Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 55
Found at i:1162716 original size:19 final size:19
Alignment explanation
Indices: 1162692--1162731 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1162682 AACCTAGTCC
1162692 ACAACCCGATTCAGGCCCA
1 ACAACCCGATTCAGGCCCA
*
1162711 ACAACCTGATTCAGGCCCA
1 ACAACCCGATTCAGGCCCA
1162730 AC
1 AC
1162732 TCAACAGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.40, G:0.15, T:0.12
Consensus pattern (19 bp):
ACAACCCGATTCAGGCCCA
Found at i:1163832 original size:14 final size:15
Alignment explanation
Indices: 1163815--1163843 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1163805 ATATAATCCC
1163815 TTAATTTT-AATATT
1 TTAATTTTAAATATT
1163829 TTAATTTTAAATATT
1 TTAATTTTAAATATT
1163844 ATTTTTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTTTAAATATT
Found at i:1170910 original size:20 final size:20
Alignment explanation
Indices: 1170887--1170995 Score: 105
Period size: 20 Copynumber: 5.5 Consensus size: 20
1170877 AGTTTCTCAT
*
1170887 TCATTTGTAAAACCTCTGGG
1 TCATTTGTAAAACCTCCGGG
***
1170907 TCATTTGTAAAACCT--AAT
1 TCATTTGTAAAACCTCCGGG
* *
1170925 TCATTTGTACAACCTCCAGG
1 TCATTTGTAAAACCTCCGGG
* *
1170945 TCATTTGCAAAACTTCCGGG
1 TCATTTGTAAAACCTCCGGG
*
1170965 TTATTTGTAAAACCTCCGGG
1 TCATTTGTAAAACCTCCGGG
* *
1170985 TAATTTATAAA
1 TCATTTGTAAA
1170996 TCCTTCAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
18 14 0.19
20 58 0.81
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
TCATTTGTAAAACCTCCGGG
Found at i:1170939 original size:38 final size:38
Alignment explanation
Indices: 1170885--1170957 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
1170875 AAAGTTTCTC
** *
1170885 ATTCATTTGTAAAACCTCTGGGTCATTTGTAAAACCTA
1 ATTCATTTGTAAAACCTCCAGGTCATTTGCAAAACCTA
*
1170923 ATTCATTTGTACAACCTCCAGGTCATTTGCAAAAC
1 ATTCATTTGTAAAACCTCCAGGTCATTTGCAAAAC
1170958 TTCCGGGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (38 bp):
ATTCATTTGTAAAACCTCCAGGTCATTTGCAAAACCTA
Found at i:1171090 original size:36 final size:36
Alignment explanation
Indices: 1171043--1171559 Score: 679
Period size: 36 Copynumber: 14.4 Consensus size: 36
1171033 AAGTCCTATA
* *
1171043 GAAGAGTAGTGAAG-TAAGTAATTTCCAACCTTCACG
1 GAAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACG
*
1171079 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCATG
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
* * *
1171115 GAAGAGTAGTGAAG-TAAGTAATTTCCAACCTTCACA
1 GAAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACG
* * *
1171151 TAAGAGTAGTGAAGTTCATCATTTCAAACCTTCACT
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
*
1171187 AAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
*
1171223 GAAGAGTAGTGAAGTTCATCATTTCTAACCTTCACG
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
* * *
1171259 GAAGAGT-GTGAAGTTCATCATTTCTAGCCTTCACA
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
* *
1171294 GAAGAGTAATGAAGTTTATCATTTCCAACCTTCACG
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
*
1171330 GAAGAGTAGTGAAGTTCATTATTTCCAACCTTCACG
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
1171366 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
*
1171402 GAAGAGTAGTGAAGTTCATCATTTCCATCCTTCACG
1 GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
* *
1171438 GAAGAGTAGTGAA-ATCAGTCATTTTCAACCTTCACG
1 GAAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACG
* **
1171474 GAAGAGTAGTGAAG-TCGGTCATTTTAAACCTTCACG
1 GAAGAGTAGTGAAGTTC-ATCATTTCCAACCTTCACG
* * * *
1171510 AAAGAGTAGTGAA-TTGATTCA-ATCCAGCCTTCACG
1 GAAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACG
* *
1171545 AAAGAGTAGTAAAGT
1 GAAGAGTAGTGAAGT
1171560 AAGATTAGAT
Statistics
Matches: 429, Mismatches: 42, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
35 60 0.14
36 365 0.85
37 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (36 bp):
GAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACG
Found at i:1171422 original size:215 final size:216
Alignment explanation
Indices: 1171043--1171562 Score: 673
Period size: 215 Copynumber: 2.4 Consensus size: 216
1171033 AAGTCCTATA
* * * * * *
1171043 GAAGAGTAGTGAAG-TAAGTAATTTCCAACCTTCACGGAAGAGTAGTGAAGTTCATCATTTCCAA
1 GAAGAGTAGTGAAGTTCA-TCATTTCTAGCCTTCACAGAAGAGTAATGAAGTTCATCATTTCCAA
* *
1171107 CCTTCATGGAAGAGTAGTGAAGTAAGTAATTTCCAACCTTCACATAAGAGTAGTGAAGTTCATCA
65 CCTTCACGGAAGAGTAGTGAAGTAAGTAATTTCCAACCTTCACAGAAGAGTAGTGAAGTTCATCA
*
1171172 TTTCAAACCTTCACTAAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGGAAGAGTAGTGAAG
130 TTTCAAACCTTCACGAAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGGAAGAGTAGTGAA-
*
1171237 TTCA-TCA-TTTCTAACCTTCACG
194 ATCAGTCATTTTC-AACCTTCACG
*
1171259 GAAGAGT-GTGAAGTTCATCATTTCTAGCCTTCACAGAAGAGTAATGAAGTTTATCATTTCCAAC
1 GAAGAGTAGTGAAGTTCATCATTTCTAGCCTTCACAGAAGAGTAATGAAGTTCATCATTTCCAAC
* * *
1171323 CTTCACGGAAGAGTAGTGAAGTTCA-TTATTTCCAACCTTCACGGAAGAGTAGTGAAGTTCATCA
66 CTTCACGGAAGAGTAGTGAAG-TAAGTAATTTCCAACCTTCACAGAAGAGTAGTGAAGTTCATCA
* * *
1171387 TTTCCAACCTTCACGGAAGAGTAGTGAAGTTCATCATTTCCATCCTTCACGGAAGAGTAGTGAAA
130 TTTCAAACCTTCACGAAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGGAAGAGTAGTGAAA
1171452 TCAGTCATTTTCAACCTTCACG
195 TCAGTCATTTTCAACCTTCACG
* * * * *
1171474 GAAGAGTAGTGAAG-TCGGTCATTT-TAAACCTTCAC-GAAAGAGTAGTGAA-TTGATTCA-ATC
1 GAAGAGTAGTGAAGTTC-ATCATTTCT-AGCCTTCACAG-AAGAGTAATGAAGTTCA-TCATTTC
* * *
1171534 CAGCCTTCACGAAAGAGTAGTAAAGTAAG
62 CAACCTTCACGGAAGAGTAGTGAAGTAAG
1171563 ATTAGATCAA
Statistics
Matches: 268, Mismatches: 26, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
214 5 0.02
215 214 0.80
216 49 0.18
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (216 bp):
GAAGAGTAGTGAAGTTCATCATTTCTAGCCTTCACAGAAGAGTAATGAAGTTCATCATTTCCAAC
CTTCACGGAAGAGTAGTGAAGTAAGTAATTTCCAACCTTCACAGAAGAGTAGTGAAGTTCATCAT
TTCAAACCTTCACGAAAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGGAAGAGTAGTGAAAT
CAGTCATTTTCAACCTTCACG
Found at i:1171744 original size:2 final size:2
Alignment explanation
Indices: 1171737--1171767 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1171727 CGTTATAAAT
1171737 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1171768 ATTACAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1173041 original size:14 final size:15
Alignment explanation
Indices: 1173024--1173052 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1173014 ATATAATCCC
1173024 TTAATTTT-AATATT
1 TTAATTTTAAATATT
1173038 TTAATTTTAAATATT
1 TTAATTTTAAATATT
1173053 ATTTTAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTTTAAATATT
Found at i:1174950 original size:14 final size:15
Alignment explanation
Indices: 1174922--1174962 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1174912 ATCAAATCAA
1174922 AGAAAA-AAG-AAAG
1 AGAAAAGAAGAAAAG
*
1174935 AGCAAAG-AGAAAAG
1 AGAAAAGAAGAAAAG
1174949 AGAAAAGAAGAAAA
1 AGAAAAGAAGAAAA
1174963 TAAAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.30
14 10 0.43
15 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAGAAAAG
Found at i:1176070 original size:44 final size:44
Alignment explanation
Indices: 1175981--1176070 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
1175971 TGCTGAAGCA
* * * * * *
1175981 AGAAATGATGAATGTTGGGGCATTTTTGAGGGCTCGTGTCATCC
1 AGAAATGATAAATGTTAGGGCATTTTTGAAGACTCATATCATCC
*
1176025 AGAAATGATAAATGTTAGGGCATTTTTGAAGACTCATATCTTCC
1 AGAAATGATAAATGTTAGGGCATTTTTGAAGACTCATATCATCC
1176069 AG
1 AG
1176071 GAAGACGATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (44 bp):
AGAAATGATAAATGTTAGGGCATTTTTGAAGACTCATATCATCC
Found at i:1177396 original size:75 final size:75
Alignment explanation
Indices: 1177301--1177448 Score: 242
Period size: 75 Copynumber: 2.0 Consensus size: 75
1177291 GACTAGACAA
* * * * *
1177301 CCTCATCATGAAGGAACAATGTCATCCACATATTTGACATCCTGAAGTAAACGATTAGATCTTTT
1 CCTCAACATAAAGGAACAATGCCATCCACAGATTTGACATCCTGAAGTAAACGATCAGATCTTTT
1177366 AAAGGCAATT
66 AAAGGCAATT
*
1177376 CCTCAACATAAAGGAACAATGCCATCCACAGATTTGACATCCTGAAGTGAACGATCAGATCTTTT
1 CCTCAACATAAAGGAACAATGCCATCCACAGATTTGACATCCTGAAGTAAACGATCAGATCTTTT
1177441 AAAGGCAA
66 AAAGGCAA
1177449 CTAGATCTCC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (75 bp):
CCTCAACATAAAGGAACAATGCCATCCACAGATTTGACATCCTGAAGTAAACGATCAGATCTTTT
AAAGGCAATT
Found at i:1177575 original size:36 final size:36
Alignment explanation
Indices: 1177492--1177588 Score: 92
Period size: 36 Copynumber: 2.7 Consensus size: 36
1177482 TATCACCTTT
* *
1177492 GAGATTGTTTTTCTCT-AAACAAAGTTTCGTCTCGCTA
1 GAGATTGTTTTTCT-TAAAACAAA-ATTCGTCTCACTA
**
1177529 GAGACAGTTTTTCTTAAAACAAAATT-GATCTCACTA
1 GAGATTGTTTTTCTTAAAACAAAATTCG-TCTCACTA
*
1177565 GAGATTG-TTTTCTTATAAAAAAAA
1 GAGATTGTTTTTCTTA-AAACAAAA
1177589 AATTTCTTAC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
35 9 0.18
36 22 0.44
37 19 0.38
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (36 bp):
GAGATTGTTTTTCTTAAAACAAAATTCGTCTCACTA
Found at i:1177736 original size:67 final size:67
Alignment explanation
Indices: 1177608--1177744 Score: 163
Period size: 67 Copynumber: 2.0 Consensus size: 67
1177598 CTTGAGACAA
* * * *
1177608 TTTTTCTTAAAAACAAATTTAATCTCATTTGAGACAGTCTTCCTTGAGACACGAACATTTGAGAT
1 TTTTTCATAAAAACAAATTTAATCTCATTTGAGACAGTCTTCCTAGAAACACGAACATTTGAAAT
1177673 TG
66 TG
** *
1177675 TTTTTCATAAAAACAAATTTCGTCTCATTTGAGACAGT-TTCCCCTAGAAATAC-AA-ATTTTGA
1 TTTTTCATAAAAACAAATTTAATCTCATTTGAGACAGTCTT--CCTAGAAACACGAACA-TTTGA
1177737 AATTG
63 AATTG
1177742 TTT
1 TTT
1177745 CACTTGAAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
66 3 0.05
67 49 0.82
68 8 0.13
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (67 bp):
TTTTTCATAAAAACAAATTTAATCTCATTTGAGACAGTCTTCCTAGAAACACGAACATTTGAAAT
TG
Found at i:1177872 original size:99 final size:101
Alignment explanation
Indices: 1177661--1178064 Score: 372
Period size: 99 Copynumber: 3.9 Consensus size: 101
1177651 TTGAGACACG
* * * * *
1177661 AACATTTGAGATTGTTTTTCATAAAAACAAATTTCGTCTCATTTGAGACAGTTTCCCCTAGAAAT
1 AACATTTGAGATTG--TTTCATAAAAACAAATTTCGTCTCACTTGAGACAATTTCTCCTCGAAAC
* *
1177726 ACAAATTTTGAAATTGTTTCACTTGAAACAAAATTTAT
64 ACAAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
** * * * *
1177764 CTCACTTGAGATTG-TTC-TCAAAACAAATTTCGTCTCACTTGAGACAATTTTTCTTCGAAACAC
1 AACATTTGAGATTGTTTCATAAAAACAAATTTCGTCTCACTTGAGACAATTTCTCCTCGAAACAC
1177827 AAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
66 AAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
* * * *
1177863 AACATTTGAGATTTTTTTCTTAAAAACAAA-TTCTGTCTCGCTTGAGACAATTT-TCACTCAAAA
1 AACATTTGAGA-TTGTTTCATAAAAACAAATTTC-GTCTCACTTGAGACAATTTCTC-CTCGAAA
*
1177926 CAAAAAAAAATTC-GAAATTGTTTCACTTGAAACAAAATTGAT
63 C----ACAAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
* * * * * * * *
1177968 AAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCT-CTTGAAAC
1 -AACATTTGAGATTGTTTC-ATAAAAACAAATTTCGTCTCACTTGAGACAATTTCTCCTCGAAAC
* * * *
1178032 ATAAACCTT-TGAGATTTTTTCTCTTGAAACAAA
64 ACAAA--TTCTGAAATTGTTTCACTTGAAACAAA
1178065 TTTTGTCTCG
Statistics
Matches: 250, Mismatches: 35, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
99 80 0.32
100 5 0.02
101 12 0.05
102 33 0.13
103 33 0.13
105 41 0.16
106 43 0.17
107 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (101 bp):
AACATTTGAGATTGTTTCATAAAAACAAATTTCGTCTCACTTGAGACAATTTCTCCTCGAAACAC
AAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
Found at i:1178022 original size:36 final size:36
Alignment explanation
Indices: 1177982--1178265 Score: 211
Period size: 36 Copynumber: 8.2 Consensus size: 36
1177972 CTTTGACATT
* * *
1177982 GTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCACTTGAGATA
* * *
1178018 GTTTCTCTTGAAACATAA-----AC-C-TTTGAGATT
1 GTTTCTCTTGAAACA-AATTTTGTCTCACTTGAGATA
* * *
1178048 TTTTCTCTTGAAACAAATTTTGTCTCGCTTGATATA
1 GTTTCTCTTGAAACAAATTTTGTCTCACTTGAGATA
*
1178084 GTTTCTCTTGAAACAAATTTTTTCTCACTTGAG-TCA
1 GTTTCTCTTGAAACAAATTTTGTCTCACTTGAGAT-A
* * * *
1178120 TTTTCTCTTGAAACATAA-----AC-C-TTTGAGATT
1 GTTTCTCTTGAAACA-AATTTTGTCTCACTTGAGATA
* * * *
1178150 GTTTCCCTTCAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCACTTGAGATA
* *
1178186 ATTTCTCTTGAAACAAATTTTATCTCACTTGAGATA
1 GTTTCTCTTGAAACAAATTTTGTCTCACTTGAGATA
* ** *
1178222 GTTTCTCTTGAAACGAATTTAATCTCACTTGAGATT
1 GTTTCTCTTGAAACAAATTTTGTCTCACTTGAGATA
1178258 GTTATCTC
1 GTT-TCTC
1178266 CAAAGTATCC
Statistics
Matches: 194, Mismatches: 35, Indels: 37
0.73 0.13 0.14
Matches are distributed among these distances:
29 4 0.02
30 37 0.19
31 3 0.02
32 2 0.01
34 2 0.01
35 3 0.02
36 135 0.70
37 8 0.04
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCACTTGAGATA
