Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 121 of 344
Found at i:40988350 original size:120 final size:119
Alignment explanation
Indices: 40988098--40988355 Score: 380
Period size: 120 Copynumber: 2.2 Consensus size: 119
40988088 AACCCAAGTA
* *
40988098 CCTTCGAAAT-TTAGCCGGATATAGCAACTCGCACGAATGCCTTCGGGACTTAGCCCGGACATAA
1 CCTTCG-AATCTTAGCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGACATAA
*
40988162 TCACTAGCACAAATGCCTTCAGGACTTAGCCCGGATATAGTCACTAGCACAAATG
65 TCACTAGCACAAATGCCTTCAGGACTTAGCCCGGATATAATCACTAGCACAAATG
* * *
40988217 CCTTTGAGA-CTTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGA-ATCTTAG-CCGGATAT-AGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGACAT
40988280 AATCACTAGCACAAATGCCTTC-GGATCTTAGCCCGGATATAATCACTAGCACAAATG
63 AATCACTAGCACAAATGCCTTCAGGA-CTTAGCCCGGATATAATCACTAGCACAAATG
40988337 CCTTCGAATCTTAGTCCGG
1 CCTTCGAATCTTAG-CCGG
40988356 TTATCATTCG
Statistics
Matches: 125, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
118 1 0.01
119 14 0.11
120 108 0.86
121 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (119 bp):
CCTTCGAATCTTAGCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGACATAAT
CACTAGCACAAATGCCTTCAGGACTTAGCCCGGATATAATCACTAGCACAAATG
Found at i:40991264 original size:27 final size:27
Alignment explanation
Indices: 40991219--40991451 Score: 287
Period size: 27 Copynumber: 8.6 Consensus size: 27
40991209 TTATCCCACG
* *
40991219 AGGGTATCTCGGTAATTCTACCCTACA
1 AGGGTATTTCAGTAATTCTACCCTACA
*
40991246 AGGGTATTTCAGTATTTCTACCCTACA
1 AGGGTATTTCAGTAATTCTACCCTACA
40991273 AGGGTATTTC-GATAATTCTACCCTACA
1 AGGGTATTTCAG-TAATTCTACCCTACA
* *
40991300 GGGGTATTTC-GATAATTCTACCTTACA
1 AGGGTATTTCAG-TAATTCTACCCTACA
40991327 AGGGTATTTCAGTAATTCTACCCTACA
1 AGGGTATTTCAGTAATTCTACCCTACA
*
40991354 AGGGTATTTCGGTAATTCTA-CCTA-A
1 AGGGTATTTCAGTAATTCTACCCTACA
* *
40991379 CAGAGGTATTTTAGTAATTCTACCTTAC-
1 -AG-GGTATTTCAGTAATTCTACCCTACA
*
40991407 AGAGGTATTTCAGTAATTCTACCTTACA
1 AG-GGTATTTCAGTAATTCTACCCTACA
* *
40991435 GGGGTATTTTAGTAATT
1 AGGGTATTTCAGTAATT
40991452 TTACAAATCA
Statistics
Matches: 184, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.01
26 7 0.04
27 171 0.93
28 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTCTACCCTACA
Found at i:40991339 original size:81 final size:81
Alignment explanation
Indices: 40991220--40991443 Score: 319
Period size: 81 Copynumber: 2.8 Consensus size: 81
40991210 TATCCCACGA
* * * *
40991220 GGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGA
1 GGGTATTTCGATAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGA
40991285 TAATTCTACCCT-ACAG
66 TAATTCTA-CCTAACAG
*
40991301 GGGTATTTCGATAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGG
1 GGGTATTTCGATAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGA
40991366 TAATTCTACCTAACAG
66 TAATTCTACCTAACAG
* * * *
40991382 AGGTATTT-TAGTAATTCTACCTTAC-AGAGGTATTTCAGTAATTCTACCTTACAGGGGTATTT
1 GGGTATTTCGA-TAATTCTACCTTACAAG-GGTATTTCAGTAATTCTACCCTACAAGGGTATTT
40991444 TAGTAATTTT
Statistics
Matches: 131, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
80 6 0.05
81 125 0.95
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (81 bp):
GGGTATTTCGATAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGA
TAATTCTACCTAACAG
Found at i:40991463 original size:27 final size:27
Alignment explanation
Indices: 40991433--40991533 Score: 132
Period size: 27 Copynumber: 3.7 Consensus size: 27
40991423 TTCTACCTTA
*
40991433 CAGGGGTATTTTAGTAATTTTACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAT
* *
40991460 CAGGGGTATTTGGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAT
* *
40991487 CAGGGGTATTTTGGTAATTTTGCTAAT
1 CAGGGGTATTTTGGTAATTTTACAAAT
*
40991514 C-GAGGGTATTTTTGTAATTT
1 CAG-GGGTATTTTGGTAATTT
40991534 GGTGAACTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
26 1 0.02
27 64 0.98
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.42
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAT
Found at i:40991468 original size:54 final size:54
Alignment explanation
Indices: 40991230--40991505 Score: 272
Period size: 54 Copynumber: 5.1 Consensus size: 54
40991220 GGGTATCTCG
* * * * * *
40991230 GTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGTA-TTTC
1 GTAATTCTACCATACAGGGGTATTTCAGTAATTCTACCTTACAGGGGTATTTTA
* * *
40991283 GATAATTCTACCCTACAGGGGTATTTC-GATAATTCTACCTTACAAGGGTATTTCA
1 G-TAATTCTACCATACAGGGGTATTTCAG-TAATTCTACCTTACAGGGGTATTTTA
* * * * *
40991338 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTAACAGAGGTATTTTA
1 GTAATTCTACCATACAGGGGTATTTCAGTAATTCTACCTTACAGGGGTATTTTA
* *
40991392 GTAATTCTACCTTACAGAGGTATTTCAGTAATTCTACCTTACAGGGGTATTTTA
1 GTAATTCTACCATACAGGGGTATTTCAGTAATTCTACCTTACAGGGGTATTTTA
* * ** * ** *
40991446 GTAATTTTA-CAAATCAGGGGTATTTGGGTAATTTTA-CAAACCAGGGGTATTTTG
