Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 130 of 163
Found at i:41885794 original size:42 final size:42
Alignment explanation
Indices: 41885608--41885818 Score: 201
Period size: 42 Copynumber: 5.0 Consensus size: 42
41885598 GGCGCTTACA
* *
41885608 GAAAAAAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAG
1 GAAAAAAACACCGCTAAAAGTAATGTTCTTTAGCGGCGCTT-G
* * *
41885651 GAAAAAAACGCCGCT-AATGATCATGTTCTTTAGCGGCGCTTG
1 GAAAAAAACACCGCTAAAAG-TAATGTTCTTTAGCGGCGCTTG
* * * * * *
41885693 GGAGAAAACACCGCT-AAAGAAACATGATCTTTAGCGGCGTTTA
1 GAAAAAAACACCGCTAAAAG-TA-ATGTTCTTTAGCGGCGCTTG
* * *
41885736 GAAAAAAACGCCGCTAAAAGTAATGTTCTATAGTGGCGCTTG
1 GAAAAAAACACCGCTAAAAGTAATGTTCTTTAGCGGCGCTTG
* * * * *
41885778 GTAAAAAACACCGCTAAAAGTAGTGCTCTTTCGCGGTGCTT
1 GAAAAAAACACCGCTAAAAGTAATGTTCTTTAGCGGCGCTT
41885819 ATTTCACAAA
Statistics
Matches: 137, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
42 68 0.50
43 65 0.47
44 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (42 bp):
GAAAAAAACACCGCTAAAAGTAATGTTCTTTAGCGGCGCTTG
Found at i:41887317 original size:114 final size:113
Alignment explanation
Indices: 41887118--41887678 Score: 863
Period size: 114 Copynumber: 4.9 Consensus size: 113
41887108 CACAACTGAT
*
41887118 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACT-AAACCCAGACGACGTTATTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACG-TCTTTGGAG
* * *
41887182 AAACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCTGCTAATAATA
65 ACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATA
* * * * *
41887231 TGAGTATTAGTGGTGTTTCTGTAAAAATGCCGCAAAAACTAAAACCCAGAAGACGTCGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTC-TTTGGAG
41887296 ACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATA
65 ACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATA
* * * *
41887345 TGAGTATTTGCGGCGTTTTTATAAAAATGCCGCAAAAACTAAAACCCAGAAGACGTCGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTC-TTTGGAG
41887410 ACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATA
65 ACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATA
* * *
41887459 TGAGTATTAGCGGCGTTTCTACATAAACGCCGGAAAAACTAAAACCCAGACGACGTCTTCTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCTT-TGGAG
** *
41887524 ACACTTCGGTGACATTAGTGGCGTTTTCCGAGTAGCGCCGCTAATAATA
65 ACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATA
* *
41887573 TGAGTATTAGAGGCGTTTTGTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCTTCTGGA
1 TGAGTATTAGCGGCG-TTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCTT-TGGA
*
41887638 GACACTTCGGTGACATTAGTGGCATTTTTTGAATAGCGCCG
64 GACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCG
41887679 NNNNNNNNNN
Statistics
Matches: 411, Mismatches: 33, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
113 39 0.09
114 290 0.71
115 82 0.20
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (113 bp):
TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCTTTGGAGA
CACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATA
Found at i:41902449 original size:29 final size:29
Alignment explanation
Indices: 41902418--41902480 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
41902408 AAAACCCTTA
* *
41902418 TTTAAAAAGATTTGACCTTTATTTAACCAT
1 TTTAAAAAG-TTTGACCCTAATTTAACCAT
* *
41902448 TTTAAAATGTTTGACCCTAATTTAA-AAT
1 TTTAAAAAGTTTGACCCTAATTTAACCAT
41902476 TTTAA
1 TTTAA
41902481 CCTTATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.24
29 14 0.48
30 8 0.28
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.44
Consensus pattern (29 bp):
TTTAAAAAGTTTGACCCTAATTTAACCAT
Found at i:41911280 original size:21 final size:20
Alignment explanation
Indices: 41911242--41911280 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
41911232 ATAGTGTACC
* *
41911242 CATGTTTAAATTTTTTCACA
1 CATGTTTAAATATGTTCACA
41911262 CATGTTTTAAATATGTTCA
1 CATG-TTTAAATATGTTCA
41911281 ATGTCATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.49
Consensus pattern (20 bp):
CATGTTTAAATATGTTCACA
Found at i:41915332 original size:4 final size:4
Alignment explanation
Indices: 41915323--41915352 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
41915313 TAATGGGTGC
41915323 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TT
41915353 GCAGTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:41916918 original size:61 final size:61
Alignment explanation
Indices: 41916849--41916971 Score: 219
Period size: 61 Copynumber: 2.0 Consensus size: 61
41916839 ATGGAAAAAC
**
41916849 ATAGAAAACTTTAGGGTATATCCATGTTGGGCACATAAGTTCCTCTAAGCCTAGGAAAAGT
1 ATAGAAAACTCGAGGGTATATCCATGTTGGGCACATAAGTTCCTCTAAGCCTAGGAAAAGT
*
41916910 ATAGAAAACTCGGGGGTATATCCATGTTGGGCACATAAGTTCCTCTAAGCCTAGGAAAAGT
1 ATAGAAAACTCGAGGGTATATCCATGTTGGGCACATAAGTTCCTCTAAGCCTAGGAAAAGT
41916971 A
1 A
41916972 AGTTCCCACT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (61 bp):
ATAGAAAACTCGAGGGTATATCCATGTTGGGCACATAAGTTCCTCTAAGCCTAGGAAAAGT
Found at i:41918978 original size:45 final size:45
Alignment explanation
Indices: 41918916--41919002 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
41918906 TATAAAAATA
41918916 TTTTTTATAATTAAAATAAGA-TATATTATTTAAAGATATTTTAAT
1 TTTTTTATAATTAAAATAA-ATTATATTATTTAAAGATATTTTAAT
* *
41918961 TTTTTTATAATTAAAATAAATTATATTATTTGAATATATTTT
1 TTTTTTATAATTAAAATAAATTATATTATTTAAAGATATTTT
41919003 TACAAAAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (45 bp):
TTTTTTATAATTAAAATAAATTATATTATTTAAAGATATTTTAAT
Found at i:41919251 original size:32 final size:30
Alignment explanation
Indices: 41919208--41919284 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 30
41919198 TGTATTTAAT
41919208 ATTTAATTAATTTTAT-AAATAGTATATTTTTA
1 ATTTAA-TAATTTTATAAAATA--ATATTTTTA
* *
41919240 ATTATAATAATTAGTATAAAATAATATTTTTC
1 ATT-TAATAATT-TTATAAAATAATATTTTTA
41919272 ATTTAA-AATTTTA
1 ATTTAATAATTTTA
41919285 AATATGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
29 2 0.05
30 4 0.10
31 3 0.08
32 19 0.49
33 6 0.15
34 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTAATAATTTTATAAAATAATATTTTTA
Found at i:41919319 original size:16 final size:17
Alignment explanation
Indices: 41919294--41919327 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41919284 AAATATGATT
41919294 AAAATATATT-AATATA
1 AAAATATATTGAATATA
*
41919310 AAAATTTATTGAATATA
1 AAAATATATTGAATATA
41919327 A
1 A
41919328 TTAAAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAATATATTGAATATA
Found at i:41927617 original size:16 final size:16
Alignment explanation
Indices: 41927598--41927631 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41927588 TGTCTAATAT
41927598 TTAATTATTTCCTCAA
1 TTAATTATTTCCTCAA
41927614 TTAATTATTTCCTCAA
1 TTAATTATTTCCTCAA
41927630 TT
1 TT
41927632 GATGTTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTATTTCCTCAA
Found at i:41927863 original size:16 final size:16
Alignment explanation
Indices: 41927844--41927877 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41927834 TGTCTAATAT
41927844 TTAATTATTTCCTCAA
1 TTAATTATTTCCTCAA
41927860 TTAATTATTTCCTCAA
1 TTAATTATTTCCTCAA
41927876 TT
1 TT
41927878 GATGTTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTATTTCCTCAA
Found at i:41927921 original size:246 final size:246
Alignment explanation
Indices: 41927486--41927977 Score: 975
Period size: 246 Copynumber: 2.0 Consensus size: 246
41927476 AAAAAATAAA
41927486 AAAAATTATCATTATACCAAAGAATCATTGGCAAGGTTTTCATATTATACTCGAAAAAAAATTTC
1 AAAAATTATCATTATACCAAAGAATCATTGGCAAGGTTTTCATATTATACTCGAAAAAAAATTTC
41927551 GTCAGAAATCTGTAAAAGCATATATAAATAGTTAAAATGTCTAATATTTAATTATTTCCTCAATT
66 GTCAGAAATCTGTAAAAGCATATATAAATAGTTAAAATGTCTAATATTTAATTATTTCCTCAATT
*
41927616 AATTATTTCCTCAATTGATGTTCACAATTAATCTTAAAAATTTATACTCACATATTTGGAAAAGA
131 AATTATTTCCTCAATTGATGTTCACAATTAATCTTAAAAATTTATACTCACACATTTGGAAAAGA
41927681 AATTATTAATAAAGTAAAAATCCAATAACAAAGTCAGGTGGGGAAATTTTT
196 AATTATTAATAAAGTAAAAATCCAATAACAAAGTCAGGTGGGGAAATTTTT
41927732 AAAAATTATCATTATACCAAAGAATCATTGGCAAGGTTTTCATATTATACTCGAAAAAAAATTTC
1 AAAAATTATCATTATACCAAAGAATCATTGGCAAGGTTTTCATATTATACTCGAAAAAAAATTTC
41927797 GTCAGAAATCTGTAAAAGCATATATAAATAGTTAAAATGTCTAATATTTAATTATTTCCTCAATT
66 GTCAGAAATCTGTAAAAGCATATATAAATAGTTAAAATGTCTAATATTTAATTATTTCCTCAATT
41927862 AATTATTTCCTCAATTGATGTTCACAATTAATCTTAAAAATTTATACTCACACATTTGGAAAAGA
131 AATTATTTCCTCAATTGATGTTCACAATTAATCTTAAAAATTTATACTCACACATTTGGAAAAGA