Found at i:1178053 original size:66 final size:66
Alignment explanation
Indices: 1177966--1178098 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
1177956 AACAAAATTG
1177966 ATAAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1178031 C
66 C
* * * * *
1178032 ATAAACCTTTGAGATTTTTTCTCTTGAAACAAATTTTGTCTCGCTTGATATAGTTTCTCTTGAAA
1 ATAAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1178097 C
66 C
1178098 A
1 A
1178099 AATTTTTTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (66 bp):
ATAAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
C
Found at i:1178100 original size:208 final size:203
Alignment explanation
Indices: 1177661--1178124 Score: 431
Period size: 208 Copynumber: 2.3 Consensus size: 203
1177651 TTGAGACACG
* * * * * * * *
1177661 AACATTTGAGATTGTTTTTCATAAAAACAAATT-TCGTCTCATTTGAGACAGTTTC-CCCTAGA-
1 AACACTTGAGA-TGTTTCTCTTAAAAACAAATTCT-GTCTCACTTGAGACATTTTCACTCAAAAC
* * * * * ** *
1177723 AATACAAATTTTGAAATTGTTTCACTTGAAACAAAATTTATCTCACTTGAGATTGTTCTCAAAAC
64 AAAAAAAAATTCGAAATTGTTTCACTTGAAACAAAATTGATAACACTTGACATTGTTCTCAAAAC
*
1177788 AAATTTCGTCTCACTTGAGACAATTTTTCTTCGAAACACAAATTCTGAAATTGTTTCACTTGAAA
129 AAATTTCGTCTCACTTGAGACAATTTCTCTTCGAAACACAAATTCTGAAATTGTTTCACTTGAAA
1177853 CAAAATTGAT
194 CAAAATTGAT
* * * *
1177863 AACATTTGAGATTTTTTTCTTAAAAACAAATTCTGTCTCGCTTGAGACAATTTTCACTCAAAACA
1 AACACTTGAGATGTTTCTCTTAAAAACAAATTCTGTCTCACTTGAGAC-ATTTTCACTCAAAACA
1177928 AAAAAAAATTCGAAATTGTTTCACTTGAAACAAAATTGATAA-ACCTTTGACATTGTTTCTCTTA
65 AAAAAAAATTCGAAATTGTTTCACTTGAAACAAAATTGATAACA-C-TTGACATTG-TTCTC--A
* * * * * * *
1177992 AAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTT-GAAACATAAACCTT-TGAGATTTTTTCTC
125 AAACAAATTTCGTCTCACTTGAGACAATTTCTCTTCGAAACACAAA--TTCTGAAATTGTTTCAC
*
1178055 TTGAAACAAATTTTG-T
188 TTGAAACAAA-ATTGAT
** * * * * * *
1178071 CTCGCTTGATATAGTTTCTCTT-GAAACAAATTTTTTCTCACTTGAGTCATTTTC
1 AACACTTGAGAT-GTTTCTCTTAAAAACAAATTCTGTCTCACTTGAGACATTTTC
1178125 TCTTGAAACA
Statistics
Matches: 212, Mismatches: 37, Indels: 21
0.79 0.14 0.08
Matches are distributed among these distances:
201 31 0.15
202 17 0.08
203 5 0.02
204 37 0.17
205 8 0.04
206 5 0.02
207 15 0.07
208 82 0.39
209 12 0.06
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (203 bp):
AACACTTGAGATGTTTCTCTTAAAAACAAATTCTGTCTCACTTGAGACATTTTCACTCAAAACAA
AAAAAAATTCGAAATTGTTTCACTTGAAACAAAATTGATAACACTTGACATTGTTCTCAAAACAA
ATTTCGTCTCACTTGAGACAATTTCTCTTCGAAACACAAATTCTGAAATTGTTTCACTTGAAACA
AAATTGAT
Found at i:1178115 original size:102 final size:102
Alignment explanation
Indices: 1177982--1178235 Score: 391
Period size: 102 Copynumber: 2.5 Consensus size: 102
1177972 CTTTGACATT
* * *
1177982 GTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
* * * * *
1178047 TTTTTCTCTTGAAACAAATTTTGTCTCGCTTGATATA
66 TGTTTCCCTTCAAACAAATTTTGTCTCGCTTGAGACA
* * *
1178084 GTTTCTCTTGAAACAAATTTTTTCTCACTTGAGTCATTTTCTCTTGAAACATAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
1178149 TGTTTCCCTTCAAACAAATTTTGTCTCGCTTGAGACA
66 TGTTTCCCTTCAAACAAATTTTGTCTCGCTTGAGACA
* *
1178186 ATTTCTCTTGAAACAAATTTTATCTCACTTGAGATAGTTTCTCTTGAAAC
1 GTTTCTCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCTCTTGAAAC
1178236 GAATTTAATC
Statistics
Matches: 137, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 137 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (102 bp):
GTTTCTCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
TGTTTCCCTTCAAACAAATTTTGTCTCGCTTGAGACA
Found at i:1178770 original size:278 final size:278
Alignment explanation
Indices: 1178257--1178969 Score: 971
Period size: 278 Copynumber: 2.6 Consensus size: 278
1178247 CACTTGAGAT
* * * * *
1178257 TGTTATCTCCAAAGTATCCCTAAAGATGACTAGACATCCTCATCACATAGGAACAATGTCGTCCA
1 TGTTGTCTCCAATGTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
** * * * * *
1178322 CTTACCAGATCTCCAAAACACGTAGGAGCAGCTTCATCATCAGATAACCAGACTTCCTCATCACA
66 CCGACCAGATCTCCTAAACACGTAGGAGCAGCATCATCCTCAGATAATCAGACTTCCTCATCACG
* * *
1178387 TAGGAATCATGTTGTCTCTC-AAGTATCCCTAAAGACGACTAGACATCCTCATCACGTTGGAACA
131 TAGGAACCATGTTGTCTC-CAAATTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACA
* * * * *
1178451 ATATCGTCCACCGACCAGATCTCCTCAACATATAGGAGCAGCGTTATCATTAGATAA-CATAACT
195 ATATCGTCCACCGACCAGATCTCCTCAACACATAAGAGCAGCATTATCATCAGACAATCAT-ACT
*
1178515 TCCTTATCACGTAGGAACCA
259 TCCTCATCACGTAGGAACCA
* * *
1178535 TGTTGTCTCCACTGTATCCCTAAAGATGGCTAAATGTCCTCATCACGTAGGAACAATGTCGTCCA
1 TGTTGTCTCCAATGTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
* * * *
1178600 CCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCGGATAATCAAACTTCCTCATCATG
66 CCGACCAGATCTCCTAAACACGTAGGAGCAGCATCATCCTCAGATAATCAGACTTCCTCATCACG
* * * * *
1178665 TAAGAACCTTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAATAA
131 TAGGAACCATGTTGTCTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAA
* * * * *
1178730 TATCGTCCACTGACCAGATCTCCTCAACGCATAAGAGCAGCATTATCCTCAGGCAATCATACTTT
196 TATCGTCCACCGACCAGATCTCCTCAACACATAAGAGCAGCATTATCATCAGACAATCATACTTC
* *
1178795 CTCATCATGTAGGAACCC
261 CTCATCACGTAGGAACCA
*
1178813 TGTTGTCTCCAATTTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
1 TGTTGTCTCCAATGTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
* ** *
1178878 CCGACCAGATCTCCTTAACACGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACG
66 CCGACCAGATCTCCTAAACACGTAGGAGCAGCATCATCCTCAGATAATCAGACTTCCTCATCACG
* *
1178943 TAGGAACCGTGTTGTCACCAAATTATC
131 TAGGAACCATGTTGTCTCCAAATTATC
1178970 TCCAGATTAA
Statistics
Matches: 379, Mismatches: 54, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
277 1 0.00
278 375 0.99
279 3 0.01
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (278 bp):
TGTTGTCTCCAATGTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
CCGACCAGATCTCCTAAACACGTAGGAGCAGCATCATCCTCAGATAATCAGACTTCCTCATCACG
TAGGAACCATGTTGTCTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAA
TATCGTCCACCGACCAGATCTCCTCAACACATAAGAGCAGCATTATCATCAGACAATCATACTTC
CTCATCACGTAGGAACCA
Found at i:1178969 original size:139 final size:139
Alignment explanation
Indices: 1178257--1178969 Score: 865
Period size: 139 Copynumber: 5.1 Consensus size: 139
1178247 CACTTGAGAT
* * * * *
1178257 TGTTATCTCCAAAGTATCCCTAAAGATGACTAGACATCCTCATCACATAGGAACAATGTCGTCCA
1 TGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
** ** * * * * *
1178322 CTTACCAGATCTCCAAAACACGTAGGAGCAGCTTCATCATCAGATAACCAGACTTCCTCATCACA
66 CCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGATAATCAAACTTCCTCATCACG
*
1178387 TAGGAATCA
131 TAGGAACCA
* * * * * *
1178396 TGTTGTCTCTC-AAGTATCCCTAAAGACGACTAGACATCCTCATCACGTTGGAACAATATCGTCC
1 TGTTGTCTC-CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCC
** * * * * *
1178460 ACCGACCAGATCTCCTCAACATATAGGAGCAGCGTTATCATTAGATAA-CATAACTTCCTTATCA
65 ACCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGATAATCA-AACTTCCTCATCA
1178524 CGTAGGAACCA
129 CGTAGGAACCA
* * *
1178535 TGTTGTCTCC-ACTGTATCCCTAAAGATGGCTAAATGTCCTCATCACGTAGGAACAATGTCGTCC
1 TGTTGTCTCCAAAT-TATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCC
* *
1178599 ACCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCGGATAATCAAACTTCCTCATCAT
65 ACCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGATAATCAAACTTCCTCATCAC
* *
1178664 GTAAGAACCT
130 GTAGGAACCA
* * *
1178674 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAATAATATCGTCCA
1 TGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
* * * * * ** * * *
1178739 CTGACCAGATCTCCTCAACGCATAAGAGCAGCATTATCCTCAGGCAATCATACTTTCTCATCATG
66 CCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGATAATCAAACTTCCTCATCACG
*
1178804 TAGGAACCC
131 TAGGAACCA
*
1178813 TGTTGTCTCCAATTTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
1 TGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
* ** * *
1178878 CCGACCAGATCTCCTTAACACGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACG
66 CCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGATAATCAAACTTCCTCATCACG
*
1178943 TAGGAACCG
131 TAGGAACCA
*
1178952 TGTTGTCACCAAATTATC
1 TGTTGTCTCCAAATTATC
1178970 TCCAGATTAA
Statistics
Matches: 494, Mismatches: 75, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
138 4 0.01
139 485 0.98
140 5 0.01
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (139 bp):
TGTTGTCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCA
CCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGATAATCAAACTTCCTCATCACG
TAGGAACCA
Found at i:1179222 original size:3 final size:3
Alignment explanation
Indices: 1179216--1179256 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1179206 TAATTTTTTT
*
1179216 TTA TTA TTA TTA TTA CTA TTA TTA TT- TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1179257 TTAATTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1185090 original size:20 final size:20
Alignment explanation
Indices: 1185067--1185195 Score: 136
Period size: 20 Copynumber: 6.5 Consensus size: 20
1185057 AGTTTCTCAT
1185067 TCATTTGTAAAACCTCCGGG
1 TCATTTGTAAAACCTCCGGG
* **
1185087 TCATTTGAAAAACCTCTTGG
1 TCATTTGTAAAACCTCCGGG
**
1185107 TCATTTGTAAAACCT-C-AT
1 TCATTTGTAAAACCTCCGGG
*
1185125 TCATTTGTACAACCTCCGGG
1 TCATTTGTAAAACCTCCGGG
* * *
1185145 TCATTTGCAAAACTTTCGGG
1 TCATTTGTAAAACCTCCGGG
*
1185165 TTATTTGTAAAACCTCCGGG
1 TCATTTGTAAAACCTCCGGG
* *
1185185 TAATTTATAAA
1 TCATTTGTAAA
1185196 TCCTTCGGGG
Statistics
Matches: 87, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
18 14 0.16
19 1 0.01
20 72 0.83
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (20 bp):
TCATTTGTAAAACCTCCGGG
Found at i:1185127 original size:58 final size:57
Alignment explanation
Indices: 1185062--1185180 Score: 177
Period size: 58 Copynumber: 2.1 Consensus size: 57
1185052 TTCAAAGTTT
1185062 CTCATTCATTTGTAAAACCTCCGGGTCATTTGAAAAACCTCTT-GGTCATTTGTAAAAC
1 CTCATTCATTTGTAAAACCTCCGGGTCATTTGAAAAA-CT-TTCGGTCATTTGTAAAAC
* * *
1185120 CTCATTCATTTGTACAACCTCCGGGTCATTTGCAAAACTTTCGGGTTATTTGTAAAAC
1 CTCATTCATTTGTAAAACCTCCGGGTCATTTGAAAAACTTTC-GGTCATTTGTAAAAC
1185178 CTC
1 CTC
1185181 CGGGTAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
56 2 0.04
57 2 0.04
58 52 0.93
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (57 bp):
CTCATTCATTTGTAAAACCTCCGGGTCATTTGAAAAACTTTCGGTCATTTGTAAAAC
Found at i:1185204 original size:20 final size:20
Alignment explanation
Indices: 1185153--1185204 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1185143 GGTCATTTGC
* * *
1185153 AAAACTTTCGGGTTATTTGT
1 AAAACCTTCGGGTAATTTAT
*
1185173 AAAACCTCCGGGTAATTTAT
1 AAAACCTTCGGGTAATTTAT
*
1185193 AAATCCTTCGGG
1 AAAACCTTCGGG
1185205 GCATCTGTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (20 bp):
AAAACCTTCGGGTAATTTAT
Found at i:1185292 original size:36 final size:36
Alignment explanation
Indices: 1185245--1185762 Score: 704
Period size: 36 Copynumber: 14.4 Consensus size: 36
1185235 AGTCCTACGA
* * *
1185245 AAGAGTAGTGAAG-TAAGTAATTTCTAACCTTCACGG
1 AAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACGG
* *
1185281 AAGAGTAGTGAAG-TAAGTAATTTCCAACCTTCACGG
1 AAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACGG
1185317 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
* * *
1185353 AAGAGTAATGAAG-TCAGTCATTTCCATCCTTCACGT
1 AAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACGG
* *
1185389 AAGAGTAGTGAAGTTCATCATTTCAAACCTTCACTG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
*
1185425 AAGAGTAGTGAAGTTAATCATTTCCAACCTTCACGG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
*
1185461 AAGAGTAGTGAAGTTCATCATTTCTAACCTTCACGG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
* * **
1185497 AAGAGTAGTGAAGTTCATCATTTCTAGCCTTCAAAG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
* * *
1185533 AAGTGTAATGAAGTTCATCATTTCCAACCTTTACGG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
*
1185569 AAGAGTAGTGAAGTTCATTATTTCCAACCTTCACGG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
1185605 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
*
1185641 AAGAGTAGTGAAGTTCATCATTTCCAGCCTTCACGG
1 AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
* ** *
1185677 AAGAGTAGTGAA-ATCAGTCATTTTTAACCTTCATGG
1 AAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACGG
** *
1185713 AAGAGTAGTGAAG-TCAGTCATTTTAAACCTTCACGA
1 AAGAGTAGTGAAGTTCA-TCATTTCCAACCTTCACGG
1185749 AAGAGTAGTGAAGT
1 AAGAGTAGTGAAGT
1185763 GATTCAATCC
Statistics
Matches: 436, Mismatches: 40, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
35 6 0.01
36 425 0.97
37 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (36 bp):
AAGAGTAGTGAAGTTCATCATTTCCAACCTTCACGG
Found at i:1187271 original size:14 final size:15
Alignment explanation