1 GTAATTCTACCATA-CAGGGGTATTTCAGTAATTCTACCTTA-CAGGGGTATTTTA
40991500 GTAATT
1 GTAATT
40991506 TTGCTAATCG
Statistics
Matches: 191, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
53 6 0.03
54 181 0.95
55 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (54 bp):
GTAATTCTACCATACAGGGGTATTTCAGTAATTCTACCTTACAGGGGTATTTTA
Found at i:40991477 original size:81 final size:80
Alignment explanation
Indices: 40991220--40991478 Score: 299
Period size: 81 Copynumber: 3.2 Consensus size: 80
40991210 TATCCCACGA
* * * *
40991220 GGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGTA-TTTCG
1 GGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTTAG
**
40991284 ATAATTCTACCCTACAG
66 -TAATTCTACAAT-CAG
* **
40991301 GGGTATTTCGATAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGG
1 GGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTTAG
40991366 TAATTCTACCTAA-CAG
66 TAATTCTA-C-AATCAG
* ** * *
40991382 AGGTATTTTAGTAATTCTACCTTAC-AGAGGTATTTCAGTAATTCTACCTTACAGGGGTATTTTA
1 GGGTATTTCGGTAATTCTACCTTACAAG-GGTATTTCAGTAATTCTACCCTACAAGGGTATTTTA
*
40991446 GTAATTTTACAAATCAG
65 GTAATTCTAC-AATCAG
*
40991463 GGGTATTTGGGTAATT
1 GGGTATTTCGGTAATT
40991479 TTACAAACCA
Statistics
Matches: 152, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
80 5 0.03
81 143 0.94
82 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (80 bp):
GGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTTAG
TAATTCTACAATCAG
Found at i:40994392 original size:27 final size:27
Alignment explanation
Indices: 40994362--40994566 Score: 277
Period size: 27 Copynumber: 7.6 Consensus size: 27
40994352 TATCCCACGA
* *
40994362 GGGTATCTCGGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTATAG
* * *
40994389 GGGTATTTCAGTATTTCTACCCTACAA
1 GGGTATTTCAGTAATTCTACCCTATAG
* *
40994416 GGGTATTTC-GATAATTCTACCTTACAG
1 GGGTATTTCAG-TAATTCTACCCTATAG
40994443 GGGTATTTCAGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTATAG
** * *
40994470 GGGTATTTTGGTAATTCTACCTTACAG
1 GGGTATTTCAGTAATTCTACCCTATAG
*
40994497 GGGTATTTTAGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTATAG
*
40994524 GGGTATTTCAGTAATTCTACCTTATAG
1 GGGTATTTCAGTAATTCTACCCTATAG
40994551 GGGTATTTCAGTAATT
1 GGGTATTTCAGTAATT
40994567 TTACAAATCA
Statistics
Matches: 157, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 155 0.99
28 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCCTATAG
Found at i:40994582 original size:27 final size:27
Alignment explanation
Indices: 40994525--40994639 Score: 76
Period size: 27 Copynumber: 4.3 Consensus size: 27
40994515 ACCCTATAGG
* ** *
40994525 GGTATTTCAGTAATTCTACCTTAT-AGG
1 GGTATTTCAGTAATTTTA-CAAATCAGA
40994552 GGTATTTCAGTAATTTTACAAATCAGA
1 GGTATTTCAGTAATTTTACAAATCAGA
* *
40994579 GGTACTTT-GGTAATTTTACAAA-CTAGG
1 GGTA-TTTCAGTAATTTTACAAATC-AGA
** * *
40994606 GGTATTTTGGTAATTTTGCTAATC-GA
1 GGTATTTCAGTAATTTTACAAATCAGA
40994632 GGGTATTT
1 -GGTATTT
40994640 TTTTAATTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
26 8 0.11
27 61 0.84
28 4 0.05
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (27 bp):
GGTATTTCAGTAATTTTACAAATCAGA
Found at i:40994592 original size:81 final size:80
Alignment explanation
Indices: 40994362--40994593 Score: 263
Period size: 81 Copynumber: 2.9 Consensus size: 80
40994352 TATCCCACGA
* * *
40994362 GGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCAGT-ATTTCTACCCTACA-AGGGTATTTC
1 GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCAGTAATTT-TACCATACAGA-GGTATTT-
* *
40994425 GATAATTCTACCTTACAG
63 GGTAATTCTACCCTACAG
** * * * *
40994443 GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTTGGTAATTCTACCTTACAGGGGTATTTTAG
1 GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCAGTAATTTTACCATACAGAGGTA-TTTGG
*
40994508 TAATTCTACCCTATAG
65 TAATTCTACCCTACAG
* *
40994524 GGGTATTTCAGTAATTCTACCTTATAGGGGTATTTCAGTAATTTTA-CAAATCAGAGGTACTTTG
1 GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCAGTAATTTTACCATA-CAGAGGTA-TTTG
40994588 GTAATT
64 GTAATT
40994594 TTACAAACTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
80 2 0.02
81 119 0.94
82 6 0.05
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (80 bp):
GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCAGTAATTTTACCATACAGAGGTATTTGGT
AATTCTACCCTACAG
Found at i:40994640 original size:27 final size:27
Alignment explanation
Indices: 40994551--40994702 Score: 157
Period size: 27 Copynumber: 5.6 Consensus size: 27
40994541 TACCTTATAG
** *
40994551 GGGTATTTCAGTAATTTTACAAATC-A
1 GGGTATTTTGGTAATTTTACTAATCGA
* * *
40994577 GAGGTACTTTGGTAATTTTAC-AAACTA
1 G-GGTATTTTGGTAATTTTACTAATCGA
*
40994604 GGGGTATTTTGGTAATTTTGCTAATCGA
1 -GGGTATTTTGGTAATTTTACTAATCGA
**
40994632 GGGTATTTTTTTAATTTTTA-TAATCGA
1 GGGTATTTTGGTAA-TTTTACTAATCGA
**
40994659 GGGTATTTTGGTAATTTTGTTAATCGA
1 GGGTATTTTGGTAATTTTACTAATCGA
