Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 16
Found at i:1016697 original size:19 final size:20
Alignment explanation
Indices: 1016660--1016699 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1016650 ATAATCCTAT
*
1016660 TATTTCAAAATTATAAAAAA
1 TATTTCAAAAATATAAAAAA
1016680 TATTT-AAAAATATCAAAAAA
1 TATTTCAAAAATAT-AAAAAA
1016700 GGACTTCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TATTTCAAAAATATAAAAAA
Found at i:1018267 original size:3 final size:3
Alignment explanation
Indices: 1018251--1018362 Score: 118
Period size: 3 Copynumber: 36.7 Consensus size: 3
1018241 TTTGGGCTTG
* ** * *
1018251 TAA TAA TATT TAA TAA TAA TTT TAA TAA TAAA TAA TAA TAT TAG TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * *
1018298 TTA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1018346 TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
1018363 TTTAAATGAA
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.02
3 81 0.90
4 7 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1018654 original size:36 final size:40
Alignment explanation
Indices: 1018617--1018697 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 40
1018607 TCATTGTGAA
* *
1018617 CTTCTTCTTTTTCAGAT-TAGTTCTTCTCATTATGAACTT
1 CTTCTTCTTCTTCAGATAGAGTTCTTCTCATTATGAACTT
1018656 CTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACT
1 CTTCTT-CTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACT
1018698 CTACCTGGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 6 0.17
40 10 0.28
43 20 0.56
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (40 bp):
CTTCTTCTTCTTCAGATAGAGTTCTTCTCATTATGAACTT
Found at i:1018854 original size:113 final size:114
Alignment explanation
Indices: 1018637--1019303 Score: 872
Period size: 113 Copynumber: 5.9 Consensus size: 114
1018627 TTCAGATTAG
1018637 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTAC
* *
1018702 CTGGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
64 CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
*
1018753 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACT-TTCTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAC-C
* * * * * *
1018816 TGG-ATAAGATAATCCATCAAGTGAT-ATATTTGAGCAAAAGGTTGAACAAA
65 TGGCA-ATGTTAATCCATCAAATGATGA-ATTTAAACAAAAAGTTGAACAAA
1018866 TTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTAC
*
1018927 CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAATGTTGAACAAA
64 CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
* *
1018978 TTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACT-TTCTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAC-C
* * * * * * * *
1019041 TGGAAAAGCTGATCCAACAAATGATGGATTTGAGC-AAAAGATTGAACAAA
65 TGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAAG-TTGAACAAA
* *
1019091 TTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTAC
* *
1019156 CTGGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
64 CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
* *
1019207 TTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACTCTAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCT
* * ** *
1019271 GGAAAAGTTAATCCATTGAATGATGGATTTAAA
66 GGCAATGTTAATCCATCAAATGATGAATTTAAA
1019304 TCTTTGCCAA
Statistics
Matches: 481, Mismatches: 50, Indels: 43
0.84 0.09 0.07
Matches are distributed among these distances:
109 11 0.02
110 5 0.01
111 1 0.00
112 88 0.18
113 225 0.47
114 1 0.00
115 5 0.01
116 139 0.29
117 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCT
GGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAA
Found at i:1019221 original size:229 final size:227
Alignment explanation
Indices: 1018637--1019300 Score: 1107
Period size: 225 Copynumber: 2.9 Consensus size: 227
1018627 TTCAGATTAG
1018637 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAA-TTCTTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
*
1018702 CTGGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
64 CTGGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATG
* *
1018767 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGATAAGATAATCCA
129 AACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCA
* ** *
1018832 TCAAGTGATATATTTGAGCAAAAGGTTGAACAAA
194 TCAAATGATGGATTTGAGCAAAAGATTGAACAAA
1018866 TTCTTCTCATTATGAA-T-TTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
1 TTCTTCTCATTATGAATTCTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
* *
1018929 GGCAATGTTAATCCATCAAATGATGAATTTAAACAAAATGTTGAACAAATTCTTCTCATTATGAA
66 GGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
* * *
1018994 CTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCAAC
131 CTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATC
1019059 AAATGATGGATTTGAGCAAAAGATTGAACAAA
196 AAATGATGGATTTGAGCAAAAGATTGAACAAA
1019091 TTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAA-TTCTTCTTC-TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
*
1019156 CTGGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATG
64 CTGGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATG
* ** *
1019221 AACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGTTAATCCA
129 AACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCA
**
1019286 TTGAATGATGGATTT
194 TCAAATGATGGATTT
1019301 AAATCTTTGC
Statistics
Matches: 409, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
225 207 0.51
226 5 0.01
227 2 0.00
228 6 0.01
229 189 0.46
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (227 bp):
TTCTTCTCATTATGAATTCTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
GGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
CTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATC
AAATGATGGATTTGAGCAAAAGATTGAACAAA
Found at i:1020430 original size:83 final size:83
Alignment explanation
Indices: 1020079--1020432 Score: 546
Period size: 83 Copynumber: 4.3 Consensus size: 83
1020069 CTTATTTCTA
* * * *
1020079 CTATGATCAAATTCATCTTTTAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
1020144 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * *
1020162 CTATGAGCATATTCCTCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
*
1020227 GAACACTTCTAGAAGATG
66 GAACACTTCCAGAAGATG
* * * * *
1020245 CTATGAGCATATTCCTCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
1020310 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * *
1020328 CTATGAGCACATTCATCTTTCAAATTAAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
1020393 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
1020411 CTATGAGCACATTCATCTTTCA
1 CTATGAGCACATTCATCTTTCA
1020433 GTTAATGTTT
Statistics
Matches: 252, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 252 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:1021601 original size:29 final size:29
Alignment explanation
Indices: 1021565--1021660 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 29
1021555 TGACCCCTCA
1021565 TTTT-TTTTCTTTTTTTCTTT-TATCTCTT
1 TTTTCTTTTCTTTTTTTCTTTCT-TCTCTT
1021593 TTTTCTTTTTCTTTCTTTTTCTTTCTT-T-TT
1 TTTTC-TTTTC-TT-TTTTTCTTTCTTCTCTT
1021623 TTTTC-TTTCTTTTTTT-TTTCTCTCTCTTT
1 TTTTCTTTTCTTTTTTTCTTTCT-TCTC-TT
1021652 TTTTCTTTT
1 TTTTCTTTT
1021661 TCTTCAAGCA
Statistics
Matches: 58, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
25 5 0.09
26 6 0.10
27 3 0.05
28 8 0.14
29 7 0.12
30 15 0.26
31 3 0.05
32 10 0.17
33 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTCTTTTCTTTTTTTCTTTCTTCTCTT
Found at i:1021657 original size:39 final size:37
Alignment explanation
Indices: 1021572--1021661 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 37
1021562 TCATTTTTTT
*
1021572 TCTTTTTTTC-TTTTATCTCTTTTTTCTTTTTCTTTC
1 TCTTTTTTTCTTTTTATCTCTTTTTTCTTTTTCTCTC
* * *
1021608 T-TTTTCTTTCTTTTTTTTTCTTTCTTTTTTTTTTCTCTC
1 TCTTTT-TTTCTTTTTATCTC-TT-TTTTCTTTTTCTCTC
1021647 TCTTTTTTTCTTTTT
1 TCTTTTTTTCTTTTT
1021662 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
35 4 0.09
36 5 0.11
37 7 0.16
38 2 0.04
39 23 0.51
40 4 0.09
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (37 bp):
TCTTTTTTTCTTTTTATCTCTTTTTTCTTTTTCTCTC
Found at i:1021664 original size:14 final size:14
Alignment explanation
Indices: 1021568--1021664 Score: 106
Period size: 14 Copynumber: 6.6 Consensus size: 14
1021558 CCCCTCATTT
1021568 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
1021582 TTTTATCTCTTTTTTC
1 TTTT-TCT-TTTTTTC
1021598 TTTTTCTTTCTTTTTC
1 TTTTTC-TT-TTTTTC
1021614 TTTCTT-TTTTTTTC
1 TTT-TTCTTTTTTTC
*
1021628 TTTCTTTTTTTTTTC
1 TTT-TTCTTTTTTTC
* *
1021643 TCTCTCTTTTTTTC
1 TTTTTCTTTTTTTC
1021657 TTTTTCTT
1 TTTTTCTT
1021665 CAAGCATAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
14 31 0.43
15 18 0.25
16 21 0.29
17 2 0.03
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:1029022 original size:15 final size:15
Alignment explanation
Indices: 1028999--1029030 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1028989 TGAAATGAAT
1028999 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1029014 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1029029 AA
1 AA
1029031 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1034446 original size:3 final size:3
Alignment explanation
Indices: 1034430--1034511 Score: 92
Period size: 3 Copynumber: 26.7 Consensus size: 3
1034420 TTTGGGCTTG
* * * *
1034430 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAT TAG TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* *
1034477 TTA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1034512 TAAATAATTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
3 61 0.92
4 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1034457 original size:9 final size:9
Alignment explanation
Indices: 1034443--1034519 Score: 63
Period size: 9 Copynumber: 8.8 Consensus size: 9
1034433 TAATATTTAA
1034443 TAATAATAT
1 TAATAATAT
*
1034452 TAATAATAAA
1 TAATAAT-AT
1034462 TAATAATAT
1 TAATAATAT
*
1034471 TAGT-A-AT
1 TAATAATAT
1034478 T-ATAAT-T
1 TAATAATAT
*
1034485 ATAATAATAA
1 -TAATAATAT
*
1034495 TAATAATAA
1 TAATAATAT
1034504 TAATAATAT
1 TAATAATAT
*
1034513 AAATAAT
1 TAATAAT
1034520 TTTTTTAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
6 1 0.02
7 5 0.09
8 2 0.04
9 39 0.71
10 8 0.15
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (9 bp):
TAATAATAT
Found at i:1039901 original size:215 final size:215
Alignment explanation
Indices: 1039530--1039960 Score: 684
Period size: 215 Copynumber: 2.0 Consensus size: 215
1039520 CTTAGAGTGA
* * * * *
1039530 ATTTATCCCCACATTTGTATCATAGTCCATTTGTTCTTCTATAATCCACCAATGTTTTCTTGTTT
1 ATTTATCCCCACATTTGTAACACAGTCCATGTGTTCTTCTATAATCCACCAATGTTTGCCTGTTT
* *
1039595 TGGATTGTATTCTAGGGAACTCTTTTCTATGGCTGGTTAACTACTGTGTTAGGAGACTTATAAGT
66 TGGATTGTATTCTAGGGAACTCCTTTCTATGGCTGGTTAACAACTGTGTTAGGAGACTTATAAGT
* * *
1039660 GAAGTTATATTCTGTTGATGTTACTTTGGGTTGATATCTAAGTTTCTTATTC-CCAACCTACCAA
131 GAAGTTATATCCTATTGATGTTACTTTGGGTTGATATCTAAGTTTCATATTCTCC-ACCTACCAA
1039724 GTCAGTTCAAATGGCTTAGCC
195 GTCAGTTCAAATGGCTTAGCC
* *