Indices: 1187254--1187282 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1187244 ATATAATCCC
1187254 TTAATTTT-AATATT
1 TTAATTTTAAATATT
1187268 TTAATTTTAAATATT
1 TTAATTTTAAATATT
1187283 ATTTTAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTTTAAATATT
Found at i:1191744 original size:37 final size:36
Alignment explanation
Indices: 1191693--1191849 Score: 149
Period size: 37 Copynumber: 4.3 Consensus size: 36
1191683 CTTTTAGATT
*
1191693 GTTTTTCTCT-AAACAAAGTTTCGTCTCGCTAGAGACA
1 GTTTTTCT-TAAAACAAA-TTTCGTCTCACTAGAGACA
* **
1191730 GTTTTTCTTAAAACAAAATT-GATCTCACTAGAGATT
1 GTTTTTCTTAAAACAAATTTCG-TCTCACTAGAGACA
* * *
1191766 G-TTTTCTTATAAACAAATTTTGTCTTACTTGAGACA
1 GTTTTTCTTA-AAACAAATTTCGTCTCACTAGAGACA
* *
1191802 ATTTTTCTTAAAAACAAATTTCGTCTCACTTGAGACA
1 GTTTTTCTT-AAAACAAATTTCGTCTCACTAGAGACA
* *
1191839 GTCTTCCTTAA
1 GTTTTTCTTAA
1191850 GACACGAACA
Statistics
Matches: 99, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
35 9 0.09
36 36 0.36
37 53 0.54
38 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (36 bp):
GTTTTTCTTAAAACAAATTTCGTCTCACTAGAGACA
Found at i:1191779 original size:73 final size:73
Alignment explanation
Indices: 1191688--1191836 Score: 178
Period size: 73 Copynumber: 2.0 Consensus size: 73
1191678 GTCACCTTTT
* * *
1191688 AGATTGTTTTTCTCTAAACAAAGTTTCGTCTCGCTAGAGACAGTTTTTCTT-AAAACAAAATT-G
1 AGATTGTTTTTCTATAAACAAA-TTTCGTCTCACTAGAGACAATTTTTCTTAAAAACAAAATTCG
1191751 ATCTCACTAG
65 -TCTCACTAG
* * * *
1191761 AGATTG-TTTTCTTATAAACAAATTTTGTCTTACTTGAGACAATTTTTCTTAAAAACAAATTTCG
1 AGATTGTTTTTC-TATAAACAAATTTCGTCTCACTAGAGACAATTTTTCTTAAAAACAAAATTCG
*
1191825 TCTCACTTG
65 TCTCACTAG
1191834 AGA
1 AGA
1191837 CAGTCTTCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
72 28 0.43
73 36 0.55
74 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (73 bp):
AGATTGTTTTTCTATAAACAAATTTCGTCTCACTAGAGACAATTTTTCTTAAAAACAAAATTCGT
CTCACTAG
Found at i:1191938 original size:66 final size:67
Alignment explanation
Indices: 1191803--1191968 Score: 166
Period size: 66 Copynumber: 2.5 Consensus size: 67
1191793 CTTGAGACAA
* * * *
1191803 TTTTTCTTAAAAACAAATTTCGTCTCACTTGAGACAGTCTTCCTTAAGACACGAACATTTGAGAT
1 TTTTTCATAAAAACAAATTTCGTCTCACTTGAGACAGTCTTCCCTAAAACACGAACATTTGAAAT
1191868 TG
66 TG
* *
1191870 TTTTTCATAAAAACAAATTTCGTCTC-TTTGAGACAGT-TTCCCCTAGAAATAC-AA-ATTTTGA
1 TTTTTCATAAAAACAAATTTCGTCTCACTTGAGACAGTCTT-CCCTA-AAACACGAACA-TTTGA
1191931 AATTG
63 AATTG
* *
1191936 --TTTCACTTAAAACAAAATTT-ATCTCACTTGAGA
1 TTTTTCA-TAAAAAC-AAATTTCGTCTCACTTGAGA
1191969 TTGTTCTCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
64 5 0.06
65 13 0.15
66 37 0.44
67 29 0.35
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (67 bp):
TTTTTCATAAAAACAAATTTCGTCTCACTTGAGACAGTCTTCCCTAAAACACGAACATTTGAAAT
TG
Found at i:1192031 original size:99 final size:97
Alignment explanation
Indices: 1191879--1192250 Score: 342
Period size: 99 Copynumber: 3.8 Consensus size: 97
1191869 GTTTTTCATA
* * * * * *
1191879 AAAACAAATTTCGTCTC-TTTGAGACAGTTTCCCCTAGAAATACAAATTTTGAAATTGTTTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACAATTTCTCTTCGAAACACAAA-TTTGAAATTGTTTCACT
* * * *
1191943 TAAAACAAAATTTATCTCACTTGAGATTGTTCTC
65 TGAAACAAAATTGAT-ACACTTGACATTGTTCTC
* * *
1191977 AAAACAAATTTCGTCTCACTTGAGATAATTTTTCTTCGAAACACAAATTCTGAAATTGTTTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACAATTTCTCTTCGAAACACAAATT-TGAAATTGTTTCACT
* * * *
1192042 TGAAACAAAATTGATAACATTTGATATTTTTTTCTTA
65 TGAAACAAAATTGAT-ACACTTGACA--TTGTTC-TC
* * *
1192079 AAAACAAATTTCGTCTCGCTTGAGACAATTT-TC-ACTAAA-A-AAATTGGAAATTGTTTCACTT
1 AAAACAAATTTCGTCTCGCTTGAGACAATTTCTCTTCGAAACACAAATTTGAAATTGTTTCACTT
*
1192140 GAAACAAAATTGATAAACCTTTGACATTGTTTCTC
66 GAAACAAAATTGATACA-C-TTGACATTG-TTCTC
* * * *
1192175 TTAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTT-GAAACATAAACCTTTGAGATTTTTTC
1 --AAAACAAATTTCGTCTCGCTTGAGACAATTTCTCTTCGAAACACAAA--TTTGAAATTGTTTC
*
1192239 TCTTGAAACAAA
62 ACTTGAAACAAA
1192251 TTTTGTCTCG
Statistics
Matches: 225, Mismatches: 33, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
96 5 0.02
97 32 0.14
98 59 0.26
99 62 0.28
100 5 0.02
101 10 0.04
102 30 0.13
103 22 0.10
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (97 bp):
AAAACAAATTTCGTCTCGCTTGAGACAATTTCTCTTCGAAACACAAATTTGAAATTGTTTCACTT
GAAACAAAATTGATACACTTGACATTGTTCTC
Found at i:1192185 original size:200 final size:199
Alignment explanation
Indices: 1191856--1192250 Score: 471
Period size: 200 Copynumber: 2.0 Consensus size: 199
1191846 TTAAGACACG
* * *
1191856 AACATTTGAGATTGTTTTTCATAAAAACAAATTTCGTCTCTTTGAGACAGTTTCCCCTAGAAATA
1 AACATTTGAGATTGTTTTTCATAAAAACAAATTTCGTCTCCTTGAGACAATTTCCACTA-AAATA
* * ** *
1191921 CAAATTTTGAAATTGTTTCACTTAAAACAAAATTTATCTCACTTGAGATTGTTCTCAAAACAAAT
65 CAAATTTGGAAATTGTTTCACTTAAAACAAAATTGATAACACTTGACATTGTTCTCAAAACAAAT
* *
1191986 TTCGTCTCACTTGAGATAATTTTTCTTCGAAACACAAA-TTCTGAAATTGTTTCACTTGAAACAA
130 TTCGTCTCACTTGAGACAATTTCTCTT-GAAACACAAACTT-TGAAATTGTTTCACTTGAAACAA
1192050 AATTGAT
193 AATTGAT
* * *
1192057 AACATTTGATATT-TTTTTCTTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTCACT-AAA-A
1 AACATTTGAGATTGTTTTTCATAAAAACAAATTTCGTCTC-CTTGAGACAATTTCCACTAAAATA
*
1192119 -AAA-TTGGAAATTGTTTCACTTGAAACAAAATTGATAA-ACCTTTGACATTGTTTCTCTTAAAA
65 CAAATTTGGAAATTGTTTCACTTAAAACAAAATTGATAACA-C-TTGACATTG-TTCTC--AAAA
* * * * * *
1192181 CAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATTTTTTCTCTTGAA
125 CAAATTTCGTCTCACTTGAGACAATTTCTCTTGAAACACAAA-CTTTGAAATTGTTTCACTTGAA
1192246 ACAAA
189 ACAAA
1192251 TTTTGTCTCG
Statistics
Matches: 166, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
195 1 0.01
196 30 0.18
197 11 0.07
198 6 0.04
199 12 0.07
200 78 0.47
201 28 0.17
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (199 bp):
AACATTTGAGATTGTTTTTCATAAAAACAAATTTCGTCTCCTTGAGACAATTTCCACTAAAATAC
AAATTTGGAAATTGTTTCACTTAAAACAAAATTGATAACACTTGACATTGTTCTCAAAACAAATT
TCGTCTCACTTGAGACAATTTCTCTTGAAACACAAACTTTGAAATTGTTTCACTTGAAACAAAAT
TGAT
Found at i:1192203 original size:98 final size:101
Alignment explanation
Indices: 1191860--1192207 Score: 349
Period size: 99 Copynumber: 3.5 Consensus size: 101
1191850 GACACGAACA
* * * * * * *
1191860 TTTGAGATTGTTTTTCATAAAAACAAATTTCGTCTC-TTTGAGACAGTTTCCCCTA-GAAATACA
1 TTTGACATTGTTTCTC-TTAAAACAAATTTCGTCTCGCTTGAGACAATTT--TCTACGAAACACA
** * * **
1191923 AATTTTGAAATTGTTTCACTTAAAACAAAATTTATCTCAC
63 AATTCGGAAATTGTTTCACTTGAAACAAAATTGATAAC-C
* * * *
1191963 -TTGAGATTG-TTCTC--AAAACAAATTTCGTCTCACTTGAGATAATTTTTCTTCGAAACACAAA
1 TTTGACATTGTTTCTCTTAAAACAAATTTCGTCTCGCTTGAGACAA-TTTTCTACGAAACACAAA
* *
1192024 TTCTGAAATTGTTTCACTTGAAACAAAATTGATAACA
65 TTCGGAAATTGTTTCACTTGAAACAAAATTGATAACC
* * *
1192061 TTTGATATT-TTTTTCTTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTC-ACTAAA-A-AAA
1 TTTGACATTGTTTCTCTT-AAAACAAATTTCGTCTCGCTTGAGACAATTTTCTACGAAACACAAA
1192122 TT-GGAAATTGTTTCACTTGAAACAAAATTGATAAACC
65 TTCGGAAATTGTTTCACTTGAAACAAAATTGAT-AACC
*
1192159 TTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAATTT
1 TTTGACATTGTTTCTCTTAAAACAAATTTCGTCTCGCTTGAGACAATTT
1192208 CTCTTGAAAC
Statistics
Matches: 211, Mismatches: 24, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
97 29 0.14
98 65 0.31
99 66 0.31
100 7 0.03
101 9 0.04
102 35 0.17
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (101 bp):
TTTGACATTGTTTCTCTTAAAACAAATTTCGTCTCGCTTGAGACAATTTTCTACGAAACACAAAT
TCGGAAATTGTTTCACTTGAAACAAAATTGATAACC
Found at i:1192229 original size:66 final size:66
Alignment explanation
Indices: 1192152--1192284 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
1192142 AACAAAATTG
1192152 ATAAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
1 ATAAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
1192217 C
66 C
* * * * *
1192218 ATAAACCTTTGAGATTTTTTCTCTTGAAACAAATTTTGTCTCGCTTGATACAGTTTCTCTTGAAA
1 ATAAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
1192283 C
66 C
1192284 A
1 A
1192285 ATTTTTTTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (66 bp):
ATAAACCTTTGACATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
C
Found at i:1192285 original size:102 final size:102
Alignment explanation
Indices: 1192168--1192420 Score: 389
Period size: 102 Copynumber: 2.5 Consensus size: 102
1192158 CTTTGACATT
* *
1192168 GTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGAT
* * *
1192233 TTTTTCTCTTGAAACAAATTTTGTCTCGCTTGATACA
66 TGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
* * * *
1192270 GTTTCTCTTGAAACAATTTTTTTCTCGCTTGAGCCATTTTCTCTTGAAACATAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGAT
1192335 TGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
66 TGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
* * * *
1192372 ATTTCTCTTGAAACAAATTTTATCTCGCTTGAGATAGTTTCTTTTGAAA
1 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAATTTCTCTTGAAA
1192421 AGAATTTAAT
Statistics
Matches: 136, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 136 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.42
Consensus pattern (102 bp):
GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGAT
TGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
Found at i:1192398 original size:36 final size:36
Alignment explanation
Indices: 1192168--1192441 Score: 209
Period size: 36 Copynumber: 7.9 Consensus size: 36
1192158 CTTTGACATT
* *
1192168 GTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACA
* * **
1192204 ATTTCTCTTGAAACATAA----A-C-C-TTTGAGATT
1 GTTTCTCTTGAAACA-AATTTTATCTCGCTTGAGACA
* * *
1192234 TTTTCTCTTGAAACAAATTTTGTCTCGCTTGATACA
1 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACA
* * *
1192270 GTTTCTCTTGAAACAATTTTTTTCTCGCTTGAGCCA
1 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACA
* * **
1192306 TTTTCTCTTGAAACATAA----A-C-C-TTTGAGATT
1 GTTTCTCTTGAAACA-AATTTTATCTCGCTTGAGACA
* *
1192336 GTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACA
* *
1192372 ATTTCTCTTGAAACAAATTTTATCTCGCTTGAGATA
1 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACA
* * *
1192408 GTTTCTTTTGAAA-AGAATTTAATCTCACTTGAGA
1 GTTTCTCTTGAAACA-AATTTTATCTCGCTTGAGA
1192442 TTTTTATCTC
Statistics
Matches: 183, Mismatches: 38, Indels: 34
0.72 0.15 0.13
Matches are distributed among these distances:
29 4 0.02
30 38 0.21
31 2 0.01
32 2 0.01
34 2 0.01
35 3 0.02
36 129 0.70
37 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACA
Found at i:1192402 original size:21 final size:20
Alignment explanation
Indices: 1192342--1192403 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
1192332 GATTGTTTCC
1192342 CTTGAAACAAATTTTGTCTCG
1 CTTGAAACAAATTTT-TCTCG
*
1192363 CTTGAGAC-AA--TTTCT--
1 CTTGAAACAAATTTTTCTCG
1192378 CTTGAAACAAATTTTATCTCG
1 CTTGAAACAAATTTT-TCTCG
1192399 CTTGA
1 CTTGA
1192404 GATAGTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 7 0.21
16 2 0.06
17 3 0.09
18 4 0.12
19 3 0.09
20 2 0.06
21 12 0.36
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (20 bp):
CTTGAAACAAATTTTTCTCG
Found at i:1192701 original size:139 final size:139
Alignment explanation
Indices: 1192448--1193155 Score: 861
Period size: 139 Copynumber: 5.1 Consensus size: 139
1192438 GAGATTTTTA
* * * * * *
1192448 TCTCCAAAGTATCCCTAAAGACGACTAGACGTCCTCATCACATAGGAATAATGTCGTCCACCGAC
1 TCTCCCAATTATCCCTAAAGATGACTAGACGTCCTCATCACGTAGGAACAATATCGTCCACCGAC
* * * *
1192513 CAGATCTCCTCAACACGTAGGAGCAGCTTCATCATCAGATAACCAGACTTCCTCATCACGTAGGA
66 CAGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGATAATCACACTTCCTCATCACGTAGGA
*
1192578 ATCATGTTG
131 ACCATGTTG
* * * *
1192587 TCTCCCAAGTATCCCTAAAGATGACTAGACATCTTCATCACGTTGGAACAATATCGTCCACCGAC
1 TCTCCCAATTATCCCTAAAGATGACTAGACGTCCTCATCACGTAGGAACAATATCGTCCACCGAC
* * * * * * *
1192652 CAGATCTCCTCGACACATAGGAGCAGCGTTATCATTAGATAA-CATGACTTCCTTATCACGTA-G
66 CAGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGATAATCA-CACTTCCTCATCACGTAGG
1192715 ACACCATGTTG
130 A-ACCATGTTG
* * * *
1192726 TCT-CCACATTATCCCTAAAGATGGCTAAATGTCCTCATCACGTAGGAACAATGA-CGTCCTCCG
1 TCTCCCA-ATTATCCCTAAAGATGACTAGACGTCCTCATCACGTAGGAACAAT-ATCGTCCACCG
* * * *
1192789 ACCAGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCGGATAATCAAACTTCCTCATCATGTAA
64 ACCAGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGATAATCACACTTCCTCATCACGTAG
1192854 GAACCATGTTG
129 GAACCATGTTG
** * * * *
1192865 TCTCTAAATTACCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAATAATATCGTCCACTGAC
1 TCTCCCAATTATCCCTAAAGATGACTAGACGTCCTCATCACGTAGGAACAATATCGTCCACCGAC
* * * **
1192930 CAGATCTCCTCAACGCATAGGAGCAGCATCATCCTCAGGCAATCACACTTCCTCATCACGTAGGA
66 CAGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGATAATCACACTTCCTCATCACGTAGGA