40994686 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
40994703 GATAAACTAA
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
26 8 0.08
27 89 0.84
28 9 0.08
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.45
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACTAATCGA
Found at i:41003103 original size:5 final size:5
Alignment explanation
Indices: 41003093--41003135 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
41003083 GAATACCTTG
41003093 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCT
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCT
41003136 CTTTCAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCTTC
Found at i:41005841 original size:39 final size:41
Alignment explanation
Indices: 41005750--41005841 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 41
41005740 TGTCACTAAG
* * *
41005750 ATGGGCTCAGG-CCCACACTGATACTGATACTGATACTGTA
1 ATGGGCTAAGGCCCCACACTGAAACTGATACCGATACTGTA
*
41005790 ATGGGCTAAGGCCCCA-ACTGAAACTGA-ACCGTTACTG-A
1 ATGGGCTAAGGCCCCACACTGAAACTGATACCGATACTGTA
*
41005828 ATTGGGCTTAGGCC
1 A-TGGGCTAAGGCC
41005842 TAGACTGTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 2 0.04
39 19 0.42
40 20 0.44
41 4 0.09
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (41 bp):
ATGGGCTAAGGCCCCACACTGAAACTGATACCGATACTGTA
Found at i:41010690 original size:30 final size:30
Alignment explanation
Indices: 41010656--41010753 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 30
41010646 TAAACTAAAA
41010656 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
41010686 TGAGCTGAGGC-TAAACTCCT-AGGCTGAGGT
1 TGAGCT-AAGCTTTAGCTCGTGA-GCTAAAGT
* *
41010716 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
41010746 TGAGCTAA
1 TGAGCTAA
41010754 AAGTGAGCTC
Statistics
Matches: 49, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
29 3 0.06
30 40 0.82
31 6 0.12
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:41013015 original size:30 final size:30
Alignment explanation
Indices: 41012950--41013017 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
41012940 TCTCACTCGA
*
41012950 TTCTTTTTCACTCTCAAATTTCTTTTCGTT
1 TTCTTTTTCAATCTCAAATTTCTTTTCGTT
* * *
41012980 CTCTTTTTCAATCTC-ATTTTCTTTTTCTTT
1 TTCTTTTTCAATCTCAAATTTC-TTTTCGTT
41013010 TTCTTTTT
1 TTCTTTTT
41013018 GATTTTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.10, C:0.22, G:0.01, T:0.66
Consensus pattern (30 bp):
TTCTTTTTCAATCTCAAATTTCTTTTCGTT
Found at i:41013096 original size:5 final size:5
Alignment explanation
Indices: 41013086--41013142 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
41013076 TTCTTGCCTC
*
41013086 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
41013133 TCTTT TCTTT
1 TCTTT TCTTT
41013143 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:41013126 original size:15 final size:14
Alignment explanation
Indices: 41013086--41013142 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
41013076 TTCTTGCCTC
*
41013086 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
41013101 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
41013116 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
41013133 TCTTTTCTTT
1 TCTTTTCTTT
41013143 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:41013143 original size:21 final size:21
Alignment explanation
Indices: 41013086--41013153 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
41013076 TTCTTGCCTC
* *
41013086 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
41013107 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
41013128 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
41013148 CTCTTT
1 -TCTTT
41013154 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:41014238 original size:82 final size:80
Alignment explanation
Indices: 41014093--41014245 Score: 180
Period size: 82 Copynumber: 1.9 Consensus size: 80
41014083 TCTTATATAC
* * ** *
41014093 TTTTTTTTATAACTACTAAAATGATAATTACAAAACAATACTCGAATCTCACGAAGTAGTTTTTT
1 TTTTTTTTATAACTACTAAAAAGATAAATACAAAACAATACTCGAATCTCACGAAACAATTTTTT
*
41014158 TGTATATATATATTT
66 TCTATATATATATTT
* ** * * *
41014173 TTTTTGTTTATAAACTACTAAAAAGGTAAATACAGTATAATACTTGAATTTCACGAAACAATTTT
1 TTTTT-TTTAT-AACTACTAAAAAGATAAATACAAAACAATACTCGAATCTCACGAAACAATTTT
41014238 TTTCTATA
64 TTTCTATA
41014246 CTATTTTTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
80 5 0.08
81 5 0.08
82 49 0.83
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (80 bp):
TTTTTTTTATAACTACTAAAAAGATAAATACAAAACAATACTCGAATCTCACGAAACAATTTTTT
TCTATATATATATTT
Found at i:41015338 original size:17 final size:16
Alignment explanation
Indices: 41015279--41015338 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
41015269 GAGACAGCCA
* *
41015279 CCATACATGCATTTAAG
1 CCATTCATGCATTT-AT
41015296 CCATTCATGCATTCTAT