1039745 ATTTATCTCCACATTTGTAACACAGTCCATGTGTTCTTCTATACTCCACCAATGTTTGCCTGTTT
1 ATTTATCCCCACATTTGTAACACAGTCCATGTGTTCTTCTATAATCCACCAATGTTTGCCTGTTT
* *
1039810 TGGATTGTATTCTGGGGAACTCCTTTCTATGGTTGGTTAACAACTGTGTTAGGAGACTTATAAGT
66 TGGATTGTATTCTAGGGAACTCCTTTCTATGGCTGGTTAACAACTGTGTTAGGAGACTTATAAGT
* * * *
1039875 GAAGTTGTATCCTATTGATGTTACTTTTGGTTGATATCTAAGTTTCATGTTCTCCACCTTCCAAG
131 GAAGTTATATCCTATTGATGTTACTTTGGGTTGATATCTAAGTTTCATATTCTCCACCTACCAAG
1039940 TCAGTTCAAATGGCTTAGCC
196 TCAGTTCAAATGGCTTAGCC
1039960 A
1 A
1039961 ACCTGAAAGC
Statistics
Matches: 197, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
215 195 0.99
216 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (215 bp):
ATTTATCCCCACATTTGTAACACAGTCCATGTGTTCTTCTATAATCCACCAATGTTTGCCTGTTT
TGGATTGTATTCTAGGGAACTCCTTTCTATGGCTGGTTAACAACTGTGTTAGGAGACTTATAAGT
GAAGTTATATCCTATTGATGTTACTTTGGGTTGATATCTAAGTTTCATATTCTCCACCTACCAAG
TCAGTTCAAATGGCTTAGCC
Found at i:1041757 original size:22 final size:22
Alignment explanation
Indices: 1041732--1041775 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1041722 CCGGACTGGG
1041732 AATGCACAAGATCAAGTGAGGA
1 AATGCACAAGATCAAGTGAGGA
1041754 AATGCACAAGATCAAGTGAGGA
1 AATGCACAAGATCAAGTGAGGA
1041776 TCAGGCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.27, T:0.14
Consensus pattern (22 bp):
AATGCACAAGATCAAGTGAGGA
Found at i:1048047 original size:19 final size:18
Alignment explanation
Indices: 1048023--1048058 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1048013 AGCAAAACTT
1048023 AAAAAGTAAAAACAAAAAG
1 AAAAAGTAAAAA-AAAAAG
1048042 AAAAAGTAAAAAAAAAA
1 AAAAAGTAAAAAAAAAA
1048059 CTTTTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.83, C:0.03, G:0.08, T:0.06
Consensus pattern (18 bp):
AAAAAGTAAAAAAAAAAG
Found at i:1065693 original size:36 final size:36
Alignment explanation
Indices: 1065607--1065707 Score: 121
Period size: 36 Copynumber: 2.8 Consensus size: 36
1065597 TTTCGTCCTT
* * * *
1065607 CTAGAATTCAAACTCCTAAAAATAGGACAGAATTTTG
1 CTAGGATTCAAACTCCT-AAAATAGGATAGAATTCTA
*
1065644 CTAGGATTCAAACTCCTAAAATAGGATAGAGTTCTA
1 CTAGGATTCAAACTCCTAAAATAGGATAGAATTCTA
* *
1065680 CTATGATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAA-ATAGGAT
1065708 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 33 0.59
37 23 0.41
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAATAGGATAGAATTCTA
Found at i:1066255 original size:19 final size:19
Alignment explanation
Indices: 1066178--1066264 Score: 58
Period size: 19 Copynumber: 4.6 Consensus size: 19
1066168 TTTTTTACAC
*
1066178 TATATAT-TA-TTATTATA
1 TATATATATATTTATTATT
*
1066195 TATACATATATGTT-TTATT
1 TATATATATAT-TTATTATT
* *
1066214 TATAT-TCATTTGGTTATTTTT
1 TATATAT-ATAT--TTATTATT
1066235 TA-ATACTATATTTATTATT
1 TATATA-TATATTTATTATT
1066254 TATATATATAT
1 TATATATATAT
1066265 ACTTTTTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
17 6 0.11
18 3 0.06
19 25 0.46
20 10 0.19
21 9 0.17
22 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:1066313 original size:2 final size:2
Alignment explanation
Indices: 1066306--1066364 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1066296 GTATTATTAC
1066306 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
1066348 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1066365 TATCTTTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1066624 original size:16 final size:15
Alignment explanation
Indices: 1066609--1066664 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
1066599 CATTTATTTA
1066609 TTTATTTTTCCTTTT
1 TTTATTTTTCCTTTT
*
1066624 ATTTATTTTTACTTATT
1 -TTTATTTTTCCTT-TT
* *
1066641 TTTATTCTTCATTTT
1 TTTATTTTTCCTTTT
1066656 TTTATTTTT
1 TTTATTTTT
1066665 TCAGTTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 10 0.29
16 22 0.65
17 2 0.06
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTTCCTTTT
Found at i:1071135 original size:15 final size:15
Alignment explanation
Indices: 1071110--1071149 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1071100 AGATCTAATC
1071110 AAGAACAAAAAAGAA-
1 AAGAA-AAAAAAGAAG
*
1071125 AAGAAACAAAAGAAG
1 AAGAAAAAAAAGAAG
1071140 AAGAAAAAAA
1 AAGAAAAAAA
1071150 CAAAGGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAGAAG
Found at i:1071137 original size:14 final size:14
Alignment explanation
Indices: 1071116--1071149 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1071106 AATCAAGAAC
1071116 AAAAAAGAA-AAGA
1 AAAAAAGAAGAAGA
1071129 AACAAAAGAAGAAGA
1 AA-AAAAGAAGAAGA
1071144 AAAAAA
1 AAAAAA
1071150 CAAAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 11 0.58
15 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAGAAGA
Found at i:1071152 original size:19 final size:18
Alignment explanation
Indices: 1071118--1071191 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 18
1071108 TCAAGAACAA
1071118 AAAAGAAAAGAAACAAAAG
1 AAAAGAAAA-AAACAAAAG
*
1071137 AAGAAGAAAAAAACAAAGG
1 AA-AAGAAAAAAACAAAAG
* *
1071156 AAAA-AGAGAAACAAAAG
1 AAAAGAAAAAAACAAAAG
*
1071173 AAAAAAATAAAGAACAAAA
1 AAAAGAA-AAA-AACAAAA
1071192 ATCAAAAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
17 14 0.31
18 3 0.07
19 14 0.31
20 14 0.31
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.01
Consensus pattern (18 bp):
AAAAGAAAAAAACAAAAG
Found at i:1072907 original size:106 final size:106
Alignment explanation
Indices: 1072776--1073832 Score: 1578
Period size: 106 Copynumber: 10.0 Consensus size: 106
1072766 ATATCGTGCC
* * * * *
1072776 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1072841 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1072882 ACTCCAGACAAGGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1072947 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1072988 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
**
1073053 AATTTCAGAGCCAATTTCAACTTCACAGTAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1073094 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1073159 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1073200 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1073265 AATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1073306 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1073370 AATTTCAGAGCCAGTTTCAACTTCGCAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1073411 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1073476 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1073517 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1073582 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * ** * * *
1073623 AC-CTAAGACAACACAAGCCCAACTTCACGACGAAGGG-GCGACTGATTGTTAA-AAA-AA--TC
1 ACTC-CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTC
* *
1073682 TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** ** * *
1073723 ACTAGAGACAACATAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCC
* * * *
1073787 CGATTCCAGAGCCAAGTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1073829 ACTC
1 ACTC
1073833 GGAACAATGC
Statistics
Matches: 870, Mismatches: 69, Indels: 24
0.90 0.07 0.02
Matches are distributed among these distances:
100 77 0.09
101 4 0.00
102 5 0.01
104 5 0.01
105 102 0.12
106 677 0.78
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1073568 original size:423 final size:422
Alignment explanation
Indices: 1072776--1073832 Score: 1675
Period size: 423 Copynumber: 2.5 Consensus size: 422
1072766 ATATCGTGCC
* *
1072776 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGAC-GCTGGTTGTCAACAAACAACTTCTC
* **
1072841 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAGGCAAGTTCAACT
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* * * *
1072906 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
130 TCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTCCCAATTTCAGAGCCAGTTTCAACTTC
*
1072971 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTG
194 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
1073036 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGTAAAGGATATTGGACTCCAG
259 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAG
1073101 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
324 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
1073166 GAGCCAATTTCAACTTCACAGCGAAGGATATTGG
389 GAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1073200 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGAC-GCTGGTTGTCAACAAACAACTTCTC
*
1073265 AATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
*
1073330 TCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCAGTTTCAACTTCG
130 TCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCAGTTTCAACTTCA
*
1073395 CAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGT
195 CAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* *
1073460 CAATAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
260 CAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGA
1073525 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
325 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* *
1073590 AGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
390 AGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * *
1073623 AC-CTAAGACAACACAAGCCCAACTTCACGACGAAGGGGCGACTGATTGTTAA-AAA-AA--TCT
1 ACTC-AAGACAACACAAGTTCAACTTCACGACGAAGGGACG-CTGGTTGTCAACAAACAACTTCT
* *
1073683 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACT-AGAGACAACATAAGTTCAA
64 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA-AGACAACACAAGTTCAA
* * *
1073745 CTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCCAAG-TTCAAC
128 CTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAGCC-AGTTTCAAC
*
1073809 TTCAC-GACGGAGGATATTGGACTC
191 TTCACAG-CGAAGGATATTGGACTC
1073833 GGAACAATGC
Statistics
Matches: 590, Mismatches: 37, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
416 1 0.00
417 86 0.15
418 48 0.08
419 6 0.01
421 2 0.00
422 5 0.01
423 295 0.50
424 147 0.25
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (422 bp):
ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACGCTGGTTGTCAACAAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTT
CACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCAGTTTCAACTTCAC
AGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
AATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGAC
AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGA
GCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1074588 original size:37 final size:37
Alignment explanation
Indices: 1074533--1074626 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
1074523 TTTTGTCCTT
* * *
1074533 CTAGTATTCAAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTA
*
1074570 CTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTA
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTA
* *
1074607 CTATGATTTAAACTCCTAAA
1 CTAGGATTCAAACTCCTAAA
1074627 GATATGATCC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTA
Found at i:1075135 original size:63 final size:66