*
1192995 ACCCTGTTG
131 ACCATGTTG
* * **
1193004 TCT-CCAATTTATCCCTAAAGA-CAGCTAGACGTCCTTATCACGTAGGAACAATATTATCCACCG
1 TCTCCCAA-TTATCCCTAAAGATGA-CTAGACGTCCTCATCACGTAGGAACAATATCGTCCACCG
* *
1193067 ACCAGATCTCCTCAACACGTAGGAGCAGTGTCATCCTCAGACAATCACACTTCCTCATCACGTAG
64 ACCAGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGATAATCACACTTCCTCATCACGTAG
*
1193132 GAACCGTGTTG
129 GAACCATGTTG
* *
1193143 TCACCAAATTATC
1 TCTCCCAATTATC
1193156 TCCAGATTGA
Statistics
Matches: 490, Mismatches: 68, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
138 10 0.02
139 471 0.96
140 9 0.02
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (139 bp):
TCTCCCAATTATCCCTAAAGATGACTAGACGTCCTCATCACGTAGGAACAATATCGTCCACCGAC
CAGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGATAATCACACTTCCTCATCACGTAGGA
ACCATGTTG
Found at i:1193407 original size:3 final size:3
Alignment explanation
Indices: 1193399--1193476 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
1193389 TTCTAATTTT
1193399 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1193447 CTA TTA CTA TTA TTA TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1193477 TTAATTACAT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.06
3 65 0.94
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1198708 original size:2 final size:2
Alignment explanation
Indices: 1198695--1198739 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1198685 TGTCTCTGTC
*
1198695 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1198737 TA T
1 TA T
1198740 TCCTCCAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1199274 original size:5 final size:5
Alignment explanation
Indices: 1199264--1199289 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1199254 TATTATTATT
1199264 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
1199290 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1200263 original size:22 final size:24
Alignment explanation
Indices: 1200238--1200281 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1200228 TTTAAGTTAG
*
1200238 TATTTTTT-TTAA-ATAGTTATTA
1 TATTTTTTATTAATATAATTATTA
1200260 TATTTTTTATTAATATAATTAT
1 TATTTTTTATTAATATAATTAT
1200282 ATAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTTTTTATTAATATAATTATTA
Found at i:1200296 original size:30 final size:33
Alignment explanation
Indices: 1200260--1200332 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 33
1200250 ATAGTTATTA
*
1200260 TATTTTTTATTAATATAAT-TATATA-AAT-AT
1 TATTTTTTATTAAAATAATATATATATAATGAT
* *
1200290 TATTTTTAATTAAAATAATATTTATATAATGAT
1 TATTTTTTATTAAAATAATATATATATAATGAT
1200323 TATTTATTTA
1 TATTT-TTTA
1200333 AATTTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 17 0.49
31 5 0.14
32 3 0.09
33 7 0.20
34 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
TATTTTTTATTAAAATAATATATATATAATGAT
Found at i:1202644 original size:19 final size:19
Alignment explanation
Indices: 1202606--1202644 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1202596 AATATTCCAA
* *
1202606 TTGAAATTTAAAATTGTAT
1 TTGAAATTCAAAATTATAT
*
1202625 TTGAAATTCAAAGTTATAT
1 TTGAAATTCAAAATTATAT
1202644 T
1 T
1202645 CCAATTATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (19 bp):
TTGAAATTCAAAATTATAT
Found at i:1203509 original size:139 final size:138
Alignment explanation
Indices: 1203061--1204255 Score: 1374
Period size: 139 Copynumber: 8.6 Consensus size: 138
1203051 CAGCGTCTCC
* * * * ** *
1203061 GGGGACATGACTCACATAATAGGGCAATGATAACATATTCTCTGACATAATAA-TCAAAGGCACG
1 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATTGGAAGGCGCG
** *** * * ** * *
1203125 CCCCCTAAAACGCGCTTTTGTCACTTTCCTGCGTTCTTTCAAACATGATAGGTACTGACACGAAT
66 CCCCCGGAAACGCGCTTTCACCACTTT-TTGCGTCCCCTCAAACATAATAGGTACTGACATGAAT
*
1203190 AATGCCCCCG
130 AGTG-CCCCG
* * * *
1203200 GGGGACATGAGTGACATAATAGGGCAATGATAACGTATTCTCTGAAAAAATAA-TAGAAGGCGCG
1 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATTGGAAGGCGCG
* * * * *
1203264 CCCCCGGAAACGCGC-TTCACCATTTTGTTGCGTCCCCTAAAAAATAATAGGTACTGATATAAAT
66 CCCCCGGAAACGCGCTTTCACCACTTT-TTGCGTCCCCTCAAACATAATAGGTACTGACATGAAT
1203328 AGTGCCACCG
130 AGTGCC-CCG
* * * *
1203338 GGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATATAATAATTGG-AGGCGCG
1 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATTGGAAGGCGCG
* * * * *
1203402 CCCCCTGAAACGCGCTTTTACCACTTTTCTACTTCCCCTCAAACATGATAGGTACTGACATGAAT
66 CCCCCGGAAACGCGCTTTCACCACTTTT-TGCGTCCCCTCAAACATAATAGGTACTGACATGAAT
*
1203467 AGTACCCCTG
130 AGTGCCCC-G
* * *
1203477 GGGGACATGAGTAACATAATAAGGTAATGATAACATATTCTCTGACAAAATAA-TGGAAGGCAC-
1 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATTGGAAGGCGCG
* * *
1203540 CCACCCGGAAATGCGCTTTCACCACGTTGTTGCGTCACCTCAAACATAATAGGTACTGACATGAA
66 CC-CCCGGAAACGCGCTTTCACCAC-TTTTTGCGTCCCCTCAAACATAATAGGTACTGACATGAA
1203605 TAGTGCCCCGG
129 TAGTGCCCC-G
* *
1203616 GGGGACATGAGTGACATAATAAGGCAATTATAACATATTCTCTGACAAAATAATAT--AAGGCGT
1 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAAT-TGGAAGGCGC
* * * *
1203679 GGCCCCGGAAACACGCTTTCACCACTTTGTTGCGTCCCATCAAACATAATAGGTACTAACATGAA
65 GCCCCCGGAAACGCGCTTTCACCACTTT-TTGCGTCCCCTCAAACATAATAGGTACTGACATGAA
1203744 TAGTGCTCCCG
129 TAGTGC-CCCG
* * * * *
1203755 GGGGAAATGAGTGACATAAT-AGGGAATTGATAATATATTCTCTGACAAAATAA-TGGAATGAGC
1 GGGGACATGAGTGACATAATAAGGCAA-TGATAACATATTCTCTGACAAAATAATTGGAAGGCGC
* * * * *
1203818 ACCCCAGGAAACGCGCTTTCACCACTTTGTTGAGTCCCCTCAAACATAACAGGTACTGATATGAA
65 GCCCCCGGAAACGCGCTTTCACCACTTT-TTGCGTCCCCTCAAACATAATAGGTACTGACATGAA
1203883 TAGTGCCCCTG
129 TAGTGCCCC-G
* *
1203894 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAA-TGGAAGACGCA
1 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATTGGAAGGCGCG
* *
1203958 CCCCCGGAAACGCGCTTTCACCACTTTGATGCGTCCCCTCAAACATAATAGGTACTGACATAAAT
66 CCCCCGGAAACGCGCTTTCACCACTTT-TTGCGTCCCCTCAAACATAATAGGTACTGACATGAAT
1204023 AGTGCTCCCG
130 AGTGC-CCCG
* * * * * * * * *
1204033 AGGGATATGAGTGATATAATAGGGAAATAATAACATATTCTCTGACAGAATAA-TGGAAGGTGTG
1 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATTGGAAGGCGCG
* * * *
1204097 CCCCTGGAAACGTGCTTTCACCACTTTGTTGTGTCCCCTCAAACATAATAGGTATTGACATGAAT
66 CCCCCGGAAACGCGCTTTCACCACTTT-TTGCGTCCCCTCAAACATAATAGGTACTGACATGAAT
1204162 AGTGCCCCG
130 AGTGCCCCG
* *
1204171 GGGGACATGAGTAACATAAT-AGGTCAATGATAACATATTCTCTGACAAAATAA-TGGAAGGCAC
1 GGGGACATGAGTGACATAATAAGG-CAATGATAACATATTCTCTGACAAAATAATTGGAAGGCGC
* * * *
1204234 GTCCACGGAAATGCGCATTCAC
65 GCCCCCGGAAACGCGCTTTCAC
1204256 ATGAATAGTA
Statistics
Matches: 903, Mismatches: 133, Indels: 41
0.84 0.12 0.04
Matches are distributed among these distances:
137 5 0.01
138 197 0.22
139 685 0.76
140 15 0.02
141 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (138 bp):
GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATTGGAAGGCGCG
CCCCCGGAAACGCGCTTTCACCACTTTTTGCGTCCCCTCAAACATAATAGGTACTGACATGAATA
GTGCCCCG
Found at i:1203884 original size:417 final size:412
Alignment explanation
Indices: 1203061--1204230 Score: 1515
Period size: 417 Copynumber: 2.8 Consensus size: 412
1203051 CAGCGTCTCC
* * * * **
1203061 GGGGACATGACTCACATAATAGGGCAATGATAACATATTCTCTGACATAATAATCAAAGGCACGC
1 GGGGACATGAGTAACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCAC-C
** *** ** ** * *
1203126 CCCCTAAAACGCGCTTTTGTCACTTTCCTGCGTTCTTTCAAACATGATAGGTACTGACACGAATA
65 CCCCGGAAACGCGCTTTCACCACTTTGATGCG-TCCCTCAAACATAATAGGTACTGACATGAATA
* * * *
1203191 ATGCCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACGTATTCTCTGAAAAAATAATAG
129 GTG-CCCCGGGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATAG
* * * * *
1203256 AAGGCGCGCCCCCGGAAACGCGC-TTCACCATTTTGTTGCGTCCCCTAAAAAATAATAGGTACTG
193 AAGGCGTGGCCCCGGAAACGCGCTTTCACCACTTTGTTGCGTCCCCTCAAACATAATAGGTACTG
* * * *
1203320 ATATAAATAGTGCCACCGGGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATA
258 ACATGAATAGTGCC-CCGGGGGAAATGAGTGACATAATAGGG-AATGATAACATATTCTCTGACA
* * * ** * * *
1203385 TAATAATTGG-AGGCGCGCCCCCTGAAACGCGCTTTTACCACTTTTCTACTTCCCCTCAAACATG
321 AAATAA-TGGAAGGAGCACCCCAGGAAACGCGCTTTCACCACTTTTCTACGTCCCCTCAAACATA
*
1203449 ATAGGTACTGACATGAATAGTACCCCTG
385 ACAGGTACTGACATGAATAGTACCCCTG
*
1203477 GGGGACATGAGTAACATAATAAGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCACCC
1 GGGGACATGAGTAACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCACCC
* * *
1203542 ACCCGGAAATGCGCTTTCACCACGTTGTTGCGTCACCTCAAACATAATAGGTACTGACATGAATA
66 -CCCGGAAACGCGCTTTCACCACTTTGATGCGTC-CCTCAAACATAATAGGTACTGACATGAATA
* * *
1203607 GTGCCCCGGGGGGACATGAGTGACATAATAAGGCAATTATAACATATTCTCTGACAAAATAATAT
129 GTGCCCC-GGGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATAG
* * *
1203672 AAGGCGTGGCCCCGGAAACACGCTTTCACCACTTTGTTGCGTCCCATCAAACATAATAGGTACTA
193 AAGGCGTGGCCCCGGAAACGCGCTTTCACCACTTTGTTGCGTCCCCTCAAACATAATAGGTACTG
*
1203737 ACATGAATAGTGCTCCCGGGGGAAATGAGTGACATAATAGGGAATTGATAATATATTCTCTGACA
258 ACATGAATAGTGC-CCCGGGGGAAATGAGTGACATAATAGGGAA-TGATAACATATTCTCTGACA
*
1203802 AAATAATGGAATGAGCACCCCAGGAAACGCGCTTTCACCACTTTGT-TGA-GTCCCCTCAAACAT
321 AAATAATGGAAGGAGCACCCCAGGAAACGCGCTTTCACCACTTT-TCT-ACGTCCCCTCAAACAT
* *
1203865 AACAGGTACTGATATGAATAGTGCCCCTG
384 AACAGGTACTGACATGAATAGTACCCCTG
*
1203894 GGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCA-
1 GGGGACATGAGTAACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATGGAAG--GCAC
*
1203958 CCCCCGGAAACGCGCTTTCACCACTTTGATGCGTCCCCTCAAACATAATAGGTACTGACATAAAT
64 CCCCCGGAAACGCGCTTTCACCACTTTGATGCGT-CCCTCAAACATAATAGGTACTGACATGAAT
* * * * * *
1204023 AGTGCTCCCGAGGGATATGAGTGATATAATAGGGAAATAATAACATATTCTCTGACAGAATAATG
128 AGTGC-CCCGGGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATA
* * * *
1204088 GAAGGTGT-GCCCCTGGAAACGTGCTTTCACCACTTTGTTGTGTCCCCTCAAACATAATAGGTAT
192 GAAGGCGTGGCCCC-GGAAACGCGCTTTCACCACTTTGTTGCGTCCCCTCAAACATAATAGGTAC
* * *
1204152 TGACATGAATAGTGCCCCGGGGGACATGAGTAACATAATAGGTCAATGATAACATATTCTCTGAC
256 TGACATGAATAGTGCCCCGGGGGAAATGAGTGACATAATAGG-GAATGATAACATATTCTCTGAC
1204217 AAAATAATGGAAGG
320 AAAATAATGGAAGG
1204231 CACGTCCACG
Statistics
Matches: 661, Mismatches: 78, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
415 8 0.01
416 244 0.37
417 397 0.60
418 9 0.01
419 3 0.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (412 bp):
GGGGACATGAGTAACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCACCC
CCCGGAAACGCGCTTTCACCACTTTGATGCGTCCCTCAAACATAATAGGTACTGACATGAATAGT
GCCCCGGGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATAGAAG
GCGTGGCCCCGGAAACGCGCTTTCACCACTTTGTTGCGTCCCCTCAAACATAATAGGTACTGACA
TGAATAGTGCCCCGGGGGAAATGAGTGACATAATAGGGAATGATAACATATTCTCTGACAAAATA
ATGGAAGGAGCACCCCAGGAAACGCGCTTTCACCACTTTTCTACGTCCCCTCAAACATAACAGGT
ACTGACATGAATAGTACCCCTG
Found at i:1207500 original size:19 final size:19
Alignment explanation
Indices: 1207420--1207501 Score: 51
Period size: 19 Copynumber: 4.1 Consensus size: 19
1207410 ATTGGTAATT
*
1207420 TTTTAAAATGATTAATTATAA
1 TTTTAAAAT-ATT-ATAATAA
* *
1207441 TTATT-GAATATAATAATTATA
1 TT-TTAAAATATTATAA-TA-A
* *
1207462 TTATAAAAT-TTATTATTAA
1 TTTTAAAATATTA-TAATAA
1207481 TTTTAAAATATTATAATAA
1 TTTTAAAATATTATAATAA
1207500 TT
1 TT
1207502 CCACCTTCTA
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
19 19 0.41
20 12 0.26
21 13 0.28
22 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTAAAATATTATAATAA
Found at i:1208238 original size:17 final size:17
Alignment explanation
Indices: 1208213--1208252 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1208203 CCAGCTAAAA
* *
1208213 CCCAAGTAAAGTGCGTC
1 CCCAGGTAAAGCGCGTC
1208230 CCCAGGTAAAGCGCGTC
1 CCCAGGTAAAGCGCGTC
1208247 CCCAGG
1 CCCAGG
1208253 GATGCGCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.35, G:0.28, T:0.12
Consensus pattern (17 bp):
CCCAGGTAAAGCGCGTC
Found at i:1208796 original size:32 final size:32
Alignment explanation
Indices: 1208753--1208820 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 32
1208743 TTTTTTTTGC
1208753 AATAATATAGGC-TTTTTACTTTGTTATATAT
1 AATAATATAGGCTTTTTTACTTTGTTATATAT
1208784 AATATATATAGGCTGATTTTTTACTTTGTTATATAT
1 AATA-ATATAGGC---TTTTTTACTTTGTTATATAT
1208820 A
1 A
1208821 TTTGAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 4 0.12
32 8 0.25
36 20 0.62
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.51
Consensus pattern (32 bp):
AATAATATAGGCTTTTTTACTTTGTTATATAT
Found at i:1213353 original size:6 final size:6
Alignment explanation
Indices: 1213342--1213372 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1213332 GAGATAAGGG
1213342 TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA T
1 TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA T
1213373 ATTCTACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.19