1 CCATTCATGCATT-TAT
*
41015313 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTT-AT
41015330 CCATTCATG
1 CCATTCATG
41015339 GACTAGACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.11
17 27 0.77
18 4 0.11
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (16 bp):
CCATTCATGCATTTAT
Found at i:41015769 original size:30 final size:30
Alignment explanation
Indices: 41015735--41015831 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
41015725 TAAACTAAAA
*
41015735 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCCTGAGCTAAAGT
* * * * *
41015765 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCCTGAGCTAAAGT
* * *
41015795 TGAGCTAAGGTTTAGCTCTTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCCTGAGCT-AAAGT
41015825 TGAGCTA
1 TGAGCTA
41015832 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCCTGAGCTAAAGT
Found at i:41021543 original size:36 final size:36
Alignment explanation
Indices: 41021496--41021570 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
41021486 ATCGAATGAG
*
41021496 GCTGATGTGTTTTAAAAACTTCAAAACTCATACCTT
1 GCTGATATGTTTTAAAAACTTCAAAACTCATACCTT
*
41021532 GCTGATATGTTTTAAAGACTTCAAAACTCATACCTT
1 GCTGATATGTTTTAAAAACTTCAAAACTCATACCTT
41021568 GCT
1 GCT
41021571 TACCTTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
GCTGATATGTTTTAAAAACTTCAAAACTCATACCTT
Found at i:41024241 original size:23 final size:22
Alignment explanation
Indices: 41024189--41024241 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41024179 TCCACGTCTT
*
41024189 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
41024211 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
41024234 TTTCTTTT
1 TTTCTTTT
41024242 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:41029017 original size:20 final size:19
Alignment explanation
Indices: 41028994--41029058 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41028984 AAGCTCAAAC
41028994 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41029014 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41029034 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41029054 GAGCT
1 GAGCT
41029059 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41029278 original size:40 final size:42
Alignment explanation
Indices: 41029208--41029295 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 42
41029198 TTGCTCAATA
* *
41029208 TCTTTTCTCTCTTCAGACTCAATTTCTTTTTC-TTCTCACAT
1 TCTTTTCACTCTTCAGACTCAATCTCTTTTTCTTTCTCACAT
* * * *
41029249 TCTTTTCACTC-TCAGTCTCGATCTCTTTTTCTTTTTCACTT
1 TCTTTTCACTCTTCAGACTCAATCTCTTTTTCTTTCTCACAT
41029290 TCTTTT
1 TCTTTT
41029296 TCAATTTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 17 0.43
41 23 0.57
ACGTcount: A:0.11, C:0.28, G:0.03, T:0.57
Consensus pattern (42 bp):
TCTTTTCACTCTTCAGACTCAATCTCTTTTTCTTTCTCACAT
Found at i:41029291 original size:12 final size:12
Alignment explanation
Indices: 41029276--41029310 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
41029266 TCGATCTCTT
*
41029276 TTTCTTTTTCAC
1 TTTCTTTTTCAA
41029288 TTTCTTTTTCAA
1 TTTCTTTTTCAA
41029300 TTTCATTTTTC
1 TTTC-TTTTTC
41029311 TTTTTCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:41029295 original size:18 final size:19
Alignment explanation
Indices: 41029272--41029317 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
41029262 AGTCTCGATC
*
41029272 TCTTTTTCTTTTTCA-CTT
1 TCTTTTTCTATTTCATCTT
* *
41029290 TCTTTTTCAATTTCATTTT
1 TCTTTTTCTATTTCATCTT
41029309 TCTTTTTCT
1 TCTTTTTCT
41029318 CATTCTCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.72
Consensus pattern (19 bp):
TCTTTTTCTATTTCATCTT
Found at i:41031974 original size:20 final size:20
Alignment explanation
Indices: 41031928--41031965 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41031918 AGCTGAAAAG
41031928 AAGCT-AAATCAAGCTCAAAT
1 AAGCTGAAA-CAAGCTCAAAT
41031948 AAGCTGAAACAAGCTCAA
1 AAGCTGAAACAAGCTCAA
41031966 GTGAGCTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.50, C:0.21, G:0.13, T:0.16
Consensus pattern (20 bp):
AAGCTGAAACAAGCTCAAAT
Found at i:41039777 original size:10 final size:10
Alignment explanation
Indices: 41039762--41039823 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
41039752 TTTGAACCAT
*
41039762 TACCAATTCG
1 TACCAATTCA
*
41039772 TACCAAATACCA
1 TACC-AAT-TCA
*
41039784 TACCATTTCA
1 TACCAATTCA
41039794 TACCAATTCCA
1 TACCAATT-CA
* *
41039805 TACCATTTCG
1 TACCAATTCA
41039815 TACCAATTC
1 TACCAATTC
41039824 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:41039807 original size:21 final size:21
Alignment explanation
Indices: 41039762--41039824 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
41039752 TTTGAACCAT
* *
41039762 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
41039784 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