Alignment explanation
Indices: 1075068--1075211 Score: 156
Period size: 67 Copynumber: 2.2 Consensus size: 66
1075058 TATATATACG
*
1075068 TATGTTTTTTTAAATGATTTTCAATT-G-ATTTTTT-ACACTATATATTATTA-TTATATATACA
1 TATGTTTTTTTAAATGATATTCAATTGGTATTTTTTAACACTATAT-TTATTATTTATATATACA
1075129 TA
65 TA
* * * * *
1075131 TATGTTTTATTT-ATTTATATTCATTTGGTTATTTTTTAATACTATATTTATTATTTATATATAT
1 TATGTTTT-TTTAAATGATATTCAATTGG-TATTTTTTAACACTATATTTATTATTTATATATAC
1075195 ATA
64 ATA
1075198 TACT-TTTTTTTAAA
1 TA-TGTTTTTTTAAA
1075212 ATATTTTACT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
63 18 0.27
64 4 0.06
66 16 0.24
67 27 0.41
68 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (66 bp):
TATGTTTTTTTAAATGATATTCAATTGGTATTTTTTAACACTATATTTATTATTTATATATACAT
A
Found at i:1075187 original size:19 final size:19
Alignment explanation
Indices: 1075106--1075196 Score: 53
Period size: 19 Copynumber: 4.6 Consensus size: 19
1075096 TTTTTTACAC
*
1075106 TATATAT-TA-TTATTATA
1 TATATATATATTTATTATT
*
1075123 TATACATATATGTT-TTATT
1 TATATATATAT-TTATTATT
* *
1075142 TATTTATATTCATTTGGTTATTT
1 TATATATA-T-ATTT-ATTA-TT
*
1075165 TTTAATACTATATTTATTATT
1 TAT-ATA-TATATTTATTATT
1075186 TATATATATAT
1 TATATATATAT
1075197 ATACTTTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
17 6 0.11
18 2 0.04
19 15 0.27
20 8 0.14
21 6 0.11
22 6 0.11
23 8 0.14
24 3 0.05
25 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:1075246 original size:2 final size:2
Alignment explanation
Indices: 1075239--1075283 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1075229 GTATTATTAC
1075239 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
1075281 TA T
1 TA T
1075284 TGTAATTATC
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:1075428 original size:23 final size:23
Alignment explanation
Indices: 1075383--1075437 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1075373 TATGTATACT
1075383 TTTATATTTGGTTTATATATTTA
1 TTTATATTTGGTTTATATATTTA
* * * *
1075406 TTTATTTTTGGTTTTTTTTTTTA
1 TTTATATTTGGTTTATATATTTA
1075429 TATTATATT
1 T-TTATATT
1075438 ATATTTTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (23 bp):
TTTATATTTGGTTTATATATTTA
Found at i:1075449 original size:18 final size:19
Alignment explanation
Indices: 1075423--1075458 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1075413 TTGGTTTTTT
*
1075423 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
1075441 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
1075459 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:1075530 original size:4 final size:4
Alignment explanation
Indices: 1075517--1075613 Score: 51
Period size: 4 Copynumber: 24.2 Consensus size: 4
1075507 TATATTTTAA
*
1075517 TATT TCATT TATT TATT TATT TATT T-TT CCT-TT TATT T-TT T-TT TACT
1 TATT T-ATT TATT TATT TATT TATT TATT --TATT TATT TATT TATT TATT
* * * * * *
1075564 TATT TTTAT TCTT CATT T-TT TCATT TATT CATT TATT CATT TATT CATT
1 TATT TAT-T TATT TATT TATT T-ATT TATT TATT TATT TATT TATT TATT
1075613 T
1 T
1075614 TTCCCTCTAA
Statistics
Matches: 72, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
3 12 0.17
4 47 0.65
5 13 0.18
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:1075542 original size:16 final size:16
Alignment explanation
Indices: 1075517--1075613 Score: 67
Period size: 16 Copynumber: 6.1 Consensus size: 16
1075507 TATATTTTAA
*
1075517 TATTTCATTTATTTATT
1 TATTT-ATTTATTCATT
*
1075534 TATTTATTT-TTCCTTT
1 TATTTATTTATT-CATT
* *
1075550 TATTT-TTT-TTTACT
1 TATTTATTTATTCATT
* *
1075564 TATTTTTATTCTTCATT
1 TATTTAT-TTATTCATT
1075581 T-TTTCATTTATTCATT
1 TATTT-ATTTATTCATT
*
1075597 TATTCATTTATTCATT
1 TATTTATTTATTCATT
1075613 T
1 T
1075614 TTCCCTCTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 6 0.09
15 8 0.12
16 37 0.58
17 13 0.20
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTATTTATTCATT
Found at i:1079375 original size:29 final size:31
Alignment explanation
Indices: 1079324--1079396 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1079314 AAATTTTGGA
* *
1079324 TAGTGACCAAAATGCAAA-TTTTG-AAAGTT
1 TAGTGACCAAAATACAAACTTTGGAAAAGTT
* *
1079353 TAGTGACCAAAGTATAAACTTTGGAAAAGTT
1 TAGTGACCAAAATACAAACTTTGGAAAAGTT
*
1079384 TAGGGACCAAAAT
1 TAGTGACCAAAAT
1079397 GGTATTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 15 0.42
30 4 0.11
31 17 0.47
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.27
Consensus pattern (31 bp):
TAGTGACCAAAATACAAACTTTGGAAAAGTT
Found at i:1088809 original size:48 final size:48
Alignment explanation
Indices: 1088738--1088834 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
1088728 GCTCCAGCTG
*
1088738 GAGCTGCCGCCGTTGGACGCTGATGCATTATTCATGGTCCACGAGGCT
1 GAGCTGCCGCCGTTGGACGCTGATGCATTATTCATGGTCAACGAGGCT
* *
1088786 GAGCTGCCGCCGTTGGACGCTGATGCATTTTTCATGGTCAACGTGGCT
1 GAGCTGCCGCCGTTGGACGCTGATGCATTATTCATGGTCAACGAGGCT
1088834 G
1 G
1088835 CCTTTCGGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (48 bp):
GAGCTGCCGCCGTTGGACGCTGATGCATTATTCATGGTCAACGAGGCT
Found at i:1091437 original size:35 final size:36
Alignment explanation
Indices: 1091393--1091463 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
1091383 TAACTGTGTT
1091393 TTTTACATATACGGAGAAATTAAATATAGTTTGTAA
1 TTTTACATATACGGAGAAATTAAATATAGTTTGTAA
1091429 TTTT-CATATACGGAGAAATTAAATATAGTTTGTAA
1 TTTTACATATACGGAGAAATTAAATATAGTTTGTAA
1091464 ATTAATTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 31 0.89
36 4 0.11
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (36 bp):
TTTTACATATACGGAGAAATTAAATATAGTTTGTAA
Found at i:1091465 original size:18 final size:18
Alignment explanation
Indices: 1091409--1091468 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1091399 ATATACGGAG
1091409 AAATTAAATATAGTTTGT
1 AAATTAAATATAGTTTGT
* ** **
1091427 AATTTTCATATACG-GAG-
1 AAATTAAATATA-GTTTGT
1091444 AAATTAAATATAGTTTGT
1 AAATTAAATATAGTTTGT
1091462 AAATTAA
1 AAATTAA
1091469 TTTGATAGTT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 1 0.03
17 10 0.34
18 17 0.59
19 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (18 bp):
AAATTAAATATAGTTTGT
Found at i:1091942 original size:21 final size:21
Alignment explanation
Indices: 1091903--1091942 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1091893 AAATATTTAA
*
1091903 TTAGGTATATTAATTTTAAAT
1 TTAGATATATTAATTTTAAAT
1091924 TTAGATAT-TTAATTATTAA
1 TTAGATATATTAATT-TTAA
1091943 TAAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TTAGATATATTAATTTTAAAT
Found at i:1093184 original size:7 final size:7
Alignment explanation
Indices: 1093172--1093238 Score: 61
Period size: 7 Copynumber: 10.0 Consensus size: 7
1093162 ATTTTAAAAA
1093172 ATATTTT
1 ATATTTT
1093179 ATATTTT
1 ATATTTT
1093186 ATATTTT
1 ATATTTT
*
1093193 ATGTTTT
1 ATATTTT
1093200 -TATTTT
1 ATATTTT
*
1093206 -TGTTTT
1 ATATTTT
1093212 -TATTTTT
1 ATA-TTTT
*
1093219 AAATTTT
1 ATATTTT
1093226 AT-TTTT
1 ATATTTT
*
1093232 AAATTTT
1 ATATTTT
1093239 TTAAAAATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
6 16 0.32
7 33 0.66
8 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (7 bp):
ATATTTT
Found at i:1093211 original size:12 final size:12
Alignment explanation
Indices: 1093182--1093218 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
1093172 ATATTTTATA
1093182 TTTTATATTTTATG
1 TTTT-TATTTT-TG
1093196 TTTTTATTTTTG
1 TTTTTATTTTTG
1093208 TTTTTATTTTT
1 TTTTTATTTTT
1093219 AAATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.57
13 6 0.26
14 4 0.17
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (12 bp):
TTTTTATTTTTG
Found at i:1093212 original size:20 final size:19
Alignment explanation
Indices: 1093175--1093232 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1093165 TTAAAAAATA
1093175 TTTTATATTTTATATTTTATGT
1 TTTTAT-TTTTAT-TTTTAT-T
*
1093197 TTTTATTTTTGTTTTTATT
1 TTTTATTTTTATTTTTATT
* *
1093216 TTTAAATTTTATTTTTA
1 TTTTATTTTTATTTTTA
1093233 AATTTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.47
20 6 0.19
21 5 0.16
22 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTATTTTTATTTTTATT
Found at i:1093225 original size:13 final size:13
Alignment explanation
Indices: 1093209--1093238 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1093199 TTATTTTTGT
1093209 TTTTATTTTTAAA
1 TTTTATTTTTAAA
1093222 TTTTATTTTTAAA
1 TTTTATTTTTAAA
1093235 TTTT
1 TTTT
1093239 TTAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATTTTTAAA
Found at i:1093238 original size:33 final size:34
Alignment explanation
Indices: 1093175--1093239 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
1093165 TTAAAAAATA
* *
1093175 TTTTATATTTTATATTTTATGTTTTTATTTTTGT
1 TTTTATATTTTAAATTTTATGTTTTAATTTTTGT
1093209 TTTTAT-TTTTAAATTTTAT-TTTTAAATTTTT
1 TTTTATATTTTAAATTTTATGTTTT-AATTTTT
1093240 TAAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.14
33 18 0.64
34 6 0.21
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (34 bp):
TTTTATATTTTAAATTTTATGTTTTAATTTTTGT
Found at i:1094213 original size:20 final size:21
Alignment explanation
Indices: 1094179--1094222 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1094169 AAGGGTGGAG
*
1094179 GAGATGGAGAGGAGAAGAGTT
1 GAGATGGAGAAGAGAAGAGTT
1094200 GAGA-GGAGAAGAGAAGAGTT
1 GAGATGGAGAAGAGAAGAGTT
1094220 GAG
1 GAG
1094223 CGAAGCAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.48, T:0.11
Consensus pattern (21 bp):
GAGATGGAGAAGAGAAGAGTT
Found at i:1094232 original size:20 final size:20
Alignment explanation
Indices: 1094190--1094234 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1094180 AGATGGAGAG
*
1094190 GAGAAGAGTTGAGAGGAGAA
1 GAGAAGAGTTGAGAGAAGAA
* *
1094210 GAGAAGAGTTGAGCGAAGCA
1 GAGAAGAGTTGAGAGAAGAA
1094230 GAGAA
1 GAGAA
1094235 TGGGAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.42, T:0.09
Consensus pattern (20 bp):
GAGAAGAGTTGAGAGAAGAA
Found at i:1097047 original size:14 final size:14
Alignment explanation
Indices: 1097028--1097056 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1097018 GATAGAAATA
1097028 TTAGGAAACTTTGC
1 TTAGGAAACTTTGC
1097042 TTAGGAAACTTTGC
1 TTAGGAAACTTTGC
1097056 T
1 T
1097057 GAGAACCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (14 bp):
TTAGGAAACTTTGC
Found at i:1110029 original size:90 final size:90
Alignment explanation
Indices: 1109920--1110098 Score: 340
Period size: 90 Copynumber: 2.0 Consensus size: 90
1109910 AATGGAGCAA
1109920 ATCAAGCAAAAAGAAGGGATTTTTATTTCTAACATTTTTTCAACAAAAATGCATGTATGACATTT
1 ATCAAGCAAAAAGAAGGGATTTTTATTTCTAACATTTTTTCAACAAAAATGCATGTATGACATTT
1109985 AATGAACCAAGGACTTCTAGTAAAT
66 AATGAACCAAGGACTTCTAGTAAAT
1110010 ATCAAGCAAAAAGAAGGGATTTTTATTTCTAACATTTTTTCAACAAAAATGCATGTATGACATTT
1 ATCAAGCAAAAAGAAGGGATTTTTATTTCTAACATTTTTTCAACAAAAATGCATGTATGACATTT
* *
1110075 AATGGACCAAGGACTTTTAGTAAA
66 AATGAACCAAGGACTTCTAGTAAA
1110099 GAACATGATT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (90 bp):
ATCAAGCAAAAAGAAGGGATTTTTATTTCTAACATTTTTTCAACAAAAATGCATGTATGACATTT
AATGAACCAAGGACTTCTAGTAAAT