Consensus pattern (6 bp):
TGGCAA
Found at i:1215599 original size:4 final size:4
Alignment explanation
Indices: 1215590--1215640 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
1215580 ACTGCACATA
1215590 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1215638 TAT
1 TAT
1215641 ATTAACACTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1220751 original size:21 final size:21
Alignment explanation
Indices: 1220725--1220766 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1220715 CCAGAATGGG
*
1220725 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
1220746 GGGAATTGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1220767 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1222430 original size:19 final size:20
Alignment explanation
Indices: 1222387--1222434 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1222377 TCTAAATCAT
*
1222387 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1222407 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1222426 TTTTCAAAA
1 TTTTCAAAA
1222435 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1223672 original size:21 final size:21
Alignment explanation
Indices: 1223646--1223687 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1223636 CCAGAATGGG
*
1223646 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1223667 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1223688 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1223827 original size:20 final size:20
Alignment explanation
Indices: 1223799--1223873 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
1223789 AAACCATTCA
*
1223799 GGGGAGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
1223819 GGGGGGAATCTGT--TCCC-
1 GGGGGGAATCTGTACCCCCT
1223836 --GGGGAATC-GATACCCCCT
1 GGGGGGAATCTG-TACCCCCT
*
1223854 GGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCTGTACCCCCT
1223874 AGGCAATCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
14 1 0.02
15 9 0.20
17 3 0.07
18 3 0.07
20 27 0.61
21 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:1225431 original size:24 final size:25
Alignment explanation
Indices: 1225403--1225452 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1225393 TAATGTAAAA
* *
1225403 TTTATA-TTAAAATTATTTTAATTT
1 TTTATATTTAAAAATAATTTAATTT
1225427 TTTATATTTAAAAATAATTTAATTT
1 TTTATATTTAAAAATAATTTAATTT
1225452 T
1 T
1225453 AATAAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTATATTTAAAAATAATTTAATTT
Found at i:1230456 original size:78 final size:78
Alignment explanation
Indices: 1230357--1230514 Score: 262
Period size: 78 Copynumber: 2.0 Consensus size: 78
1230347 AATTCAGTGT
*
1230357 GATTTATGTAGGGGTGAGTAAAACTCGATTCAACTAGAATTGAATTTGAATTATAATTTAATAAA
1 GATTGATGTAGGGGTGAGTAAAACTCGATTCAACTAGAATTGAATTTGAATTATAATTTAATAAA
1230422 CTCGACTAAACTC
66 CTCGACTAAACTC
* * * *
1230435 GATTGATGTAGGGGTGAGTAAAACTCGATTCAACTCGAATTGACTTTGAATTGTAATTTCATAAA
1 GATTGATGTAGGGGTGAGTAAAACTCGATTCAACTAGAATTGAATTTGAATTATAATTTAATAAA
*
1230500 CTCGACTAGACTC
66 CTCGACTAAACTC
1230513 GA
1 GA
1230515 AAATTTTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (78 bp):
GATTGATGTAGGGGTGAGTAAAACTCGATTCAACTAGAATTGAATTTGAATTATAATTTAATAAA
CTCGACTAAACTC
Found at i:1233690 original size:19 final size:18
Alignment explanation
Indices: 1233666--1233713 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1233656 TGATGCATCG
1233666 GTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGGA-A
*
1233685 GTGCATCGGTGCATGGAA
1 GTGCATCGATGCATGGAA
1233703 -TGCATTCGATG
1 GTGCA-TCGATG
1233714 TTCAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 4 0.15
18 6 0.23
19 16 0.62
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (18 bp):
GTGCATCGATGCATGGAA
Found at i:1234087 original size:49 final size:49
Alignment explanation
Indices: 1234015--1234111 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
1234005 CCCCTTTTTG
1234015 ATATAACAAAACATTTGAATAATTTTAAGATTTGTTTAAGAAATTATTA
1 ATATAACAAAACATTTGAATAATTTTAAGATTTGTTTAAGAAATTATTA
1234064 ATATAACAAAACATTTGAATAATTTTAAGATTTGTTTAAGAAATTATT
1 ATATAACAAAACATTTGAATAATTTTAAGATTTGTTTAAGAAATTATT
1234112 TTTGAAATCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.41
Consensus pattern (49 bp):
ATATAACAAAACATTTGAATAATTTTAAGATTTGTTTAAGAAATTATTA
Found at i:1240243 original size:22 final size:21
Alignment explanation
Indices: 1240201--1240240 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1240191 GAGGTTGTTT
*
1240201 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1240222 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1240241 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1242237 original size:64 final size:64
Alignment explanation
Indices: 1242184--1242346 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
1242174 CGGTGCACCA
*
1242184 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
1242248 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
1242313 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1242347 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:1242318 original size:19 final size:19
Alignment explanation
Indices: 1242294--1242344 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1242284 GAAAATATTC
1242294 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1242313 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1242332 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1242345 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1243444 original size:64 final size:64
Alignment explanation
Indices: 1243374--1243516 Score: 178
Period size: 64 Copynumber: 2.2 Consensus size: 64
1243364 ATCCATTATC
* * * *
1243374 GCATTCAAATAATACATAGCAGAGTCAATATTGCATTTAGATAATGCATAGCAGAGTTAGTGTT
1 GCATTCAAATAATACATAACAAAGTCAATATTGCATTTAGATAATGCACAACAGAGTTAGTGTT
* * ** * * *
1243438 GTATTCATATAATGTATAATAAAGTCAGTATTGCATTTAGATGATGCACAACAGAGTTAGTGTT
1 GCATTCAAATAATACATAACAAAGTCAATATTGCATTTAGATAATGCACAACAGAGTTAGTGTT
*
1243502 GCATTCAGATAATAC
1 GCATTCAAATAATAC
1243517 CCATGAATGC
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (64 bp):
GCATTCAAATAATACATAACAAAGTCAATATTGCATTTAGATAATGCACAACAGAGTTAGTGTT
Found at i:1243450 original size:32 final size:32
Alignment explanation
Indices: 1243343--1243514 Score: 121
Period size: 32 Copynumber: 5.4 Consensus size: 32
1243333 ATCAAAATTA
* ** * *
1243343 CATTCAGATAGTGCATAGTAGA-TCCATTATCG
1 CATTCAGATAATGCATAACAGAGT-CAGTATTG
* * * *
1243375 CATTCAAATAATACATAGCAGAGTCAATATTG
1 CATTCAGATAATGCATAACAGAGTCAGTATTG
* * * *
1243407 CATTTAGATAATGCATAGCAGAGTTAGTGTTG
1 CATTCAGATAATGCATAACAGAGTCAGTATTG
* * * * *
1243439 TATTCATATAATGTATAATAAAGTCAGTATTG
1 CATTCAGATAATGCATAACAGAGTCAGTATTG
* * * * *
1243471 CATTTAGATGATGCACAACAGAGTTAGTGTTG
1 CATTCAGATAATGCATAACAGAGTCAGTATTG
1243503 CATTCAGATAAT
1 CATTCAGATAAT
1243515 ACCCATGAAT
Statistics
Matches: 106, Mismatches: 33, Indels: 2
0.75 0.23 0.01
Matches are distributed among these distances:
32 105 0.99
33 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
CATTCAGATAATGCATAACAGAGTCAGTATTG
Found at i:1243531 original size:64 final size:63
Alignment explanation
Indices: 1243402--1243551 Score: 167
Period size: 64 Copynumber: 2.3 Consensus size: 63
1243392 GCAGAGTCAA
* * * * * *
1243402 TATTGCATTTAGATAATGCATAGCAGAGTTAGTGTTGTATTCATATAATGTATAATAAAGTCAG
1 TATTGCATTTAGATAATGCACAACAGAGTTAGTGTTGCATTCAGATAA-GTACAATAAAGCCAG
* * *
1243466 TATTGCATTTAGATGATGCACAACAGAGTTAGTGTTGCATTCAGATAA-TACCCATGAATGCCAG
1 TATTGCATTTAGATAATGCACAACAGAGTTAGTGTTGCATTCAGATAAGTA-CAAT-AAAGCCAG
**
1243530 TATCACATTTAGATAATGCACA
1 TATTGCATTTAGATAATGCACA
1243552 TCATATATAG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
62 2 0.03
63 2 0.03
64 68 0.94
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (63 bp):
TATTGCATTTAGATAATGCACAACAGAGTTAGTGTTGCATTCAGATAAGTACAATAAAGCCAG
Found at i:1249061 original size:32 final size:32
Alignment explanation
Indices: 1248998--1249106 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 32
1248988 TATAAAAGAT
** ** *
1248998 TCAGTATCACATTCAGATAATACATAATAGAG
1 TCAGTATTGCATTCAGATAATGTATACTAGAG
*
1249030 TCAGTATTGTATTCAGATAATGTATACTAGAG
1 TCAGTATTGCATTCAGATAATGTATACTAGAG
* * * *
1249062 TTACTGTTGCATTCATATAATGTATAGC-AGAG
1 TCAGTATTGCATTCAGATAATGTATA-CTAGAG
*
1249094 TCAGTGTTGCATT
1 TCAGTATTGCATT
1249107 TGAATGATGC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
32 62 0.98
33 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (32 bp):
TCAGTATTGCATTCAGATAATGTATACTAGAG
Found at i:1256245 original size:21 final size:20
Alignment explanation
Indices: 1256221--1256300 Score: 56
Period size: 20 Copynumber: 3.8 Consensus size: 20
1256211 AACCTCACTA
1256221 TGTATCGATACACTATG-ATAG
1 TGTATCGATACACT-TGAAT-G
*
1256242 TGTATAGATACATTCCTTGAATG
1 TGTATCGATACA---CTTGAATG
*
1256265 TGTATCGATACACTCTGCA-G
1 TGTATCGATACACT-TGAATG
* *
1256285 TGTACCAATACACTTG
1 TGTATCGATACACTTG
1256301 TCGTTTTTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.04
20 15 0.31
21 14 0.29
23 14 0.29
24 4 0.08
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (20 bp):
TGTATCGATACACTTGAATG
Found at i:1258292 original size:20 final size:20
Alignment explanation
Indices: 1258255--1258311 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
1258245 TTATATATAT
* *
1258255 ATTTGGTTTTGACT-ATTTGA
1 ATTTGG-TTTGATTAATTTCA
*
1258275 ATTTGGTTTGATTAATTTCT
1 ATTTGGTTTGATTAATTTCA
*
1258295 A-TTGGTTTTATTAATTT
1 ATTTGGTTTGATTAATTT
1258312 TTGCATCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.21, C:0.04, G:0.16, T:0.60
Consensus pattern (20 bp):
ATTTGGTTTGATTAATTTCA
Found at i:1258565 original size:12 final size:13
Alignment explanation
Indices: 1258533--1258579 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
1258523 AGGGGGAGTA
*
1258533 ATTTTCAAAAGTG
1 ATTTTCAAAAATG
1258546 ATTTTCAAAAATG
1 ATTTTCAAAAATG
1258559 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1258571 ATTTTCAAA
1 ATTTTCAAA
1258580 GAAAATCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1260917 original size:15 final size:15
Alignment explanation
Indices: 1260897--1260933 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1260887 ACTTGAAGAG
1260897 GAAAATGGGAGAGAA
1 GAAAATGGGAGAGAA
1260912 GAAAATGGGAGAGAA
1 GAAAATGGGAGAGAA
1260927 GAAAATG
1 GAAAATG
1260934 AGAAGAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (15 bp):
GAAAATGGGAGAGAA
Found at i:1260929 original size:18 final size:16
Alignment explanation
Indices: 1260891--1260941 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
1260881 TATGTCACTT
*
1260891 GAAGAGGAAAATGGGA
1 GAAGAAGAAAATGGGA
1260907 G-AGAAGAAAATGGGA
1 GAAGAAGAAAATGGGA
1260922 G-AGAAGAAAAT--GA
1 GAAGAAGAAAATGGGA
1260935 GAAGAAG
1 GAAGAAG
1260942 TGAATGAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 3 0.09
14 5 0.15
15 24 0.73
16 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (16 bp):
GAAGAAGAAAATGGGA
Found at i:1267821 original size:75 final size:73
Alignment explanation
Indices: 1267729--1267934 Score: 235
Period size: 76 Copynumber: 2.8 Consensus size: 73
1267719 AATTAAACTC
* *
1267729 AAGTTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAAGTTTTAGT
1 AAGTTTAGGATATTATTTTAAATATTATATTTTAT-TTTGTATTTTAGTTTAAATAAGTTTTAGT
1267794 ATTTTAATT
65 ATTTTAATT
* * * *
1267803 AAGTCTTAGGATATTATTTT-TATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT
1 AAGT-TTAGGATATTATTTTAAATATTATAT-TTTATTTT--GTATTTTAGTTTAAATAAGTTTT
1267867 AGTATTTTAATT
62 AGTATTTTAATT
* * *
1267879 AGGATTTAGAATATTATTTTAAATATTAT-TTTTA---GGTATTTTAGTTTAAAT-AGTTT
1 AAG-TTTAGGATATTATTTTAAATATTATATTTTATTTTGTATTTTAGTTTAAATAAGTTT
1267935 AAACTGTTTT
Statistics
Matches: 113, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
69 4 0.04
70 16 0.14
74 14 0.12
75 21 0.19
76 51 0.45
77 7 0.06
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (73 bp):
AAGTTTAGGATATTATTTTAAATATTATATTTTATTTTGTATTTTAGTTTAAATAAGTTTTAGTA
TTTTAATT
Found at i:1268643 original size:15 final size:14
Alignment explanation
Indices: 1268627--1268685 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
1268617 TTTACTACTA
1268627 TTATTTATTATTTT
1 TTATTTATTATTTT
***
1268641 ATTATTT-TCCCTTT
1 -TTATTTATTATTTT
*
1268655 TTATTTATTATTAT
1 TTATTTATTATTTT
1268669 TTATTTTATTATTTT
1 TTA-TTTATTATTTT
1268684 TT
1 TT
1268686 CTTTTTAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 6 0.18
14 10 0.29
15 18 0.53
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTATTATTTT
Found at i:1268673 original size:35 final size:36
Alignment explanation
Indices: 1268625--1268711 Score: 115