41927927 AATTATTAATAAAGTAAAAATCCAATAACAAAGTCAGGTGGGGAAATTTTT
196 AATTATTAATAAAGTAAAAATCCAATAACAAAGTCAGGTGGGGAAATTTTT
41927978 TTTCAATTTT
Statistics
Matches: 245, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 245 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (246 bp):
AAAAATTATCATTATACCAAAGAATCATTGGCAAGGTTTTCATATTATACTCGAAAAAAAATTTC
GTCAGAAATCTGTAAAAGCATATATAAATAGTTAAAATGTCTAATATTTAATTATTTCCTCAATT
AATTATTTCCTCAATTGATGTTCACAATTAATCTTAAAAATTTATACTCACACATTTGGAAAAGA
AATTATTAATAAAGTAAAAATCCAATAACAAAGTCAGGTGGGGAAATTTTT
Found at i:41934373 original size:22 final size:22
Alignment explanation
Indices: 41934325--41934375 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
41934315 ATTGAGTTTG
*
41934325 ATTTTTATATATTTGTATTGAT
1 ATTTTTATATATTTGTATTGAA
* *
41934347 TTTTTTATATATTTTTATTGAA
1 ATTTTTATATATTTGTATTGAA
41934369 ATTTTTA
1 ATTTTTA
41934376 ATTCTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (22 bp):
ATTTTTATATATTTGTATTGAA
Found at i:41936525 original size:2 final size:2
Alignment explanation
Indices: 41936514--41936544 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
41936504 GAGAATTTTA
41936514 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
41936545 TACAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41939166 original size:10 final size:10
Alignment explanation
Indices: 41939130--41939169 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
41939120 AATTCTAACT
*
41939130 AAATATACAA
1 AAATATATAA
41939140 AAATAT-TAA
1 AAATATATAA
41939149 AAA-A-ATAA
1 AAATATATAA
41939157 AAATATATAA
1 AAATATATAA
41939167 AAA
1 AAA
41939170 GTTCCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 7 0.27
9 6 0.23
10 13 0.50
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATATATAA
Found at i:41941555 original size:82 final size:82
Alignment explanation
Indices: 41941418--41941575 Score: 255
Period size: 82 Copynumber: 1.9 Consensus size: 82
41941408 AGCCAGATGC
* * *
41941418 TTAAAGTTATTTGAAAGAAAATTAGGCATACCAACAAGTTTTGAGTTTTATGTTTGGAGACGACA
1 TTAAAGTTATTTAAAAGAAAATTAGGCATACCAACAAGTTTTGAGTATAATGTTTGGAGACGACA
41941483 TTGTTAGAAATAACTGA
66 TTGTTAGAAATAACTGA
* *
41941500 TTAAAGTTATTTAAAAGAAAATTAGGCATATCAAC-AGATTTTGAGTATAATGTTTGGATACGAC
1 TTAAAGTTATTTAAAAGAAAATTAGGCATACCAACAAG-TTTTGAGTATAATGTTTGGAGACGAC
41941564 ATTGTTAGAAAT
65 ATTGTTAGAAAT
41941576 TATATTCAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
81 2 0.03
82 68 0.97
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (82 bp):
TTAAAGTTATTTAAAAGAAAATTAGGCATACCAACAAGTTTTGAGTATAATGTTTGGAGACGACA
TTGTTAGAAATAACTGA
Found at i:41945905 original size:10 final size:11
Alignment explanation
Indices: 41945872--41945903 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
41945862 ACTTAAAATT
41945872 TATTTTAAAAA
1 TATTTTAAAAA
41945883 TATTTTAAAAA
1 TATTTTAAAAA
41945894 TATTTTAAAA
1 TATTTTAAAA
41945904 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:41947092 original size:19 final size:21
Alignment explanation
Indices: 41947054--41947092 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41947044 AATTTTATTC
*
41947054 ATTATTTTTATAATAATTAAT
1 ATTATTTTTATAAGAATTAAT
41947075 ATTATTTTT-T-AGAATTAA
1 ATTATTTTTATAAGAATTAA
41947093 ATTTACGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
ATTATTTTTATAAGAATTAAT
Found at i:41950913 original size:16 final size:16
Alignment explanation
Indices: 41950878--41950912 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41950868 AGAATATAGT
41950878 AAAATATTAAAATAAA
1 AAAATATTAAAATAAA
*
41950894 AAAATATT-TAATAAA
1 AAAATATTAAAATAAA
41950909 AAAA
1 AAAA
41950913 AGTCACGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATATTAAAATAAA
Found at i:41960604 original size:14 final size:14
Alignment explanation
Indices: 41960570--41960596 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41960560 GCTACTATTT
41960570 TACTATTATGTTGC
1 TACTATTATGTTGC
41960584 TACTATTATGTTG
1 TACTATTATGTTG
41960597 TTATTATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (14 bp):
TACTATTATGTTGC
Found at i:41960666 original size:30 final size:30
Alignment explanation
Indices: 41960630--41960692 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
41960620 ATTTATTTTA
*
41960630 TTGTTAATTTTATTAATATTTTAAAGGTAT
1 TTGTTAATTTTATTAATATTTTAAAGGCAT
* * *
41960660 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTAATATTTTAAAGGCAT
41960690 TTG
1 TTG
41960693 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTAATATTTTAAAGGCAT
Found at i:41961709 original size:20 final size:23
Alignment explanation
Indices: 41961676--41961720 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
41961666 CGCCACCACA
41961676 TCTTAGTTGCCTT-CAC-CTTTC
1 TCTTAGTTGCCTTCCACTCTTTC
*
41961697 TCTTATTTG-CTTCCACTCTTTC
1 TCTTAGTTGCCTTCCACTCTTTC
41961719 TC
1 TC
41961721 AACTCGGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 11 0.52
22 7 0.33
ACGTcount: A:0.09, C:0.33, G:0.07, T:0.51
Consensus pattern (23 bp):
TCTTAGTTGCCTTCCACTCTTTC
Found at i:41980766 original size:28 final size:24
Alignment explanation
Indices: 41980708--41980766 Score: 57
Period size: 28 Copynumber: 2.3 Consensus size: 24
41980698 GATAAATTCT
41980708 ATTTT-AAGTAAATTTTTACATAA
1 ATTTTAAAGTAAATTTTTACATAA
**
41980731 ATCATAAAGATAAATTATATTATCATAA
1 ATTTTAAAG-TAAATT-T-TTA-CATAA
41980759 ATTTTAAA
1 ATTTTAAA
41980767 AAAACATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 3 0.11
24 3 0.11
25 6 0.22
26 1 0.04
27 3 0.11
28 11 0.41
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (24 bp):
ATTTTAAAGTAAATTTTTACATAA
Found at i:41996450 original size:10 final size:10
Alignment explanation
Indices: 41996432--41996466 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
41996422 CATGACCCTG
41996432 TTTTGTTTTT
1 TTTTGTTTTT
*
41996442 TTTTTTTTTT
1 TTTTGTTTTT
*
41996452 TTTTGGTTTT
1 TTTTGTTTTT
41996462 TTTTG
1 TTTTG
41996467 GGAAAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:41996571 original size:122 final size:121
Alignment explanation
Indices: 41996350--41996577 Score: 438
Period size: 122 Copynumber: 1.9 Consensus size: 121
41996340 AGAAAGCCAT
41996350 AAAAGTTGTTTGGACCCAGTGGTCCAATTACAGAAGGAATTTCATCATACAAATCTACAATTCAA
1 AAAAGTTGTTTGGACCCAGTGGTCCAATTACAGAAGGAATTTCATCATACAAATCTACAATTCAA
*
41996415 AGAAGCACATGACCCTGTTTTGTTTTTTTTTTTTTTTTTTTGGTTTTTTTTGGGAA
66 AGAAGCACATGACCCTGTTTTGTTTTGTTTTTTTTTTTTTTGGTTTTTTTTGGGAA
41996471 AAAATGTTGTTTGGACCCAGTGGTCCAATTACAGAAGGAATTTCATCATACAAATCTACAATTCA
1 AAAA-GTTGTTTGGACCCAGTGGTCCAATTACAGAAGGAATTTCATCATACAAATCTACAATTCA
41996536 AAGAAGCACATGACCCTGTTTTGTTTTGTTTTTTTTTTTTTT
65 AAGAAGCACATGACCCTGTTTTGTTTTGTTTTTTTTTTTTTT
41996578 TTTTTTGGTT
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
121 4 0.04
122 101 0.96
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (121 bp):
AAAAGTTGTTTGGACCCAGTGGTCCAATTACAGAAGGAATTTCATCATACAAATCTACAATTCAA
AGAAGCACATGACCCTGTTTTGTTTTGTTTTTTTTTTTTTTGGTTTTTTTTGGGAA
Found at i:41997647 original size:27 final size:28
Alignment explanation
Indices: 41997617--41997680 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
41997607 TTATGTTTTG
*
41997617 TCATTTTCAGT-AAATAGAAAATAAAAA
1 TCATTTTCAGTAAAATAAAAAATAAAAA
** *
41997644 TCA-TTTCCTTAAAATAAAAAATAGAAA
1 TCATTTTCAGTAAAATAAAAAATAAAAA
*
41997671 TTATTTTCAG
1 TCATTTTCAG
41997681 AAAGCAAATG
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
26 5 0.18
27 19 0.68
28 4 0.14
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (28 bp):
TCATTTTCAGTAAAATAAAAAATAAAAA
Found at i:41998604 original size:20 final size:20
Alignment explanation
Indices: 41998580--41998721 Score: 114
Period size: 21 Copynumber: 7.0 Consensus size: 20
41998570 TAATAAATAC
41998580 AAAAAATTTATTTTAAAAATT
1 AAAAAA-TTATTTTAAAAATT
*
41998601 AAAAAAATATTTTAAAAATATTT
1 AAAAAATTATTTT-AAAA-A-TT
* * *
41998624 TAAAAATT-TTTTAATAATAC
1 AAAAAATTATTTTAAAAAT-T
41998644 AAAAAATTTATTTTAAAAATT
1 AAAAAA-TTATTTTAAAAATT
*
41998665 AAAAAAATATTTT-AAAATT
1 AAAAAATTATTTTAAAAATT
*
41998684 AAAAAA--A-TTAAAACAATT
1 AAAAAATTATTTTAAA-AATT
*
41998702 AAAAAAAGTATTTTAAAAAT
1 -AAAAAATTATTTTAAAAAT
41998722 ATTTTAAAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
16 2 0.02
17 3 0.03
18 4 0.04
19 19 0.19
20 18 0.18
21 25 0.26
22 19 0.19
23 8 0.08
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (20 bp):
