Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008078.1 Hibiscus syriacus cultivar Beakdansim tig00110580_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: 1434613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1123909 original size:9 final size:9
Alignment explanation
Indices: 1123895--1123929 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1123885 TTTTATAGCC
1123895 CCGCCGTCG
1 CCGCCGTCG
1123904 CCGCCGTCG
1 CCGCCGTCG
* *
1123913 CCACCATCG
1 CCGCCGTCG
1123922 CCGCCGTC
1 CCGCCGTC
1123930 ACAAAGTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.06, C:0.57, G:0.26, T:0.11
Consensus pattern (9 bp):
CCGCCGTCG
Found at i:1124493 original size:34 final size:35
Alignment explanation
Indices: 1124416--1124504 Score: 126
Period size: 35 Copynumber: 2.6 Consensus size: 35
1124406 TAATACTTAC
* * * *
1124416 TTTATTTTGTTGATTTGGTTGGATTTTTTTTTGAT
1 TTTATTTTGTTAATTTTGTTGGATTTTTTGTTGAA
*
1124451 TTTTTTTTGTTAATTTTGTTGGATTTTTTGTT-AA
1 TTTATTTTGTTAATTTTGTTGGATTTTTTGTTGAA
1124485 TTTATTTTGTTAATTTTGTT
1 TTTATTTTGTTAATTTTGTT
1124505 TATTATCATT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 20 0.42
35 28 0.58
ACGTcount: A:0.13, C:0.00, G:0.16, T:0.71
Consensus pattern (35 bp):
TTTATTTTGTTAATTTTGTTGGATTTTTTGTTGAA
Found at i:1141457 original size:22 final size:22
Alignment explanation
Indices: 1141432--1141478 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1141422 TATATTATTT
* *
1141432 AAATTATTTATGTTTATGTGTA
1 AAATTATTTACGTTTATGTGCA
1141454 AAATTATTTACGTTTATGTGCA
1 AAATTATTTACGTTTATGTGCA
1141476 AAA
1 AAA
1141479 AATTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (22 bp):
AAATTATTTACGTTTATGTGCA
Found at i:1142922 original size:14 final size:14
Alignment explanation
Indices: 1142896--1142944 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1142886 ATATTCCTCT
1142896 TTTAT-TTAT-TTA
1 TTTATATTATATTA
1142908 TTTATATTATATTA
1 TTTATATTATATTA
*
1142922 TTTTTATTATATATA
1 TTTATATTATAT-TA
1142937 TCTTATAT
1 T-TTATAT
1142945 CATTATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 5 0.16
13 4 0.13
14 14 0.45
15 3 0.10
16 5 0.16
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATATTATATTA
Found at i:1146380 original size:26 final size:27
Alignment explanation
Indices: 1146334--1146386 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
1146324 AAAAAAGAGA
1146334 AAAAAGAGAAAAAAAGCAAAGGGAAAAT
1 AAAAAGAGAAAAAAAGCAAA-GGAAAAT
1146362 AAAAAGAG-AAAAAA-CAAAGGAAAAT
1 AAAAAGAGAAAAAAAGCAAAGGAAAAT
1146387 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 6 0.24
28 8 0.32
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.04
Consensus pattern (27 bp):
AAAAAGAGAAAAAAAGCAAAGGAAAAT
Found at i:1148177 original size:36 final size:36
Alignment explanation
Indices: 1148130--1148355 Score: 207
Period size: 36 Copynumber: 6.4 Consensus size: 36
1148120 ATTGAAAACA
* *
1148130 TTTCCCTTGAAATAAATTTCATCTCTCCTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
**
1148166 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
* *
1148202 TTTCCCTTGAAACAAA----A--TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACA-G
*** * *
1148231 TTTTATTTGAAACAAATTTCATCTCCCTTAAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
** * * **
1148267 TTTCTTTTGGAACTAAGTTTTTTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCATCTCTCTTGAGACAG
* *
1148304 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
1148340 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
1148356 ATCTTTGAAT
Statistics
Matches: 152, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
30 2 0.01
33 1 0.01
35 1 0.01
36 97 0.64
37 31 0.20
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
Found at i:1148241 original size:101 final size:101
Alignment explanation
Indices: 1148054--1148319 Score: 320
Period size: 101 Copynumber: 2.6 Consensus size: 101
1148044 TTTTATTTCA
* * *
1148054 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAA
* *
1148119 CATTGAAAACATTTCCCTTGAAATAAATTTCATCTCTC
65 CATTGAAAACATTTCACTTGAAACAAATTTCATCTC-C
* *
1148157 C-TGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 CTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAC
* ** * *
1148220 ATTTGAATATGTTTTATTTGAAACAAATTTCATCTCC
66 A-TTGAAAACATTTCACTTGAAACAAATTTCATCTCC
* ** * * * *
1148257 CTTAAGACAGTTTCTTTTGGAACTAAGTTTTTTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 CTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1148320 TTTCGTCTCT
Statistics
Matches: 141, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
100 6 0.04
101 78 0.55
102 56 0.40
103 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (101 bp):
CTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAC
ATTGAAAACATTTCACTTGAAACAAATTTCATCTCC
Found at i:1148403 original size:138 final size:138
Alignment explanation
Indices: 1148151--1148409 Score: 392
Period size: 138 Copynumber: 1.9 Consensus size: 138
1148141 ATAAATTTCA
*
1148151 TCTCTCCTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCCTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* * ** *
1148216 AAATATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACT
66 AAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACT
1148281 AAGTTTTT
131 AAGTTTTT
* *
1148289 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCCTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* * * ** *
1148354 AAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGACAGTTTCT
1148410 CTTGAAACAT
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 107 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (138 bp):
TCTCTCCTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
AAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACT
AAGTTTTT
Found at i:1149395 original size:110 final size:110
Alignment explanation
Indices: 1149190--1149442 Score: 282
Period size: 110 Copynumber: 2.3 Consensus size: 110
1149180 GATTCCCAGT
* *
1149190 TTCAGAGACAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAAATTCA
1 TTCAGAGACAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* * * *
1149255 TAACGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAATTTCA
66 CAACGAAGGGGCGACTGACTATCAAAAAACAACTTTTCAATTTCA
* * * * *
1149300 TTCAGAGTCAATTTCAACTTTACAGTGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGACAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* * * * * *
1149365 CAGCGAATGGGC-AGCTGGCTATCAAAAAACAA-TTTCCCAGTTC-
66 CAACGAAGGGGCGA-CTGACTATCAAAAAACAACTTTTCAATTTCA
* * *
1149408 --CAGAGCCAATTTCAACTTCACGGCGGAGGATATTG
1 TTCAGAGACAATTTCAACTTCACAGCGAAGGATATTG
1149443 GACTAGAAAC
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
106 30 0.25
109 9 0.08
110 81 0.68
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (110 bp):
TTCAGAGACAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
CAACGAAGGGGCGACTGACTATCAAAAAACAACTTTTCAATTTCA
Found at i:1150761 original size:13 final size:13
Alignment explanation
Indices: 1150711--1150765 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
1150701 TGAATCTTAA
1150711 TCTTT-AATTTAC
1 TCTTTAAATTTAC
1150723 -CTTTAAATTTAC
1 TCTTTAAATTTAC
*
1150735 CCTTTAAATTTAC
1 TCTTTAAATTTAC
*
1150748 TCTTTAATTTTAC
1 TCTTTAAATTTAC
1150761 T-TTTA
1 TCTTTA
1150766 TATTAATTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 4 0.10
12 11 0.28
13 24 0.62
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.56
Consensus pattern (13 bp):
TCTTTAAATTTAC
Found at i:1150855 original size:17 final size:18
Alignment explanation
Indices: 1150835--1150909 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 18
1150825 ATTCCTCTTT
1150835 TTATTTATTTATT-TATA
1 TTATTTATTTATTATATA
*
1150852 TTATTTTTTTATTATATA
1 TTATTTATTTATTATATA
*
1150870 -TATCTTATATATATATATA
1 TTAT-TTATTTAT-TATATA
* *
1150889 TATATATATATATATATATA
1 T-TATTTATTTAT-TATATA
1150909 T
1 T
1150910 ATATATATAG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
17 15 0.31
18 10 0.20
19 6 0.12
20 15 0.31
21 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATTTATTTATTATATA
Found at i:1150860 original size:25 final size:26
Alignment explanation
Indices: 1150805--1150879 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
1150795 TTAATTATAT
* * *
1150805 TTTTTTTATTTTTTTA-CTATATTCC
1 TTTTTTTATTTATTTATTTATATTCA
*
1150830 TCTTTTTATTTATTTATTTATATT-A
1 TTTTTTTATTTATTTATTTATATTCA
*
1150855 TTTTTTTATTATATATATCTTATAT
1 TTTTTTTATT-TATTTAT-TTATAT
1150880 ATATATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 23 0.56
26 12 0.29
27 6 0.15
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTTTTATTTATTTATTTATATTCA
Found at i:1150869 original size:2 final size:2
Alignment explanation
Indices: 1150864--1150918 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
1150854 ATTTTTTTAT
*
1150864 TA TA TA TA TC T- 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
1150905 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1150919 GATGTATTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1151065 original size:42 final size:44
Alignment explanation
Indices: 1150948--1151039 Score: 117
Period size: 39 Copynumber: 2.2 Consensus size: 44
1150938 ATTTGCTATG
1150948 TATATATATATTTTCTTAATA-T-TA---TATTTTTTATGTTTT