41039805 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
41039825 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:41044667 original size:10 final size:10
Alignment explanation
Indices: 41044652--41044713 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
41044642 TTTGAACCAT
*
41044652 TACCAATTCG
1 TACCAATTCA
*
41044662 TACCAAATACCA
1 TACC-AAT-TCA
*
41044674 TACCATTTCA
1 TACCAATTCA
41044684 TACCAATTCCA
1 TACCAATT-CA
* *
41044695 TACCATTTCG
1 TACCAATTCA
41044705 TACCAATTC
1 TACCAATTC
41044714 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:41044697 original size:21 final size:21
Alignment explanation
Indices: 41044652--41044714 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
41044642 TTTGAACCAT
* *
41044652 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
41044674 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
41044695 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
41044715 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:41045048 original size:13 final size:13
Alignment explanation
Indices: 41045032--41045056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41045022 AAGGAGTTCG
41045032 AAAAAAAAATTGA
1 AAAAAAAAATTGA
41045045 AAAAAAAAATTG
1 AAAAAAAAATTG
41045057 CATACGGTTT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:41047957 original size:22 final size:22
Alignment explanation
Indices: 41047906--41047971 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
41047896 GGTATTTGGG
* *
41047906 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
41047927 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
41047949 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
41047972 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:41051187 original size:22 final size:22
Alignment explanation
Indices: 41051159--41051202 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41051149 TTTTGAACCA
41051159 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41051181 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41051203 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41053143 original size:17 final size:17
Alignment explanation
Indices: 41053118--41053164 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
41053108 TCTCTTTTCA
*
41053118 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
41053135 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
*
41053152 TTCTTTTCTTTTG
1 TTCTTTTTTTTTG
41053165 TATTGTCGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:41055374 original size:20 final size:19
Alignment explanation
Indices: 41055351--41055415 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41055341 AAGCTCAAAC
41055351 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41055371 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41055391 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41055411 GAGCT
1 GAGCT
41055416 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41056627 original size:30 final size:30
Alignment explanation
Indices: 41056593--41056689 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
41056583 AGCTCACTCC
41056593 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
41056623 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
41056653 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
41056683 TAGCTCA
1 TAGCTCA
41056690 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:41059308 original size:37 final size:37
Alignment explanation
Indices: 41059257--41059327 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
41059247 CATTCTTGTA
41059257 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
41059294 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
41059328 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:41059327 original size:6 final size:6
Alignment explanation
Indices: 41059267--41059316 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
41059257 AAGAGAAAAC
*
41059267 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
41059316 A
1 A
41059317 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:41059454 original size:30 final size:30
Alignment explanation
Indices: 41059420--41059476 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41059410 AAAAAGAAAA
* *
41059420 TGAAAAAGGAA-ATGAAAAGAAATTTGAGAG
1 TGAAAAA-GAATATGAAAAAAAAATTGAGAG
41059450 TGAAAAAGAATATGAAAAAAAAATTGA
1 TGAAAAAGAATATGAAAAAAAAATTGA
41059477 AACAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (30 bp):
TGAAAAAGAATATGAAAAAAAAATTGAGAG
Found at i:41060012 original size:30 final size:30
Alignment explanation
Indices: 41059978--41060074 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
41059968 AGCTCACTCC
41059978 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