Period size: 35 Copynumber: 2.4 Consensus size: 36
1268615 TCTTTACTAC
*
1268625 TATTATT-TATTATTTTATTATTTTCCCTTTTT-ATT
1 TATTATTAT-TTATTTTATTATTTTCCCTTTTTAAAT
**
1268660 TATTATTATTTATTTTATTATTTTTTCTTTTTAAAT
1 TATTATTATTTATTTTATTATTTTCCCTTTTTAAAT
*
1268696 TATAATTATTTATTTT
1 TATTATTATTTATTTT
1268712 GTTTTATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
35 28 0.61
36 18 0.39
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (36 bp):
TATTATTATTTATTTTATTATTTTCCCTTTTTAAAT
Found at i:1273437 original size:75 final size:72
Alignment explanation
Indices: 1273348--1273548 Score: 235
Period size: 76 Copynumber: 2.7 Consensus size: 72
1273338 TAAACTCAAG
* *
1273348 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATATTATTTTAAATATT-TATTTT-T-TTTGTATTTTAGTTTAAATAGGTTTTAGTATT
*
1273413 TTAATTAAGT
63 TTAATTAAGA
* *
1273423 TTTAGGATATTATTTT-TATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAAGTTTTAGTA
1 TTTAGGATATTATTTTAAATA-TTTAT-TTT-TTTT--GTATTTTAGTTTAAATAGGTTTTAGTA
*
1273487 TTTTAATTAGGA
61 TTTTAATTAAGA
* **
1273499 TTTAGAATATTATTTTAAATA-TTATTTTTTAGGTATTTTAGTTTAAATAG
1 TTTAGGATATTATTTTAAATATTTATTTTTTTTGTATTTTAGTTTAAATAG
1273549 TTTAAAGTGT
Statistics
Matches: 109, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
71 17 0.16
73 2 0.02
74 11 0.10
75 25 0.23
76 51 0.47
77 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.56
Consensus pattern (72 bp):
TTTAGGATATTATTTTAAATATTTATTTTTTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTA
ATTAAGA
Found at i:1274186 original size:18 final size:18
Alignment explanation
Indices: 1274163--1274205 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1274153 TTTTAGATTA
1274163 TTTATTTAATTATTT-TCT
1 TTTATTTAATT-TTTATCT
1274181 TTTATTTAATTTTTATCT
1 TTTATTTAATTTTTATCT
1274199 TTTATTT
1 TTTATTT
1274206 TAAACAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTTTTATCT
Found at i:1274285 original size:36 final size:39
Alignment explanation
Indices: 1274245--1274342 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 39
1274235 TCTTTACTAC
*
1274245 TATTATTTA-TTATTTTATTATTTTCCCTTTTT-TATT-
1 TATTATTTATTTATTTTATTATTTTCCCTTTTTAAATTA
**
1274281 TATTA-TTATTTATTTTATTATTTTTTCTTTTTAAATTA
1 TATTATTTATTTATTTTATTATTTTCCCTTTTTAAATTA
1274319 TAATTATTTATTTTATTTTATTAT
1 T-ATTATTTA-TTTATTTTATTAT
1274343 ATCTTTTCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
35 3 0.06
36 26 0.49
37 3 0.06
38 1 0.02
39 4 0.08
40 3 0.06
41 13 0.25
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (39 bp):
TATTATTTATTTATTTTATTATTTTCCCTTTTTAAATTA
Found at i:1274291 original size:10 final size:9
Alignment explanation
Indices: 1274274--1274336 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
1274264 ATTTTCCCTT
1274274 TTTTATTTA
1 TTTTATTTA
1274283 TTATTATTTA
1 TT-TTATTTA
1274293 TTTTA-TTA
1 TTTTATTTA
1274301 TTTT-TTCT-
1 TTTTATT-TA
*
1274309 TTTTAAATTA
1 TTTT-ATTTA
*
1274319 TAATTATTTA
1 T-TTTATTTA
1274329 TTTTATTT
1 TTTTATTT
1274337 TATTATATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
8 12 0.28
9 13 0.30
10 16 0.37
11 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1275582 original size:14 final size:14
Alignment explanation
Indices: 1275563--1275590 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1275553 TCCTTAGTGT
1275563 GGATATCTAAGTTA
1 GGATATCTAAGTTA
1275577 GGATATCTAAGTTA
1 GGATATCTAAGTTA
1275591 CTAGATGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
GGATATCTAAGTTA
Found at i:1283296 original size:29 final size:30
Alignment explanation
Indices: 1283262--1283319 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1283252 TGAATATTTA
1283262 ATTATGACAT-TAAATATTT-AAAAAAAATT
1 ATTATGACATGT-AATATTTGAAAAAAAATT
*
1283291 ATTATGACATGTAATATTTGAAATAAAAT
1 ATTATGACATGTAATATTTGAAAAAAAAT
1283320 AAATTCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (30 bp):
ATTATGACATGTAATATTTGAAAAAAAATT
Found at i:1284901 original size:25 final size:26
Alignment explanation
Indices: 1284846--1284905 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
1284836 GCTTTTCTTA
* *
1284846 TTCTTCAACCTATTCCCCATCTTCTTT
1 TTCTTC-ACCTATTCCCCATCTTCATC
1284873 TTCTTCACCT-TTCCCC-TCGTTCATC
1 TTCTTCACCTATTCCCCATC-TTCATC
1284898 TTCTTCAC
1 TTCTTCAC
1284906 GAATCCAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 2 0.07
25 18 0.60
26 4 0.13
27 6 0.20
ACGTcount: A:0.12, C:0.40, G:0.02, T:0.47
Consensus pattern (26 bp):
TTCTTCACCTATTCCCCATCTTCATC
Found at i:1295173 original size:40 final size:40
Alignment explanation
Indices: 1295127--1295211 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
1295117 TTAAAATATG
*
1295127 AAATTCAAATTAACTTGATTTGCAAAAAAATGAAACTTAT
1 AAATTCAAATTAACTTGATTTACAAAAAAATGAAACTTAT
*
1295167 AAATTCAAATTAACTTGATTTACAAAAAAATGAAGCTTAT
1 AAATTCAAATTAACTTGATTTACAAAAAAATGAAACTTAT
1295207 AAATT
1 AAATT
1295212 ATCGATTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (40 bp):
AAATTCAAATTAACTTGATTTACAAAAAAATGAAACTTAT
Found at i:1298669 original size:29 final size:29
Alignment explanation
Indices: 1298627--1298713 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
1298617 GTCCCGGGGG
*
1298627 TAGGTCGCCATGCACGCCCGGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
* **
1298656 TAGGTCGCCATGCACGCCCAACGACCTGG
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
* *
1298685 TAGGTCGCCATGCATGCCCTGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
1298714 CAGCACCTCC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.18, C:0.39, G:0.26, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCTAC
Found at i:1298752 original size:30 final size:30
Alignment explanation
Indices: 1298718--1298834 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
1298708 ACCTACCAGC
1298718 ACCTCCATGCACGCCCAGGCACGCCCAACG
1 ACCTCCATGCACGCCCAGGCACGCCCAACG
*
1298748 ACCTCCATGACCTACCAGCACCTCCATGCACGCCCAACG
1 ACCTCCATG--C-A-C-G---C-CCAGGCACGCCCAACG
* * *
1298787 ACCTCCATGAATGCCCAGACACGCCCAACG
1 ACCTCCATGCACGCCCAGGCACGCCCAACG
1298817 ACCTCCATGCACGCCCAG
1 ACCTCCATGCACGCCCAG
1298835 CTCGCCAAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
30 39 0.55
31 1 0.01
32 1 0.01
33 1 0.01
34 2 0.03
35 1 0.01
36 1 0.01
38 1 0.01
39 24 0.34
ACGTcount: A:0.26, C:0.48, G:0.16, T:0.10
Consensus pattern (30 bp):
ACCTCCATGCACGCCCAGGCACGCCCAACG
Found at i:1298792 original size:20 final size:20
Alignment explanation
Indices: 1298736--1298795 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
1298726 GCACGCCCAG
1298736 GCACGCCCAACGACCTCCAT
1 GCACGCCCAACGACCTCCAT
*
1298756 G-AC-CTACCAGC-ACCTCCAT
1 GCACGC--CCAACGACCTCCAT
1298775 GCACGCCCAACGACCTCCAT
1 GCACGCCCAACGACCTCCAT
1298795 G
1 G
1298796 AATGCCCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 1 0.03
19 15 0.45
20 16 0.48
21 1 0.03
ACGTcount: A:0.25, C:0.48, G:0.15, T:0.12
Consensus pattern (20 bp):
GCACGCCCAACGACCTCCAT
Found at i:1298802 original size:20 final size:20
Alignment explanation
Indices: 1298740--1298803 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1298730 GCCCAGGCAC
*
1298740 GCCCAACGACCTCCATGACCT
1 GCCCAACGACCTCCATGA-AT
* * * *
1298761 -ACCAGC-ACCTCCATGCAC
1 GCCCAACGACCTCCATGAAT
1298779 GCCCAACGACCTCCATGAAT
1 GCCCAACGACCTCCATGAAT
1298799 GCCCA
1 GCCCA
1298804 GACACGCCCA
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.27, C:0.47, G:0.14, T:0.12
Consensus pattern (20 bp):
GCCCAACGACCTCCATGAAT
Found at i:1299519 original size:23 final size:22
Alignment explanation
Indices: 1299470--1299520 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 22
1299460 ACAGAAATTT
1299470 AGTTA-ATTAGTTTGTAGTATA
1 AGTTATATTAGTTTGTAGTATA
*
1299491 A--T-TATTAGTTTGTTAGTTTA
1 AGTTATATTAGTTTG-TAGTATA
1299511 AGTTATATTA
1 AGTTATATTA
1299521 TATTAAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
19 10 0.42
20 7 0.29
21 1 0.04
22 1 0.04
23 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (22 bp):
AGTTATATTAGTTTGTAGTATA
Found at i:1299625 original size:42 final size:47
Alignment explanation
Indices: 1299528--1299625 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 47
1299518 TTATATTAAA
* *
1299528 TTGTTAGTTTAAGTTATATATTAGATTATAAAAAATTAGTTAATTAGT
1 TTGTTAGTTTAAGTTATATA-TAGATTATAAAAAATTAGTTAATGAAT
* * *
1299576 TTCTTAGTTTAAGTTAT-TA-A-A-TGTAAAAAA-TATTTAATGAAT
1 TTGTTAGTTTAAGTTATATATAGATTATAAAAAATTAGTTAATGAAT
1299618 TTGTTAGT
1 TTGTTAGT
1299626 GTGTTTAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
42 16 0.36
43 8 0.18
44 1 0.02
45 1 0.02
47 2 0.05
48 16 0.36
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (47 bp):
TTGTTAGTTTAAGTTATATATAGATTATAAAAAATTAGTTAATGAAT
Found at i:1302722 original size:10 final size:11
Alignment explanation
Indices: 1302697--1302783 Score: 52
Period size: 11 Copynumber: 7.6 Consensus size: 11
1302687 TATGATTTGA
1302697 TAGTAATGATT
1 TAGTAATGATT
1302708 TAGTAATGATT
1 TAGTAATGATT
* *
1302719 AGTAATAATGAAT
1 --TAGTAATGATT
* * *
1302732 TATTATTAATT
1 TAGTAATGATT
*
1302743 T-TTAATGATTT
1 TAGTAATGA-TT
*
1302754 GATATTAATGATT
1 --TAGTAATGATT
1302767 TAGTAATGA-T
1 TAGTAATGATT
1302777 TAGTAAT
1 TAGTAAT
1302784 AATGAAATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
10 13 0.21
11 29 0.48
13 12 0.20
14 7 0.11
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:1302750 original size:21 final size:21
Alignment explanation
Indices: 1302724--1302810 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
1302714 TGATTAGTAA
1302724 TAATGAATTATTATTAATTTT
1 TAATGAATTATTATTAATTTT
* *
1302745 TAATGATTTGA-TATTAATGATT
1 TAATGAATT-ATTATTAAT-TTT
* * *
1302767 TAGT-AATGATTAGTAA----
1 TAATGAATTATTATTAATTTT
1302783 TAATGAAATTATTATTAATTTT
1 TAATG-AATTATTATTAATTTT
1302805 TAATGA
1 TAATGA
1302811 TTTGATAGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
16 3 0.06
18 10 0.21
20 1 0.02
21 23 0.48
22 11 0.23
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.49
Consensus pattern (21 bp):
TAATGAATTATTATTAATTTT
Found at i:1302786 original size:119 final size:119
Alignment explanation
Indices: 1302649--1302948 Score: 488
Period size: 119 Copynumber: 2.6 Consensus size: 119
1302639 AGTAATTTGA
*
1302649 TAGTAATGATTATAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTATAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAATGATTTAGTA
* *
1302713 ATGATTAGTAATAATG-AATTATTATTAATT-TTTAATGATTTGATATTAATGATT
65 ATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATT
*
1302767 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTACTA
1 TAGTAATGATTA-TAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
1302832 ATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATT
65 ATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATT
1302887 TAGTAATGATTATAAT-A--AAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAA
1 TAGTAATGATTATAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAA
1302948 T
66 T
1302949 AATAATTATT
Statistics
Matches: 173, Mismatches: 5, Indels: 11
0.92 0.03 0.06
Matches are distributed among these distances:
115 7 0.04
116 37 0.21
118 15 0.09
119 67 0.39
120 45 0.26
121 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (119 bp):
TAGTAATGATTATAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAA
TGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATT
Found at i:1302823 original size:60 final size:60
Alignment explanation
Indices: 1302649--1302948 Score: 483
Period size: 60 Copynumber: 5.1 Consensus size: 60
1302639 AGTAATTTGA
*
1302649 TAGTAATGATTA-TAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAATGATT
*
1302708 TAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1302767 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* *
1302827 TACTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAATGATT
1302887 TAGTAATGATTA-TAAT-A--AAATTATTATTAATTTTTAATGATTTGATAGTAATGA-T
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1302942 TAGTAAT
1 TAGTAAT
1302949 AATAATTATT
Statistics
Matches: 229, Mismatches: 7, Indels: 14
0.92 0.03 0.06
Matches are distributed among these distances:
55 10 0.04
56 33 0.14
58 3 0.01
59 70 0.31
60 111 0.48
61 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (60 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
Found at i:1302967 original size:44 final size:44
Alignment explanation
Indices: 1302887--1302977 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 44
1302877 AGTAATGATT
* *
1302887 TAGTAATGATTATAATAAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTATAAT-AAATAATTATTAATATTTAATGATTTGA
1302932 TAGTAATGATTAGTAAT-AATAATTATTAATATTTAATGATTTGA
1 TAGTAATGATTA-TAATAAATAATTATTAATATTTAATGATTTGA
1302976 TA
1 TA