1 TATATATATATTTTCTTAATATTCTATTTTATTTTTTATGTTTT
1150987 TATATATATATTTTCTTAATATTCTATTTT-TGTTTTTAT-TTATT
1 TATATATATATTTTCTTAATATTCTATTTTAT-TTTTTATGTT-TT
1151031 TATATATAT
1 TATATATAT
1151040 TATATTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
39 21 0.46
40 1 0.02
41 2 0.04
43 3 0.07
44 19 0.41
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (44 bp):
TATATATATATTTTCTTAATATTCTATTTTATTTTTTATGTTTT
Found at i:1160562 original size:15 final size:15
Alignment explanation
Indices: 1160542--1160572 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1160532 CAACAAATAG
1160542 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1160557 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1160572 A
1 A
1160573 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1163992 original size:177 final size:177
Alignment explanation
Indices: 1163696--1164050 Score: 710
Period size: 177 Copynumber: 2.0 Consensus size: 177
1163686 TTAGCTGTAT
1163696 ATTAGAAAGAAAAAAAAGGGAAAATCTTGCTCTTGCATAACTAGATCTGTGAGCAGCATTGCTTA
1 ATTAGAAAGAAAAAAAAGGGAAAATCTTGCTCTTGCATAACTAGATCTGTGAGCAGCATTGCTTA
1163761 AGTGGTGTCGTGGTTGCTTGTTTTTTACAAATATGTTATTTATATTGATCTTGTTTTAATTCTAA
66 AGTGGTGTCGTGGTTGCTTGTTTTTTACAAATATGTTATTTATATTGATCTTGTTTTAATTCTAA
1163826 TATGATTGGGTTGCAAATAGATCGAAGATATATTTGAAGTCAAGTCA
131 TATGATTGGGTTGCAAATAGATCGAAGATATATTTGAAGTCAAGTCA
1163873 ATTAGAAAGAAAAAAAAGGGAAAATCTTGCTCTTGCATAACTAGATCTGTGAGCAGCATTGCTTA
1 ATTAGAAAGAAAAAAAAGGGAAAATCTTGCTCTTGCATAACTAGATCTGTGAGCAGCATTGCTTA
1163938 AGTGGTGTCGTGGTTGCTTGTTTTTTACAAATATGTTATTTATATTGATCTTGTTTTAATTCTAA
66 AGTGGTGTCGTGGTTGCTTGTTTTTTACAAATATGTTATTTATATTGATCTTGTTTTAATTCTAA
1164003 TATGATTGGGTTGCAAATAGATCGAAGATATATTTGAAGTCAAGTCA
131 TATGATTGGGTTGCAAATAGATCGAAGATATATTTGAAGTCAAGTCA
1164050 A
1 A
1164051 CAGATCTAGA
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 178 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (177 bp):
ATTAGAAAGAAAAAAAAGGGAAAATCTTGCTCTTGCATAACTAGATCTGTGAGCAGCATTGCTTA
AGTGGTGTCGTGGTTGCTTGTTTTTTACAAATATGTTATTTATATTGATCTTGTTTTAATTCTAA
TATGATTGGGTTGCAAATAGATCGAAGATATATTTGAAGTCAAGTCA
Found at i:1177078 original size:134 final size:134
Alignment explanation
Indices: 1176913--1177163 Score: 457
Period size: 134 Copynumber: 1.9 Consensus size: 134
1176903 GATGACATTG
* *
1176913 CTCATACGTGATAAAGTGTTTTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGA
1 CTCATACGTGATAAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGA
*
1176978 GGACGGCTGGTTATCTAGGGGTGACACGACTCATACGTGATGAAGAGATATGTTCGGGGGATGGC
66 GGACGGCTGGTTATCTAGGAGTGACACGACTCATACGTGATGAAGAGATATGTTCGGGGGATGGC
1177043 ACGA
131 ACGA
*
1177047 CTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGA
1 CTCATACGTGATAAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGA
*
1177112 GGACGGCTGGTTATCTAGTAGTGACACGACTCATACGTGATGAAGAGATATG
66 GGACGGCTGGTTATCTAGGAGTGACACGACTCATACGTGATGAAGAGATATG
1177164 GTCAAGGGAT
Statistics
Matches: 112, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 112 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (134 bp):
CTCATACGTGATAAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGA
GGACGGCTGGTTATCTAGGAGTGACACGACTCATACGTGATGAAGAGATATGTTCGGGGGATGGC
ACGA
Found at i:1177210 original size:134 final size:134
Alignment explanation
Indices: 1176938--1177214 Score: 414
Period size: 134 Copynumber: 2.1 Consensus size: 134
1176928 GTGTTTTGGT
*
1176938 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGAC
1 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGAGTGAC
* ** * *
1177003 ACGACTCATACGTGATGAAGAGATATGTTCGGGGGATGGCACGACTCATACGTGATGAAGAGTTC
66 ACGACTCATACGTGATGAAGAGATATGGTCAAGGGATGACACGACTCATACGTGATGAAGAGTGC
**
1177068 TGGT
131 TGAC
*
1177072 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGTAGTGAC
1 CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGAGTGAC
* * *
1177137 ACGACTCATACGTGATGAAGAGATATGGTCAAGGGATGACAC-AGTTCCTACGTGATGAGGACG-
66 ACGACTCATACGTGATGAAGAGATATGGTCAAGGGATGACACGA-CTCATACGTGATGAAGA-GT
1177200 GCTGAC
129 GCTGAC
1177206 CATCTTTAG
1 CATCTTTAG
1177215 TGATTATGGT
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
133 1 0.01
134 127 0.98
135 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (134 bp):
CATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGAGTGAC
ACGACTCATACGTGATGAAGAGATATGGTCAAGGGATGACACGACTCATACGTGATGAAGAGTGC
TGAC
Found at i:1177263 original size:28 final size:28
Alignment explanation
Indices: 1177223--1177362 Score: 124
Period size: 29 Copynumber: 4.9 Consensus size: 28
1177213 AGTGATTATG
**
1177223 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACCGACTCAAAGATTT
* *
1177251 GTTTCAAAAGAAACAGACTCAAAGGTTT
1 GTTTCAAAAGAAACCGACTCAAAGATTT
* *
1177279 TTTTCAAAAGAAA-CAACTCAAAGATTTTT
1 GTTTCAAAAGAAACCGACTCAAAGA--TTT
* *
1177308 ATTTCAAAAGAAA-CAACTCACAA-ACTTTT
1 GTTTCAAAAGAAACCGACTCA-AAGA--TTT
* *
1177337 GTTTCAAGAGAAACAGACTCAAAGAT
1 GTTTCAAAAGAAACCGACTCAAAGAT
1177363 AGGTTTTGTT
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
27 8 0.09
28 37 0.40
29 40 0.43
30 8 0.09
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (28 bp):
GTTTCAAAAGAAACCGACTCAAAGATTT
Found at i:1177321 original size:29 final size:29
Alignment explanation
Indices: 1177239--1177412 Score: 169
Period size: 29 Copynumber: 5.9 Consensus size: 29
1177229 AGGGAAACCG
1177239 ACTCAAAGA--TTTGTTTCAAAAGAAACA
1 ACTCAAAGATTTTTGTTTCAAAAGAAACA
*
1177266 GACTCAAAG-GTTTT-TTTCAAAAGAAACA
1 -ACTCAAAGATTTTTGTTTCAAAAGAAACA
*
1177294 ACTCAAAGATTTTTATTTCAAAAGAAACA
1 ACTCAAAGATTTTTGTTTCAAAAGAAACA
* *
1177323 ACTCACAA-ACTTTTGTTTCAAGAGAAACA
1 ACTCA-AAGATTTTTGTTTCAAAAGAAACA
**
1177352 GACTCAAAGATAGGTTTTGTTTCAAGGGAAACA
1 -ACTCAAAGAT---TTTTGTTTCAAAAGAAACA
* * *
1177385 ATCTCAAAGATGTTTGTTTTAAGAGAAA
1 A-CTCAAAGATTTTTGTTTCAAAAGAAA
1177413 TTGTCTCAAA
Statistics
Matches: 126, Mismatches: 9, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
27 8 0.06
28 26 0.21
29 42 0.33
30 22 0.17
32 1 0.01
33 27 0.21
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (29 bp):
ACTCAAAGATTTTTGTTTCAAAAGAAACA
Found at i:1177539 original size:36 final size:36
Alignment explanation
Indices: 1177498--1177570 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
1177488 AAGAGACAGA
1177498 ATTTTGTTTCAA-AGAAACATACTCAAAGATTCTTTC
1 ATTTTGTTTCAAGAGAAACATACTCAAAGATT-TTTC
* *
1177534 ATTTTGTTTTAAGTGAAACATACTCAAAGATTTTTC
1 ATTTTGTTTCAAGAGAAACATACTCAAAGATTTTTC
1177570 A
1 A
1177571 AGAAAATCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 16 0.47
37 18 0.53
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (36 bp):
ATTTTGTTTCAAGAGAAACATACTCAAAGATTTTTC
Found at i:1177653 original size:30 final size:31
Alignment explanation
Indices: 1177599--1177657 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1177589 GAGACAAAGT
1177599 TTTGTTTAAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTAAAAAGAAATAGACTCAAAGATCC
*
1177630 TTTGTTTCAAAAGAAAT-GACTCAAAGAT
1 TTTGTTTAAAAAGAAATAGACTCAAAGAT
1177658 GATGCTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTAAAAAGAAATAGACTCAAAGATCC
Found at i:1177735 original size:36 final size:36
Alignment explanation
Indices: 1177695--1177832 Score: 138
Period size: 36 Copynumber: 3.8 Consensus size: 36
1177685 ATAATTTGGA
* *
1177695 AAATTGTCTTAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * * *
1177731 AAATTTTCTTAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
1177767 AAATTGTCTCAAGCGAGACAA-AGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACA-TTTGTTTTTAGAG
** *
1177802 AAAACGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
1177833 AATGTGAAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
35 8 0.09
36 75 0.87
37 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:1178432 original size:16 final size:16
Alignment explanation
Indices: 1178411--1178450 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1178401 ATCATGTAAT
**
1178411 ATGTATGTATGTGTTG
1 ATGTATGTATGCATTG
1178427 ATGTATGTATGCATTG
1 ATGTATGTATGCATTG
1178443 ATGTATGT
1 ATGTATGT
1178451 TTTCTCGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.47
Consensus pattern (16 bp):
ATGTATGTATGCATTG
Found at i:1183233 original size:44 final size:45
Alignment explanation
Indices: 1183112--1183237 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
1183102 TATAAAATCT
1183112 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
1183157 CTTACCATTTAAATTCCATAAGGTCGTAAGCTTATTTTTCTAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1183204 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1183238 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 37 0.52
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1187252 original size:16 final size:15
Alignment explanation
Indices: 1187231--1187278 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
1187221 GTGAAATATT
1187231 TTTTTTTCATTTCTCA
1 TTTTTTTC-TTTCTCA
1187247 TTTTTTTC--TCT-A
1 TTTTTTTCTTTCTCA
1187259 TTTCTTTTCTTTCTCA
1 TTT-TTTTCTTTCTCA
1187275 TTTT
1 TTTT
1187279 CATTTTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.14
13 8 0.29
15 4 0.14
16 12 0.43
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTCTTTCTCA
Found at i:1187283 original size:6 final size:6
Alignment explanation
Indices: 1187234--1187328 Score: 58
Period size: 6 Copynumber: 15.7 Consensus size: 6
1187224 AAATATTTTT
1187234 TTTTCA TTTCTCA TTTT-- TTTCTC- TATTTC- TTTTC- TTTCTCA TTTTCA
1 TTTTCA TTT-TCA TTTTCA TTT-TCA T-TTTCA TTTTCA TTT-TCA TTTTCA
* * *
1187281 TTTTCA TTTTCTC TTTTC- TTCTTCA TTTTCT TTTTCT TTTTCTA TTTT
1 TTTTCA TTTTC-A TTTTCA TT-TTCA TTTTCA TTTTCA TTTTC-A TTTT
1187329 TTTTCTTATA
Statistics
Matches: 76, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
4 3 0.04
5 10 0.13
6 41 0.54
7 22 0.29
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCA
Found at i:1187296 original size:31 final size:31
Alignment explanation
Indices: 1187261--1187334 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1187251 TTTCTCTATT
1187261 TCTTTTCTTTCTCATTTTCATTTTCATTTTC
1 TCTTTTCTTTCTCATTTTCATTTTCATTTTC
* *
1187292 TCTTTTC-TTCTTCATTTTCTTTTTCTTTTTC
1 TCTTTTCTTTC-TCATTTTCATTTTCATTTTC
* *
1187323 TATTTTTTTTCT
1 TCTTTTCTTTCT
1187335 TATAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 31 0.84
32 3 0.08
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (31 bp):
TCTTTTCTTTCTCATTTTCATTTTCATTTTC
Found at i:1187321 original size:12 final size:12
Alignment explanation
Indices: 1187249--1187335 Score: 70
Period size: 12 Copynumber: 7.2 Consensus size: 12
1187239 ATTTCTCATT
1187249 TTTTTCTCTATTTC
1 TTTTTCT-T-TTTC
*
1187263 -TTTTCTTTCTC
1 TTTTTCTTTTTC
* *
1187274 ATTTTCATTTTC
1 TTTTTCTTTTTC
*
1187286 ATTTTCTCTTTTC
1 TTTTTCT-TTTTC
* *
1187299 TTCTTCATTTTC
1 TTTTTCTTTTTC
1187311 TTTTTCTTTTTC
1 TTTTTCTTTTTC
*
1187323 TATTT-TTTTTC
1 TTTTTCTTTTTC
1187334 TT
1 TT
1187336 ATAATATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
11 10 0.17
12 35 0.58
13 15 0.25
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:1187344 original size:2 final size:2
Alignment explanation
Indices: 1187335--1187364 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1187325 TTTTTTTTCT
1187335 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1187365 TTAGCTCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1188222 original size:16 final size:16
Alignment explanation
Indices: 1188201--1188232 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1188191 AATCGTAACC
1188201 ATTGTTGATATCACTT
1 ATTGTTGATATCACTT
*
1188217 ATTGTTGATTTCACTT
1 ATTGTTGATATCACTT
1188233 TTTCATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (16 bp):
ATTGTTGATATCACTT
Found at i:1190280 original size:44 final size:46
Alignment explanation
Indices: 1190161--1190284 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 46
1190151 TAAAATCTCT
*
1190161 TACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACA
1 TACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACA
* * ** *
1190206 TACCATTTAAATTCCATAAGGTCGTAAGCTTATTTTTCCATTATACT
1 TACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACA
* * *
1190253 TGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 TACCATTTAATTCCATAAGCTCGTAAGCTTATTT
1190285 GCATGGTTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
44 22 0.33
45 8 0.12
46 2 0.03
47 35 0.52
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.39
Consensus pattern (46 bp):
TACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACA
Found at i:1196196 original size:2 final size:2
Alignment explanation
Indices: 1196189--1196271 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
1196179 ATAATAAGAG
1196189 TA TA TA 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
1196231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1196272 CATGTTTGTA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1198375 original size:16 final size:16
Alignment explanation
Indices: 1198354--1198384 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1198344 TTTTTTCAAC
1198354 TATTTAATTATATATG
1 TATTTAATTATATATG
*
1198370 TATTTATTTATATAT
1 TATTTAATTATATAT
1198385 ACATTTTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTTAATTATATATG
Found at i:1198672 original size:34 final size:35
Alignment explanation
Indices: 1198634--1198700 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
1198624 ATATTTAATT
* * *
1198634 TATTTCATTTTTTA-TTATTTTTTTTCTTTTTTTG
1 TATTTCATTATTTATTTACTTATTTTCTTTTTTTG
**
1198668 TATTTTGTTATTTATTTACTTATTTTCTTTTTT
1 TATTTCATTATTTATTTACTTATTTTCTTTTTT
1198701 CCTTTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 11 0.41
35 16 0.59
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.78
Consensus pattern (35 bp):
TATTTCATTATTTATTTACTTATTTTCTTTTTTTG
Found at i:1198679 original size:42 final size:40
Alignment explanation
Indices: 1198632--1198750 Score: 109
Period size: 42 Copynumber: 2.8 Consensus size: 40
1198622 CTATATTTAA
*
1198632 TTTATTTCATTTTTTATTATTTTTTTTCTTTTTT-TGTATTT
1 TTTATTT-ATTTTTTATTATTTTTTTTCTTTTTTCTGT-TTC
*
1198673 TGTTATTTATTTACTTATT-TTCTTTTTTCCTTTTTTCTGTTTC
1 T-TTATTTATTT-TTTATTATT-TTTTTT-CTTTTTTCTGTTTC
*
1198716 TTTATTTATATTTTGTA-TATTTTATTTACTTTTTT
1 TTTATTTAT-TTTT-TATTATTTT-TTTTCTTTTTT
1198751 ATATCATTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
41 7 0.11
42 36 0.55
43 19 0.29
44 3 0.05
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (40 bp):
TTTATTTATTTTTTATTATTTTTTTTCTTTTTTCTGTTTC
Found at i:1198749 original size:20 final size:19
Alignment explanation
Indices: 1198716--1198754 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1198706 TTTCTGTTTC
1198716 TTTATTTATATTTTGTATAT
1 TTTATTTATATTTT-TATAT
1198736 TTTATTTACT-TTTTTATAT
1 TTTATTTA-TATTTTTATAT
1198755 CATTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 12 0.67
21 1 0.06
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTATTTATATTTTTATAT
Found at i:1204096 original size:36 final size:36
Alignment explanation
Indices: 1204056--1204173 Score: 110
Period size: 36 Copynumber: 3.2 Consensus size: 36
1204046 ATACTTTGCC
1204056 TCACTCGAGATTGTTTTACTCGAAAGAAGATTTATT
1 TCACTCGAGATTGTTTTACTCGAAAGAAGATTTATT
* * ** * * *
1204092 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTCGAGATTGTTTTACTCGAAAGAAGATTTATT
* * *
1204128 TCGCTTGAGACTGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTCGAGATTGTTTT-ACTCGAAAGAA-G-ATTT-ATT
1204168 TCACTC
1 TCACTC
1204174 AAGACTATTT
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
36 42 0.71
37 7 0.12
38 1 0.02
39 4 0.07
40 5 0.08
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (36 bp):
TCACTCGAGATTGTTTTACTCGAAAGAAGATTTATT
Found at i:1204143 original size:72 final size:74
Alignment explanation
Indices: 1204012--1204211 Score: 223
Period size: 72 Copynumber: 2.7 Consensus size: 74
1204002 TAATGCAGAT
* * * * * * *
1204012 GATTTATCTCACTTAAGATTGTTTTTCTTAAAACATA-CTTTGCCTCACTCGAGATTGTTTT-AC
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACA-AGATTTGTCTCGCTTGAGACTGTTTTCAC
1204075 TCGAAAGAA-
65 TCGAAAGAAG
1204084 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACTGTTTTCACT
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACTGTTTTCACT
1204149 CGAAAGAAG
66 CGAAAGAAG
* * * *
1204158 GCATTTCATTTCACTCAAGACT-ATTTT-TT-ATAGAAGATTTTGTCTCGCTTGAGA
1 G-ATTT-ATTTCACTCAAGATTGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGA
1204212 TAGTTTCTCT
Statistics
Matches: 111, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 52 0.47
73 17 0.15
74 19 0.17
75 8 0.07
76 14 0.13
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (74 bp):
GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACTGTTTTCACT
CGAAAGAAG
Found at i:1204247 original size:39 final size:39
Alignment explanation
Indices: 1204191--1204270 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
1204181 TTTTTTATAG
* * *
1204191 AAGATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAACAA
* *
1204230 AAGATTTTATCTTGCTTGAGATAATTTCCCTTGAAACAA
1 AAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAACAA
1204269 AA
1 AA
1204271 TTTTGTCAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAACAA
Found at i:1204356 original size:36 final size:36
Alignment explanation
Indices: 1204309--1204392 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
1204299 ATTGAAAACA
* * *
1204309 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAG
1204345 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAG
*
1204381 TTTCTCTTGAAA
1 TTTCCCTTGAAA
1204393 CATAAACTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAG
Found at i:1204559 original size:30 final size:30
Alignment explanation
Indices: 1204525--1204586 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1204515 TTTATCTCCC
1204525 TTGAGACAGTTTCTCTTGAAACACCAACCT
1 TTGAGACAGTTTCTCTTGAAACACCAACCT
1204555 TTGAGACAGTTTCTCTTGAAACACCAACCT
1 TTGAGACAGTTTCTCTTGAAACACCAACCT
1204585 TT
1 TT
1204587 AAGATTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (30 bp):
TTGAGACAGTTTCTCTTGAAACACCAACCT
Found at i:1204599 original size:96 final size:97
Alignment explanation
Indices: 1204458--1204642 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 97
1204448 TGAAATGAGT
* * * *
1204458 TTTGAGACAGTTTCCCTTAAAACACCCACATTTGAGATTGTTTCCCTTGAAACATATTT-TATCT
1 TTTGAGACAGTTTCCCTTAAAACACCAACATTTAAGATTATTTCCCTTGAAACAAATTTCT-TCT
*
1204522 CCCTTGAGAC-AGTTTCTCTTGAAACACCAACC