AAAAAATTATTTTAAAAATT
Found at i:41998619 original size:11 final size:11
Alignment explanation
Indices: 41998603--41998642 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
41998593 TAAAAATTAA
41998603 AAAAATATTTT
1 AAAAATATTTT
41998614 AAAAATATTTT
1 AAAAATATTTT
*
41998625 AAAAATTTTTT
1 AAAAATATTTT
*
41998636 AATAATA
1 AAAAATA
41998643 CAAAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:41998672 original size:9 final size:9
Alignment explanation
Indices: 41998658--41998708 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
41998648 AATTTATTTT
41998658 AAAAATTAA
1 AAAAATTAA
**
41998667 AAAAATATTT
1 AAAAAT-TAA
*
41998677 TAAAATTAA
1 AAAAATTAA
41998686 AAAAATTAA
1 AAAAATTAA
*
41998695 AACAATTAA
1 AAAAATTAA
41998704 AAAAA
1 AAAAA
41998709 GTATTTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAAATTAA
Found at i:42000378 original size:20 final size:19
Alignment explanation
Indices: 42000362--42000429 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
42000352 ACAAAAAATT
42000362 TATTTTAAAAATTAAAAAAA
1 TATTTT-AAAATTAAAAAAA
42000382 TATTTTAAAATT-AAAAAA
1 TATTTTAAAATTAAAAAAA
**
42000400 -ATTAAAACAATTAAAAAAA
1 TATTTTAA-AATTAAAAAAA
42000419 GTATTTTAAAA
1 -TATTTTAAAA
42000430 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.12
18 10 0.25
19 12 0.30
20 8 0.20
21 5 0.12
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (19 bp):
TATTTTAAAATTAAAAAAA
Found at i:42000382 original size:9 final size:9
Alignment explanation
Indices: 42000368--42000418 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
42000358 AATTTATTTT
42000368 AAAAATTAA
1 AAAAATTAA
**
42000377 AAAAATATTT
1 AAAAAT-TAA
*
42000387 TAAAATTAA
1 AAAAATTAA
42000396 AAAAATTAA
1 AAAAATTAA
*
42000405 AACAATTAA
1 AAAAATTAA
42000414 AAAAA
1 AAAAA
42000419 GTATTTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAAATTAA
Found at i:42000659 original size:18 final size:18
Alignment explanation
Indices: 42000636--42000673 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42000626 AAGCGCATTA
42000636 TAAGAGTTAAGGAGGGGC
1 TAAGAGTTAAGGAGGGGC
42000654 TAAGAGTTAAGGAGGGGC
1 TAAGAGTTAAGGAGGGGC
42000672 TA
1 TA
42000674 TGGTAGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.42, T:0.18
Consensus pattern (18 bp):
TAAGAGTTAAGGAGGGGC
Found at i:42003657 original size:32 final size:32
Alignment explanation
Indices: 42003591--42003655 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
42003581 TAAACTCTTC
* * *
42003591 TTAATTATTAGATCAAGAGGATTTTGGATTTT
1 TTAATTATTAGATCAAGAAGATTGTCGATTTT
*
42003623 TTAATTATTA-ATTAAGAAGATTGTCGATTTT
1 TTAATTATTAGATCAAGAAGATTGTCGATTTT
42003654 TT
1 TT
42003656 TATTCACGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.49
Consensus pattern (32 bp):
TTAATTATTAGATCAAGAAGATTGTCGATTTT
Found at i:42009018 original size:13 final size:13
Alignment explanation
Indices: 42009000--42009065 Score: 96
Period size: 13 Copynumber: 5.1 Consensus size: 13
42008990 AGCTCTTCAT
42009000 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
42009013 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
42009026 TGCTGTGGAAAAA
1 TGCTTTTGAAAAG
*
42009039 TGCTTTTGATAAG
1 TGCTTTTGAAAAG
42009052 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
42009065 T
1 T
42009066 TTGGTTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:42011090 original size:17 final size:17
Alignment explanation
Indices: 42011065--42011097 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42011055 AATATATCAA
42011065 AAAAACAAAAAAAAAAC
1 AAAAACAAAAAAAAAAC
*
42011082 AAAACCAAAAAAAAAA
1 AAAAACAAAAAAAAAA
42011098 ATCAGACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAAAAAAC
Found at i:42011201 original size:4 final size:4
Alignment explanation
Indices: 42011192--42011232 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
42011182 CAGAAGGATT
*
42011192 GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAA
42011233 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 28 0.85
5 4 0.12
6 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:42017180 original size:3 final size:3
Alignment explanation
Indices: 42017172--42017356 Score: 370
Period size: 3 Copynumber: 61.7 Consensus size: 3
42017162 TCTTCATACT
42017172 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
42017220 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
42017268 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
42017316 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
42017357 TAATAATAAT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 182 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:42017361 original size:3 final size:3
Alignment explanation
Indices: 42017355--42017392 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
42017345 CAACAACAAC
*
42017355 AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
42017393 CTTTTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42017462 original size:19 final size:21
Alignment explanation
Indices: 42017438--42017476 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
42017428 ACTAAAACAA
*
42017438 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
42017457 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
42017477 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:42017640 original size:27 final size:28
Alignment explanation
Indices: 42017610--42017683 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 28
42017600 AATACGAGTA
* *
42017610 GTGCCACCAATTAG-TTTGGCACCATTG
1 GTGCCGCCAATTAGCATTGGCACCATTG
* *
42017637 GTGCCGCCAA-TGGCATTGGCACCTTTG
1 GTGCCGCCAATTAGCATTGGCACCATTG
*
42017664 GTGCCGCCAATT-CCATTGGC
1 GTGCCGCCAATTAGCATTGGC
42017684 GTCACCAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 37 0.93
28 1 0.03
ACGTcount: A:0.18, C:0.30, G:0.26, T:0.27
Consensus pattern (28 bp):
GTGCCGCCAATTAGCATTGGCACCATTG
Found at i:42017775 original size:28 final size:29
Alignment explanation
Indices: 42017735--42017805 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
42017725 TTTTTTTGAC
*
42017735 ATATTTTGATAAAT-AAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
42017762 TATATTTTGGTAAATAAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAAGTTGTA
*
42017792 ATATTTTAGTAAAT
1 ATATTTTGGTAAAT
42017806 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 13 0.33
29 24 0.62
30 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAGTTGTA
Found at i:42032610 original size:2 final size:2
Alignment explanation
Indices: 42032603--42032639 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42032593 TACCATCTCA
42032603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42032640 GTGGAAAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42038649 original size:18 final size:18
Alignment explanation
Indices: 42038628--42038675 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
42038618 TAGGCCCAGT
* *
42038628 GATTACTCCCGGCCTAGC
1 GATTACTCCAGACCTAGC
* *
42038646 GATTACTCTAGACCTAGT
1 GATTACTCCAGACCTAGC
42038664 GATTACTCCAGA
1 GATTACTCCAGA
42038676 TGGGGTTCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (18 bp):
GATTACTCCAGACCTAGC
Found at i:42043935 original size:3 final size:3
Alignment explanation
Indices: 42043927--42043951 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42043917 TTTTAACAGA
42043927 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
42043952 ATAATGTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:42044471 original size:20 final size:20
Alignment explanation
Indices: 42044425--42044474 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
42044415 TATTTTTTTA
42044425 TTTTAAAATATTTTTAAAAT
1 TTTTAAAATATTTTTAAAAT
***
42044445 AAATAAAATACTTTTT-AAAT
1 TTTTAAAATA-TTTTTAAAAT
42044465 TTTTAAAATA
1 TTTTAAAATA
42044475 AATTTTTGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTAAAATATTTTTAAAAT
Found at i:42046823 original size:14 final size:15
Alignment explanation
Indices: 42046799--42046827 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42046789 TTTTTCTGTG
42046799 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
42046814 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
42046828 AGTTTCGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:42048561 original size:41 final size:41
Alignment explanation
Indices: 42048505--42048646 Score: 164