Found at i:1110677 original size:76 final size:75
Alignment explanation
Indices: 1110582--1110809 Score: 332
Period size: 76 Copynumber: 3.0 Consensus size: 75
1110572 TTCCAGATTA
* * * * *
1110582 ATTCTAGTATGTCGGAATATATGTCAGAATTGAGTCTCTGACTGAATTTCTCCTTTCCAAGTATT
1 ATTCTAGTATGTAGAAATATCTGTCAGAATTGAGTCTCTGACTGAATTT-TCATTTCCATGTATT
*
1110647 CAGCCAAATGG
65 GAGCCAAATGG
*
1110658 ATTCTAGTATGTAGAAATATCTGTAAGAATTGAGTCTCTGACTGAATTTTCATTTCCATGTATTG
1 ATTCTAGTATGTAGAAATATCTGTCAGAATTGAGTCTCTGACTGAATTTTCATTTCCATGTATTG
1110723 AGCCAAATAGG
66 AGCCAAAT-GG
* * *
1110734 -TTCTAGTATGCAGAAATATCTGTCAGAATTGAGCCTCTGACTGAATTTTTCATGTCCATGTATT
1 ATTCTAGTATGTAGAAATATCTGTCAGAATTGAGTCTCTGACTGAA-TTTTCATTTCCATGTATT
1110798 GAGCCAAATGG
65 GAGCCAAATGG
1110809 A
1 A
1110810 AAAAGAAAAT
Statistics
Matches: 138, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
75 65 0.47
76 73 0.53
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (75 bp):
ATTCTAGTATGTAGAAATATCTGTCAGAATTGAGTCTCTGACTGAATTTTCATTTCCATGTATTG
AGCCAAATGG
Found at i:1132299 original size:27 final size:28
Alignment explanation
Indices: 1132269--1132322 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
1132259 AGTGTACTCT
*
1132269 TATA-TGCACTTAAAAGTGCCTCGTAGA
1 TATATTGCACTCAAAAGTGCCTCGTAGA
*
1132296 TATATTTGCACTCGAAAGTGCCTCGTA
1 TATA-TTGCACTCAAAAGTGCCTCGTA
1132323 AAATTGCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
29 19 0.83
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (28 bp):
TATATTGCACTCAAAAGTGCCTCGTAGA
Found at i:1132555 original size:66 final size:66
Alignment explanation
Indices: 1132364--1132557 Score: 237
Period size: 66 Copynumber: 2.9 Consensus size: 66
1132354 ATCATATAGT
* * * *
1132364 CACTCCACCTTATGCACCACAAGGGTAC-TCAAGTCTCATTGAGTGATCAGTACAATATTCAATT
1 CACTCCACCTCATGCACCACAAAGGTACAT-GAGTCTCATTGAGTGATCTGTACAATATTCAATT
1132428 AC
65 AC
* * * * *
1132430 CACTCCATCTCATACGCCACAAAGGTACAAGAGTCTCATTGAGTGATCTGTATAATATTCAATTA
1 CACTCCACCTCATGCACCACAAAGGTACATGAGTCTCATTGAGTGATCTGTACAATATTCAATTA
*
1132495 T
66 C
* * * * *
1132496 TACTCCACCTCATGCACCACAAAGGTACATGAGTCTTATTGAGTGATTTGCACAGTATTCAA
1 CACTCCACCTCATGCACCACAAAGGTACATGAGTCTCATTGAGTGATCTGTACAATATTCAA
1132558 CAATCATTCC
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
66 107 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (66 bp):
CACTCCACCTCATGCACCACAAAGGTACATGAGTCTCATTGAGTGATCTGTACAATATTCAATTA
C
Found at i:1140727 original size:11 final size:11
Alignment explanation
Indices: 1140711--1140744 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1140701 CAACACCATG
1140711 CATTGCATTTA
1 CATTGCATTTA
*
1140722 CATTGCATCTA
1 CATTGCATTTA
*
1140733 TATTGCATTTA
1 CATTGCATTTA
1140744 C
1 C
1140745 TTTTCACATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (11 bp):
CATTGCATTTA
Found at i:1144077 original size:19 final size:20
Alignment explanation
Indices: 1144053--1144094 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
1144043 TTTTCATATT
1144053 TTTATCATTCTTT-ACA-TTC
1 TTTATCATT-TTTGACACTTC
1144072 TTTATCATTTTTGACACTTC
1 TTTATCATTTTTGACACTTC
1144092 TTT
1 TTT
1144095 TGTTATTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.19, C:0.19, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTATCATTTTTGACACTTC
Found at i:1145618 original size:14 final size:12
Alignment explanation
Indices: 1145601--1145759 Score: 113
Period size: 12 Copynumber: 12.2 Consensus size: 12
1145591 TACCACACTC
1145601 GAAAAAGAAAAAGA
1 GAAAAA-AAAAA-A
1145615 GAAAAAAAAGAAA
1 GAAAAAAAA-AAA
*
1145628 GAAAAAAATAGAAG
1 GAAAAAAA-A-AAA
1145642 GAAATAAAAAAAA
1 GAAA-AAAAAAAA
* *
1145655 GAATATAAAAAA
1 GAAAAAAAAAAA
1145667 GAAAGAAAGAAAAAA
1 G-AA-AAA-AAAAAA
1145682 GAAAAAAGAAAAAA
1 G-AAAAA-AAAAAA
*
1145696 GAAAAGAAAAAA
1 GAAAAAAAAAAA
*
1145708 GAAAAAAGAAAA
1 GAAAAAAAAAAA
1145720 GAAAAAAGAATAAA
1 GAAAAAA-AA-AAA
**
1145734 -AAAGGAAAAAA
1 GAAAAAAAAAAA
*
1145745 GAAAGAAAGAAAA
1 GAAA-AAAAAAAA
1145758 GA
1 GA
1145760 TAGATAAGGA
Statistics
Matches: 120, Mismatches: 15, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
11 3 0.03
12 36 0.30
13 35 0.29
14 32 0.27
15 14 0.12
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:1145650 original size:18 final size:17
Alignment explanation
Indices: 1145602--1145737 Score: 69
Period size: 17 Copynumber: 8.4 Consensus size: 17
1145592 ACCACACTCG
*
1145602 AAAAAGAA--AAAGAGA
1 AAAAAGAAGGAAAGAAA
1145617 AAAAA-AA-GAAAGAAA
1 AAAAAGAAGGAAAGAAA
*
1145632 AAAATAGAAGGAAATAAA
1 AAAA-AGAAGGAAAGAAA
*
1145650 AAAAAGAA-TATAA-AAA
1 AAAAAGAAGGA-AAGAAA
* * *
1145666 AGAAAGAAAGAAAAAAGA
1 AAAAAGAAGGAAAGAA-A
*
1145684 AAAAAGAA-AAAAGAAA
1 AAAAAGAAGGAAAGAAA
1145700 AGAAAA-AA-GAAA-AAA
1 A-AAAAGAAGGAAAGAAA
* *
1145715 GAAAAGAA-AAAAGAATA
1 AAAAAGAAGGAAAGAA-A
1145732 AAAAAG
1 AAAAAG
1145738 GAAAAAAGAA
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.06
15 23 0.24
16 23 0.24
17 26 0.27
18 19 0.20
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (17 bp):
AAAAAGAAGGAAAGAAA
Found at i:1145678 original size:60 final size:57
Alignment explanation
Indices: 1145602--1145757 Score: 163
Period size: 60 Copynumber: 2.6 Consensus size: 57
1145592 ACCACACTCG
* * *
1145602 AAAAAGAAAAAGAGAAAAAAAAGAAAGAAAAAAATAGAAGGAAATAA-AAAAAAGAATATA
1 AAAAAGAAAAA-AGAAAAAAAAGAAAGAAAAAAA-A-AA-GAAAAAAGAAAAAAGAAAAGA
*
1145662 AAAAAGAAAGAAAGAAAAAAGAAAAAAGAAAAAAGAAAAGAAAAAAGAAAAAAGAAAAGA
1 AAAAAGAAA-AAAGAAAAAA-AAGAAAGAAAAAA-AAAAGAAAAAAGAAAAAAGAAAAGA
*
1145722 AAAAAGAATAAAA-AAGGAAAAAAGAAAGAAAGAAAA
1 AAAAAGAA-AAAAGAA--AAAAAAGAAAGAAAAAAAA
1145758 GATAGATAAG
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
59 10 0.12
60 52 0.63
61 20 0.24
62 1 0.01
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (57 bp):
AAAAAGAAAAAAGAAAAAAAAGAAAGAAAAAAAAAAGAAAAAAGAAAAAAGAAAAGA
Found at i:1145684 original size:7 final size:7
Alignment explanation
Indices: 1145602--1145757 Score: 130
Period size: 7 Copynumber: 22.4 Consensus size: 7
1145592 ACCACACTCG
1145602 AAAAAGA
1 AAAAAGA
1145609 AAAAGAGA
1 AAAA-AGA
1145617 AAAAA-A
1 AAAAAGA
*
1145623 AGAAAGA
1 AAAAAGA
1145630 AAAAA-A
1 AAAAAGA
* *
1145636 TAGAAGGA
1 -AAAAAGA
*
1145644 AATAA-A
1 AAAAAGA
1145650 AAAAAG-
1 AAAAAGA
* *
1145656 -AATATA
1 AAAAAGA
1145662 AAAAAGA
1 AAAAAGA
1145669 AAGAAAGA
1 AA-AAAGA
1145677 AAAAAGA
1 AAAAAGA
1145684 AAAAAGA
1 AAAAAGA
1145691 AAAAAG-
1 AAAAAGA
1145697 -AAAAGA
1 AAAAAGA
1145703 AAAAAGA
1 AAAAAGA
1145710 AAAAAGA
1 AAAAAGA
1145717 AAAGAA-A
1 AAA-AAGA
*
1145724 AAAGAATA
1 AAA-AAGA
1145732 AAAAAGGA
1 AAAAA-GA
1145740 AAAAAGA
1 AAAAAGA
1145747 AAGAAAGA
1 AA-AAAGA
1145755 AAA
1 AAA
1145758 GATAGATAAG
Statistics
Matches: 122, Mismatches: 13, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
5 8 0.07
6 11 0.09
7 69 0.57
8 34 0.28
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:1145769 original size:30 final size:27
Alignment explanation
Indices: 1145668--1145770 Score: 97
Period size: 26 Copynumber: 3.7 Consensus size: 27
1145658 TATAAAAAAG
*
1145668 AAAG-AAAGA-AAAAAGAAAAAAGAAA
1 AAAGAAAAGATAAAAGGAAAAAAGAAA
*
1145693 AAAGAAAAGA-AAAAAGAAAAAAGAAA
1 AAAGAAAAGATAAAAGGAAAAAAGAAA
1145719 AGAA-AAAAGAATAAAAAAGGAAAAAAGAAA
1 A-AAGAAAAG-ATAAA--AGGAAAAAAGAAA
1145749 GAAAGAAAAGATAGATAAGGAA
1 -AAAGAAAAGATA-A-AAGGAA
1145771 GAGCAAAAGG
Statistics
Matches: 67, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
25 4 0.06
26 27 0.40
27 3 0.04
28 3 0.04
30 22 0.33
31 7 0.10
32 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (27 bp):
AAAGAAAAGATAAAAGGAAAAAAGAAA
Found at i:1148383 original size:134 final size:134
Alignment explanation
Indices: 1148154--1148867 Score: 748
Period size: 134 Copynumber: 5.3 Consensus size: 134
1148144 ACAAATAGAA
* * *
1148154 CTCGATTTAATCTTCCCTGAGTGATAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATTCCCAGATCTGATTTTCCCTCA
* * * ** *
1148219 AGAAGAAACATAA-ACTATCCATCTCTTTCAATATTTAATATTCCCTTAGTAGTAGTGGAACAAG
66 AGAAGAAACATAACA-TATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAA
* *
1148283 CCTGC
130 TCTAC
* * * * *
1148288 CTCGATT-ATATTTTCCATGAGTGACAATGGAATGAATAAACATTCCCAGATATGATTTTCCCTC
1 CTCGATTCA-ATCTTCCCTGAGTGACAGTGGAATGAATCAACATTCCCAGATCTGATTTTCCCTC
* * * *
1148352 AAGAAGAAGCATAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAATAATAGTGGAACAAA
65 AAGAAGAAACATAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAA
1148417 TCTAC
130 TCTAC
* *
1148422 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATC-A-ATGTCCTCATATCTTATTTTCCCT
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACAT-TCC-CAGATCTGATTTTCCCT
* *** ** * * *
1148485 CAAAAAGAAATGGAACAGGTTCATCCCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
64 CAAGAAGAAACATAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
* * *
1148550 GTATGC
129 ATCTAC
* *
1148556 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGA--CCCCGAATCTGATTTTCCAT
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAAC-ATTCCCAG-ATCTGATTTTCCCT
* * * **
1148619 CAAGAA-AAA-GTGAA-ATAAATCCATCTCTTTCAAGAGTTGATATTCCCTGAATAACAGTTAAA
64 CAAGAAGAAACAT-AACAT--ATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAA
*
1148681 AAAATCTAC
126 CAAATCTAC
* * * * * *
1148690 CTCGATTCAATCTTCCCTGAGTGACAATGGAATGAATCAAC-GTCCTGAGATATAATTTTCCCTT
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATTCC-CAGATCTGATTTTCCCTC
* * * *
1148754 AAGAAGAAACAGAACATATCCATCTCTTTCAAGAATTGATATTCCCTGAGTAACAGTGGAATAAG
65 AAGAAGAAACATAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAA
*
1148819 TATAC
130 TCTAC
* * *
1148824 CTCGATTCAATCTTTCCTGAAG-AACAGTGGAATGAGTCAACATT
1 CTCGATTCAATCTTCCCTG-AGTGACAGTGGAATGAATCAACATT
1148868 TCTCGATCTG
Statistics
Matches: 480, Mismatches: 80, Indels: 39
0.80 0.13 0.07
Matches are distributed among these distances:
132 4 0.01
133 11 0.02
134 450 0.94
135 12 0.03
136 2 0.00
137 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATTCCCAGATCTGATTTTCCCTCA
AGAAGAAACATAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAAT
CTAC
Found at i:1148879 original size:268 final size:267
Alignment explanation
Indices: 1148154--1148879 Score: 879
Period size: 268 Copynumber: 2.7 Consensus size: 267
1148144 ACAAATAGAA
* * * * *
1148154 CTCGATTTAATCTTCCCTGAGTGATAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTCCTCAGATCTAATTTTCCCTCA
* * * * **
1148219 AGAAGAAACATAA-ACTATCCATCTCTTTCAATATTTAATATTCCCTTAGTAGTAGTGGAACAAG
66 AGAAGAAACAGAACA-TATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
** * * *
1148283 CCTGCCTCGATT-ATAT-TTTCCATGAGTGACAATGGAATGAATAAACATTCCCAGATATGATTT
130 TATGCCTCGATTCA-ATCTTTCC-TGAGTGACAGTGGAATGAATCAACATTCCC-GATCTGATTT
* * * * * * *
1148346 TCCCTCAAGAAGAAGCATAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAATAATAGTGG
192 TCCATCAAGAAAAAGCATAACAAATCCATCTCTTTCAAGAGTTGATATTCCCTGAATAACAGTGA
*
1148411 AACAAATCTAC
257 AAAAAATCTAC
* * *
1148422 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAATGTCCTCATATCTTATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTCCTCAGATCTAATTTTCCCTCA