65 CCCTTGAGACAAGTTTCCCTTGAAACACCAACC
* * *
1204554 TTTGAGACAGTTTCTCTTGAAACACCAACCTTTAAGATTATTTCCCTTGAAACAAATTTCTTCTC
1 TTTGAGACAGTTTCCCTTAAAACACCAACATTTAAGATTATTTCCCTTGAAACAAATTTCTTCTC
* *
1204619 TCTTGAGACAATTTTCCCTTGAAA
66 CCTTGAGACAAGTTTCCCTTGAAA
1204643 TAAGAAATGT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
96 64 0.83
97 13 0.17
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (97 bp):
TTTGAGACAGTTTCCCTTAAAACACCAACATTTAAGATTATTTCCCTTGAAACAAATTTCTTCTC
CCTTGAGACAAGTTTCCCTTGAAACACCAACC
Found at i:1204603 original size:30 final size:30
Alignment explanation
Indices: 1204528--1204607 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
1204518 ATCTCCCTTG
*
1204528 AGACAGTTTCTCTTGAAACACCAACCTTTG
1 AGACAGTTTCTCTTGAAACACCAACCTTTA
1204558 AGACAGTTTCTCTTGAAACACCAACCTTTA
1 AGACAGTTTCTCTTGAAACACCAACCTTTA
* *
1204588 AGATTA-TTTCCCTTGAAACA
1 AGA-CAGTTTCTCTTGAAACA
1204608 AATTTCTTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 45 0.98
31 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (30 bp):
AGACAGTTTCTCTTGAAACACCAACCTTTA
Found at i:1205907 original size:16 final size:17
Alignment explanation
Indices: 1205884--1205927 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
1205874 AATATGTGAT
1205884 TATATAATGTATATATA
1 TATATAATGTATATATA
1205901 T-TATAATGTATATATA
1 TATATAATGTATATATA
1205917 TATATATATGT
1 TATATA-ATGT
1205928 TATTTACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.64
17 5 0.20
18 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
TATATAATGTATATATA
Found at i:1207198 original size:16 final size:16
Alignment explanation
Indices: 1207177--1207210 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1207167 TACTATTTAA
* *
1207177 TTATATATGTATCTAT
1 TTATATATATATATAT
1207193 TTATATATATATATAT
1 TTATATATATATATAT
1207209 TT
1 TT
1207211 CCATTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (16 bp):
TTATATATATATATAT
Found at i:1207316 original size:12 final size:12
Alignment explanation
Indices: 1207290--1207341 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
1207280 TCCTTTTATT
1207290 TATTT-TATTAA
1 TATTTATATTAA
*
1207301 TATTTATATTAG
1 TATTTATATTAA
1207313 TATTTATA-TACA
1 TATTTATATTA-A
* *
1207325 TATATATATTAT
1 TATTTATATTAA
1207337 TATTT
1 TATTT
1207342 TGTTTTCCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
11 7 0.21
12 24 0.73
13 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (12 bp):
TATTTATATTAA
Found at i:1207332 original size:24 final size:22
Alignment explanation
Indices: 1207293--1207341 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
1207283 TTTTATTTAT
*
1207293 TTTATTAATATTTATATTAGTA
1 TTTATTAATATATATATTAGTA
*
1207315 TTTATATACATATATATATTATTA
1 TTTAT-TA-ATATATATATTAGTA
1207339 TTT
1 TTT
1207342 TGTTTTCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 2 0.09
24 16 0.70
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTATTAATATATATATTAGTA
Found at i:1225832 original size:48 final size:48
Alignment explanation
Indices: 1225780--1225910 Score: 253
Period size: 48 Copynumber: 2.7 Consensus size: 48
1225770 CCTAACATCG
1225780 TTTATCTCTTTCTTCATCTTTAGTTGATATGTGATCATACTAGTTTTA
1 TTTATCTCTTTCTTCATCTTTAGTTGATATGTGATCATACTAGTTTTA
1225828 TTTATCTCTTTCTTCATCTTTAGTTGATATGTGATCATACTAGTTTTA
1 TTTATCTCTTTCTTCATCTTTAGTTGATATGTGATCATACTAGTTTTA
*
1225876 TTTATCTCTTTCTTTATCTTTAGTTGATATGTGAT
1 TTTATCTCTTTCTTCATCTTTAGTTGATATGTGAT
1225911 GACACTAATT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.56
Consensus pattern (48 bp):
TTTATCTCTTTCTTCATCTTTAGTTGATATGTGATCATACTAGTTTTA
Found at i:1226420 original size:2 final size:2
Alignment explanation
Indices: 1226413--1226453 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1226403 GTAATTTTGA
1226413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1226454 ATAAAACTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1227002 original size:21 final size:21
Alignment explanation
Indices: 1226976--1227016 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1226966 AGCGCGTGGA
1226976 GATTGGATCTCCGAAGACCGG
1 GATTGGATCTCCGAAGACCGG
1226997 GATTGGATCTCCGAAGACCG
1 GATTGGATCTCCGAAGACCG
1227017 AACCTAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (21 bp):
GATTGGATCTCCGAAGACCGG
Found at i:1227044 original size:14 final size:14
Alignment explanation
Indices: 1227025--1227059 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1227015 CGAACCTAAC
1227025 TAATTTTACAAACA
1 TAATTTTACAAACA
1227039 TAATTTTACAAACA
1 TAATTTTACAAACA
1227053 TAATTTT
1 TAATTTT
1227060 TCACATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATTTTACAAACA
Found at i:1238989 original size:229 final size:227
Alignment explanation
Indices: 1238584--1239032 Score: 783
Period size: 229 Copynumber: 2.0 Consensus size: 227
1238574 GTAAATTATC
* * *
1238584 TATCCTTTTTATAAAAGAGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGAGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1238649 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
1238714 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1238779 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
1238812 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGAGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
1238877 TTAATATTGTTAAATTT-AAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
65 TTAATATTGTTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
* *
1238941 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
1239006 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
1239033 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 43 0.20
229 167 0.80
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGAGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1239120 original size:20 final size:19
Alignment explanation
Indices: 1239097--1239141 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
1239087 GATATACCAT
1239097 GTAAAAATATGATAAAACCG
1 GTAAAAA-ATGATAAAACCG
1239117 GTAACAAAATGATAAAACCG
1 GTAA-AAAATGATAAAACCG
1239137 GTAAA
1 GTAAA
1239142 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.18
Consensus pattern (19 bp):
GTAAAAAATGATAAAACCG
Found at i:1239286 original size:20 final size:19
Alignment explanation
Indices: 1239263--1239309 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1239253 CGATATAACA
1239263 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1239283 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1239303 GGTAAAA
1 GGTAAAA
1239310 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1239311 original size:17 final size:19
Alignment explanation
Indices: 1239272--1239314 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1239262 AGGTAAAAAT
1239272 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1239292 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1239309 ATGATA
1 ATGATA
1239315 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1240890 original size:25 final size:25
Alignment explanation
Indices: 1240856--1240906 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1240846 ACAACAAATC
*
1240856 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
1240881 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
1240906 A
1 A
1240907 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:1241176 original size:18 final size:18
Alignment explanation
Indices: 1241155--1241191 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1241145 GTAATTGGAG
1241155 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1241173 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1241191 T
1 T
1241192 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1241199 original size:24 final size:24
Alignment explanation
Indices: 1241147--1241193 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1241137 TTTCATATGT
* *
1241147 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1241171 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1241194 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1241494 original size:39 final size:39
Alignment explanation
Indices: 1241451--1241537 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1241441 TCCGATGCTC
*
1241451 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
1241490 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1241529 ATCAAAATC
1 ATCAAAATC
1241538 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:1249808 original size:17 final size:18
Alignment explanation
Indices: 1249765--1249805 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1249755 AAATTATATT
1249765 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1249782 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1249800 ATTAAA
1 AGTAAA
1249806 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1251169 original size:31 final size:31
Alignment explanation
Indices: 1251131--1251192 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1251121 GTTGGTGGGA
1251131 ATAGCAATTTGTGTTACAATCATTCTGTTTT
1 ATAGCAATTTGTGTTACAATCATTCTGTTTT
1251162 ATAGCAATTTGTGTTACAATCATTCTGTTTT
1 ATAGCAATTTGTGTTACAATCATTCTGTTTT
1251193 GTCATCGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (31 bp):
ATAGCAATTTGTGTTACAATCATTCTGTTTT