Period size: 41 Copynumber: 3.5 Consensus size: 41
42048495 TTGAGATTTT
* *
42048505 TCAGGC-TTATGCCTAGCAGGCTTGATGTCGGTGAATTACA
1 TCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTATA
* *
42048545 TCAGGCTTTATGCCTAGAAGGC-TCAGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTGA-TGCCGGTGAATTATA
* * * *
42048586 TCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGC-TTGATGCCGGTGAATTATA
*
42048627 TCAGGCTTTGTGCCTAGCAG
1 TCAGGCTTTATGCCTAGCAG
42048647 ACTATATGTC
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
40 8 0.09
41 76 0.89
43 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTATA
Found at i:42049368 original size:41 final size:41
Alignment explanation
Indices: 42049319--42049642 Score: 632
Period size: 41 Copynumber: 7.9 Consensus size: 41
42049309 ATATATTTAT
42049319 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
42049360 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
42049401 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
42049442 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
42049483 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
42049524 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
42049565 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
*
42049606 TTTTTTAATTTTAAAATATTTTTAAAATA-CTTTTTTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTA
42049643 ATTTTTAAAA
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
40 7 0.02
41 275 0.98
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.63
Consensus pattern (41 bp):
TTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTATTA
Found at i:42049395 original size:30 final size:30
Alignment explanation
Indices: 42049338--42049660 Score: 132
Period size: 30 Copynumber: 11.5 Consensus size: 30
42049328 TTTAAAATAT
** *
42049338 TTTTAAAATATATTTTTTATTATTTTTTAA
1 TTTTAAAATATATTTTAAAATATTTTTTAA
*
42049368 TTTTAAAATAT-TTTTAAAATATATTTTTTA
1 TTTTAAAATATATTTTAAAATAT-TTTTTAA
***
42049398 TTATT-TTTTA-ATTTTAAAATA-----T--
1 TT-TTAAAATATATTTTAAAATATTTTTTAA
** *
42049420 TTTTAAAATATATTTTTTATTATTTTTTAA
1 TTTTAAAATATATTTTAAAATATTTTTTAA
*
42049450 TTTTAAAATAT-TTTTAAAATATATTTTTTA
1 TTTTAAAATATATTTTAAAATAT-TTTTTAA
***
42049480 TTATT-TTTTA-ATTTTAAAATA-----T--
1 TT-TTAAAATATATTTTAAAATATTTTTTAA
** *
42049502 TTTTAAAATATATTTTTTATTATTTTTTAA
1 TTTTAAAATATATTTTAAAATATTTTTTAA
*
42049532 TTTTAAAATAT-TTTTAAAATATATTTTTTA
1 TTTTAAAATATATTTTAAAATAT-TTTTTAA
***
42049562 TTATT-TTTTA-ATTTTAAAATA-----T--
1 TT-TTAAAATATATTTTAAAATATTTTTTAA
** *
42049584 TTTTAAAATATATTTTTTATTATTTTTTAA
1 TTTTAAAATATATTTTAAAATATTTTTTAA
42049614 TTTTAAAATAT-TTTTAAAATACTTTTTTAA
1 TTTTAAAATATATTTTAAAATA-TTTTTTAA
*
42049644 TTTTTAAAATAAATTTT
1 -TTTTAAAATATATTTT
42049661 TGGTATTTAT
Statistics
Matches: 211, Mismatches: 43, Indels: 76
0.64 0.13 0.23
Matches are distributed among these distances:
21 6 0.03
22 12 0.06
23 24 0.11
24 3 0.01
28 3 0.01
29 31 0.15
30 112 0.53
31 16 0.08
32 4 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTAAAATATATTTTAAAATATTTTTTAA
Found at i:42049660 original size:20 final size:20
Alignment explanation
Indices: 42049623--42049661 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42049613 ATTTTAAAAT
**
42049623 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
42049643 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
42049662 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:42052642 original size:9 final size:9
Alignment explanation
Indices: 42052628--42052652 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42052618 CTATTCTCTT
42052628 TTTCTTTTA
1 TTTCTTTTA
42052637 TTTCTTTTA
1 TTTCTTTTA
42052646 TTTCTTT
1 TTTCTTT
42052653 ACTTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTTA
Found at i:42052731 original size:23 final size:23
Alignment explanation
Indices: 42052704--42052751 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
42052694 TAATAAGTAC
42052704 ATACATATATTAATTACAAATGT
1 ATACATATATTAATTACAAATGT
* *
42052727 ATACATATATTTATTACACATGT
1 ATACATATATTAATTACAAATGT
42052750 AT
1 AT
42052752 TTATAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (23 bp):
ATACATATATTAATTACAAATGT
Found at i:42053152 original size:19 final size:18
Alignment explanation
Indices: 42053124--42053175 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
42053114 AAAATAATAA
*
42053124 TAAAA-ATATAAAAAATC
1 TAAAATATATAAAAAAGC
* *
42053141 TAATATGTTATAAAAAAGC
1 TAAAAT-ATATAAAAAAGC
42053160 TAAAATATATAAAAAA
1 TAAAATATATAAAAAA
42053176 ATACTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 15 0.54
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (18 bp):
TAAAATATATAAAAAAGC
Found at i:42053182 original size:20 final size:20
Alignment explanation
Indices: 42053114--42053184 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 20
42053104 TTTACATGTC
* *
42053114 AAAATAATAATAAAA-ATAT
1 AAAAAAATACTAAAATATAT
* *
42053133 -AAAAAAT-CTAATATGT-T
1 AAAAAAATACTAAAATATAT
*
42053150 ATAAAAAA-GCTAAAATATAT
1 A-AAAAAATACTAAAATATAT
42053170 AAAAAAATACTAAAA
1 AAAAAAATACTAAAA
42053185 AAGTATGTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
17 5 0.13
18 7 0.18
19 19 0.49
20 8 0.21
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAAAATACTAAAATATAT
Found at i:42056115 original size:3 final size:3
Alignment explanation
Indices: 42056107--42056153 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
42056097 AAGCTCATAT
* * * *
42056107 GAA GAA GAA GAA GAA CAA GAA GAA GAA CAA GAA CAA GAA CAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
42056154 GGAAAGGAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.09, G:0.26, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42056118 original size:6 final size:6
Alignment explanation
Indices: 42056111--42056151 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
42056101 TCATATGAAG
* *
42056111 AAGAAG AAGAAC AAGAAG AAGAAC AAGAAC AAGAAC AAGAA
1 AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAGAA
42056152 GAGGAAAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.68, C:0.10, G:0.22, T:0.00
Consensus pattern (6 bp):
AAGAAC
Found at i:42056128 original size:12 final size:12
Alignment explanation
Indices: 42056111--42056153 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
42056101 TCATATGAAG
42056111 AAGAAGAAGAAC
1 AAGAAGAAGAAC
42056123 AAGAAGAAGAAC
1 AAGAAGAAGAAC
*
42056135 AAGAACAAGAAC
1 AAGAAGAAGAAC
42056147 AAGAAGA
1 AAGAAGA
42056154 GGAAAGGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.67, C:0.09, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAC
Found at i:42061032 original size:9 final size:9
Alignment explanation
Indices: 42061018--42061042 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42061008 TCCCGAGAGG
42061018 AAGAAGAAC
1 AAGAAGAAC
42061027 AAGAAGAAC
1 AAGAAGAAC
42061036 AAGAAGA
1 AAGAAGA
42061043 TGAAAGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (9 bp):
AAGAAGAAC
Found at i:42062150 original size:8 final size:8
Alignment explanation
Indices: 42062139--42062168 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
42062129 AATATAAATA
42062139 TATTTTAT
1 TATTTTAT
42062147 TATTTTAT
1 TATTTTAT
42062155 TATTTTAT
1 TATTTTAT
42062163 TATTTT
1 TATTTT
42062169 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TATTTTAT
Found at i:42067830 original size:23 final size:22
Alignment explanation
Indices: 42067787--42067832 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
42067777 TGTAACAATA
**
42067787 TTTTTATTTAACATGTTTAATT
1 TTTTTATTTAACATGAATAATT
*
42067809 TTTTTAATTTAACTTGAATAATT
1 TTTTT-ATTTAACATGAATAATT
42067832 T
1 T
42067833 CACTCAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTTATTTAACATGAATAATT
Found at i:42074170 original size:61 final size:62
Alignment explanation
Indices: 42073990--42074172 Score: 189
Period size: 62 Copynumber: 3.0 Consensus size: 62
42073980 TTTACATAAT
* * ** * *
42073990 AACAAATTTAGCTCTACAATAATTACAGATTCTATCAATTTGGTCTTAATTCTAAAAAAA-TC
1 AACAAATTTAACCCTACAATGTTTGCA-ATTCTATCAATTTGATCTTAATTCTAAAAAAATTC
* *
42074052 AACAAATTTAACCCTACAATGTTTGCAGATTCTATCAAATTGATCCTAATTCT--AAAAATTC
1 AACAAATTTAACCCTACAATGTTTGCA-ATTCTATCAATTTGATCTTAATTCTAAAAAAATTC
* * *
42074113 AACAAATTTAACCCTTA-AAT-TTATGC-ATTCTATCTATTTAATCTTGATTCTAAAAAAATT
1 AACAAATTTAACCC-TACAATGTT-TGCAATTCTATCAATTTGATCTTAATTCTAAAAAAATT