* ** ** * * *
1148487 AAAAGAAATGGAACAGGTTCATCCCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
66 AGAAGAAACAGAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
* *
1148552 ATGCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGA-CCCCGAATCTGATTTTC
131 ATGCCTCGATTCAATCTTTCCTGAGTGACAGTGGAATGAATCAAC-ATTCCCG-ATCTGATTTTC
* * *
1148616 CATCAAGAAAAAGTGA-AATAAATCCATCTCTTTCAAGAGTTGATATTCCCTGAATAACAGTTAA
194 CATCAAGAAAAAG-CATAACAAATCCATCTCTTTCAAGAGTTGATATTCCCTGAATAACAGTGAA
1148680 AAAAATCTAC
258 AAAAATCTAC
* * * *
1148690 CTCGATTCAATCTTCCCTGAGTGACAATGGAATGAATCAACGTCCTGAGATATAATTTTCCCTTA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTCCTCAGATCTAATTTTCCCTCA
* *
1148755 AGAAGAAACAGAACATATCCATCTCTTTCAAGAATTGATATTCCCTGAGTAACAGTGGAATAAGT
66 AGAAGAAACAGAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
* * * *
1148820 ATACCTCGATTCAATCTTTCCTGAAG-AACAGTGGAATGAGTCAACATTTCTCGATCTGAT
131 ATGCCTCGATTCAATCTTTCCTG-AGTGACAGTGGAATGAATCAACA-TTCCCGATCTGAT
1148880 CTCCCCTAAA
Statistics
Matches: 387, Mismatches: 62, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
267 2 0.01
268 372 0.96
269 13 0.03
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (267 bp):
CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTCCTCAGATCTAATTTTCCCTCA
AGAAGAAACAGAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
ATGCCTCGATTCAATCTTTCCTGAGTGACAGTGGAATGAATCAACATTCCCGATCTGATTTTCCA
TCAAGAAAAAGCATAACAAATCCATCTCTTTCAAGAGTTGATATTCCCTGAATAACAGTGAAAAA
AATCTAC
Found at i:1149045 original size:3 final size:3
Alignment explanation
Indices: 1149037--1149091 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1149027 TCTGGATATC
1149037 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1149085 TAT TAT T
1 TAT TAT T
1149092 TAGTTTTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1149852 original size:18 final size:18
Alignment explanation
Indices: 1149829--1149869 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1149819 TTCTCTCTCT
1149829 AAAAATAAAAAAAAATGA
1 AAAAATAAAAAAAAATGA
* *
1149847 AAAAATATAAAAATATGA
1 AAAAATAAAAAAAAATGA
1149865 AAAAA
1 AAAAA
1149870 ATATTGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAAAAAATGA
Found at i:1151516 original size:14 final size:14
Alignment explanation
Indices: 1151497--1151524 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1151487 TGATAGTTGG
1151497 AAAATGTTTTCCAA
1 AAAATGTTTTCCAA
1151511 AAAATGTTTTCCAA
1 AAAATGTTTTCCAA
1151525 TGTTTGATAG
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:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
AAAATGTTTTCCAA
Found at i:1151548 original size:42 final size:44
Alignment explanation
Indices: 1151474--1151587 Score: 139
Period size: 42 Copynumber: 2.7 Consensus size: 44
1151464 GGTTTTCCTC
** * *
1151474 GTTTTCCTGTGTTTGATAGTTGGAAAAT-GTTTT-CCAAAAA-AT
1 GTTTTCCAATGTTTGATAGTT-GTAATTGGTTTTACCAAAAACAT
*
1151516 GTTTTCCAATGTTTGATAGTTGTAATTGGTTTTACGAAAAACAT
1 GTTTTCCAATGTTTGATAGTTGTAATTGGTTTTACCAAAAACAT
1151560 -TTTT-CAATGTTTGATAGTTGTAATTGGT
1 GTTTTCCAATGTTTGATAGTTGTAATTGGT
1151588 AATCCTAAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
41 4 0.06
42 48 0.75
43 10 0.16
44 2 0.03
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (44 bp):
GTTTTCCAATGTTTGATAGTTGTAATTGGTTTTACCAAAAACAT
Found at i:1152355 original size:22 final size:22
Alignment explanation
Indices: 1152329--1152373 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1152319 TGTAATTCAT
* *
1152329 TTTATGTAAAATAATTTTTAGG
1 TTTATATAAAACAATTTTTAGG
*
1152351 TTTATATAAAACAGTTTTTAGG
1 TTTATATAAAACAATTTTTAGG
1152373 T
1 T
1152374 AATTCATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
TTTATATAAAACAATTTTTAGG
Found at i:1154208 original size:251 final size:251
Alignment explanation
Indices: 1153750--1154252 Score: 927
Period size: 251 Copynumber: 2.0 Consensus size: 251
1153740 ATTGTAAAAT
1153750 ATAATAATTTAAAATAATATATATCTTTAAGTTACTAAAAAATAAATCTTATACATTGAAAAATA
1 ATAATAATTTAAAATAATATATATCTTTAAGTTACTAAAAAATAAATCTTATACATTGAAAAATA
* *
1153815 ATATTTTTGTCCACTTGAGATCACAATATTATTTTTTTTCATATTATATTATATTTTATATAGAT
66 ATATCTTTGTCCACTTAAGATCACAATATTATTTTTTTTCATATTATATTATATTTTATATAGAT
*
1153880 AAAAATGATACTTATAAAAATTATTTAAATACAAATTTGATATACTAATTATATTAATTATATAT
131 AAAAATGATACTTATAAAAATTATTTAAATACAAAGTTGATATACTAATTATATTAATTATATAT
*
1153945 TAAATTTATTTTTCTCAAAAGTTAGATAGTATAACAATTAAAATATTTATATGTTA
196 TAAATGTATTTTTCTCAAAAGTTAGATAGTATAACAATTAAAATATTTATATGTTA
*
1154001 ATAATTATATTAAAATAATATATATCTTTAAGTTACTAAAAAATAAATCTTATACATTGAAAAAT
1 ATAATAAT-TTAAAATAATATATATCTTTAAGTTACTAAAAAATAAATCTTATACATTGAAAAAT
1154066 AATATCTTTGTCCACTTAAGATCACAATATTA-TTTTTTTCATATTATATTATATTTTATATAGA
65 AATATCTTTGTCCACTTAAGATCACAATATTATTTTTTTTCATATTATATTATATTTTATATAGA
*
1154130 TAAATATGATACTTATAAAAATTATTTAAATACAAAGTTGATATACTAATTATATTAATTATATA
130 TAAAAATGATACTTATAAAAATTATTTAAATACAAAGTTGATATACTAATTATATTAATTATATA
*
1154195 TTAAATGTATTTTTCTCAAAAGTTAGATAGTATAATAATTAAAATATTTATATGTTA
195 TTAAATGTATTTTTCTCAAAAGTTAGATAGTATAACAATTAAAATATTTATATGTTA
1154252 A
1 A
1154253 AATGTGTAAG
Statistics
Matches: 244, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
251 158 0.65
252 86 0.35
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (251 bp):
ATAATAATTTAAAATAATATATATCTTTAAGTTACTAAAAAATAAATCTTATACATTGAAAAATA
ATATCTTTGTCCACTTAAGATCACAATATTATTTTTTTTCATATTATATTATATTTTATATAGAT
AAAAATGATACTTATAAAAATTATTTAAATACAAAGTTGATATACTAATTATATTAATTATATAT
TAAATGTATTTTTCTCAAAAGTTAGATAGTATAACAATTAAAATATTTATATGTTA
Found at i:1154805 original size:189 final size:188
Alignment explanation
Indices: 1154487--1154826 Score: 554
Period size: 189 Copynumber: 1.8 Consensus size: 188
1154477 AATAAAATCA
* **
1154487 TTTTACGATTCAAACTTAAATAGGTATTATTTTAATTTGAAATATACAAAAGTATATAATTATTT
1 TTTTACGATTCAAACTTAAACAAATATTATTTTAATTTGAAATATACAAAAGTATATAATTATTT
* * * * *
1154552 TTAATATTCAAAGTTAAAAAGATAACAAATATCTTTTTAAATTGACATATTCATAGAGTAATTAT
66 TTAATATTCAAAATTAAAAAGATAAAAAATACCTTTTTAAATTGACATATTAAAAGAGTAATTAT
1154617 CCTACTAATATTCAAATTAAATAATAGATTTAATTTGCAATGGTCAAAGGTAAACTAT
131 CCTACTAATATTCAAATTAAATAATAGATTTAATTTGCAATGGTCAAAGGTAAACTAT
*
1154675 TTTTACTATTCAAACTTAAACAAATATTATTTTAATTTGAAATATACAAAAGTATATAATTATCT
1 TTTTACGATTCAAACTTAAACAAATATTATTTTAATTTGAAATATACAAAAGTATATAATTAT-T
* ** *
1154740 TTTAATATTCAAAATTATAAAGATAAAAAATACCTTTTTAAATTGATTTATTAAAATAGTAATTA
65 TTTAATATTCAAAATTAAAAAGATAAAAAATACCTTTTTAAATTGACATATTAAAAGAGTAATTA
1154805 TCCTACTAATATTCAAATTAAA
130 TCCTACTAATATTCAAATTAAA
1154827 AATTATCTTT
Statistics
Matches: 138, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
188 59 0.43
189 79 0.57
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (188 bp):
TTTTACGATTCAAACTTAAACAAATATTATTTTAATTTGAAATATACAAAAGTATATAATTATTT
TTAATATTCAAAATTAAAAAGATAAAAAATACCTTTTTAAATTGACATATTAAAAGAGTAATTAT
CCTACTAATATTCAAATTAAATAATAGATTTAATTTGCAATGGTCAAAGGTAAACTAT
Found at i:1155240 original size:12 final size:13
Alignment explanation
Indices: 1155216--1155244 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1155206 TTTTTAAAAT
1155216 AAAACATTATTTA
1 AAAACATTATTTA
1155229 AAAACATT-TTTA
1 AAAACATTATTTA
1155241 AAAA
1 AAAA
1155245 TTTTGATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAACATTATTTA
Found at i:1155907 original size:2 final size:2
Alignment explanation
Indices: 1155896--1155931 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1155886 AATTATTAAA
1155896 AT AT -T 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 A
1155932 ACTTTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1156459 original size:14 final size:14
Alignment explanation
Indices: 1156442--1156518 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
1156432 TTTTCAGAAA
1156442 ATGTAATTCATTTT
1 ATGTAATTCATTTT
*
1156456 ATGTAA--AATATTT
1 ATGTAATTCAT-TTT
* *
1156469 AGGTAATTCATTTG
1 ATGTAATTCATTTT
**
1156483 ATGTAAAACAATTTTT
1 ATGTAATTC-A-TTTT
*
1156499 AGGTAATTCATTTT
1 ATGTAATTCATTTT
*
1156513 ACGTAA
1 ATGTAA
1156519 ATTATTTTCC
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
12 2 0.04
13 8 0.17
14 23 0.50
15 4 0.09
16 9 0.20
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (14 bp):
ATGTAATTCATTTT
Found at i:1156502 original size:30 final size:27
Alignment explanation
Indices: 1156444--1156525 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 27
1156434 TTCAGAAAAT
*
1156444 GTAATTCATTTTATGTAAAATATTTAG
1 GTAATTCATTTGATGTAAAATATTTAG
*
1156471 GTAATTCATTTGATGTAAAACAATTTTTAG
1 GTAATTCATTTGATGT--AA-AATATTTAG
* * *
1156501 GTAATTCATTTTACGTAAATTATTT
1 GTAATTCATTTGATGTAAAATATTT
1156526 TCCAAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
27 20 0.43
28 2 0.04
29 2 0.04
30 22 0.48
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (27 bp):
GTAATTCATTTGATGTAAAATATTTAG
Found at i:1158106 original size:9 final size:9
Alignment explanation
Indices: 1158094--1158119 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1158084 CAAGCTTTCC
1158094 TCTTCTTCA
1 TCTTCTTCA
1158103 TCTTCTTCA
1 TCTTCTTCA
1158112 TCTTCTTC
1 TCTTCTTC
1158120 TTAAGCAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.58
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:1173389 original size:40 final size:40
Alignment explanation
Indices: 1173334--1173415 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1173324 TTATCACTGC
1173334 CTAGGTAAACATATTTAAGATGCCCTGGCAAAGGCTTTAG
1 CTAGGTAAACATATTTAAGATGCCCTGGCAAAGGCTTTAG
1173374 CTAGGTAAACATATTTAAGATGCCCTGGCAAAGGCTTTAG
1 CTAGGTAAACATATTTAAGATGCCCTGGCAAAGGCTTTAG
1173414 CT
1 CT
1173416 CTAGGGTAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (40 bp):
CTAGGTAAACATATTTAAGATGCCCTGGCAAAGGCTTTAG
Found at i:1178059 original size:20 final size:21
Alignment explanation
Indices: 1178008--1178060 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1177998 CAACCTGTGG
*
1178008 GTATCGATAC-CAGGAGTTCA
1 GTATCGATACTGAGGAGTTCA
* *
1178028 TTATCAATACTGAGGAG-TCA
1 GTATCGATACTGAGGAGTTCA
1178048 GTATCGATACTGA
1 GTATCGATACTGA
1178061 CAGATAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (21 bp):
GTATCGATACTGAGGAGTTCA
Found at i:1188175 original size:21 final size:21
Alignment explanation
Indices: 1188145--1188197 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1188135 AAGTTACCCT
*
1188145 AGTATCGATACCCCTATGGAG
1 AGTATTGATACCCCTATGGAG
1188166 AGTATTGATACCCCTATGGAG
1 AGTATTGATACCCCTATGGAG
1188187 AGTATTGATAC
1 AGTATTGATAC
1188198 TCCTGCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (21 bp):
AGTATTGATACCCCTATGGAG
Found at i:1195341 original size:21 final size:21
Alignment explanation
Indices: 1195317--1195368 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1195307 AAAATACCCT
* *
1195317 AGTATTGATACCCCTATGGAG
1 AGTATTAATACCCCTACGGAG
*
1195338 AGTATTAATACCCCTACGGGG
1 AGTATTAATACCCCTACGGAG
*
1195359 AGTATCAATA
1 AGTATTAATA
1195369 TTTTATGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (21 bp):