Found at i:1253750 original size:44 final size:44
Alignment explanation
Indices: 1253693--1253782 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
1253683 ATTTTATAAT
* *
1253693 AATATGAGATAATGGGTATAATTTTATCCTTAACAATATTTATA
1 AATATGAGATAATGAGTATAATATTATCCTTAACAATATTTATA
* *
1253737 AATATGAGATAATGAGTATAATATTATCCTTAATAATATTTTTA
1 AATATGAGATAATGAGTATAATATTATCCTTAACAATATTTATA
1253781 AA
1 AA
1253783 AATAAATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (44 bp):
AATATGAGATAATGAGTATAATATTATCCTTAACAATATTTATA
Found at i:1255590 original size:12 final size:12
Alignment explanation
Indices: 1255573--1255597 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1255563 AATACATAAG
1255573 ATACAACCAACA
1 ATACAACCAACA
1255585 ATACAACCAACA
1 ATACAACCAACA
1255597 A
1 A
1255598 AACACCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (12 bp):
ATACAACCAACA
Found at i:1259464 original size:28 final size:28
Alignment explanation
Indices: 1259433--1259489 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1259423 CCCTCTGACC
*
1259433 ACTAATGAACAAGCTCAACTCTTCAAAA
1 ACTAATGAACAAACTCAACTCTTCAAAA
1259461 ACTAATGAACAAACTCAACTCTTCAAAA
1 ACTAATGAACAAACTCAACTCTTCAAAA
1259489 A
1 A
1259490 AAAACTATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.21
Consensus pattern (28 bp):
ACTAATGAACAAACTCAACTCTTCAAAA
Found at i:1263252 original size:31 final size:32
Alignment explanation
Indices: 1263203--1263264 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
1263193 CGAATTTAAC
**
1263203 TTTATATTTTTTTGAATCGAGTCAAACTCAAT
1 TTTATATTTTTTAAAATCGAGTCAAACTCAAT
**
1263235 TTTATA-TTTTTAAAATCGAGTTGAACTCAA
1 TTTATATTTTTTAAAATCGAGTCAAACTCAA
1263265 CACTATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (32 bp):
TTTATATTTTTTAAAATCGAGTCAAACTCAAT
Found at i:1267060 original size:19 final size:19
Alignment explanation
Indices: 1267038--1267077 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1267028 TACCAAAACC
*
1267038 CCCTTGGGCCCTCAAAGCT
1 CCCTTGAGCCCTCAAAGCT
1267057 CCCTTGAGCCCTCAAAGCT
1 CCCTTGAGCCCTCAAAGCT
1267076 CC
1 CC
1267078 ACCCCTACCG
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:0.17, C:0.45, G:0.17, T:0.20
Consensus pattern (19 bp):
CCCTTGAGCCCTCAAAGCT
Found at i:1267443 original size:10 final size:10
Alignment explanation
Indices: 1267429--1267500 Score: 65
Period size: 10 Copynumber: 7.2 Consensus size: 10
1267419 CAAAAAACAG
1267429 AAAAAGAAAAT
1 AAAAA-AAAAT
1267440 AAAAAAAAAT
1 AAAAAAAAAT
* *
1267450 AAAAAATAAC
1 AAAAAAAAAT
*
1267460 AAAAACAAA-
1 AAAAAAAAAT
* *
1267469 AATAACAAAT
1 AAAAAAAAAT
*
1267479 AACAAAAAAT
1 AAAAAAAAAT
*
1267489 AACAAAAAAT
1 AAAAAAAAAT
1267499 AA
1 AA
1267501 TAATATGTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
9 8 0.15
10 40 0.75
11 5 0.09
ACGTcount: A:0.82, C:0.07, G:0.01, T:0.10
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:1267454 original size:22 final size:22
Alignment explanation
Indices: 1267420--1267487 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1267410 ATAATGTAAC
*
1267420 AAAAAACAGAAAAAGAA-AATAAA
1 AAAAAATA-AAAAAGAACAA-AAA
*
1267443 AAAAAATAAAAAATAACAAAAA
1 AAAAAATAAAAAAGAACAAAAA
* * *
1267465 CAAAAATAACAAATAACAAAAA
1 AAAAAATAAAAAAGAACAAAAA
1267487 A
1 A
1267488 TAACAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 30 0.77
23 9 0.23
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.07
Consensus pattern (22 bp):
AAAAAATAAAAAAGAACAAAAA
Found at i:1267486 original size:32 final size:32
Alignment explanation
Indices: 1267435--1267496 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1267425 ACAGAAAAAG
*
1267435 AAAATAAAAAAAAATAAAAAATAACAAAAACA
1 AAAATAAAAAAAAACAAAAAATAACAAAAACA
* *
1267467 AAAATAACAAATAACAAAAAATAACAAAAA
1 AAAATAAAAAAAAACAAAAAATAACAAAAA
1267497 ATAATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (32 bp):
AAAATAAAAAAAAACAAAAAATAACAAAAACA
Found at i:1268791 original size:17 final size:18
Alignment explanation
Indices: 1268757--1268789 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1268747 TTTTGTTTGT
1268757 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
1268775 AATTT-TTTAA-TATTT
1 AATTTATTTAAGTATTT
1268790 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTTATTTAAGTATTTA
Found at i:1269358 original size:35 final size:33
Alignment explanation
Indices: 1269319--1269403 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
1269309 ATATTTTTGT
1269319 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
1269354 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
1269389 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1269404 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:1271639 original size:23 final size:23
Alignment explanation
Indices: 1271563--1271650 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
1271553 AGCTCATATA
1271563 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
1271586 AAATTGTC-CTGAAAG-ACCGCGTAG
1 -AATTG-CACCG-AAGTGCCACGTAG
*
1271610 AAATGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1271633 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1271651 TATAAGATTG
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
22 4 0.08
23 29 0.57
24 14 0.27
25 4 0.08
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1275606 original size:2 final size:2
Alignment explanation
Indices: 1275599--1275630 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1275589 CAAACTATCC
1275599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1275631 CTTTCCAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1276819 original size:18 final size:18
Alignment explanation
Indices: 1276796--1276840 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1276786 AATTGAAAAC
1276796 ACATCATAATATCATTTA
1 ACATCATAATATCATTTA
1276814 ACATCATAATATCATTTA
1 ACATCATAATATCATTTA
*
1276832 AAATCATAA
1 ACATCATAA
1276841 AACCTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (18 bp):
ACATCATAATATCATTTA
Found at i:1277491 original size:2 final size:2
Alignment explanation
Indices: 1277484--1277512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1277474 TACCATTTAC
1277484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1277513 CATTTAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1278151 original size:24 final size:24
Alignment explanation
Indices: 1278124--1278209 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
1278114 CACCACAACT
* *
1278124 CGTATAAATTGCACCGAAGTTCCA
1 CGTAGAAATTGCACCGAAGTACCA
*
1278148 CGTAGAAATTGTC-CCGAA-TGACCG
1 CGTAGAAATTG-CACCGAAGT-ACCA
*
1278172 CGTAGAAA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTACCA
1278195 CGTAG-AATTGCACCG
1 CGTAGAAATTGCACCG
1278210 TAGTGCCATA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
22 3 0.06
23 22 0.42
24 26 0.50
25 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTACCA
Found at i:1278198 original size:23 final size:24
Alignment explanation
Indices: 1278124--1278217 Score: 106
Period size: 23 Copynumber: 4.0 Consensus size: 24
1278114 CACCACAACT
* *
1278124 CGTATAAATTGCACCGAAGTTCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
1278148 CGTAGAAATTGTC-CCGAA-TGACCG
1 CGTAGAAATTG-CACCGAAGTG-CCA
1278172 CGTAGAAA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
1278195 CGTAG-AATTGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
1278218 TATAAGATTG
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
22 3 0.05
23 29 0.48
24 27 0.45
25 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:1279360 original size:54 final size:54
Alignment explanation
Indices: 1279302--1279440 Score: 224
Period size: 54 Copynumber: 2.6 Consensus size: 54
1279292 AGTTTTCTCA
* * * *
1279302 TAAGGTGTGAGCACGGCTTATTCATTTTGAGCTTTCGCAGAAGAGGTCTTTAGT
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAGATATCGCAGAAGAGGTCTTTAGT
* *
1279356 TAAGGCGTGGGCACGGCTTATTCATTCTAAGATATCGCAGAAGAGGTCTTTAGT
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAGATATCGCAGAAGAGGTCTTTAGT
1279410 TAAGGCGTGGGCACGGCTTATTCATTTTGAG
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAG
1279441 TTATTGCATC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (54 bp):
TAAGGCGTGGGCACGGCTTATTCATTTTGAGATATCGCAGAAGAGGTCTTTAGT
Found at i:1280622 original size:29 final size:29
Alignment explanation
Indices: 1280586--1280665 Score: 117
Period size: 29 Copynumber: 2.7 Consensus size: 29
1280576 TATTGCTGTT
1280586 AAAATTATAATTTGAAATTTTAAAAAAG-
1 AAAATTATAATTTGAAATTTTAAAAAAGC
1280614 AAACATTATAATTTGAAATTTTAAAAAAGC
1 AAA-ATTATAATTTGAAATTTTAAAAAAGC
*
1280644 AAAATTACAATTTAGAATATTT
1 AAAATTATAATTT-GAA-ATTT
1280666 CAAGAGTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 3 0.06
29 34 0.72
30 6 0.13
31 4 0.09
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAATTATAATTTGAAATTTTAAAAAAGC
Found at i:1284595 original size:25 final size:25
Alignment explanation
Indices: 1284547--1284595 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1284537 TGAACAGTAA
* * *
1284547 TGAACAGTAACTTGTTACATTACCG
1 TGAACAGTAACCTGCTACAGTACCG
*
1284572 TGAACAGTAACCTGCTATAGTACC
1 TGAACAGTAACCTGCTACAGTACC
1284596 CAAAATGTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (25 bp):
TGAACAGTAACCTGCTACAGTACCG