42074173 AAAAATAAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
59 20 0.19
60 7 0.07
61 29 0.28
62 47 0.46
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.37
Consensus pattern (62 bp):
AACAAATTTAACCCTACAATGTTTGCAATTCTATCAATTTGATCTTAATTCTAAAAAAATTC
Found at i:42075984 original size:16 final size:15
Alignment explanation
Indices: 42075963--42075994 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
42075953 GTGGATTTTA
42075963 TAGTTAGTTAATTAAT
1 TAGTTAGTT-ATTAAT
42075979 TAGTTAGTTATTAAT
1 TAGTTAGTTATTAAT
42075994 T
1 T
42075995 TAATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TAGTTAGTTATTAAT
Found at i:42077340 original size:16 final size:17
Alignment explanation
Indices: 42077308--42077340 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42077298 CACTTTGATC
*
42077308 TTTTAATTTTTATAAAA
1 TTTTAATTTTAATAAAA
42077325 TTTTAA-TTTAATAAAA
1 TTTTAATTTTAATAAAA
42077341 ATAAAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAATTTTAATAAAA
Found at i:42077342 original size:17 final size:17
Alignment explanation
Indices: 42077308--42077340 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42077298 CACTTTGATC
*
42077308 TTTTAATTTTTATAAAA
1 TTTTAATTTATATAAAA
42077325 TTTTAATTTA-ATAAAA
1 TTTTAATTTATATAAAA
42077341 ATAAAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAATTTATATAAAA
Found at i:42078823 original size:13 final size:13
Alignment explanation
Indices: 42078805--42078831 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42078795 AATTTATCTT
42078805 ATAAAAATTCTAA
1 ATAAAAATTCTAA
42078818 ATAAAAATTCTAA
1 ATAAAAATTCTAA
42078831 A
1 A
42078832 GAGAACTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAAAATTCTAA
Found at i:42085333 original size:6 final size:6
Alignment explanation
Indices: 42085324--42085349 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42085314 GTTTAAATTT
42085324 ATTTAG ATTTAG ATTTAG ATTTAG AT
1 ATTTAG ATTTAG ATTTAG ATTTAG AT
42085350 ATATTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATTTAG
Found at i:42089998 original size:34 final size:35
Alignment explanation
Indices: 42089943--42090009 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
42089933 CAAACACCAG
*
42089943 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
42089978 AAAACATTTTCCCG-AAATCATTTTACTGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
42090010 TATTTTACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42091869 original size:16 final size:16
Alignment explanation
Indices: 42091848--42091880 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42091838 TTTGTAAAGA
42091848 TGGTTGCTTTGGTTTC
1 TGGTTGCTTTGGTTTC
42091864 TGGTTGCTTTGGTTTC
1 TGGTTGCTTTGGTTTC
42091880 T
1 T
42091881 TATTTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.30, T:0.58
Consensus pattern (16 bp):
TGGTTGCTTTGGTTTC
Found at i:42103475 original size:17 final size:19
Alignment explanation
Indices: 42103441--42103477 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
42103431 ATTTGTCTGC
42103441 ATATACAATATATAATGTT
1 ATATACAATATATAATGTT
*
42103460 ATAT-CAATA-ATTATGTT
1 ATATACAATATATAATGTT
42103477 A
1 A
42103478 ATAATTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
ATATACAATATATAATGTT
Found at i:42103795 original size:2 final size:2
Alignment explanation
Indices: 42103788--42103814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42103778 TTGTTTGGGC
42103788 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 A
42103815 GTTAATAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42107247 original size:16 final size:17
Alignment explanation
Indices: 42107214--42107250 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
42107204 TTTTTACAAT
42107214 AAATTAATATTAAATAA
1 AAATTAATATTAAATAA
*
42107231 AAATTAA-ATTTAATAA
1 AAATTAATATTAAATAA
42107247 AAAT
1 AAAT
42107251 GTGCATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTAATATTAAATAA
Found at i:42110276 original size:6 final size:6
Alignment explanation
Indices: 42110267--42110291 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42110257 CGTAATTCAC
42110267 CATCTT CATCTT CATCTT CATCTT C
1 CATCTT CATCTT CATCTT CATCTT C
42110292 TTCTAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (6 bp):
CATCTT
Found at i:42114109 original size:2 final size:2
Alignment explanation
Indices: 42114102--42114128 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42114092 CAAACATGAA
42114102 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 A
42114129 GTTGATGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42115639 original size:55 final size:55
Alignment explanation
Indices: 42115571--42115679 Score: 141
Period size: 55 Copynumber: 2.0 Consensus size: 55
42115561 GAGGAGAGTA
* *
42115571 ATTAGACCCAGACTCTAATA-C-CTTGTTGAGTTAGGATTCATTGAAACCCAATTCG
1 ATTAGACCCAGACTCCAA-AGCGC-TGTTGAATTAGGATTCATTGAAACCCAATTCG
** *
42115626 ATTAGACTTAGACTCCAAAGCGCTGTTGAATTAGGATTCGTTGAAACCCAATTC
1 ATTAGACCCAGACTCCAAAGCGCTGTTGAATTAGGATTCATTGAAACCCAATTC
42115680 AAATCTATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
54 1 0.02
55 45 0.96
56 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (55 bp):
ATTAGACCCAGACTCCAAAGCGCTGTTGAATTAGGATTCATTGAAACCCAATTCG
Found at i:42118490 original size:22 final size:22
Alignment explanation
Indices: 42118463--42118511 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
42118453 TCTTTTTTTT
*
42118463 TAAAAACAACAATAATTGTAA-AA
1 TAAAAATAA-AATAA-TGTAACAA
42118486 TAAAAATAAAATAATGTAACAA
1 TAAAAATAAAATAATGTAACAA
42118508 TAAA
1 TAAA
42118512 TAGAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 5 0.21
22 11 0.46
23 8 0.33
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.22
Consensus pattern (22 bp):
TAAAAATAAAATAATGTAACAA
Found at i:42118518 original size:22 final size:22
Alignment explanation
Indices: 42118463--42118518 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
42118453 TCTTTTTTTT
*
42118463 TAAAAACAACAATAATTGTAAAA
1 TAAAAAGAA-AATAATTGTAAAA
*
42118486 TAAAAATAAAATAA-TGTAACAA
1 TAAAAAGAAAATAATTGTAA-AA
*
42118508 TAAATAGAAAA
1 TAAAAAGAAAA
42118519 ATCATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.17
22 16 0.55
23 8 0.28
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (22 bp):
TAAAAAGAAAATAATTGTAAAA
Found at i:42118931 original size:17 final size:17
Alignment explanation
Indices: 42118898--42118929 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42118888 CTTGCCCTCT
42118898 TCTTTCTTATTTTTTTC
1 TCTTTCTTATTTTTTTC
42118915 TCTTT-TTATTTTTTT
1 TCTTTCTTATTTTTTT
42118930 TCATAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (17 bp):
TCTTTCTTATTTTTTTC
Found at i:42146411 original size:11 final size:11
Alignment explanation
Indices: 42146397--42146422 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42146387 AAAAATAAAA
42146397 AAAAACATTTT
1 AAAAACATTTT
42146408 AAAAACATTTT
1 AAAAACATTTT
42146419 AAAA
1 AAAA
42146423 TAAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAACATTTT
Found at i:42159317 original size:13 final size:13
Alignment explanation
Indices: 42159299--42159323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42159289 GTTGTTTTAA
42159299 TTTTTAATTAATG
1 TTTTTAATTAATG
42159312 TTTTTAATTAAT
1 TTTTTAATTAAT
42159324 AAATATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:42160406 original size:144 final size:144
Alignment explanation
Indices: 42160146--42160435 Score: 571
Period size: 144 Copynumber: 2.0 Consensus size: 144
42160136 CTAACAAAGA
*
42160146 TAACTTCTATCTTATAACCTTCTCAAATTCTAATATATTTACTCTTGATTTAACATGGTTCATAA
1 TAACTTCTATCTTATAACCTTCTCAAATTCTAAAATATTTACTCTTGATTTAACATGGTTCATAA
42160211 CTCAAGGGTATTGGGGATGCTACATGAATTTTTTCCACTTTTGTTGTATTTTTATTAATTCATTT
66 CTCAAGGGTATTGGGGATGCTACATGAATTTTTTCCACTTTTGTTGTATTTTTATTAATTCATTT
42160276 TGATTTATTATAAC
131 TGATTTATTATAAC
42160290 TAACTTCTATCTTATAACCTTCTCAAATTCTAAAATATTTACTCTTGATTTAACATGGTTCATAA
1 TAACTTCTATCTTATAACCTTCTCAAATTCTAAAATATTTACTCTTGATTTAACATGGTTCATAA
42160355 CTCAAGGGTATTGGGGATGCTACATGAATTTTTTCCACTTTTGTTGTATTTTTATTAATTCATTT
66 CTCAAGGGTATTGGGGATGCTACATGAATTTTTTCCACTTTTGTTGTATTTTTATTAATTCATTT
42160420 TGATTTATTATAAC
131 TGATTTATTATAAC
42160434 TA
1 TA
42160436 TTGATACTAG
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.47
Consensus pattern (144 bp):
TAACTTCTATCTTATAACCTTCTCAAATTCTAAAATATTTACTCTTGATTTAACATGGTTCATAA