AGTATTAATACCCCTACGGAG
Found at i:1195514 original size:12 final size:12
Alignment explanation
Indices: 1195497--1195521 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1195487 TACCCCAAAC
1195497 TCACCATTGAGG
1 TCACCATTGAGG
1195509 TCACCATTGAGG
1 TCACCATTGAGG
1195521 T
1 T
1195522 GCAAAACCCC
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TCACCATTGAGG
Found at i:1196337 original size:21 final size:22
Alignment explanation
Indices: 1196296--1196351 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
1196286 TCAAGAGTAG
1196296 TGGTTTCAAAACCCGCTCTTTA
1 TGGTTTCAAAACCCGCTCTTTA
* * *
1196318 TGGTTTTAAAATCC-CTCTTTT
1 TGGTTTCAAAACCCGCTCTTTA
*
1196339 TGGTTTCGAAACC
1 TGGTTTCAAAACC
1196352 ATTTGGGCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (22 bp):
TGGTTTCAAAACCCGCTCTTTA
Found at i:1200629 original size:13 final size:13
Alignment explanation
Indices: 1200611--1200639 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1200601 TCCGTTGAAA
1200611 TTTTTGGATAAGC
1 TTTTTGGATAAGC
1200624 TTTTTGGATAAGC
1 TTTTTGGATAAGC
1200637 TTT
1 TTT
1200640 CAAACCCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (13 bp):
TTTTTGGATAAGC
Found at i:1201051 original size:23 final size:22
Alignment explanation
Indices: 1201025--1201085 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
1201015 TTATTTGTTT
*
1201025 TTTAAAAACT-AAAATATTTAAAA
1 TTTAAAAA-TAAAAATA-TAAAAA
1201048 TTTAAAATATAAAAATATAAAAA
1 TTTAAAA-ATAAAAATATAAAAA
*
1201071 ATTAAAAATTAAAAA
1 TTTAAAAA-TAAAAA
1201086 AATGATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 25 0.76
24 7 0.21
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TTTAAAAATAAAAATATAAAAA
Found at i:1201070 original size:16 final size:15
Alignment explanation
Indices: 1201026--1201086 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
1201016 TATTTGTTTT
* *
1201026 TTAAAAACTAAAATA
1 TTAAAAATTAAAAAA
* *
1201041 TTTAAAATT-TAAAA
1 TTAAAAATTAAAAAA
1201055 TATAAAAATATAAAAAA
1 T-TAAAAAT-TAAAAAA
1201072 TTAAAAATTAAAAAA
1 TTAAAAATTAAAAAA
1201087 ATGATTAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 4 0.11
15 20 0.54
16 8 0.22
17 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAAATTAAAAAA
Found at i:1201071 original size:24 final size:23
Alignment explanation
Indices: 1201026--1201085 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
1201016 TATTTGTTTT
* **
1201026 TTAAAAACT-AAAATATTTAAAA
1 TTAAAAATTAAAAATATAAAAAA
*
1201048 TTTAAAATATAAAAATATAAAAAA
1 TTAAAAAT-TAAAAATATAAAAAA
1201072 TTAAAAATTAAAAA
1 TTAAAAATTAAAAA
1201086 AATGATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 6 0.19
23 7 0.23
24 18 0.58
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
TTAAAAATTAAAAATATAAAAAA
Found at i:1201085 original size:7 final size:7
Alignment explanation
Indices: 1201026--1201085 Score: 57
Period size: 7 Copynumber: 8.0 Consensus size: 7
1201016 TATTTGTTTT
1201026 TTAAAAA
1 TTAAAAA
*
1201033 CTAAAATA
1 TTAAAA-A
*
1201041 TTTAAAA
1 TTAAAAA
*
1201048 TTTAAAA
1 TTAAAAA
1201055 TATAAAAA
1 T-TAAAAA
1201063 TATAAAAAA
1 T-T-AAAAA
1201072 TTAAAAA
1 TTAAAAA
1201079 TTAAAAA
1 TTAAAAA
1201086 AATGATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 26 0.57
8 14 0.30
9 6 0.13
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:1201182 original size:23 final size:23
Alignment explanation
Indices: 1201138--1201193 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1201128 TATATTTAAT
*
1201138 TTTAAATTATTATTATTATTTTA
1 TTTAAATTATTATTATCATTTTA
*
1201161 TTTAATTTATTATT-TCACTTTTTA
1 TTTAAATTATTATTATCA--TTTTA
*
1201185 TTGAAATTA
1 TTTAAATTA
1201194 CAACAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.07
23 13 0.48
24 12 0.44
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTAAATTATTATTATCATTTTA
Found at i:1203478 original size:32 final size:32
Alignment explanation
Indices: 1203410--1203528 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 32
1203400 GAGAGTACAA
* * *
1203410 TGGGGTCTTAGAGCTTACCCAAGGAA-TACCT
1 TGGGGCCTTAGAGCCTACCCAAGGAAGAACCT
*
1203441 TGGGGCCTTAGGGCCTACCCAAGGAAGAACCT
1 TGGGGCCTTAGAGCCTACCCAAGGAAGAACCT
* * *
1203473 TGGGGCCTGATAGCCTACCTAAGG--GAACATCT
1 TGGGGCCTTAGAGCCTACCCAAGGAAGAAC--CT
* *
1203505 CGGGGCCTAAGAGCCTACCCAAGG
1 TGGGGCCTTAGAGCCTACCCAAGG
1203529 GTCAGGGTAG
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
30 4 0.05
31 23 0.32
32 46 0.63
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.18
Consensus pattern (32 bp):
TGGGGCCTTAGAGCCTACCCAAGGAAGAACCT
Found at i:1205939 original size:55 final size:55
Alignment explanation
Indices: 1205846--1206469 Score: 808
Period size: 55 Copynumber: 11.3 Consensus size: 55
1205836 CCATGTCTAC
* *
1205846 TATCGACACTAAGTGTGCAAAACCAC-AGAATTCATAATAAGTTTATGAACGATCG
1 TATCGACACTAAGTGTGCAAAACCACGA-AATTCATAATATGTTTATGAACGACCG
* * * *
1205901 TATTGACATTAAGTGTGTAAAACCACGAAATTAATAATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
* * * * *
1205956 TATTGGCACTAAGTGTGCGAAACCACGGAATTCATAATATGTTTATGAACAACCG
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
1206011 TATCGACACTAAGTGTGCAAAACCAC-AGAATTCATAATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACGA-AATTCATAATATGTTTATGAACGACCG
* * *
1206066 TATGGACACTAAGTGTGCAAAACCACTG-AATTCATAATAAGTTTATGAACGATCG
1 TATCGACACTAAGTGTGCAAAACCAC-GAAATTCATAATATGTTTATGAACGACCG
* * * * * *
1206121 TATCGGCACTAAGTATGCAAAACTATGAAATTCATAATATATTTATGAACGATCG
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
* * * * * *
1206176 TATCGATACTAAGTGTACAAAACCATGAAATTTGA-AACATGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAAAACCACGAAA-TTCATAATATGTTTATGAACGACCG
* * * *
1206231 TATCGGCACTAAGTGTACAAAACCAC-AGAATTTATAATATGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAAAACCACGA-AATTCATAATATGTTTATGAACGACCG
* * * *
1206286 TATAGGCACTAAGTGTGCAAATCCACAAAATTCATAATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
* * *
1206341 TATCGGCACTAAGTGTGCAAAACCATGAAATTCATAATATGTTTATGAACGACCA
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
* *
1206396 TATCGACACTAAGTGTGCAAAACCACAAAATTCATAATATGTTTATGAACGATCG
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
*
1206451 TATCGACACTACGTGTGCA
1 TATCGACACTAAGTGTGCA
1206470 CCTCAAAGAA
Statistics
Matches: 499, Mismatches: 61, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
54 5 0.01
55 489 0.98
56 5 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (55 bp):
TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
Found at i:1212781 original size:55 final size:54
Alignment explanation
Indices: 1212715--1213307 Score: 697
Period size: 55 Copynumber: 10.8 Consensus size: 54
1212705 GTACTATCAC
* * * * *
1212715 CACTAAGTGTACAAAATCGAAGAATTCATAATAAGTTTATAAACGACCGTATCGG
1 CACTAAGTGTGCAAAA-CCAAGAATTCATAATATGTTTATGAACGACCGTATCGA
* * *
1212770 CACTAAGTGTACAAAACTACGAAATTCATAATATGTTTATGAACGACCGTATCGA
1 CACTAAGTGTGCAAAACCAAG-AATTCATAATATGTTTATGAACGACCGTATCGA
* * *
1212825 CACTAAGTGTGCAAAACCATGAAATTCATAATATGTTTATGAACGACCATATCAA
1 CACTAAGTGTGCAAAACCAAG-AATTCATAATATGTTTATGAACGACCGTATCGA
* ** *
1212880 CACTAAGTGTGCAAAACCATGGAATTCATAATATGTTTATGAACGACATTATCGG
1 CACTAAGTGTGCAAAACCA-AGAATTCATAATATGTTTATGAACGACCGTATCGA
* * * * * *
1212935 CACTAAGTGTGCAATACCACGGAATTCATAATATGATTATGAACGATCGGATCGG
1 CACTAAGTGTGCAAAACCA-AGAATTCATAATATGTTTATGAACGACCGTATCGA
* * * *
1212990 CACTAAGTGTGCAAAACCACGGAATTCAAAATGA-GTTTATGAACGATCGTATCAA
1 CACTAAGTGTGCAAAACCA-AGAATTCATAAT-ATGTTTATGAACGACCGTATCGA
* * * *
1213045 CACTAA-TGGTGCAAAACCATGAAATTAATAATATGTTTATGAACGATCGTATCGG
1 CACTAAGT-GTGCAAAACCAAG-AATTCATAATATGTTTATGAACGACCGTATCGA
* * *
1213100 TACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGA-TGTATCGA
1 CACTAAGTGTGCAAAACCAAG-AATTCATAATATGTTTATGAACGACCGTATCGA
* * * * *
1213154 CACAAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAATGAACATATCGA
1 CACTAAGTGTGCAAAACCAAG-AATTCATAATATGTTTATGAACGACCGTATCGA
*
1213209 CACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCGTATCGG
1 CACTAAGTGTGCAAAACCA-AGAATTCATAATATGTTTATGAACGACCGTATCGA
*
1213264 CACTAAGTGTGCAAAACCACAGAATTCATAACATGTTTATGAAC
1 CACTAAGTGTGCAAAACCA-AGAATTCATAATATGTTTATGAAC
1213308 TACTATATTG
Statistics
Matches: 479, Mismatches: 50, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
54 55 0.11
55 420 0.88
56 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (54 bp):
CACTAAGTGTGCAAAACCAAGAATTCATAATATGTTTATGAACGACCGTATCGA
Found at i:1212908 original size:110 final size:110
Alignment explanation
Indices: 1212715--1213307 Score: 773
Period size: 110 Copynumber: 5.4 Consensus size: 110
1212705 GTACTATCAC
* * * * *
1212715 CACTAAGTGTACAAAATCGAAG-AATTCATAATAAGTTTATAAACGACCGTATCGGCACTAAGTG
1 CACTAAGTGTGCAAAA-CCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTG
* * *
1212779 TACAAAACTACGAAATTCATAATATGTTTATGAACGACCGTATCGA
65 TGCAAAACCACGGAATTCATAATATGTTTATGAACGACCGTATCGA
* * **
1212825 CACTAAGTGTGCAAAACCATGAAATTCATAATATGTTTATGAACGACCATATCAACACTAAGTGT
1 CACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTGT
* ** *
1212890 GCAAAACCATGGAATTCATAATATGTTTATGAACGACATTATCGG
66 GCAAAACCACGGAATTCATAATATGTTTATGAACGACCGTATCGA
* * * * *
1212935 CACTAAGTGTGCAATACCACGGAATTCATAATATGATTATGAACGATCGGATCGGCACTAAGTGT
1 CACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTGT
* * *
1213000 GCAAAACCACGGAATTCAAAATGA-GTTTATGAACGATCGTATCAA
66 GCAAAACCACGGAATTCATAAT-ATGTTTATGAACGACCGTATCGA
* * * *
1213045 CACTAA-TGGTGCAAAACCATGAAATTAATAATATGTTTATGAACGATCGTATCGGTACTAAGTG
1 CACTAAGT-GTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTG
* *
1213109 TGCAAAACCACGAAATTCATAATATGTTTATGAACGA-TGTATCGA
65 TGCAAAACCACGGAATTCATAATATGTTTATGAACGACCGTATCGA
* * * * *
1213154 CACAAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAATGAACATATCGACACTAAGTGT
1 CACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTGT
* *
1213219 GCAAAACCACAGAATTCATAATATGTTTATGAACGACCGTATCGG
66 GCAAAACCACGGAATTCATAATATGTTTATGAACGACCGTATCGA
*
1213264 CACTAAGTGTGCAAAACCAC-AGAATTCATAACATGTTTATGAAC
1 CACTAAGTGTGCAAAACCACGA-AATTCATAATATGTTTATGAAC
1213308 TACTATATTG
Statistics
Matches: 419, Mismatches: 57, Indels: 14
0.86 0.12 0.03
Matches are distributed among these distances:
109 101 0.24
110 317 0.76
111 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (110 bp):
CACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTAAGTGT
GCAAAACCACGGAATTCATAATATGTTTATGAACGACCGTATCGA
Found at i:1212996 original size:165 final size:165
Alignment explanation
Indices: 1212709--1213307 Score: 841
Period size: 165 Copynumber: 3.6 Consensus size: 165
1212699 TTATATGTAC
* * * * *
1212709 TATCACCACTAAGTGTACAAAATCGA-AGAATTCATAATAAGTTTATAAACGACCGTATCGGCAC
1 TATCAACACTAAGTGTGCAAAA-CCATAGAATTCATAATATGTTTATGAACGACCGTATCGGCAC
* * *
1212773 TAAGTGTACAAAACTACGAAATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGCA
65 TAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGATCGTATCGACACTAAGTGTGCA
* *
1212838 AAACCATGAAATTCATAATATGTTTATGAACGACCA