1302978 TTATTTAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 27 0.63
45 12 0.28
46 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (44 bp):
TAGTAATGATTATAATAAATAATTATTAATATTTAATGATTTGA
Found at i:1305553 original size:21 final size:21
Alignment explanation
Indices: 1305529--1305568 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1305519 TTTCTATATG
1305529 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1305550 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1305569 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1305781 original size:27 final size:28
Alignment explanation
Indices: 1305742--1305814 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
1305732 ATTCAACAAC
*
1305742 CAAAATAACTTAACTATTTA-ACTAACT-A
1 CAAACTAA-TTAA-TATTTAGACTAACTAA
1305770 CAAACTAATTAA-ATTTAGACTAACTAA
1 CAAACTAATTAATATTTAGACTAACTAA
*
1305797 CACACTAATTAATTATTT
1 CAAACTAATTAA-TATTT
1305815 TTTAATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 5 0.13
26 7 0.18
27 16 0.41
28 7 0.18
29 4 0.10
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.34
Consensus pattern (28 bp):
CAAACTAATTAATATTTAGACTAACTAA
Found at i:1306117 original size:12 final size:11
Alignment explanation
Indices: 1306086--1306121 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1306076 ACGTTCACGG
1306086 GCTGCAATAAT
1 GCTGCAATAAT
*
1306097 GCAGCAATAAGT
1 GCTGCAATAA-T
1306109 GCTGCAATAAT
1 GCTGCAATAAT
1306120 GC
1 GC
1306122 AGTTGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (11 bp):
GCTGCAATAAT
Found at i:1306375 original size:33 final size:33
Alignment explanation
Indices: 1306312--1306377 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1306302 AAGCATGGAC
*
1306312 TGCATGGTGACCTTTGGCGAGCTGAACGTGCAT
1 TGCATGGTGACCTTTGGCGAGATGAACGTGCAT
**
1306345 TGCATGGTGACCTTTGGCGAGATGGGCGTGCAT
1 TGCATGGTGACCTTTGGCGAGATGAACGTGCAT
1306378 GGAGGTCGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.36, T:0.27
Consensus pattern (33 bp):
TGCATGGTGACCTTTGGCGAGATGAACGTGCAT
Found at i:1306402 original size:10 final size:10
Alignment explanation
Indices: 1306366--1306431 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
1306356 CTTTGGCGAG
1306366 ATGGGCGTGC
1 ATGGGCGTGC
1306376 ATGGAG-GT-C
1 ATGG-GCGTGC
*
1306385 GTTGGGCGTGC
1 -ATGGGCGTGC
1306396 ATGGGCGTGC
1 ATGGGCGTGC
1306406 ATGGAG-GT-C
1 ATGG-GCGTGC
*
1306415 GTTGGGCGTGC
1 -ATGGGCGTGC
1306426 ATGGGC
1 ATGGGC
1306432 ATGGAGGTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
9 4 0.09
10 36 0.82
11 4 0.09
ACGTcount: A:0.11, C:0.17, G:0.50, T:0.23
Consensus pattern (10 bp):
ATGGGCGTGC
Found at i:1306402 original size:30 final size:30
Alignment explanation
Indices: 1306366--1306445 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
1306356 CTTTGGCGAG
1306366 ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
1 ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
1306396 ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
1 ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
1306426 AT--G-G-GCATGGAGGTCGTTGG
1 ATGGGCGTGCATGGAGGTCGTTGG
1306446 CTGGTAGGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
26 16 0.32
27 1 0.02
28 1 0.02
30 32 0.64
ACGTcount: A:0.11, C:0.15, G:0.50, T:0.24
Consensus pattern (30 bp):
ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
Found at i:1306711 original size:51 final size:51
Alignment explanation
Indices: 1306613--1306712 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
1306603 TAATGGAAGG
* * * * *
1306613 CGCGTCCCCGGGGATGCGCTTTCCACACGTGGCAGTCGAGCTGGCGAAAGA
1 CGCGTCCCCGGGGATGCGCCTTCCACAAGTAGCAGTCCAGCTAGCGAAAGA
*
1306664 CGCGTGCCCGGGGATGCGCCTTCCACAAGTAGCA-TCCAGCTCAGCGAAA
1 CGCGTCCCCGGGGATGCGCCTTCCACAAGTAGCAGTCCAGCT-AGCGAAA
1306713 ACACGGGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 6 0.14
51 36 0.86
ACGTcount: A:0.20, C:0.33, G:0.32, T:0.15
Consensus pattern (51 bp):
CGCGTCCCCGGGGATGCGCCTTCCACAAGTAGCAGTCCAGCTAGCGAAAGA
Found at i:1307154 original size:16 final size:17
Alignment explanation
Indices: 1307130--1307167 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1307120 GACACGTGTC
*
1307130 AAAACATTATA-ATTTA
1 AAAAAATTATATATTTA
1307146 AAAAAATTATATATTTA
1 AAAAAATTATATATTTA
1307163 AAAAA
1 AAAAA
1307168 CATAAAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAAATTATATATTTA
Found at i:1307204 original size:19 final size:18
Alignment explanation
Indices: 1307172--1307207 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1307162 AAAAAACATA
*
1307172 AAACACAAATTTTGAAAT
1 AAACACAAACTTTGAAAT
1307190 AAACACAAAACTTTGAAA
1 AAACAC-AAACTTTGAAA
1307208 ACCTTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (18 bp):
AAACACAAACTTTGAAAT
Found at i:1310334 original size:16 final size:17
Alignment explanation
Indices: 1310313--1310364 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
1310303 TTTTTAATTT
1310313 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
1310329 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
1310344 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
1310361 AATT
1 AATT
1310365 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:1320897 original size:22 final size:22
Alignment explanation
Indices: 1320852--1320897 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1320842 TTTAATGCAT
*
1320852 AAGGGATCGATCCTTTTGGTCA
1 AAGGGATCGATCCTTTTGGCCA
1320874 AAGGGATCGATCC-TTTGAGCCA
1 AAGGGATCGATCCTTTTG-GCCA
1320896 AA
1 AA
1320898 AATCCTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGGATCGATCCTTTTGGCCA
Found at i:1322014 original size:43 final size:43
Alignment explanation
Indices: 1321966--1322049 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
1321956 AGGGCTAATC
* * * *
1321966 CTATTCCTAATGACCATCCTTGTTTGAAATTTCAAATCAATAT
1 CTATTCCTAATGACCACCCATGCTTCAAATTTCAAATCAATAT
* *
1322009 CTATTCCTACTGATCACCCATGCTTCAAATTTCAAATCAAT
1 CTATTCCTAATGACCACCCATGCTTCAAATTTCAAATCAAT
1322050 GTCCACCACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (43 bp):
CTATTCCTAATGACCACCCATGCTTCAAATTTCAAATCAATAT
Found at i:1323548 original size:23 final size:22
Alignment explanation
Indices: 1323500--1323549 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1323490 TATATATATA
*
1323500 TTCTTTCATTTTCTTCTCCTCGT
1 TTCTTCCATTTTCTTCT-CTCGT
1323523 TTCTTCCATTTTTCTTCT-TCGCT
1 TTCTTCCA-TTTTCTTCTCTCG-T
1323546 TTCT
1 TTCT
1323550 CTTCAAAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 12 0.50
24 9 0.38
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (22 bp):
TTCTTCCATTTTCTTCTCTCGT
Found at i:1324035 original size:21 final size:21
Alignment explanation
Indices: 1324009--1324090 Score: 139
Period size: 21 Copynumber: 4.0 Consensus size: 21
1323999 TCAAGGTTTG
1324009 AGTATCGATACTGGGATGAAC
1 AGTATCGATACTGGGATGAAC
1324030 AGTATCGATACTGGGATGAAC
1 AGTATCGATACTGGGATGAAC
*
1324051 AGTATCGCTACTGGGATGAAC
1 AGTATCGATACTGGGATGAAC
*
1324072 AGTATCGCTACT-GGATGAA
1 AGTATCGATACTGGGATGAA
1324091 TTTGGGCAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
20 7 0.12
21 53 0.88
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (21 bp):
AGTATCGATACTGGGATGAAC
Found at i:1324146 original size:20 final size:19
Alignment explanation
Indices: 1324117--1324154 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1324107 GGATTTCAAG
1324117 CAGGGAGTATCGATACTGT
1 CAGGGAGTATCGATACTGT
1324136 CAGGAGAGTATCGATACTG
1 CAGG-GAGTATCGATACTG
1324155 CCTCTTCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (19 bp):
CAGGGAGTATCGATACTGT
Found at i:1332372 original size:21 final size:21
Alignment explanation
Indices: 1332348--1332393 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1332338 GGTGACAGCA
*
1332348 GCACGGGCTTTGGTGAGTGGC
1 GCACGGGCTCTGGTGAGTGGC
* *
1332369 GCACTGTCTCTGGTGAGTGGC
1 GCACGGGCTCTGGTGAGTGGC
1332390 GCAC
1 GCAC
1332394 TGTCTCGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.41, T:0.24
Consensus pattern (21 bp):
GCACGGGCTCTGGTGAGTGGC
Found at i:1332394 original size:21 final size:21
Alignment explanation
Indices: 1332358--1332403 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1332348 GCACGGGCTT
1332358 TGGTGAGTGGCGCACTGTCTC
1 TGGTGAGTGGCGCACTGTCTC
1332379 TGGTGAGTGGCGCACTGTCTC
1 TGGTGAGTGGCGCACTGTCTC
1332400 -GGTG
1 TGGTG
1332404 CTCTGAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.09, C:0.22, G:0.41, T:0.28
Consensus pattern (21 bp):
TGGTGAGTGGCGCACTGTCTC
Found at i:1333253 original size:83 final size:83
Alignment explanation
Indices: 1333036--1333298 Score: 332
Period size: 83 Copynumber: 3.2 Consensus size: 83
1333026 TTTAAAATGA
* * **
1333036 CCCGAAGGA-TTATTATTTTGCTCGAAAGACTTACAAATGA-CCGAAATATTTCATCATCATGCT
1 CCCGAAGGACTTATCATATTGCTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCT
1333099 CGAAAGACTTACTGATGG
66 CGAAAGACTTACTGATGG
* * *
1333117 CCCGAAGGATTCTTAATCATAATGCTCGAAAGACTTACAAATGACCTGAAGGATTTCATCATCCT
1 CCCGAAGGA--CTT-ATCATATTGCTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCAT
* *
1333182 ACTCGAAAGATTTACTGATGG
63 GCTCGAAAGACTTACTGATGG
* * * * * * *
1333203 CCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATTACCCGAAGGATTTAAGCATCATGCT
1 CCCGAAGGACTTATCATATTGCTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCT
*
1333268 CGAAAGACTTATTGATGG
66 CGAAAGACTTACTGATGG
1333286 CCCGAAGGACTTA
1 CCCGAAGGACTTA
1333299 CTAAGTGTGA
Statistics
Matches: 155, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
81 9 0.06
83 71 0.46
84 5 0.03
85 26 0.17
86 44 0.28
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (83 bp):
CCCGAAGGACTTATCATATTGCTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCT
CGAAAGACTTACTGATGG
Found at i:1333290 original size:42 final size:42
Alignment explanation
Indices: 1333054--1333294 Score: 234
Period size: 42 Copynumber: 5.7 Consensus size: 42
1333044 ATTATTATTT
** * ** *
1333054 TGCTCGAAAGACTTACAAAT-GACCGAAATATTTCATCATCA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCA
*
1333095 TGCTCGAAAGACTTACTGATGGCCCGAAGGATTCTTAATCATAA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGA-T-TTAATCATCA
** * * * *
1333139 TGCTCGAAAGACTTACAAATGACCTGAAGGATTTCATCATCC
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCA
* * * *
1333181 TACTCGAAAGATTTACTGATGGCCCGAAGGACTT-ATCATCT
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCA
* * * ** *
1333222 TGCTCTAAAGGCTTACAGATTACCCGAAGGATTTAAGCATCA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCA
*
1333264 TGCTCGAAAGACTTATTGATGGCCCGAAGGA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGA
1333295 CTTACTAAGT
Statistics
Matches: 158, Mismatches: 38, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
41 50 0.32
42 71 0.45
43 2 0.01
44 35 0.22
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (42 bp):
TGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCA
Found at i:1333499 original size:42 final size:41
Alignment explanation
Indices: 1333399--1333505 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
1333389 TACCGAAGGT
* * * * *
1333399 CTTATGGATTGCCCGAAGGACTTATCATCTTGCTCTAAAGG
1 CTTATAGATGGCCCGAAGGACTTAGCATCTTGCTCGAAAGA
* * * *
1333440 CTTACAGATGACTCGAAGGATTTAAGCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCTTGCTCGAAAGA
*
1333482 CTTATTGATGGCCCGAAGGACTTA
1 CTTATAGATGGCCCGAAGGACTTA
1333506 TTAAGTGAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
41 18 0.35
42 33 0.65
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCTTGCTCGAAAGA
Found at i:1333676 original size:209 final size:214
Alignment explanation
Indices: 1333198--1334077 Score: 1066
Period size: 209 Copynumber: 4.2 Consensus size: 214
1333188 AAGATTTACT
* *
1333198 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATTACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACTCGAAGGATTTAAGCATC
*
1333263 ATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAAGTGTGAAAATTTGGAAATCAACTTC
66 ATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAA--GTGAAAATTTGGAAATCACCTTC
* *
1333328 TTAATTTTCAAAAATTTCATCTTCTTAAAACATCATTTT-TCA---TT----TTCATGTGAAAAC
129 TTAGTTTTCAAAGATTTCATCTTCTTAAAACATCATTTTCTCATTTTTCAAATTCATGTGAAAAC
1333385 ATCCTA-CCGAAGGTCTTATG
194 ATCCTACCCGAAGGTCTTATG
*
1333405 GATTGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACTCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACTCGAAGGATTTAAGCATC
* * * *
1333470 TTGCTCGAAAGACTTATTGATGGCCCGAAGGACTTATTAAGTG-AAATTTGAAAATCGCCTTCTT
66 ATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAAGTGAAAATTTGGAAATCACCTTCTT
*
1333534 AGTTTTCAAA-ATTTCATCTTCTTAAAACATCATTTTCTCA-TTTTCAAATTCATTTGAAAACAT