41060008 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
41060038 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
41060068 TAGCTCA
1 TAGCTCA
41060075 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:41062494 original size:21 final size:21
Alignment explanation
Indices: 41062459--41062515 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
41062449 TTGGTATTTG
** *
41062459 GGAATTGGTTTGAAATAGTCT
1 GGAATTGGTACGAAATAGTAT
*
41062480 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATAGTAT
*
41062501 GGTATTTGGTACGAA
1 GG-AATTGGTACGAA
41062516 TTGGTAATGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATAGTAT
Found at i:41062510 original size:22 final size:23
Alignment explanation
Indices: 41062484--41062526 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
41062474 TAGTCTGGAA
41062484 TTGGTACGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
*
41062506 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGTAATGGT
41062527 TCAAAAGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.37
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:41065203 original size:30 final size:31
Alignment explanation
Indices: 41065169--41065234 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
41065159 GAGCTCAAAC
* *
41065169 GAGCTAAAACA-AGCTCAAAAGAG-TTGAATT
1 GAGCTAAAACAGAGCTC-AAAGAGCTGGAAAT
*
41065199 GAGCT-AGACAGAGCTCAAAGAGCTGGAAAT
1 GAGCTAAAACAGAGCTCAAAGAGCTGGAAAT
41065229 GAGCTA
1 GAGCTA
41065235 GGATCAGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.17
Consensus pattern (31 bp):
GAGCTAAAACAGAGCTCAAAGAGCTGGAAAT
Found at i:41085151 original size:13 final size:12
Alignment explanation
Indices: 41085118--41085149 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
41085108 TTGTAGATTC
41085118 AAAAAAAATCGA
1 AAAAAAAATCGA
41085130 AAAAAAAATCGA
1 AAAAAAAATCGA
41085142 AAAAAAAA
1 AAAAAAAA
41085150 ATATTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:41086834 original size:11 final size:11
Alignment explanation
Indices: 41086818--41086859 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
41086808 TTGTAGATTC
41086818 AAAAAAAATCA
1 AAAAAAAATCA
* *
41086829 AAAAAAATTGA
1 AAAAAAAATCA
*
41086840 AAAAAAAATCG
1 AAAAAAAATCA
41086851 AAAAAAAAT
1 AAAAAAAAT
41086860 ATTTTGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:41086835 original size:12 final size:12
Alignment explanation
Indices: 41086818--41086858 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
41086808 TTGTAGATTC
41086818 AAAAAAAATC--
1 AAAAAAAATCGA
*
41086828 AAAAAAAATTGA
1 AAAAAAAATCGA
41086840 AAAAAAAATCGA
1 AAAAAAAATCGA
41086852 AAAAAAA
1 AAAAAAA
41086859 TATTTTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:41088560 original size:12 final size:11
Alignment explanation
Indices: 41088524--41088565 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
41088514 TTGTAGATTC
*
41088524 AAAAAAATAAA
1 AAAAAAATGAA
41088535 AAAAAAATTG-A
1 AAAAAAA-TGAA
41088546 AAAAAAATCGAA
1 AAAAAAAT-GAA
41088558 AAAAAAAT
1 AAAAAAAT
41088566 ATTTTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 1 0.04
11 16 0.59
12 10 0.37
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:41090250 original size:11 final size:11
Alignment explanation
Indices: 41090234--41090276 Score: 77
Period size: 11 Copynumber: 3.8 Consensus size: 11
41090224 TTTAGATTCA
41090234 AAAAAAAATCG
1 AAAAAAAATCG
41090245 AAAAAAAAATCG
1 -AAAAAAAATCG
41090257 AAAAAAAATCG
1 AAAAAAAATCG
41090268 AAAAAAAAT
1 AAAAAAAAT
41090277 ATTTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.09
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:41090250 original size:12 final size:12
Alignment explanation
Indices: 41090233--41090275 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
41090223 TTTTAGATTC
41090233 AAAAAAAAATCG
1 AAAAAAAAATCG
41090245 AAAAAAAAATCG
1 AAAAAAAAATCG
41090257 -AAAAAAAATCG
1 AAAAAAAAATCG
41090268 AAAAAAAA
1 AAAAAAAA
41090276 TATTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAAAAATCG
Found at i:41095966 original size:21 final size:20
Alignment explanation
Indices: 41095940--41095996 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
41095930 TATTGGATTT
*
41095940 AAAAAAAAGAGAAGAAATTCA
1 AAAAAAAAGA-AAGAAAATCA
*
41095961 AAAAAAAAGAAAAAAAATCA
1 AAAAAAAAGAAAGAAAATCA
41095981 AAAAAAAA-AAAGAAAA
1 AAAAAAAAGAAAGAAAA
41095997 AAAAAGGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 7 0.21
20 16 0.48
21 10 0.30
ACGTcount: A:0.82, C:0.04, G:0.09, T:0.05
Consensus pattern (20 bp):
AAAAAAAAGAAAGAAAATCA
Found at i:41095975 original size:10 final size:10
Alignment explanation
Indices: 41095960--41096002 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
41095950 GAAGAAATTC
41095960 AAAAAAAAAG
1 AAAAAAAAAG
*
41095970 AAAAAAAATCAAA
1 -AAAAAAA--AAG
41095983 AAAAAAAAAG