130 AAACCACGAAATTCATAATATGTTTATGAACGAACA
* **
1212874 TATCAACACTAAGTGTGCAAAACCATGGAATTCATAATATGTTTATGAACGACATTATCGGCACT
1 TATCAACACTAAGTGTGCAAAACCATAGAATTCATAATATGTTTATGAACGACCGTATCGGCACT
* * * * *
1212939 AAGTGTGCAATACCACGGAATTCATAATATGATTATGAACGATCGGATCGGCACTAAGTGTGCAA
66 AAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGATCGTATCGACACTAAGTGTGCAA
* * * *
1213004 AACCACGGAATTCAAAATGA-GTTTATGAACGATCG
131 AACCACGAAATTCATAAT-ATGTTTATGAACGAACA
* * *
1213039 TATCAACACTAA-TGGTGCAAAACCAT-GAAATTAATAATATGTTTATGAACGATCGTATCGGTA
1 TATCAACACTAAGT-GTGCAAAACCATAG-AATTCATAATATGTTTATGAACGACCGTATCGGCA
*
1213102 CTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGAT-GTATCGACACAAAGTGTGC
64 CTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGATCGTATCGACACTAAGTGTGC
*
1213166 AAAACCACGAAATTCATAATATGTTTATGAATGAACA
129 AAAACCACGAAATTCATAATATGTTTATGAACGAACA
* *
1213203 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCGTATCGGCACT
1 TATCAACACTAAGTGTGCAAAACCATAGAATTCATAATATGTTTATGAACGACCGTATCGGCACT
*
1213268 AAGTGTGCAAAACCAC-AGAATTCATAACATGTTTATGAAC
66 AAGTGTGCAAAACCACGA-AATTCATAATATGTTTATGAAC
1213308 TACTATATTG
Statistics
Matches: 383, Mismatches: 43, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
163 2 0.01
164 143 0.37
165 237 0.62
166 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.27
Consensus pattern (165 bp):
TATCAACACTAAGTGTGCAAAACCATAGAATTCATAATATGTTTATGAACGACCGTATCGGCACT
AAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGATCGTATCGACACTAAGTGTGCAA
AACCACGAAATTCATAATATGTTTATGAACGAACA
Found at i:1215290 original size:15 final size:15
Alignment explanation
Indices: 1215272--1215348 Score: 59
Period size: 16 Copynumber: 5.0 Consensus size: 15
1215262 TTTTATATTT
1215272 TTAATATTTAAAATA
1 TTAATATTTAAAATA
*
1215287 TTAATTATTTATAAT-
1 TTAA-TATTTAAAATA
** *
1215302 TTAATGGTGAAAATA
1 TTAATATTTAAAATA
*
1215317 TTATTATTGTAAAA-A
1 TTAATATT-TAAAATA
1215332 TGTAATTATTTAAAATA
1 T-TAA-TATTTAAAATA
1215349 ATATTTAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
14 6 0.13
15 15 0.33
16 20 0.43
17 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TTAATATTTAAAATA
Found at i:1216259 original size:2 final size:2
Alignment explanation
Indices: 1216252--1216296 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1216242 TGAACCAAAT
1216252 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
1216294 TA T
1 TA T
1216297 TCAAATTGAA
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:1229442 original size:37 final size:37
Alignment explanation
Indices: 1229329--1229513 Score: 279
Period size: 37 Copynumber: 5.1 Consensus size: 37
1229319 TAATGGAAAC
*
1229329 AAGCAATGCAAATCAAGCCTTCA-TAAAAGAGTAGTG
1 AAGCAATGCAAATCAAGCCTTCACAAAAAGAGTAGTG
*
1229365 AAGCAATGCAAATCAAGCCTTCAC-AAAAGAGTAATG
1 AAGCAATGCAAATCAAGCCTTCACAAAAAGAGTAGTG
*
1229401 AAGCAATGCAAATCAAGCCTTCACAAAAAGAGTAGTT
1 AAGCAATGCAAATCAAGCCTTCACAAAAAGAGTAGTG
*
1229438 AAGCAATGCAAATTC-AGCCTTCACAAAAAGTGTAGTG
1 AAGCAATGCAAA-TCAAGCCTTCACAAAAAGAGTAGTG
*
1229475 AAGCAATGCAAATTC-AGCCTTCATAAAAAGAGTAGTG
1 AAGCAATGCAAA-TCAAGCCTTCACAAAAAGAGTAGTG
1229512 AA
1 AA
1229514 AGAAGATCAG
Statistics
Matches: 139, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
36 58 0.42
37 79 0.57
38 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (37 bp):
AAGCAATGCAAATCAAGCCTTCACAAAAAGAGTAGTG
Found at i:1230321 original size:21 final size:22
Alignment explanation
Indices: 1230267--1230313 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1230257 GGCAAACCTA
1230267 CAAGAGAACCAAACAACGAGAG
1 CAAGAGAACCAAACAACGAGAG
*
1230289 CAAGAGAACCAAATAACGA-AG
1 CAAGAGAACCAAACAACGAGAG
1230310 CAAG
1 CAAG
1230314 CAAGCCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.55, C:0.21, G:0.21, T:0.02
Consensus pattern (22 bp):
CAAGAGAACCAAACAACGAGAG
Found at i:1230918 original size:2 final size:2
Alignment explanation
Indices: 1230911--1230945 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1230901 CAATCATTAT
1230911 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 T
1230946 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1233007 original size:5 final size:5
Alignment explanation
Indices: 1232999--1233199 Score: 86
Period size: 5 Copynumber: 40.6 Consensus size: 5
1232989 AAATAACATA
*
1232999 ATAAT ATAA- ATAAT ATAAT AT-AT ATAAC AT-AT ATAGTAT ATAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT
* * * *
1233047 A-AAA AT-AT GTATAT ATAAT ATATT AT-AT ATTATT ATAAT ATAAT ATAATAT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT AT-A-AT
* * * * *
1233098 ATAAT AAAAT ATGAT ATAAT AATAAT A-ATAT AAAAT ATATT ACATAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATA-AT ATAAT ATAAT ATA-AT
* * * *
1233145 AAAAT ATACT ATACA- A-AAT ATAAT -T-AT ATAAT ATACT AT-AT ACTACT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT
1233192 ATAAT ATA
1 ATAAT ATA
1233200 TACTATGCTA
Statistics
Matches: 146, Mismatches: 26, Indels: 48
0.66 0.12 0.22
Matches are distributed among these distances:
3 3 0.02
4 27 0.18
5 88 0.60
6 19 0.13
7 9 0.06
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:1233011 original size:17 final size:18
Alignment explanation
Indices: 1232989--1233131 Score: 61
Period size: 17 Copynumber: 8.2 Consensus size: 18
1232979 TAAAAATAGA
1232989 AAATAACATAATA-ATAT
1 AAATAACATAATATATAT
*
1233006 AAATAATATAATATATAT
1 AAATAACATAATATATAT
* *
1233024 AACAT-ATATAGTATATAAT
1 AA-ATAACATAATATAT-AT
* *
1233043 ATATAA-A-AATATGTAT
1 AAATAACATAATATATAT
* * *
1233059 ATATAATATATTATATATT
1 AAATAACATAATATATA-T
* *
1233078 ATTATAATATAATATA-AT
1 A-AATAACATAATATATAT
* * *
1233096 ATATAATAAAATATGATAT
1 AAATAACATAATAT-ATAT
1233115 -AAT-A-ATAATA-ATAT
1 AAATAACATAATATATAT
1233129 AAA
1 AAA
1233132 ATATATTACA
Statistics
Matches: 104, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
14 4 0.04
15 2 0.02
16 13 0.12
17 31 0.30
18 30 0.29
19 11 0.11
20 13 0.12
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATAACATAATATATAT
Found at i:1233023 original size:2 final size:2
Alignment explanation
Indices: 1233002--1233201 Score: 72
Period size: 2 Copynumber: 109.5 Consensus size: 2
1232992 TAACATAATA
* *
1233002 AT AT AA AT A- AT AT A- AT AT AT AT A- AC AT AT AT AGT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
1233041 AT AT AT AA AA AT AT GT AT AT AT A- AT AT AT -T AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1233080 -T AT A- AT AT A- AT AT A- AT AT AT A- AT A- AA AT AT GAT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
* * *
1233116 AT A- AT A- AT A- AT AT A- AA AT AT AT -T AC AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1233152 ACT AT AC A- AA AT AT A- AT -T AT AT A- AT AT ACT AT AT ACT ACT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T A-T
1233192 AT A- AT AT AT A
1 AT AT AT AT AT A
1233202 CTATGCTATA
Statistics
Matches: 154, Mismatches: 14, Indels: 60
0.68 0.06 0.26
Matches are distributed among these distances:
1 25 0.16
2 116 0.75
3 13 0.08
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:1233038 original size:7 final size:7
Alignment explanation
Indices: 1232999--1233201 Score: 106
Period size: 7 Copynumber: 29.4 Consensus size: 7
1232989 AAATAACATA
1232999 ATAATAT
1 ATAATAT
1233006 A-AATAAT
1 ATAAT-AT
1233013 ATAATAT
1 ATAATAT
1233020 AT-ATA-
1 ATAATAT
*
1233025 A-CATAT
1 ATAATAT
*
1233031 ATAGTAT
1 ATAATAT
1233038 ATAATAT
1 ATAATAT
*
1233045 ATAAAAAT
1 AT-AATAT
*
1233053 ATGTATAT
1 AT-AATAT
1233061 ATAATAT
1 ATAATAT
*
1233068 ATTATAT
1 ATAATAT
*
1233075 ATTAT-T
1 ATAATAT
1233081 ATAATATAAT
1 AT-A-AT-AT
1233091 ATAATAT
1 ATAATAT
1233098 ATAATA-
1 ATAATAT
1233104 A-AATAT
1 ATAATAT
1233110 GAT-ATA-
1 -ATAATAT
1233116 ATAATA-
1 ATAATAT
1233122 ATAATAT
1 ATAATAT
*
1233129 AAAATAT
1 ATAATAT
* *
1233136 ATTACAT
1 ATAATAT
*
1233143 ATAAAAT
1 ATAATAT
*
1233150 ATACTAT
1 ATAATAT
* *
1233157 ACAAAAT
1 ATAATAT
1233164 ATAAT-T
1 ATAATAT
1233170 AT-ATAAT
1 ATAAT-AT
*
1233177 ATACTAT
1 ATAATAT
*
1233184 ATACTACT
1 ATAATA-T
1233192 ATAATAT
1 ATAATAT
1233199 ATA
1 ATA
1233202 CTATGCTATA
Statistics
Matches: 152, Mismatches: 25, Indels: 38
0.71 0.12 0.18
Matches are distributed among these distances:
5 12 0.08
6 23 0.15
7 88 0.58
8 25 0.16
9 1 0.01
10 3 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (7 bp):
ATAATAT
Found at i:1233178 original size:43 final size:43
Alignment explanation
Indices: 1233084--1233179 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 43
1233074 TATTATTATA
* *
1233084 ATATAATATAATATATAATAAAATATGATATAATAATAATAAT
1 ATATAATATAATACATAATAAAATATGATATAAAAATAATAAT
* *
1233127 ATAAAATATATTACAT-ATAAAATAT-ACTATACAAAAT-ATAATT
1 ATATAATATAATACATAATAAAATATGA-TATA-AAAATAATAA-T
1233170 ATATAATATA
1 ATATAATATA
1233180 CTATATACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.02
42 17 0.38
43 27 0.60
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (43 bp):
ATATAATATAATACATAATAAAATATGATATAAAAATAATAAT
Found at i:1233586 original size:31 final size:31
Alignment explanation
Indices: 1233488--1233578 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
1233478 CAATTTAAGG
1233488 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1233519 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1233550 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1233579 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:1233670 original size:19 final size:19
Alignment explanation
Indices: 1233643--1233709 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
1233633 AATGTTTTTA
* *
1233643 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
1233662 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
1233681 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
1233700 TGAACAGTAA
1 TGAACAGTAA
1233710 CCCGAGGCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1233842 original size:21 final size:21
Alignment explanation
Indices: 1233816--1233857 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1233806 ATTTGAATAT
*
1233816 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1233837 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1233858 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1233919 original size:21 final size:21
Alignment explanation
Indices: 1233886--1233925 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1233876 TTTGAGTAGA
*
1233886 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1233908 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1233926 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1234179 original size:34 final size:32
Alignment explanation
Indices: 1234140--1234209 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1234130 TTTTGTAAAG
* *
1234140 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1234174 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1234206 GGGA
1 GGGA
1234210 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1236226 original size:23 final size:23