Found at i:1284667 original size:22 final size:21
Alignment explanation
Indices: 1284625--1284669 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1284615 TATTACAAAT
*
1284625 AGGGTACCGATTCCCTACTAC
1 AGGGTACCGATCCCCTACTAC
*
1284646 AGGGTACCGATACCCCTGCTAC
1 AGGGTACCGAT-CCCCTACTAC
1284668 AG
1 AG
1284670 TACTGCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20
Consensus pattern (21 bp):
AGGGTACCGATCCCCTACTAC
Found at i:1285265 original size:21 final size:22
Alignment explanation
Indices: 1285221--1285276 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
1285211 ATTTGTGCAA
* *
1285221 AAGGACCTGTGAATATGTCCCG
1 AAGGACCTATGAATATGTCACG
*
1285243 AAGGACCTATGAGT-TGTCACG
1 AAGGACCTATGAATATGTCACG
1285264 AAGGACCTATGAA
1 AAGGACCTATGAA
1285277 ACCCTCGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (22 bp):
AAGGACCTATGAATATGTCACG
Found at i:1290845 original size:259 final size:256
Alignment explanation
Indices: 1290366--1290863 Score: 808
Period size: 259 Copynumber: 1.9 Consensus size: 256
1290356 GAAACTTTAT
*
1290366 TTTGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAATACCCGACTCGAAAATATATATAATTTTA
1 TTTGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAATACCCGACTCCAAAATATATATAATTTTA
* *
1290431 CCTTATATATTTAGTAATAATTACAATAATACCCCTCTATATATATTTTTTCAATTAAGTCACTG
66 CCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATTTTTTCAATTAAGTCACTA
1290496 CTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGATCAGGTCGGATTTCTAATTCAT
131 CTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGATCAGGTCGGATTTCTAATTCAT
1290561 ATATTCGGGTTGGGTCGAGTGAAACTTTATTTTGGTCGGGTCGATTTTTTTAAGTGTGATA
196 ATATTCGGGTTGGGTCGAGTGAAACTTTATTTTGGTCGGGTCGATTTTTTTAAGTGTGATA
*
1290622 TTTGAGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCTGACCCGAC-CCAAAA-ATATATAA
1 TTTG-GTCGGGTCGAGTTCGGGTTTAGGGTGAAAAA-A--T-ACCCGACTCCAAAATATATATAA
* *
1290685 TTTTACCTTATATATTTAGGAATAATTATAATAATACCCCTCTCTATATATTTTTTTCCAATTAA
61 TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATA-TTTTTT-CAATTAA
* * *
1290750 GTCACTATTTTTATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTCGGGTCGGGTCAGG-TTTC
124 GTCACTACTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGATCAGGTC-GGATTTC
1290813 TAATTCATATATTCGGGTTGGGTCGA-TGAAACTTTATTTTGGTCGGGTCGA
188 TAATTCATATATTCGGGTTGGGTCGAGTGAAACTTTATTTTGGTCGGGTCGA
1290864 GTCTCAGATG
Statistics
Matches: 225, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
256 4 0.02
257 30 0.13
258 1 0.00
259 80 0.36
260 71 0.32
261 39 0.17
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (256 bp):
TTTGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAATACCCGACTCCAAAATATATATAATTTTA
CCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATTTTTTCAATTAAGTCACTA
CTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGATCAGGTCGGATTTCTAATTCAT
ATATTCGGGTTGGGTCGAGTGAAACTTTATTTTGGTCGGGTCGATTTTTTTAAGTGTGATA
Found at i:1291256 original size:18 final size:18
Alignment explanation
Indices: 1291219--1291265 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1291209 TATGGAATTG
*
1291219 GATTCCAATT-CTTGACA
1 GATTCCAATTCCTTCACA
1291236 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
1291254 GATTTCAATTCC
1 GATTCCAATTCC
1291266 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1291810 original size:2 final size:2
Alignment explanation
Indices: 1291803--1291847 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1291793 ATTATATCGT
1291803 TA TA TA 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
1291845 TA T
1 TA T
1291848 TAATGATTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1293987 original size:21 final size:22
Alignment explanation
Indices: 1293961--1294005 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
1293951 TATTACAAAT
*
1293961 AGGGTACCGAT-TCCCTGCTAC
1 AGGGTACCGATACCCCTGCTAC
1293982 AGGGTACCGATACCCCTGCTAC
1 AGGGTACCGATACCCCTGCTAC
1294004 AG
1 AG
1294006 TACTGTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGTACCGATACCCCTGCTAC
Found at i:1294600 original size:21 final size:22
Alignment explanation
Indices: 1294556--1294611 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
1294546 ATTTGTGCCA
* *
1294556 AAGGACCTGTGAATATGTCCCG
1 AAGGACCTATGAATATGTCACG
*
1294578 AAGGACCTATGAGT-TGTCACG
1 AAGGACCTATGAATATGTCACG
*
1294599 AATGACCTATGAA
1 AAGGACCTATGAA
1294612 ACCCTCGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (22 bp):
AAGGACCTATGAATATGTCACG
Found at i:1311559 original size:26 final size:25
Alignment explanation
Indices: 1311515--1311565 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1311505 TTAGCATATT
1311515 TAAAAACAAAACTT-AAAAATAAAG
1 TAAAAACAAAACTTAAAAAATAAAG
*
1311539 TAAAAACCAAAAACTTGAAAAATAAAG
1 TAAAAA-C-AAAACTTAAAAAATAAAG
1311566 AAGAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.25
25 1 0.04
26 7 0.29
27 10 0.42
ACGTcount: A:0.69, C:0.10, G:0.06, T:0.16
Consensus pattern (25 bp):
TAAAAACAAAACTTAAAAAATAAAG
Found at i:1311709 original size:26 final size:26
Alignment explanation
Indices: 1311680--1311741 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
1311670 CTGACTAGAT
*
1311680 CTTCTAGAAACTACAACTGATTGGAC
1 CTTCTAAAAACTACAACTGATTGGAC
* *
1311706 CTTCTAAAAACTGCAACTGATTGGGC
1 CTTCTAAAAACTACAACTGATTGGAC
1311732 CTTCTAAAAA
1 CTTCTAAAAA
1311742 TTGTCAGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (26 bp):
CTTCTAAAAACTACAACTGATTGGAC
Found at i:1313787 original size:215 final size:216
Alignment explanation
Indices: 1313358--1314474 Score: 1673
Period size: 215 Copynumber: 5.3 Consensus size: 216
1313348 ATTTAAGAAT
*
1313358 TAAATTGAACAACTATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
1313423 GGATCAAATCGAAATAA---TAAATTGTGAGGTTGAAATTAATCCAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
1313485 CCATTTAAAAAATTATGGGCCAA-TTAAAAATAGAATTAAGTAAA-AAGTATGGATCAATTTCAG
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAG-AAATAAGTATGGGTCAATTTCAG
*
1313548 ATACAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
*
1313570 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1313635 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
1313700 CCATTTAAAAAGTT-TGGGCCAATTTAAAAGTAGAAATAAGAAATAAGCATGGGTCAATTTTAGA
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGAAATAAGTATGGGTCAATTTCAGA
* *
1313764 TGTAAATAAAAATTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* * *
1313785 TAAATTGAACAAATATTAAATTGCAAATAAAAATTTAAATAAATTAAACAACATA-A---A--AG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
1313844 GGATCAAATCAAAATAATTTTAGATTGTGATGTTGAAATTAATAC-AAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
1313908 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAA-AAGTATGGATCAATTTCAG
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAG-AAATAAGTATGGGTCAATTTCAG
1313972 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
* *
1313994 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTGAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
1314059 GGATCAAATCGAAATAAATTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * *
1314124 ACATTTAAAAAGTTATGGGCCAATTTAAAAAAAGAAATAAGTAATAAGTATGGGTCAATTTCATA
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGAAATAAGTATGGGTCAATTTCAGA
1314189 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* *
1314210 TAAATTGAATAAATATAAAATTACAAATAAAAATTTAAATAAATTAAACAACACA-A---A--AG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * *
1314269 GGGTCAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAATGTACTAATTTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * *
1314334 TCATTTAAAAATTTATGGGCCAA-TTAATAAATAGAAATAAGTAATAAGTATGAGTCAATTTCAG
131 CCATTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGAAATAAGTATGGGTCAATTTCAG
* *
1314398 ATGCAAATAAAATGTAGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
* * *
1314420 TATATTGAATAAGTATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1314475 AAAGGGATCA
Statistics
Matches: 828, Mismatches: 61, Indels: 34
0.90 0.07 0.04
Matches are distributed among these distances:
208 33 0.04
209 158 0.19
210 192 0.23
211 1 0.00
212 81 0.10
213 1 0.00
214 12 0.01
215 204 0.25
216 146 0.18
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGAAATAAGTATGGGTCAATTTCAGA
TGCAAATAAAATTTGGAGGAC
Found at i:1314562 original size:2 final size:2
Alignment explanation
Indices: 1314557--1314683 Score: 116
Period size: 2 Copynumber: 63.0 Consensus size: 2
1314547 AAAAAAACTA
1314557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1314599 AT AT AT AT AT AT GT A- AT AT AA ACT AT AT AGT TT AT AT AT AA AGT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T
* * * * *
1314643 AT AT GT AT -T AT AT TT AT AA ACT AC AT A- AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
1314684 TATGTATAAA
Statistics
Matches: 100, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
1 3 0.03
2 93 0.93
3 4 0.04
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1314701 original size:42 final size:42
Alignment explanation
Indices: 1314588--1314702 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 42
1314578 TATATATATA
* * * *
1314588 TATATATATATATATATATATATGTAATATAAACTATATAGTT
1 TATATATATATATATGTATATATGT-TTATAAACTACATAATT