1 AAAAAAAAAG
41095993 AAAAAAAAAG
1 AAAAAAAAAG
41096003 GTGAGCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 12 0.43
11 7 0.25
12 7 0.25
13 2 0.07
ACGTcount: A:0.88, C:0.02, G:0.07, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:41095987 original size:14 final size:13
Alignment explanation
Indices: 41095960--41096001 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
41095950 GAAGAAATTC
*
41095960 AAAAAAA-AAGAA
1 AAAAAAACAAAAA
*
41095972 AAAAAATCAAAAA
1 AAAAAAACAAAAA
*
41095985 AAAAAAAGAAAAA
1 AAAAAAACAAAAA
41095998 AAAA
1 AAAA
41096002 GGTGAGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.90, C:0.02, G:0.05, T:0.02
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:41097957 original size:20 final size:20
Alignment explanation
Indices: 41097932--41097975 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41097922 GGGTTAAGAT
*
41097932 TGAGTTGAATTGAGCTTGAG
1 TGAGTTGAATTGAGCTCGAG
*
41097952 TGAGTTGACTTGAGCTCGAG
1 TGAGTTGAATTGAGCTCGAG
41097972 TGAG
1 TGAG
41097976 CTGGAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGTTGAATTGAGCTCGAG
Found at i:41099702 original size:47 final size:47
Alignment explanation
Indices: 41099625--41099729 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
41099615 TTGTCTTTTC
* *
41099625 TTTCTTTTTCAATTTTCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTCTCTTT-CTCACATCCTTT-TTCAATCTCAA
* *
41099673 TTTCTTTTTCGATTTCTTTCTCTTT-TCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTT-TCTCTCTTTCTCACATCCTTTTTCAATCTCAA
41099720 TTTCTTTTTC
1 TTTCTTTTTC
41099730 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 26 0.51
48 18 0.35
49 7 0.14
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (47 bp):
TTTCTTTTTCAATTTTCTCTCTTTCTCACATCCTTTTTCAATCTCAA
Found at i:41100866 original size:28 final size:28
Alignment explanation
Indices: 41100835--41100900 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 28
41100825 TTAAACTTGA
41100835 TTTTTTTTTGCTC-ACCTTTTTTTT-CTTT
1 TTTTTTTTTGCTCGA--TTTTTTTTACTTT
41100863 TTTTTTTTTGCTCGATTTTTTTTCACTTT
1 TTTTTTTTTGCTCGATTTTTTTT-ACTTT
41100892 TTTTTTTTT
1 TTTTTTTTT
41100901 TTTTCAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 8 0.23
28 13 0.37
29 14 0.40
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.77
Consensus pattern (28 bp):
TTTTTTTTTGCTCGATTTTTTTTACTTT
Found at i:41100915 original size:34 final size:33
Alignment explanation
Indices: 41100855--41100932 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 33
41100845 CTCACCTTTT
* *
41100855 TTTTCTTTTTTTTTTTTGCTCGATTTTTTTTC-AC
1 TTTT-TTTTTTTTTTTTGCTC-AATTTTTTTCGAA
41100889 TTTTTTTTTTTTTTTT-CAATCAATTTTTTTCGAA
1 TTTTTTTTTTTTTTTTGC--TCAATTTTTTTCGAA
41100923 TTTTTTTTTT
1 TTTTTTTTTT
41100933 GATTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 1 0.03
33 21 0.54
34 17 0.44
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.76
Consensus pattern (33 bp):
TTTTTTTTTTTTTTTTGCTCAATTTTTTTCGAA
Found at i:41112805 original size:40 final size:40
Alignment explanation
Indices: 41112745--41113003 Score: 407
Period size: 40 Copynumber: 6.5 Consensus size: 40
41112735 TTCGGATGAC
*
41112745 ATCCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
41112785 ATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* * * *
41112824 ATCCGGGCTAAGCCCCGAAGGAATTTGTGCTATTGAATAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
41112864 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
41112904 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
41112944 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAT
*
41112984 ATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
41113004 TACTTGGGTT
Statistics
Matches: 206, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
39 52 0.25
40 152 0.74
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
Found at i:41112992 original size:119 final size:119
Alignment explanation
Indices: 41112745--41113003 Score: 414
Period size: 119 Copynumber: 2.2 Consensus size: 119
41112735 TTCGGATGAC
*
41112745 ATCCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATT
*
41112810 GTGCTAGTGACTATATCCGGGCTAAGCCCCGAAGGAATTTGTGCTATTGAATAT
66 GTGCTAGTGACTATATCCGGGCTAAGCCCCGAAGGAATTTGTGCGATTGAATAT
*
41112864 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA-T
* * * *
41112929 TGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTAT
65 TGTGCTAGTGACTATATCCGGGCTAAGCCCCGAAGGAATTTGTGCGA-TTGAATAT
*
41112984 ATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
41113004 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
119 76 0.58
120 51 0.39
121 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (119 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATT
GTGCTAGTGACTATATCCGGGCTAAGCCCCGAAGGAATTTGTGCGATTGAATAT