Alignment explanation
Indices: 1236199--1236246 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1236189 GTTTGGTTTG
1236199 AAAAATTCAATTTCTTAATAAAA
1 AAAAATTCAATTTCTTAATAAAA
*
1236222 AAAAATTCAATTTCTTAATGAAA
1 AAAAATTCAATTTCTTAATAAAA
1236245 AA
1 AA
1236247 GGGGGAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAATTCAATTTCTTAATAAAA
Found at i:1236503 original size:31 final size:31
Alignment explanation
Indices: 1236405--1236495 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
1236395 CAATTTAAGG
1236405 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1236436 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1236467 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1236496 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:1236587 original size:19 final size:19
Alignment explanation
Indices: 1236560--1236626 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
1236550 AATGTTTTTA
* *
1236560 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
1236579 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
1236598 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
1236617 TGAACAGTAA
1 TGAACAGTAA
1236627 CCCGAGGCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1236758 original size:21 final size:21
Alignment explanation
Indices: 1236732--1236773 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1236722 ATTTGAATAT
*
1236732 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1236753 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1236774 CCATTCTGGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1237094 original size:34 final size:32
Alignment explanation
Indices: 1237055--1237124 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1237045 TTTTGTAAAG
* *
1237055 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1237089 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1237121 GGGA
1 GGGA
1237125 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1238707 original size:98 final size:98
Alignment explanation
Indices: 1238538--1238731 Score: 325
Period size: 98 Copynumber: 2.0 Consensus size: 98
1238528 TTCTGTCAAG
* * *
1238538 GGGACTTCAAGATTGTGGCAACATTTGAATGGTTCAAAATTCCTCACAAATTATCTAGTCTCCAA
1 GGGACTTCAAGATTGTGGCAACACTTGAATGGTGCAAAATTCCTCACAAATTATCAAGTCTCCAA
1238603 AGACTTGGATACTGTGATGTTTTATCACCCTTA
66 AGACTTGGATACTGTGATGTTTTATCACCCTTA
** *
1238636 GGGACTTCAAGATTGTGGCAATGCTTGAATGGTGCAAAATTCCTCATAAATTATCAAGTCTCCAA
1 GGGACTTCAAGATTGTGGCAACACTTGAATGGTGCAAAATTCCTCACAAATTATCAAGTCTCCAA
*
1238701 AGACTTGGATATTGTGATGTTTTATCACCCT
66 AGACTTGGATACTGTGATGTTTTATCACCCT
1238732 GATCCAGGAC
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (98 bp):
GGGACTTCAAGATTGTGGCAACACTTGAATGGTGCAAAATTCCTCACAAATTATCAAGTCTCCAA
AGACTTGGATACTGTGATGTTTTATCACCCTTA
Found at i:1239906 original size:20 final size:21
Alignment explanation
Indices: 1239881--1239920 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1239871 CTTTGTATAG
*
1239881 TAGTATTGATACCA-TAGGCA
1 TAGTATCGATACCATTAGGCA
1239901 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCATTAGGC
1239921 CCTAACGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (21 bp):
TAGTATCGATACCATTAGGCA
Found at i:1243289 original size:20 final size:20
Alignment explanation
Indices: 1243261--1243320 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1243251 CAAAGGTAAG
*
1243261 GGAAGTATCTATACTCACTA
1 GGAAGTATCGATACTCACTA
* *
1243281 GGTAGTATCGATGCTCACTA
1 GGAAGTATCGATACTCACTA
1243301 GGAAGTATCGATACT-ACTA
1 GGAAGTATCGATACTCACTA
1243320 G
1 G
1243321 CAATGCTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 5 0.14
20 30 0.86
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (20 bp):
GGAAGTATCGATACTCACTA
Found at i:1246848 original size:2 final size:2
Alignment explanation
Indices: 1246801--1246832 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1246791 CAGAGTGGGA
1246801 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
1246833 GCGAGAGAAA
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:1249541 original size:25 final size:25
Alignment explanation
Indices: 1249509--1249557 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1249499 ATCCCCCATC
1249509 GTTGTGCATATTGTCTGAAACTTTT
1 GTTGTGCATATTGTCTGAAACTTTT
1249534 GTTGTGCATATTGTCTGAAACTTT
1 GTTGTGCATATTGTCTGAAACTTT
1249558 CGTTATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (25 bp):
GTTGTGCATATTGTCTGAAACTTTT
Found at i:1252650 original size:18 final size:18
Alignment explanation
Indices: 1252627--1252664 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1252617 GATGTAAATA
1252627 AAAAAAAGGAAAGAAAAC
1 AAAAAAAGGAAAGAAAAC
**
1252645 AAAAAATTGAAAGAAAAC
1 AAAAAAAGGAAAGAAAAC
1252663 AA
1 AA
1252665 TTTAGTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAAAAAGGAAAGAAAAC
Found at i:1254930 original size:5 final size:5
Alignment explanation
Indices: 1254922--1255065 Score: 67
Period size: 5 Copynumber: 29.8 Consensus size: 5
1254912 AAATAACATA
* * * * * *
1254922 ATAAT ATAA- ATAAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
1254971 AT-AT A-ACAT AT-AT A-ATAT ATAAT AT-AT AGTAA- ATACT ATAGT
1 ATAAT ATA-AT ATAAT ATA-AT ATAAT ATAAT A-TAAT ATAAT ATAAT
*
1255013 -TTAT A-ATAT ATAAT ATATAT ATAAT ATATAT ATAAT A-AAT AT-AT
1 ATAAT ATA-AT ATAAT ATA-AT ATAAT ATA-AT ATAAT ATAAT ATAAT
*
1255057 ATACT ATAA
1 ATAAT ATAA
1255066 CATATAACAT
Statistics
Matches: 113, Mismatches: 9, Indels: 34
0.72 0.06 0.22
Matches are distributed among these distances:
4 25 0.22
5 75 0.66
6 13 0.12
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:1254941 original size:20 final size:19
Alignment explanation
Indices: 1254913--1254982 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 19
1254903 GAAAATAGAA
1254913 AATAACATAATAATATAAAT
1 AATAACAT-ATAATATAAAT
* * *
1254933 AATATCATATCATATCATAT
1 AATAACATATAATAT-AAAT
* * *
1254953 CATATCATATCATAT-AAT
1 AATAACATATAATATAAAT
1254971 ATATAACATATA
1 A-ATAACATATA
1254983 TAATATATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
18 2 0.05
19 14 0.35
20 24 0.60
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAACATATAATATAAAT
Found at i:1254976 original size:7 final size:7
Alignment explanation
Indices: 1254964--1255112 Score: 99
Period size: 7 Copynumber: 20.4 Consensus size: 7
1254954 ATATCATATC
1254964 ATATAAT
1 ATATAAT
1254971 ATATAACAT
1 ATAT-A-AT
1254980 ATATAAT
1 ATATAAT
1254987 ATATAAT
1 ATATAAT
1254994 ATAT-A-
1 ATATAAT
*
1254999 GTA-AAT
1 ATATAAT
*
1255005 ACTATAGT
1 A-TATAAT
*
1255013 TTATAAT
1 ATATAAT
1255020 ATATAAT
1 ATATAAT
1255027 ATAT-AT
1 ATATAAT
1255033 ATAATATAT
1 AT-ATA-AT
1255042 ATATAAT
1 ATATAAT
1255049 AAATATATAT
1 --ATATA-AT
*
1255059 ACTATAAC
1 A-TATAAT
*
1255067 ATATAAC
1 ATATAAT
*
1255074 ATATACT
1 ATATAAT
*
1255081 ATACAAT
1 ATATAAT
1255088 ATATAATT
1 ATATAA-T
*
1255096 ACATAAT
1 ATATAAT
*
1255103 ATATTAT
1 ATATAAT
1255110 ATA
1 ATA
1255113 CTACTCTAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
5 3 0.03
6 5 0.04
7 68 0.60
8 16 0.14
9 19 0.17
10 2 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:1255010 original size:12 final size:11
Alignment explanation
Indices: 1254991--1255057 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
1254981 TATAATATAT
1254991 AATATATAGTA
1 AATATATAGTA
1255002 AATACTATAGTTTA
1 AATA-TATAG--TA
*
1255016 TAATATATAATA
1 -AATATATAGTA
* *
1255028 TATATATAATA
1 AATATATAGTA
* *
1255039 TATATATAATA
1 AATATATAGTA
1255050 AATATATA
1 AATATATA
1255058 TACTATAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
11 32 0.65
12 7 0.14
14 6 0.12
15 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (11 bp):
AATATATAGTA
Found at i:1255126 original size:2 final size:2
Alignment explanation
Indices: 1254925--1255112 Score: 84
Period size: 2 Copynumber: 96.5 Consensus size: 2
1254915 TAACATAATA
*
1254925 AT AT AA AT A- AT AT CAT AT CAT AT CAT AT CAT AT CAT AT CAT AT
1 AT AT AT AT AT AT AT -AT AT -AT AT -AT AT -AT AT -AT AT -AT AT
* *
1254968 A- AT AT AT A- AC AT AT AT A- AT AT AT A- AT AT AT AGT AA AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
*
1255008 AT AGT TT AT A- AT AT AT A- AT AT AT AT AT A- AT AT AT AT AT A-
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1255047 AT AA AT AT AT AT ACT AT A- AC AT AT A- AC AT AT ACT AT AC A- AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
1255088 AT AT A- AT -T AC AT A- AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1255113 CTACTCTAAT
Statistics
Matches: 145, Mismatches: 14, Indels: 54
0.68 0.07 0.25
Matches are distributed among these distances:
1 16 0.11
2 108 0.74
3 21 0.14
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:1263758 original size:20 final size:21
Alignment explanation
Indices: 1263735--1263776 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1263725 GTTCTGTTAC
*
1263735 AACATAAAACTTAAA-AACCA
1 AACATAAAACATAAATAACCA
*
1263755 AACATAGAACATAAATAACCA
1 AACATAAAACATAAATAACCA
1263776 A
1 A
1263777 CTCAATAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.64, C:0.19, G:0.02, T:0.14
Consensus pattern (21 bp):
AACATAAAACATAAATAACCA
Found at i:1271483 original size:179 final size:174
Alignment explanation
Indices: 1271152--1271635 Score: 569
Period size: 179 Copynumber: 2.7 Consensus size: 174
1271142 AATTTTCTGC
* * * * *
1271152 ATAACCATTATCATCTCCAAGTTCATTACCATCTTCTGCATAACCAAGAACTTATCAGAAGGGGG
1 ATAAACATTATTATTTCCAAGCTCATTATCATCTTCTGCATAACCAAGAACTT-TCAGAA---GG
* * * * *
1271217 AAAAACAACATACTTTGAACAGTAGAAACATGCTTTGATATTTTCTGACAACTTGCACTCTTGGG
62 AAAAACAACATACTTTGAACAGCAGAAGCATCCTTTGATGTTTTCTGACAACTCGCACTCTTGGG
*
1271282 TAATGAGTGGTCATTGAGCAAACTCTTCTTAGTTTCTGCATAACATAGTTA
127 TAACGAGTGGTCATTGAGCAAA--C-TCTTAGTTTCTGCATAACATAGTTA
* * * *
1271333 ATAAACATTATTATTTCTAAGCTCATTATCATCTTCTGCATAACCAATAAATTGTCAGAAGAAAA
1 ATAAACATTATTATTTCCAAGCTCATTATCATCTTCTGCATAACCAAGAACTT-TCAGAAG-GAA
* * *
1271398 AAACAACATACTTTGAACAGCAGAAGCGTCCTTTGATGTTTTCTGACGAGTCGCA-TGCTTGGGT
64 AAACAACATACTTTGAACAGCAGAAGCATCCTTTGATGTTTTCTGACAACTCGCACT-CTTGGGT
** *
1271462 TCCGAGTGGTCATTGAGCAAACTCTTAGTTTCTGCATATCATAGTTA
128 AACGAGTGGTCATTGAGCAAACTCTTAGTTTCTGCATAACATAGTTA
* * ** *
1271509 ATAACCATTATTATTTCCAAGTTCATTATCATCTTCTGCA-ATATTAAGAACTTTACAG-AGGGA
1 ATAAACATTATTATTTCCAAGCTCATTATCATCTTCTGCATA-ACCAAGAACTTT-CAGAAGGAA
* * * *
1271572 AAACGACATACTTCGAACAGCAGAAGCATCCTTTGGTGTTTTCTGACAACTTGCACTCTTGGGT
64 AAACAACATACTTTGAACAGCAGAAGCATCCTTTGATGTTTTCTGACAACTCGCACTCTTGGGT
1271636 GATGAATGAT
Statistics
Matches: 260, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
174 56 0.22
175 5 0.02
176 71 0.27
177 1 0.00
178 2 0.01
179 74 0.28
181 51 0.20
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (174 bp):
ATAAACATTATTATTTCCAAGCTCATTATCATCTTCTGCATAACCAAGAACTTTCAGAAGGAAAA
ACAACATACTTTGAACAGCAGAAGCATCCTTTGATGTTTTCTGACAACTCGCACTCTTGGGTAAC
GAGTGGTCATTGAGCAAACTCTTAGTTTCTGCATAACATAGTTA
Done.