CTCAAGGGTATTGGGGATGCTACATGAATTTTTTCCACTTTTGTTGTATTTTTATTAATTCATTT
TGATTTATTATAAC
Found at i:42177372 original size:3 final size:3
Alignment explanation
Indices: 42177366--42177390 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42177356 ATCATTTTTT
42177366 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
42177391 CAAGAAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:42179372 original size:33 final size:33
Alignment explanation
Indices: 42179334--42179444 Score: 78
Period size: 33 Copynumber: 3.2 Consensus size: 33
42179324 GTAATGGAGT
42179334 TTGGGTCTAATTACTCTTGTTTATAAATTCGAA
1 TTGGGTCTAATTACTCTTGTTTATAAATTCGAA
* * * * ** * * * *
42179367 TTGGGTTTCAGTGAATCCTAATTCAATAAGTAATGGAG
1 TTGGGTCT-AATTACT-CTTGTT-TATAA--ATTCGAA
42179405 TTTGGGTCTAATTACTCTTGTTTATAAATTCGAA
1 T-TGGGTCTAATTACTCTTGTTTATAAATTCGAA
42179439 TTGGGT
1 TTGGGT
42179445 TTCAATGAAT
Statistics
Matches: 52, Mismatches: 20, Indels: 12
0.62 0.24 0.14
Matches are distributed among these distances:
33 12 0.23
34 9 0.17
35 4 0.08
36 8 0.15
37 4 0.08
38 9 0.17
39 6 0.12
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (33 bp):
TTGGGTCTAATTACTCTTGTTTATAAATTCGAA
Found at i:42179431 original size:72 final size:73
Alignment explanation
Indices: 42179280--42179461 Score: 321
Period size: 72 Copynumber: 2.5 Consensus size: 73
42179270 CATATAATAT
* * *
42179280 TTTATAAATTCAAATTAGGTTTCAGTAAATCCTAATTCAATAACGTAATGGAGTTTGGGTCTAAT
1 TTTATAAATTCGAATTGGGTTTCAGTGAATCCTAATTCAATAACGTAATGGAGTTTGGGTCTAAT
42179345 TACTCTTG
66 TACTCTTG
42179353 TTTATAAATTCGAATTGGGTTTCAGTGAATCCTAATTCAATAA-GTAATGGAGTTTGGGTCTAAT
1 TTTATAAATTCGAATTGGGTTTCAGTGAATCCTAATTCAATAACGTAATGGAGTTTGGGTCTAAT
42179417 TACTCTTG
66 TACTCTTG
*
42179425 TTTATAAATTCGAATTGGGTTTCAATGAATCCTAATT
1 TTTATAAATTCGAATTGGGTTTCAGTGAATCCTAATT
42179462 GAACACAGAT
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 65 0.62
73 40 0.38
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (73 bp):
TTTATAAATTCGAATTGGGTTTCAGTGAATCCTAATTCAATAACGTAATGGAGTTTGGGTCTAAT
TACTCTTG
Found at i:42181439 original size:23 final size:24
Alignment explanation
Indices: 42181413--42181459 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
42181403 TCATCCAAAG
*
42181413 GAAAAACA-ATTTTTACTT-ATTTT
1 GAAAAAAATATTTTTA-TTAATTTT
42181436 GAAAAAAATATTTTTATTAATTTT
1 GAAAAAAATATTTTTATTAATTTT
42181460 ATTAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
GAAAAAAATATTTTTATTAATTTT
Found at i:42185656 original size:8 final size:9
Alignment explanation
Indices: 42185604--42185659 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 9
42185594 AATATTAAAA
42185604 ATAAAAATT
1 ATAAAAATT
*
42185613 GATATAAACTT
1 -ATA-AAAATT
42185624 ATAAAAAGTT
1 ATAAAAA-TT
42185634 ATAAAATATT
1 ATAAAA-ATT
42185644 ATAAAAA-T
1 ATAAAAATT
42185652 ATAAAAAT
1 ATAAAAAT
42185660 CTAATAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 8 0.20
9 4 0.10
10 22 0.55
11 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:42187448 original size:23 final size:23
Alignment explanation
Indices: 42187416--42187537 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
42187406 ATAAGTGCAA
42187416 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
42187439 CGCTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42187462 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42187485 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
42187508 CACTGAAACGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
42187531 CACTGAT
1 CACTGAT
42187538 CAATAACACT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:42187483 original size:46 final size:46
Alignment explanation
Indices: 42187416--42187535 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
42187406 ATAAGTGCAA
* *
42187416 CACTGATATGTAGCCGAAGCTACCGCTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
42187462 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
* *
42187508 CACTGAAACGTAGCCAAAGCTACCACTG
1 CACTGAAATGTAGCCGAAGCTACCACTG
42187536 ATCAATAACA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
Found at i:42188855 original size:29 final size:30
Alignment explanation
Indices: 42188823--42188881 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
42188813 TTCTAATTCT
* * *
42188823 AATATGTTTTTTTAATTTTA-AATATTTTA
1 AATAAGTTTTATTAATTTTATAAAATTTTA
42188852 AATAAGTTTTATTAATTTTATAAAATTTTA
1 AATAAGTTTTATTAATTTTATAAAATTTTA
42188882 TAATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
AATAAGTTTTATTAATTTTATAAAATTTTA
Found at i:42188975 original size:17 final size:17
Alignment explanation
Indices: 42188953--42189016 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
42188943 TTGTATCAAT
42188953 TTTAATATTTTTTAATA
1 TTTAATATTTTTTAATA
* *
42188970 TTTAATA-TTTTTATTT
1 TTTAATATTTTTTAATA
42188986 TTATAAT-TTTTTTATGATA
1 TT-TAATATTTTTTA--ATA
42189005 TTTAATACTTTT
1 TTTAATA-TTTT
42189017 ATGAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 9 0.24
17 17 0.46
18 4 0.11
19 3 0.08
20 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTAATATTTTTTAATA
Found at i:42192562 original size:13 final size:13
Alignment explanation
Indices: 42192546--42192608 Score: 99
Period size: 13 Copynumber: 4.8 Consensus size: 13
42192536 TTTAAACCAA
42192546 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
42192559 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
42192572 ACTTTTCCATAGC
1 ACTTTTCAAAAGC
42192585 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
42192598 ACTTTTCAAAA
1 ACTTTTCAAAA
42192609 ACAATGAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:42193590 original size:16 final size:16
Alignment explanation
Indices: 42193566--42193596 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42193556 TATTTATGAT
*
42193566 AATATTTTTTAATATG
1 AATACTTTTTAATATG
42193582 AATACTTTTTAATAT
1 AATACTTTTTAATAT
42193597 ATTTTTAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
AATACTTTTTAATATG
Found at i:42196863 original size:20 final size:21
Alignment explanation
Indices: 42196825--42196870 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
42196815 CTCGTCAACA
*
42196825 TTAAATTTTTATATATATATCT
1 TTAAATTTATATATATATAT-T
42196847 TTAAATTTAT-TAT-TATATT
1 TTAAATTTATATATATATATT
42196866 TTAAA
1 TTAAA
42196871 AAATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 3 0.13
22 9 0.39
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAATTTATATATATATATT
Found at i:42201127 original size:2 final size:2
Alignment explanation
Indices: 42201120--42201146 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42201110 TGCATGCAAC
42201120 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 T
42201147 GCAAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42202288 original size:3 final size:3
Alignment explanation
Indices: 42202280--42202320 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42202270 ATGTATCATA
42202280 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
42202321 TGTATATAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:42203509 original size:13 final size:13
Alignment explanation
Indices: 42203491--42203517 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42203481 TCTTTTTACA
42203491 ACACATGAAATGT
1 ACACATGAAATGT
42203504 ACACATGAAATGT
1 ACACATGAAATGT
42203517 A
1 A
42203518 TTATGATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (13 bp):
ACACATGAAATGT
Found at i:42210581 original size:24 final size:24
Alignment explanation
Indices: 42210534--42210581 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
42210524 TCGTTTTGTG
* *
42210534 GCAAATGATGAATTGACAGTAAAT
1 GCAAAAGATGAATTGACAGCAAAT
42210558 GCAAAAGATGAATTGA-AGGCAAAT
1 GCAAAAGATGAATTGACA-GCAAAT
42210582 TACCCAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (24 bp):
GCAAAAGATGAATTGACAGCAAAT
Found at i:42216675 original size:17 final size:16
Alignment explanation
Indices: 42216618--42216676 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
42216608 AATTTTTTAT
* *
42216618 ATTATTTTAGATTTGG
1 ATTATTTTAGGTTAGG
* *
42216634 ATTAATTTTATGTTAGT
1 ATT-ATTTTAGGTTAGG
*
42216651 ATTGTTTTAGGGTTAGG
1 ATTATTTTA-GGTTAGG
42216668 ATTATTTTA
1 ATTATTTTA
42216677 ATTTCGGGTC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
16 8 0.24
17 25 0.76
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (16 bp):
ATTATTTTAGGTTAGG