* *
1314631 TATATATAAAGTATATGTAT-TATATTTATAAACTACATAATT
1 TATATATATA-TATATGTATATATGTTTATAAACTACATAATT
*
1314673 TATATATATAT-TATGTATAAACTGTTTATA
1 TATATATATATATATGTATATA-TGTTTATA
1314703 CCATGTATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 7 0.12
41 2 0.03
42 30 0.50
43 13 0.22
44 8 0.13
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (42 bp):
TATATATATATATATGTATATATGTTTATAAACTACATAATT
Found at i:1314807 original size:42 final size:39
Alignment explanation
Indices: 1314715--1314817 Score: 98
Period size: 42 Copynumber: 2.5 Consensus size: 39
1314705 ATGTATAAAC
* * *
1314715 TATAATACTATATAGTTTATATATGAACTATTGAACTATA
1 TATAA-ACTACATAGTTTATATATAAAATATTGAACTATA
* * *
1314755 TAGAATCTACATAGTTTATATATAAATTATATTTGAATTATA
1 TATAAACTACATAGTTTATATATAAA--ATA-TTGAACTATA
* *
1314797 TATAAACTACACAATTTATAT
1 TATAAACTACATAGTTTATAT
1314818 TTATATATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
39 18 0.36
40 4 0.08
41 2 0.04
42 26 0.52
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (39 bp):
TATAAACTACATAGTTTATATATAAAATATTGAACTATA
Found at i:1314869 original size:9 final size:9
Alignment explanation
Indices: 1314847--1314896 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1314837 ATAAAAAAAA
1314847 ATATATATT
1 ATATATATT
* *
1314856 GTATAAATT
1 ATATATATT
1314865 ATATAGT-TT
1 ATATA-TATT
1314874 ATATATA-T
1 ATATATATT
*
1314882 ATATATAGT
1 ATATATATT
1314891 ATATAT
1 ATATAT
1314897 GGTTTAGGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 9 0.26
9 25 0.74
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (9 bp):
ATATATATT
Found at i:1314907 original size:7 final size:7
Alignment explanation
Indices: 1314897--1314962 Score: 69
Period size: 7 Copynumber: 9.4 Consensus size: 7
1314887 TAGTATATAT
1314897 GGTTTAG
1 GGTTTAG
1314904 GGTTTAG
1 GGTTTAG
* *
1314911 GGATTAT
1 GGTTTAG
1314918 GGTTTAG
1 GGTTTAG
*
1314925 AGTTTAG
1 GGTTTAG
* *
1314932 GGATTAT
1 GGTTTAG
*
1314939 GGTTTAT
1 GGTTTAG
*
1314946 AGTTTAG
1 GGTTTAG
1314953 GGTTTAG
1 GGTTTAG
1314960 GGT
1 GGT
1314963 ATATGTTTAT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:1314920 original size:21 final size:21
Alignment explanation
Indices: 1314894--1314954 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
1314884 ATATAGTATA
*
1314894 TATGGTTTAGGGTTTAGGGAT
1 TATGGTTTAGAGTTTAGGGAT
1314915 TATGGTTTAGAGTTTAGGGAT
1 TATGGTTTAGAGTTTAGGGAT
*
1314936 TATGGTTTATAGTTTAGGG
1 TATGGTTTAGAGTTTAGGG
1314955 TTTAGGGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TATGGTTTAGAGTTTAGGGAT
Found at i:1314967 original size:28 final size:27
Alignment explanation
Indices: 1314897--1314977 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
1314887 TAGTATATAT
* * *
1314897 GGTTTAGGGTTTAGGGATTATGGTTTAG
1 GGTTTAGGGTATATGGTTTAT-GTTTAG
*
1314925 AGTTTAGGG-ATTATGGTTTATAGTTTAG
1 GGTTTAGGGTA-TATGGTTTAT-GTTTAG
1314953 GGTTTAGGGTATAT-GTTTATGTTTA
1 GGTTTAGGGTATATGGTTTATGTTTA
1314978 TGTTCATGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 5 0.11
27 6 0.13
28 33 0.73
29 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (27 bp):
GGTTTAGGGTATATGGTTTATGTTTAG
Found at i:1314975 original size:6 final size:6
Alignment explanation
Indices: 1314965--1315017 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
1314955 TTTAGGGTAT
* *
1314965 ATGTTT ATGTTT ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC
1 ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC
1315013 ATGTT
1 ATGTT
1315018 TATGCTTATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (6 bp):
ATGTTC
Found at i:1315061 original size:20 final size:20
Alignment explanation
Indices: 1315036--1315108 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 20
1315026 TATAAACTAC
1315036 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
*
1315056 ATACTATATTTTATATTATTTAT
1 ATACTATA-ATT-TA-TATTTAT
*
1315079 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAATTTATATTTAT
*
1315101 ATATTATA
1 ATACTATA
1315109 TATATGAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 13 0.29
21 2 0.04
22 11 0.24
23 11 0.24
24 2 0.04
25 6 0.13
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:1315079 original size:23 final size:24
Alignment explanation
Indices: 1315049--1315097 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
1315039 CTATAATTTA
*
1315049 TATTTATAT-ACTATATTTTATAT
1 TATTTATATAACTATAGTTTATAT
1315072 TATTTATATAAACTATAGTTTATAT
1 TATTTATAT-AACTATAGTTTATAT
1315097 T
1 T
1315098 TATATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
25 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTATATAACTATAGTTTATAT
Found at i:1315111 original size:31 final size:31
Alignment explanation
Indices: 1315060--1315152 Score: 84
Period size: 33 Copynumber: 2.9 Consensus size: 31
1315050 ATTTATATAC
1315060 TATATTT-TATATTATTTATATAAACTATAGTT
1 TATATTTATATATTA--TATATAAACTATAGTT
*
1315092 TATATTTATATATTATATATATGAACTATTGTT
1 TATATTTATATATTATATATA--AACTATAGTT
* *
1315125 TACATATGA-ACTA-TATATATAAACTATA
1 TATAT-TTATA-TATTATATATAAACTATA
1315153 TAGTTTACAT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
31 12 0.23
32 7 0.13
33 29 0.56
34 4 0.08
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.49
Consensus pattern (31 bp):
TATATTTATATATTATATATAAACTATAGTT
Found at i:1315113 original size:33 final size:31
Alignment explanation
Indices: 1315076--1315211 Score: 166
Period size: 33 Copynumber: 4.2 Consensus size: 31
1315066 TTATATTATT
* *
1315076 TATATAAACTATAGTTTATATTTAT-ATATTATA
1 TATATAAACTATAGTTTACA--TATGA-ACTATA
* *
1315109 TATATGAACTATTGTTTACATATGAACTATA
1 TATATAAACTATAGTTTACATATGAACTATA
1315140 TATATAAACTATATAGTTTACATATGAACTATA
1 TATATAAAC--TATAGTTTACATATGAACTATA
1315173 TATATAAACTATATAGTTTACATATGAACTATA
1 TATATAAAC--TATAGTTTACATATGAACTATA
1315206 TATATA
1 TATATA
1315212 CTAAAGTTGA
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
31 16 0.17
32 1 0.01
33 77 0.82
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (31 bp):
TATATAAACTATAGTTTACATATGAACTATA
Found at i:1315169 original size:20 final size:20
Alignment explanation
Indices: 1315110--1315379 Score: 154
Period size: 18 Copynumber: 14.7 Consensus size: 20
1315100 TATATTATAT
1315110 ATATGAACTAT-T-GTTTAC
1 ATATGAACTATATAGTTTAC
1315128 ATATGAACTATATA---T--
1 ATATGAACTATATAGTTTAC
1315143 ATA--AACTATATAGTTTAC
1 ATATGAACTATATAGTTTAC
1315161 ATATGAACTATATA---T--
1 ATATGAACTATATAGTTTAC
1315176 ATA--AACTATATAGTTTAC
1 ATATGAACTATATAGTTTAC
*
1315194 ATATGAACTATATA-TATAC
1 ATATGAACTATATAGTTTAC
* *
1315213 -TA--AAGT-TGATA-TTTAT
1 ATATGAACTAT-ATAGTTTAC
1315229 ATATGAAC--TATAGTTTAC
1 ATATGAACTATATAGTTTAC
*
1315247 ATATAAACTATATAGTTT--
1 ATATGAACTATATAGTTTAC
1315265 ATAT--ACTATCTATAGTTTAC
1 ATATGAACTA--TATAGTTTAC
*
1315285 ATATAAACAATAGTTGATA-TTTAC
1 ATATGAAC--TA--T-ATAGTTTAC
1315309 ATATGAAC--TATAGTTTAC
1 ATATGAACTATATAGTTTAC
* *
1315327 ATATGAACTATATA-TATAT
1 ATATGAACTATATAGTTTAC
* *
1315346 ATATAAACTACATAGTTTAC
1 ATATGAACTATATAGTTTAC
*
1315366 ATATGACCTATATA
1 ATATGAACTATATA
1315380 TATACTATAG
Statistics
Matches: 197, Mismatches: 19, Indels: 70
0.69 0.07 0.24
Matches are distributed among these distances:
13 18 0.09
15 7 0.04
16 15 0.08
17 10 0.05
18 57 0.29
19 22 0.11
20 48 0.24
22 2 0.01
24 15 0.08
25 3 0.02
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (20 bp):
ATATGAACTATATAGTTTAC
Found at i:1315230 original size:53 final size:53
Alignment explanation
Indices: 1315173--1315494 Score: 229
Period size: 53 Copynumber: 5.9 Consensus size: 53
1315163 ATGAACTATA
*
1315173 TATATAAACTATATAGTTTACATATGAACTATATATATACTAAAGTTGATATT
1 TATATAAACTATATAGTTTACATATGAACTATATATATACTATAGTTGATATT
* * * *
1315226 TATATATGAAC--TATAGTTTACATATAAACTATATAGTTTA-TATACTATCTATAGTT
1 TATATA--AACTATATAGTTTACATATGAACTATATA-TATACTATAGT-T-GATA-TT
1315282 TACATATAAACAATAGTTGATA-TTTACATATGAACTATAGTTTACATATGAACTATA--T-ATA
1 T--ATATAAAC--TA--T-ATAGTTTACATATGAACTATA---T--ATAT--ACTATAGTTGATA
*
1315343 TA
52 TT
* *
1315345 TATATAAACTACATAGTTTACATATGACCTATATATATACTATAGTTGATATT
1 TATATAAACTATATAGTTTACATATGAACTATATATATACTATAGTTGATATT
* *
1315398 TATAT--ACTATATAGTTTACATATGACCTATATATATATACTATAGTTTATATT
1 TATATAAACTATATAGTTTACATATGAAC--TATATATATACTATAGTTGATATT
* *
1315451 TATAT--ACTATATA-TTATATATATAAACTATATATACTA-TATAGT
1 TATATAAACTATATAGTT-TACATATGAACTATATATA-TACTATAGT
1315495 ATAATTTACA
Statistics
Matches: 222, Mismatches: 16, Indels: 64
0.74 0.05 0.21
Matches are distributed among these distances:
50 6 0.03
51 35 0.16
52 9 0.04
53 86 0.39
54 5 0.02
55 6 0.03
56 9 0.04
57 16 0.07
58 5 0.02
59 2 0.01
61 8 0.04
62 17 0.08
63 5 0.02
64 3 0.01
65 1 0.00
66 3 0.01
67 1 0.00
68 1 0.00
69 4 0.02
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.43
Consensus pattern (53 bp):
TATATAAACTATATAGTTTACATATGAACTATATATATACTATAGTTGATATT
Found at i:1315245 original size:18 final size:18
Alignment explanation
Indices: 1315076--1315377 Score: 113
Period size: 18 Copynumber: 16.7 Consensus size: 18
1315066 TTATATTATT
*
1315076 TATATAAACTATAGTTTA
1 TATATGAACTATAGTTTA
*
1315094 TAT-T-TA-TATA-TTATA
1 TATATGAACTATAGTT-TA
*
1315109 TATATGAACTATTGTTTA
1 TATATGAACTATAGTTTA
*
1315127 CATATGAACTATA---TA
1 TATATGAACTATAGTTTA