131 AGTTTTCAAAGATTTCATCTTCTTAAAACATCATTTTCTCATTTTTCAAATTCATGTGAAAACAT
* *
1333597 CCT-TCCGAAGGTTTTATG
196 CCTACCCGAAGGTCTTATG
* * *
1333615 GATGG-CCGAAGGACTTATTATCTTGCTCTAAAGGCTTATAGGTGACTCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACTCGAAGGATTTAAGCATC
* *
1333679 AAGCTCGAAAGGCTTACTT-ATGGCCCGAAGGACTTACTAAGTTTGAAAATTTGGAAATCACCTT
66 ATGCTCGAAAGACTTA-TTGATGGCCCGAAGGACTTACTAAG--TGAAAATTTGGAAATCACCTT
* *
1333743 CTTAGTTTTCAAAGA-TTCATTTTCTTAAAACATCA-CTTCTCATTTTCTCAAATTCATGTG-AA
128 CTTAGTTTTCAAAGATTTCATCTTCTTAAAACATCATTTTCTCATTTT-TCAAATTCATGTGAAA
* *
1333805 ACATCATACCCGAAGGTCTTATA
192 ACATCCTACCCGAAGGTCTTATG
* * * * * *
1333828 AATGGCCCAAAGGACTTATCATCTTACTCTAAAGGTTTACAGATGAC-CTAAAGGATTT-ATCA-
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACTC-GAAGGATTTAAGCAT
* * * * *
1333890 CA--CTCGAAAGACTTAATGATGG-CCGAAGGACTT-GTATAGCGCGAAATATTGGAAATCGCCT
65 CATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTA-AGTG-AAAAT-TTGGAAATCACCT
* * * * * *
1333951 TCTTACTTTTAAAATATTTCATTTTCTT-AAA-AT-ACTTTCTCATTTTTCAATTTCATGTGAAA
127 TCTTAGTTTTCAAAGATTTCATCTTCTTAAAACATCATTTTCTCATTTTTCAAATTCATGTGAAA
*
1334013 A-TTCCTACCCGAAGGTC-TATG
192 ACATCCTACCCGAAGGTCTTATG
* **
1334034 GATGGCCCGAAGGA-TTATCATCTTACTCTAAAGAATTACAGATG
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATG
1334078 GATTGCTTCA
Statistics
Matches: 593, Mismatches: 55, Indels: 52
0.85 0.08 0.07
Matches are distributed among these distances:
203 26 0.04
204 30 0.05
205 31 0.05
206 17 0.03
207 128 0.22
208 21 0.04
209 132 0.22
210 63 0.11
211 8 0.01
212 61 0.10
213 33 0.06
214 43 0.07
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (214 bp):
GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACTCGAAGGATTTAAGCATC
ATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAAGTGAAAATTTGGAAATCACCTTCTT
AGTTTTCAAAGATTTCATCTTCTTAAAACATCATTTTCTCATTTTTCAAATTCATGTGAAAACAT
CCTACCCGAAGGTCTTATG
Found at i:1340092 original size:54 final size:53
Alignment explanation
Indices: 1340019--1340270 Score: 299
Period size: 54 Copynumber: 4.7 Consensus size: 53
1340009 AAGCATGTTT
* * * * * * *
1340019 ACTCCCTATTCCTTCAGGGAGTAGA-AACTCGAACAATCTTTTGCCTACGAGTTT
1 ACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAAT-TTTT-CTTACGGGTTC
* *
1340073 GCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATTTTCTTCTTACGGGTTC
1 ACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATTT-TTCTTACGGGTTC
** * *
1340127 ACTCATTCTTTCTTTATGGAGTATAAAACTCGAACACATTTTTCTTACGGGTTC
1 ACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACA-ATTTTTCTTACGGGTTC
* * * *
1340181 GCTTCCTCTTTCTCTAGGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTC
1 ACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACA-ATTTTTCTTACGGGTTC
1340235 ACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACA
1 ACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACA
1340271 TCTTTATCAA
Statistics
Matches: 169, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
54 153 0.91
55 16 0.09
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (53 bp):
ACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATTTTTCTTACGGGTTC
Found at i:1340225 original size:108 final size:109
Alignment explanation
Indices: 1340034--1340275 Score: 339
Period size: 108 Copynumber: 2.2 Consensus size: 109
1340024 CTATTCCTTC
* * *
1340034 AGGGAGTA-GAAACTCGAACAATCTTTTGCCTACGAGTTTGCTCCCTCTTTCTTTAGGGAGTATA
1 AGGGAGTATAAAACTCGAACAATCTTTTGCCTACGAGTTCGCTCCCTCTTTCTCTAGGGAGTATA
** *
1340098 GAACTCGAACATTTTCTTCTTACGGGTTCACTCATTCTTTCTTT
66 GAACTCGAACACATTCTTCTTACGGGTTCACTCACTCTTTCTTT
* * * *
1340142 ATGGAGTATAAAACTCGAACACAT-TTTT-CTTACGGGTTCGCTTCCTCTTTCTCTAGGGAGTAT
1 AGGGAGTATAAAACTCGAACA-ATCTTTTGCCTACGAGTTCGCTCCCTCTTTCTCTAGGGAGTAT
*
1340205 AGAACTCGAACACATTCTTCTTACGGGTTCACTCCCTCTTTCTTT
65 AGAACTCGAACACATTCTTCTTACGGGTTCACTCACTCTTTCTTT
*
1340250 AGGGAGTATAGAACTCGAAC-ATCTTT
1 AGGGAGTATAAAACTCGAACAATCTTT
1340276 ATCAATCGTG
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
106 2 0.02
107 3 0.03
108 96 0.81
109 15 0.13
110 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (109 bp):
AGGGAGTATAAAACTCGAACAATCTTTTGCCTACGAGTTCGCTCCCTCTTTCTCTAGGGAGTATA
GAACTCGAACACATTCTTCTTACGGGTTCACTCACTCTTTCTTT
Found at i:1340312 original size:108 final size:108
Alignment explanation
Indices: 1340092--1340324 Score: 253
Period size: 108 Copynumber: 2.2 Consensus size: 108
1340082 TTCTTTAGGG
** * *
1340092 AGTATAGAACTCGAACATTTTCTTCTTACGGGTTCACTCATTCTTTCTTTATGGAGTATAAAACT
1 AGTATAGAACTCGAACACATTCTTCTTACGGGTTCACTCACTCTTTCTTTAGGGAGTATAAAACT
* * * * **
1340157 CGAACACATTTTTCTTACGGGTTCGCTTCCTCTTTCTCTAGGG
66 CGAACACATTTATCATACGGGTTCGCTTCCTCTATCACTAGAA
* *
1340200 AGTATAGAACTCGAACACATTCTTCTTACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACT
1 AGTATAGAACTCGAACACATTCTTCTTACGGGTTCACTCACTCTTTCTTTAGGGAGTATAAAACT
*
1340265 CGAACATC-TTTATCA-ATCGTG-TCTGC-TCC-CTATCACTTCAGAA
66 CGAACA-CATTTATCATA-CGGGTTC-GCTTCCTCTATCAC-T-AGAA
1340308 AGTATA-AGACTCGAACA
1 AGTATAGA-ACTCGAACA
1340325 ATCTTCAACA
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
106 5 0.05
107 8 0.08
108 92 0.87
109 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (108 bp):
AGTATAGAACTCGAACACATTCTTCTTACGGGTTCACTCACTCTTTCTTTAGGGAGTATAAAACT
CGAACACATTTATCATACGGGTTCGCTTCCTCTATCACTAGAA
Found at i:1340348 original size:55 final size:55
Alignment explanation
Indices: 1340253--1340877 Score: 929
Period size: 55 Copynumber: 11.4 Consensus size: 55
1340243 TTTCTTTAGG
* *
1340253 GAGTAT-AGAACTCGAAC-ATCTTTATCAATCGTGTCTGCTCCCTA-TCACTTCAGA
1 GAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC-CTTCAGA
*
1340307 AAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
1340362 GAGTATAAGACTCGAACAACCTTCAATAATTGTGTCTGCTCTCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
1340417 GAGTATAAGACTCAAAC-ATCTTCATCAAACGGGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
1340471 GAGTATAAGACTCGAACAACCTTAAACAATCGTGTTTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* *
1340526 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTATGCTCCCTAATCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * *
1340581 GAGTATAAGACTAGAACAATATTCAACAATTGTGTTTGCTCTCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1340636 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* **
1340691 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTACTCTATATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
** *
1340746 GAGTATAAGACTCGAAC-ATCTTCTTCAATCGTGTCTACTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
*
1340800 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
*
1340855 GAGTATAAGACTCAAAC-ATCTTC
1 GAGTATAAGACTCGAACAATCTTC
1340878 TTTAAACGGG
Statistics
Matches: 516, Mismatches: 50, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
54 115 0.22
55 399 0.77
56 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (55 bp):
GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
Found at i:1340455 original size:164 final size:164
Alignment explanation
Indices: 1340253--1340877 Score: 952
Period size: 164 Copynumber: 3.8 Consensus size: 164
1340243 TTTCTTTAGG
* * *
1340253 GAGTAT-AGAACTCGAACATCTTTATCAATCGTGTCTGCTCCCTA-TCACTTCAGAAAGTATAAG
1 GAGTATAAG-ACTCAAACATCTTCATCAATCGTGTCTGCTCCCTATTC-CTTCAGAGAGTATAAG
1340316 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAA
64 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAA
* * *
1340381 CCTTCAATAATTGTGTCTGCTCTCTATTCCTTCAGA
129 TCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGA
* *
1340417 GAGTATAAGACTCAAACATCTTCATCAAACGGGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
1 GAGTATAAGACTCAAACATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
* * *
1340482 TCGAACAACCTTAAACAATCGTGTTTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATC
66 TCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATC
* * *
1340547 TTCAACAATCGTGTATGCTCCCTAATCCTTCAGA
131 TTCAACAATCGTGTCTGCTCTCTATTCCTTCAGA
* * * * *
1340581 GAGTATAAGACT-AGAACAATATTCAACAATTGTGTTTGCTCTCTATTCCTTCAGAGAGTATAAG
1 GAGTATAAGACTCA-AAC-ATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
1340645 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAA
64 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAA
* *
1340710 TCTTCAACAATCGTGTCTACTCTATATTCCTTCAGA
129 TCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGA
* * *
1340746 GAGTATAAGACTCGAACATCTTCTTCAATCGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGAC
1 GAGTATAAGACTCAAACATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
* *
1340811 TCGAACAATCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCAAAC-ATC
66 TCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATC
1340875 TTC
131 TTC
1340878 TTTAAACGGG
Statistics
Matches: 417, Mismatches: 39, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
163 7 0.02
164 259 0.62
165 151 0.36
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (164 bp):
GAGTATAAGACTCAAACATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
TCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATC
TTCAACAATCGTGTCTGCTCTCTATTCCTTCAGA
Found at i:1340663 original size:329 final size:328
Alignment explanation
Indices: 1340278--1340877 Score: 1004
Period size: 329 Copynumber: 1.8 Consensus size: 328
1340268 ACATCTTTAT
1340278 CAATCGTGTCTGCTCCCTATCACTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATCGTGTC
1 CAATCGTGTCTGCTCCCTATCACTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATCGTGTC
* * * *
1340343 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAATAATTGTGTCTGCTCTCTAT
66 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAACAATCGTGTCTACTCTATAT
*
1340408 TCCTTCAGAGAGTATAAGACTCAAACATCTTCATCAAACGGGTCTGCTCCCTATTCCTTCAGAGA
131 TCCTTCAGAGAGTATAAGACTCAAACATCTTCATCAAACGGGTCTACTCCCTATTCCTTCAGAGA
*
1340473 GTATAAGACTCGAACAACCTTAAACAATCGTGTTTGCTCCCTATTCCTTCAGAGAGTATAAGACT
196 GTATAAGACTCGAACAACCTTAAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACT
*
1340538 CGAACAATCTTCAACAATCGTGTATGCTCCCTAATCCTTCAGAGAGTATAAGACTAGAACAATAT
261 CAAAC-ATCTTCAACAATCGTGTATGCTCCCTAATCCTTCAGAGAGTATAAGACTAGAACAATAT
1340603 TCAA
325 TCAA
* * * *
1340607 CAATTGTGTTTGCTCTCTATTC-CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGT
1 CAATCGTGTCTGCTCCCTA-TCACTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATCGTGT
*
1340671 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTACTCTATA
65 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAACAATCGTGTCTACTCTATA
* * * *
1340736 TTCCTTCAGAGAGTATAAGACTCGAACATCTTCTTCAATCGTGTCTACTCCCTATTCCTTCAGAG
130 TTCCTTCAGAGAGTATAAGACTCAAACATCTTCATCAAACGGGTCTACTCCCTATTCCTTCAGAG
* * *
1340801 AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGAC
195 AGTATAAGACTCGAACAACCTTAAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
1340866 TCAAACATCTTC
260 TCAAACATCTTC
1340878 TTTAAACGGG
Statistics
Matches: 251, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
328 6 0.02
329 243 0.97
330 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (328 bp):
CAATCGTGTCTGCTCCCTATCACTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATCGTGTC
TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAACAATCGTGTCTACTCTATAT
TCCTTCAGAGAGTATAAGACTCAAACATCTTCATCAAACGGGTCTACTCCCTATTCCTTCAGAGA
GTATAAGACTCGAACAACCTTAAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACT
CAAACATCTTCAACAATCGTGTATGCTCCCTAATCCTTCAGAGAGTATAAGACTAGAACAATATT
CAA
Found at i:1342869 original size:125 final size:125
Alignment explanation
Indices: 1342646--1342885 Score: 340
Period size: 125 Copynumber: 1.9 Consensus size: 125
1342636 CGCAATATTA
* * * * *
1342646 TCTTATATTGGTATGGGCCTTCAAAATGCCCCAACATCTCATATTGTAAGGCTCACTCTCAATGC
1 TCTTATACTGGTACGAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACTCTCAATGC
*
1342711 CTTCTTGGTATAAATCTTGTCATCTCAATATGATGTGGGTTCAGTCGTGCTCCAAAATTG
66 CTTCTTGGTATAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCTCCAAAATTG
* * *
1342771 TCTTATACTGGTACGAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTATTC-ATG
1 TCTTATACTGGTACGAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACT-CTCAATG
* * *
1342835 CC-TCATTGGTTTGAATCTTGTCATCTCAACATGATGTGGGTTCATTCGTGC
65 CCTTC-TTGGTATAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGC
1342886 CCGAACATAT
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
124 2 0.02
125 97 0.96
126 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (125 bp):
TCTTATACTGGTACGAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACTCTCAATGC
CTTCTTGGTATAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCTCCAAAATTG
Done.