Found at i:42218759 original size:21 final size:21
Alignment explanation
Indices: 42218722--42218771 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
42218712 TTTTATTCAG
*
42218722 AATCTTAAACTCGAAACTTTA
1 AATCTTAAACTCGAAACCTTA
*
42218743 AATCTTAAA-TCTTAAACCTTA
1 AATCTTAAACTC-GAAACCTTA
42218764 AA-CTTAAA
1 AATCTTAAA
42218772 ACTCATAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (21 bp):
AATCTTAAACTCGAAACCTTA
Found at i:42219564 original size:15 final size:14
Alignment explanation
Indices: 42219531--42219573 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
42219521 AGCAATTTAA
* *
42219531 TTCTTTTCTTTTATG
1 TTCTTTTATTTT-TT
42219546 TTCTTTTAATTTTTT
1 TTCTTTT-ATTTTTT
42219561 TTCTTTTATTTTT
1 TTCTTTTATTTTT
42219574 CATTCTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 15 0.60
16 4 0.16
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.79
Consensus pattern (14 bp):
TTCTTTTATTTTTT
Found at i:42227971 original size:73 final size:73
Alignment explanation
Indices: 42227852--42228001 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
42227842 CGGATCATGA
42227852 GATCCCTCAAAGGCAAGTCTACCTCTCTCATAAATAACCTCCACTGTAGTATTAAATCAGTATCA
1 GATCCCTCAAAGGCAAGTCTACCTCTCTCATAAATAACCTCCACTGTAGTATTAAATCAGTATCA
42227917 GTCATATC
66 GTCATATC
42227925 GATCCCTCAAAGGCAAGTCTACCTCTCTCATAAATAACCTCCACTGTAGTATTAAATCAGTATCA
1 GATCCCTCAAAGGCAAGTCTACCTCTCTCATAAATAACCTCCACTGTAGTATTAAATCAGTATCA
42227990 GTCATATC
66 GTCATATC
42227998 GATC
1 GATC
42228002 GATATGTTTC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (73 bp):
GATCCCTCAAAGGCAAGTCTACCTCTCTCATAAATAACCTCCACTGTAGTATTAAATCAGTATCA
GTCATATC
Found at i:42232918 original size:13 final size:13
Alignment explanation
Indices: 42232900--42232928 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42232890 TACAATATTC
42232900 ATTTTTATTTTAA
1 ATTTTTATTTTAA
42232913 ATTTTTATTTTAA
1 ATTTTTATTTTAA
42232926 ATT
1 ATT
42232929 ATATCAAATA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTATTTTAA
Found at i:42242317 original size:27 final size:27
Alignment explanation
Indices: 42242287--42242365 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
42242277 AGCCAATCAC
* *
42242287 ATTGGCGACACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
*
42242314 ATTGGCGGCACCAATGGTGCCAAAGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
42242341 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
42242366 GACTAAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.32, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:42242476 original size:18 final size:19
Alignment explanation
Indices: 42242438--42242476 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42242428 TTCAACTCAT
* *
42242438 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAAATCTA
42242457 TTTTAATTTAATAAAT-TA
1 TTTTAATTTAATAAATCTA
42242475 TT
1 TT
42242477 AAGTAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAATTTAATAAATCTA
Found at i:42242728 original size:18 final size:19
Alignment explanation
Indices: 42242691--42242729 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42242681 TCAACCCATT
* *
42242691 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
42242710 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
42242728 TT
1 TT
42242730 CTCATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:42242736 original size:18 final size:19
Alignment explanation
Indices: 42242696--42242738 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
42242686 CCATTTTTTT
* *
42242696 ATTTAATAACTCTATTTTA
1 ATTTAATAACACTATTCTA
*
42242715 ATTTAATAA-ACTATTCTC
1 ATTTAATAACACTATTCTA
42242733 ATTTAA
1 ATTTAA
42242739 ATTAAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATAACACTATTCTA
Found at i:42242759 original size:19 final size:19
Alignment explanation
Indices: 42242735--42242837 Score: 122
Period size: 19 Copynumber: 5.6 Consensus size: 19
42242725 CTATTCTCAT
42242735 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
42242754 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
42242772 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
42242791 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
*
42242809 TTAAACTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
42242828 TTAAA-TAAAA
1 TTAAATTAAAA
42242838 AAATGAGTTG
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
18 34 0.49
19 35 0.51
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:42242785 original size:37 final size:37
Alignment explanation
Indices: 42242735--42242833 Score: 189
Period size: 37 Copynumber: 2.7 Consensus size: 37
42242725 CTATTCTCAT
42242735 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
42242772 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
*
42242809 TTAAACTAAAATAGAGTTATTAAAT
1 TTAAATTAAAATAGAGTTATTAAAT
42242834 AAAAAAATGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.37
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:42242821 original size:18 final size:18
Alignment explanation
Indices: 42242735--42242837 Score: 111
Period size: 18 Copynumber: 5.6 Consensus size: 18
42242725 CTATTCTCAT
42242735 TTAAATTAAAATAGAGTTA
1 TTAAA-TAAAATAGAGTTA
* *
42242754 TTAAATGAGAATAG-TTTA
1 TTAAAT-AAAATAGAGTTA
42242772 TTAAATTAAAATAGAGTTA
1 TTAAA-TAAAATAGAGTTA
* *
42242791 TTAAATGAGAATAG-TTTA
1 TTAAAT-AAAATAGAGTTA
42242809 TTAAACTAAAATAGAGTTA
1 TTAAA-TAAAATAGAGTTA
42242828 TTAAATAAAA
1 TTAAATAAAA
42242838 AAATGAGTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
18 35 0.50
19 35 0.50
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (18 bp):
TTAAATAAAATAGAGTTA
Found at i:42242943 original size:27 final size:27
Alignment explanation
Indices: 42242913--42242990 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
42242903 ATTTTAGTCA
*
42242913 TTTGGCACCATTGGTGCTGCCAATCAC
1 TTTGGCACCATTGGTGCCGCCAATCAC
** *
42242940 TTTGGCACCATTGGTGCCAACAATCTC
1 TTTGGCACCATTGGTGCCGCCAATCAC
*
42242967 TTTGGCACCTTTGGTGCCGCCAAT
1 TTTGGCACCATTGGTGCCGCCAAT
42242991 ATGATTGGCC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCGCCAATCAC
Found at i:42243118 original size:27 final size:23
Alignment explanation
Indices: 42243059--42243102 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
42243049 TTTTTTTGGT
*
42243059 ATATTTTCGTAAATAAAAAAATA
1 ATATTTTGGTAAATAAAAAAATA
42243082 ATATTTTGGTAAATAAAAAAA
1 ATATTTTGGTAAATAAAAAAA
42243103 GTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (23 bp):
ATATTTTGGTAAATAAAAAAATA
Found at i:42246183 original size:19 final size:18
Alignment explanation
Indices: 42246152--42246207 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
42246142 TAACAATTAA
*
42246152 TTAA-TTTTAAAATATTT
1 TTAACTTTTTAAATATTT
42246169 TTATACTTTTTAAATACTTT
1 TTA-ACTTTTTAAATA-TTT
* *
42246189 TTAATTTTTTAAAAATTT
1 TTAACTTTTTAAATATTT
42246207 T
1 T
42246208 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 3 0.09
18 5 0.15
19 19 0.58
20 6 0.18
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAACTTTTTAAATATTT
Found at i:42247853 original size:89 final size:90
Alignment explanation
Indices: 42247743--42247922 Score: 353
Period size: 89 Copynumber: 2.0 Consensus size: 90
42247733 TTTAAATCTA
42247743 CATTATATAAATAATCATGTTAAAAAATAAATATAATTATTTAAATATATTTATACCAGATTTAA
1 CATTATATAAATAATCATGTTAAAAAATAAATATAATTATTTAAATATATTTATACCAGATTTAA
42247808 GCGAATATTTAACGTTGAAGTTAAT
66 GCGAATATTTAACGTTGAAGTTAAT
42247833 CATTATAT-AATAATCATGTTAAAAAATAAATATAATTATTTAAATATATTTATACCAGATTTAA
1 CATTATATAAATAATCATGTTAAAAAATAAATATAATTATTTAAATATATTTATACCAGATTTAA
42247897 GCGAATATTTAACGTTGAAGTTAAT
66 GCGAATATTTAACGTTGAAGTTAAT
42247922 C
1 C
42247923 CAAAAGAAAA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 82 0.91
90 8 0.09
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (90 bp):
CATTATATAAATAATCATGTTAAAAAATAAATATAATTATTTAAATATATTTATACCAGATTTAA
GCGAATATTTAACGTTGAAGTTAAT
Found at i:42255236 original size:12 final size:12
Alignment explanation
Indices: 42255197--42255233 Score: 53
Period size: 10 Copynumber: 3.3 Consensus size: 12
42255187 CCCTCAATTA
42255197 TTTTAAAATA--
1 TTTTAAAATACT
42255207 TTTTAAAATACT
1 TTTTAAAATACT
42255219 TTTTAAAA-ACT
1 TTTTAAAATACT
42255230 TTTT
1 TTTT
42255234 TAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.40
11 7 0.28
12 8 0.32
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTAAAATACT
Found at i:42256836 original size:117 final size:117
Alignment explanation
Indices: 42256548--42257475 Score: 1276
Period size: 117 Copynumber: 8.1 Consensus size: 117
42256538 TTTTTGAAAT
* * * * * * *
42256548 TGATAAAGATGTTGATATTAACGATGGAGGAGGTGGATATGATGTACTTTCATTAGGTCCCGATG
1 TGATGAAGATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
* *
42256613 GAGGAATAGGCACACCTGTAGGTAAAATCTTGAAATTTGAACTCTTCAAAA-
66 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
42256664 -G-T---GATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
1 TGATGAAGATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
* * *
42256724 GAGGAATAGGCATACATGTAGGTAGAATCTTGAAATTTGAACTCTTCAAAAG
66 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
* *
42256776 TGATGAAGATGTCGATATTGACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACA
1 TGATGAAGATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
42256841 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
66 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
* *
42256893 TGATGAAGATGTCGATATTGACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACA
1 TGATGAAGATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
* * * *
42256958 GAGGAATAGGCATACATGTAGGTAGAATCTTGGAATTTGAACTCTTCAAAAG
66 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
* * * *
42257010 TGATAAAGATGTCGATATTGA-GTATGGAGGAGGTGGATCTGATTTACTTCCACTAGGTCCCGAC
1 TGATGAAGATGTCGATATTAACG-GTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGAC
* *
42257074 ---GG---AGGCCCACATGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAA-
65 GGAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
* *
42257120 -G-T---GATGTCAATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGGCG
1 TGATGAAGATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
*
42257180 GAGGAATAGGCACACCTGTAGGTAAAATCCTGAAATTTGAACTCTTCAAAAG
66 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
* * * **
42257232 TGATGAAGATGTCGATATCAAAGATGGAGGAGGCAGATCTGATGTACTTCCACTAGGTCCCGAC-
1 TGATGAAGATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
42257296 ----AA-AGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
66 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
* * *
42257343 TGACGAAGATGTCGATATTGACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCTCGACG
1 TGATGAAGATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
* * * **
42257408 AAGAAATAGGCACACCTGTAGGTAGAATCTTGAAATTTGAACTCTTTGAAAG
66 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
* *
42257460 CGATGAAGATATCGAT
1 TGATGAAGATGTCGAT
42257476 GTCATTAGTG
Statistics
Matches: 731, Mismatches: 55, Indels: 51
0.87 0.07 0.06
Matches are distributed among these distances:
105 50 0.07
106 1 0.00
108 3 0.00
109 1 0.00
111 281 0.38
112 2 0.00
113 2 0.00
114 5 0.01
115 1 0.00
116 3 0.00
117 382 0.52
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (117 bp):
TGATGAAGATGTCGATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAG
Found at i:42256850 original size:228 final size:225
Alignment explanation
Indices: 42256548--42257475 Score: 1294
Period size: 228 Copynumber: 4.1 Consensus size: 225
42256538 TTTTTGAAAT
* * * * *
42256548 TGATAAAGATGTTGATATTAACGATGGAGGAGGTGGATATGATGTACTTTCATTAGGTCCCGATG
1 TGATGAAGATGTCGATATTAACGATGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGA--
* * *
42256613 GAGGAATAGGCACACCTGTAGGTAAAATCTTGAAATTTGAACTCTTCAAAAGT-GATGTCGATAT
64 -CGGAA-AGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAGTAGATGTCGATAT
*
42256677 TAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACGGAGGAATAGGCATACATG
127 TAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACGGAGGAATAGGCACACATG
42256742 TAGGTAGAATCTTGAAATTTGAACTCTTCAAAAG
192 TAGGTAGAATCTTGAAATTTGAACTCTTCAAAAG
* *
42256776 TGATGAAGATGTCGATATTGACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACA
1 TGATGAAGATGTCGATATTAACGATGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGAC-
42256841 GAGGAATAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAGTGATGAAGATGTC
65 --GGAA-AGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAA--G-T--AGATGTC
* * *
42256906 GATATTGACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACAGAGGAATAGGCAT
122 GATATTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACGGAGGAATAGGCAC
*
42256971 ACATGTAGGTAGAATCTTGGAATTTGAACTCTTCAAAAG
187 ACATGTAGGTAGAATCTTGAAATTTGAACTCTTCAAAAG
* * *
42257010 TGATAAAGATGTCGATATTGA-GTATGGAGGAGGTGGATCTGATTTACTTCCACTAGGTCCCGAC
1 TGATGAAGATGTCGATATTAACG-ATGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGAC
* * *
42257074 GG--AGGCCCACATGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAGT-GATGTCAATATTAA
65 GGAAAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAGTAGATGTCGATATTAA
* *
42257136 CGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGGCGGAGGAATAGGCACACCTGTAG
130 CGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACGGAGGAATAGGCACACATGTAG
* *
42257201 GTAAAATCCTGAAATTTGAACTCTTCAAAAG
195 GTAGAATCTTGAAATTTGAACTCTTCAAAAG
* * **
42257232 TGATGAAGATGTCGATATCAAAGATGGAGGAGGCAGATCTGATGTACTTCCACTAGGTCCCGAC-
1 TGATGAAGATGTCGATATTAACGATGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
42257296 -AAAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAGTGACGAAGATGTCGATA
66 GAAAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAGT-----AGATGTCGATA
* * * * *
42257360 TTGACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCTCGACGAAGAAATAGGCACACCT
126 TTAACGGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACGGAGGAATAGGCACACAT
**
42257425 GTAGGTAGAATCTTGAAATTTGAACTCTTTGAAAG
191 GTAGGTAGAATCTTGAAATTTGAACTCTTCAAAAG
* *
42257460 CGATGAAGATATCGAT
1 TGATGAAGATGTCGAT
42257476 GTCATTAGTG
Statistics
Matches: 634, Mismatches: 47, Indels: 38
0.88 0.07 0.05
Matches are distributed among these distances:
222 201 0.32
223 1 0.00
225 1 0.00
226 1 0.00
228 259 0.41
230 1 0.00
231 3 0.00
233 1 0.00
234 166 0.26
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (225 bp):
TGATGAAGATGTCGATATTAACGATGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACG
GAAAGGCACACCTGTAGGTAGAATCCTGAAATTTGAACTCTTCAAAAGTAGATGTCGATATTAAC
GGTGGAGGAGGTGGATCTGATGTACTTCCACTAGGTCCCGACGGAGGAATAGGCACACATGTAGG
TAGAATCTTGAAATTTGAACTCTTCAAAAG
Found at i:42258205 original size:19 final size:19
Alignment explanation
Indices: 42258169--42258206 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42258159 ACCCAGCCCG
*
42258169 TATTAATTTTTTTAAAAAT
1 TATTAATTTTTATAAAAAT
42258188 TATT-ATTTTTATATAAAAT
1 TATTAATTTTTATA-AAAAT
42258207 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTAATTTTTATAAAAAT
Found at i:42260687 original size:21 final size:20
Alignment explanation
Indices: 42260663--42260711 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
42260653 TACAGAAACG
* *
42260663 GAAGAAATAAGGAAGGAAGCA
1 GAAGAAAGAAGGAAGGAA-AA
42260684 GAAGAAAAGAAGGAAGGAAAA
1 GAAG-AAAGAAGGAAGGAAAA
42260705 GAAGAAA
1 GAAGAAA
42260712 AAAATAAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 9 0.36
22 13 0.52
ACGTcount: A:0.63, C:0.02, G:0.33, T:0.02
Consensus pattern (20 bp):
GAAGAAAGAAGGAAGGAAAA
Found at i:42260713 original size:22 final size:22
Alignment explanation
Indices: 42260663--42260712 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
42260653 TACAGAAACG
* *
42260663 GAAG-AAATAAGGAAGGAAGCA
1 GAAGAAAAGAAGGAAGGAAGAA
42260684 GAAGAAAAGAAGGAAGGAA-AA
1 GAAGAAAAGAAGGAAGGAAGAA
42260705 GAAGAAAA
1 GAAGAAAA
42260713 AAATAAGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (22 bp):
GAAGAAAAGAAGGAAGGAAGAA
Found at i:42261069 original size:21 final size:21
Alignment explanation
Indices: 42261045--42261088 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
42261035 TTACAAACAC
*
42261045 AAAATTACAATATTCATATAA
1 AAAATTACAATATTCATACAA
42261066 AAAATTACAATATTCATACAA
1 AAAATTACAATATTCATACAA
42261087 AA
1 AA
42261089 TACTAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATTACAATATTCATACAA
Found at i:42261141 original size:19 final size:19
Alignment explanation
Indices: 42261122--42261159 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
42261112 AAATTTAATT
42261122 ATAAAATAATTACAATATTA
1 ATAAAA-AATTACAATATTA
*
42261142 ATACAAAATTACAATATT
1 ATAAAAAATTACAATATT
42261160 CATTGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAAATTACAATATTA
Done.