1315142 TATA--AACTATATAGTTTA
1 TATATGAAC--TATAGTTTA
*
1315160 CATATGAACTATA---TA
1 TATATGAACTATAGTTTA
1315175 TATA--AACTATATAGTTTA
1 TATATGAAC--TATAGTTTA
*
1315193 CATATGAACTATA---TA
1 TATATGAACTATAGTTTA
* *
1315208 TATACTAAAGTTGATA-TTTA
1 TATA-TGAA-CT-ATAGTTTA
1315228 TATATGAACTATAGTTTA
1 TATATGAACTATAGTTTA
* *
1315246 CATATAAACTATATAGTTTA
1 TATATGAAC--TATAGTTTA
*
1315266 TATACT-ATCTATAGTTTA
1 TATA-TGAACTATAGTTTA
* * *
1315284 CATATAAACAATAGTTGATA
1 TATATGAACTATAGTT--TA
1315304 TTTACATATGAACTATAGTTTA
1 --T--ATATGAACTATAGTTTA
*
1315326 CATATGAACTATA-TATATA
1 TATATGAACTATAGT-T-TA
*
1315345 TATATAAACTACATAGTTTA
1 TATATGAACT--ATAGTTTA
* *
1315365 CATATGACCTATA
1 TATATGAACTATA
1315378 TATATACTAT
Statistics
Matches: 214, Mismatches: 30, Indels: 80
0.66 0.09 0.25
Matches are distributed among these distances:
13 6 0.03
14 2 0.01
15 32 0.15
16 5 0.02
17 8 0.04
18 88 0.41
19 15 0.07
20 37 0.17
21 5 0.02
22 3 0.01
24 13 0.06
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (18 bp):
TATATGAACTATAGTTTA
Found at i:1315317 original size:80 final size:80
Alignment explanation
Indices: 1315216--1315369 Score: 233
Period size: 80 Copynumber: 1.9 Consensus size: 80
1315206 TATATACTAA
*
1315216 AGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGT-T-TATAT-ACTATCTAT
1 AGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATA-TATATATATAACTA-C-AT
1315278 AGTTTACATATAAACAAT
63 AGTTTACATATAAACAAT
*
1315296 AGTTGATATTTACATATGAACTATAGTTTACATATGAACTATATATATATATATAAACTACATAG
1 AGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATATATATATAT-AACTACATAG
1315361 TTTACATAT
65 TTTACATAT
1315370 GACCTATATA
Statistics
Matches: 68, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
79 1 0.01
80 44 0.65
81 18 0.26
82 1 0.01
83 4 0.06
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (80 bp):
AGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATATATATATATAACTACATAGT
TTACATATAAACAAT
Found at i:1315432 original size:2 final size:2
Alignment explanation
Indices: 1315425--1315497 Score: 58
Period size: 2 Copynumber: 34.0 Consensus size: 2
1315415 ACATATGACC
* *
1315425 TA TA TA TA TA TA CTA TA GTT TA TA TT TA TA TA CTA TA TA T- TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA
*
1315467 TA TA TA TA AA CTA TA TA TA CTA TA TA GTA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
1315498 ATTTACATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 1 0.02
2 47 0.81
3 10 0.17
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1315448 original size:20 final size:20
Alignment explanation
Indices: 1315425--1315497 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1315415 ACATATGACC
1315425 TATATATATATACTATAGT-T
1 TATATATATATACTATA-TAT
*
1315445 TATATTTATATACTATATAT
1 TATATATATATACTATATAT
*
1315465 TATATATATAAACTATATA-
1 TATATATATATACTATATAT
1315484 TACTATATAGTATA
1 TA-TATATA-TATA
1315498 ATTTACATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 3 0.07
20 40 0.87
21 3 0.07
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (20 bp):
TATATATATATACTATATAT
Found at i:1315514 original size:34 final size:36
Alignment explanation
Indices: 1315451--1315519 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
1315441 AGTTTATATT
*
1315451 TATATACTATATATTATATATATAAACTATATATAC
1 TATATACTATATATTATACATATAAACTATATATAC
* *
1315487 TATATAGTATA-ATT-TACATATGAACTATATATA
1 TATATACTATATATTATACATATAAACTATATATA
1315520 AAACCATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
35 3 0.10
36 10 0.33
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATACTATATATTATACATATAAACTATATATAC
Found at i:1315591 original size:53 final size:48
Alignment explanation
Indices: 1315374--1315589 Score: 154
Period size: 53 Copynumber: 4.2 Consensus size: 48
1315364 ACATATGACC
**
1315374 TATATATATACTATAGTTGATATTTATATACTATATAGTTTACATATGACCTA
1 TATATATATACTATAGTTGATATTTATATACTATATA-AATA-ATAT-A--TA
* *
1315427 TATATATATACTATAGTTTATATTTATATACTATAT-ATTATATATATA
1 TATATATATACTATAGTTGATATTTATATACTATATAAATA-ATATATA
* * *
1315475 AACTATATATACTATA-TAGTATAATTTACATATGAACTATATATAA-AACCATATA
1 TA-TATATATACTATAGTTG-AT-ATTT--ATAT--ACTATATA-AATAA-TATATA
*
1315530 -A-ACTATATACTATAGTTGATATTTATATACTATATAAAATAATTTATA
1 TATA-TATATACTATAGTTGATATTTATATACTATAT-AAATAATATATA
1315578 CTATAGTATATA
1 -TATA-TATATA
1315590 TAAGAGAAAA
Statistics
Matches: 134, Mismatches: 12, Indels: 36
0.74 0.07 0.20
Matches are distributed among these distances:
48 17 0.13
49 18 0.13
50 10 0.07
51 14 0.10
52 9 0.07
53 48 0.36
54 11 0.08
55 6 0.04
56 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (48 bp):
TATATATATACTATAGTTGATATTTATATACTATATAAATAATATATA
Found at i:1315809 original size:21 final size:21
Alignment explanation
Indices: 1315758--1315810 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1315748 ATTATGACTA
1315758 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1315779 TCGCGTTGCGATTTTCCCAATT
1 TCGCAATGCGATTTT-CCAATT
1315801 T-GCAATGCGA
1 TCGCAATGCGA
1315811 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1315843 original size:21 final size:21
Alignment explanation
Indices: 1315817--1315893 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
1315807 GCGAATAAGT
*
1315817 AAATCGCAATGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
1315838 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
*
1315859 AAATCGCAATGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
1315880 AAATCGCAACGCGA
1 AAATCGCAACGCGA
1315894 TACTGACTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (21 bp):
AAATCGCAACGCGAATTTGGA
Found at i:1315907 original size:20 final size:20
Alignment explanation
Indices: 1315882--1315996 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
1315872 AATTTGGAAA
1315882 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1315902 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
1315923 ATCACAACGCGATACTGGCT
1 ATCGCAACGCGATACTGACT
* * * * *
1315943 TTCACAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* * *
1315963 TTCGCAACTCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1315983 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1315997 ATACATAATC
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.03
20 57 0.77
21 14 0.19
22 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1315924 original size:41 final size:41
Alignment explanation
Indices: 1315879--1316016 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
1315869 GCGAATTTGG
*
1315879 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * * * * *
1315920 AAAATCACAACGCGATACTGGCTTTCACAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
** * * *
1315960 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
1316001 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1316017 TTTCAAAGCG
Statistics
Matches: 72, Mismatches: 24, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
40 29 0.40
41 43 0.60
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1316538 original size:20 final size:20
Alignment explanation
Indices: 1316489--1316547 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1316479 TTTATTCTCT
* **
1316489 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1316509 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
1316529 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1316548 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1316738 original size:25 final size:24
Alignment explanation
Indices: 1316684--1316738 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1316674 TGTTTATTAT
* *
1316684 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1316708 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1316734 TGTTT
1 TGTTT
1316739 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1317888 original size:18 final size:18
Alignment explanation
Indices: 1317867--1317914 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1317857 TCCACTTCGG
1317867 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1317885 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1317903 GATCCATCACCT
1 GAGCCATCACCT
1317915 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.46, G:0.10, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1318480 original size:20 final size:20
Alignment explanation
Indices: 1318455--1318500 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1318445 TAGTTTACTT
1318455 TCGCAACACAAAAATGACCA
1 TCGCAACACAAAAATGACCA
* * * *
1318475 TCGCAACGCAGAAATGGCTA
1 TCGCAACACAAAAATGACCA
1318495 TCGCAA
1 TCGCAA
1318501 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACACAAAAATGACCA
Found at i:1318509 original size:19 final size:19
Alignment explanation
Indices: 1318494--1318576 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
1318484 AGAAATGGCT
1318494 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1318513 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1318532 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1318546 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1318565 ATCGCAATGCGA
1 ATCGCAATGCGA
1318577 TTTGTGTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.71
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Done.