Found at i:41124671 original size:21 final size:22
Alignment explanation
Indices: 41124645--41124690 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
41124635 GCACCAATCA
*
41124645 CATACTCAT-AGAATAATCAAG
1 CATACTCATAAGAATAATAAAG
*
41124666 CATACTCATAATAATAATAAAG
1 CATACTCATAAGAATAATAAAG
41124688 CAT
1 CAT
41124691 TAACATTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (22 bp):
CATACTCATAAGAATAATAAAG
Found at i:41131775 original size:42 final size:43
Alignment explanation
Indices: 41131728--41131845 Score: 114
Period size: 43 Copynumber: 2.8 Consensus size: 43
41131718 TGTGGTATCA
* * **
41131728 TGTAAGACCATGTTTGGGACATTGGCATCGTATTTGATTTC-G
1 TGTAAGACCATGTCTGGGACATTGGCATCGTATTTAATGACAG
* * * *
41131770 TGTAAGACCCTATCTAGGACAATGGCATCGATATTTAATGACAG
1 TGTAAGACCATGTCTGGGACATTGGCATCG-TATTTAATGACAG
* * *
41131814 T-TAAGACCACGTCTGGGACGTTGGCATTGTAT
1 TGTAAGACCATGTCTGGGACATTGGCATCGTAT
41131846 GAGCTTTCTG
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
42 28 0.47
43 29 0.49
44 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTATTTAATGACAG
Found at i:41135881 original size:40 final size:40
Alignment explanation
Indices: 41135826--41135994 Score: 284
Period size: 40 Copynumber: 4.2 Consensus size: 40
41135816 TATGTGCACA
*
41135826 GCATTCGTGTGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
41135866 GCATTCATGCGGGTTATTATAACCGGGCTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
41135906 GCATTCGTGCGGGTTATTATAACCGGGATAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
41135946 GCATTCGTGCGAGTTATTATTACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
41135986 GCATTCGTG
1 GCATTCGTG
41135995 TTGGTTGTTA
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 121 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:41136024 original size:80 final size:80
Alignment explanation
Indices: 41135826--41136024 Score: 218
Period size: 80 Copynumber: 2.5 Consensus size: 80
41135816 TATGTGCACA
* * * ** * *
41135826 GCATTCGTGTGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCATGCGGGTTATTATAACCG
1 GCATTCGTGCGGGTTATTACAACCGAGACAAATCCCGAAGGCATTCATGCGAGTTATTATAACCG
41135891 GGCTAAGTCCCGAAG
66 GGCTAAGTCCCGAAG
* * * * * *
41135906 GCATTCGTGCGGGTTATTATAACCGGGATAAGTCCCGAAGGCATTCGTGCGAGTTATTATTACCG
1 GCATTCGTGCGGGTTATTACAACCGAGACAAATCCCGAAGGCATTCATGCGAGTTATTATAACCG
*
41135971 GGTTAAGTCCCGAAG
66 GGCTAAGTCCCGAAG
** * * * *
41135986 GCATTCGTGTTGGTTGTTACATCCGAGCCAAATTCCGAA
1 GCATTCGTGCGGGTTATTACAACCGAGACAAATCCCGAA
41136025 AGTATTTATA
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 103 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (80 bp):
GCATTCGTGCGGGTTATTACAACCGAGACAAATCCCGAAGGCATTCATGCGAGTTATTATAACCG
GGCTAAGTCCCGAAG
Found at i:41140919 original size:93 final size:93
Alignment explanation
Indices: 41140760--41140931 Score: 238
Period size: 93 Copynumber: 1.8 Consensus size: 93
41140750 GGATGGTTGA
* * * *
41140760 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCAGGGATACAAACGTCCGAACTCGTTCAGT
41140825 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
41140853 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATACGAACG-CCTGAGCTCGTTCAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCAGGGATACAAACGTCC-GAACTCGTTCAG
* *
41140917 TTGATTTCGAGTTCG
65 TTGAGTCCGAGTTCG
41140932 CTTATGGGCG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
92 2 0.03
93 66 0.97
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCAGGGATACAAACGTCCGAACTCGTTCAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41144164 original size:36 final size:36
Alignment explanation
Indices: 41144117--41144190 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
41144107 GTGATTTTTG
* *
41144117 TTGTTTAATGGTGAAATATGAAATACATGTTTTAGA
1 TTGTTTAATGGTGAAATAGGAAAGACATGTTTTAGA
41144153 TTGTTTAATGGTGAAATAGGAAAGACATGTTTTAGA
1 TTGTTTAATGGTGAAATAGGAAAGACATGTTTTAGA
41144189 TT
1 TT
41144191 AACATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.41
Consensus pattern (36 bp):
TTGTTTAATGGTGAAATAGGAAAGACATGTTTTAGA
Found at i:41156230 original size:71 final size:70
Alignment explanation
Indices: 41156096--41156225 Score: 176
Period size: 71 Copynumber: 1.9 Consensus size: 70
41156086 AGCCAATTTA
* * *
41156096 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATT
41156161 TATCTC
65 TATCTC
* *
41156167 TCTCGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 TCTCGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
41156226 TACATAGTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
68 23 0.43
69 1 0.02
70 1 0.02
71 28 0.53
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (70 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTT
ATCTC
Found at i:41156244 original size:68 final size:70
Alignment explanation
Indices: 41156094--41156251 Score: 171
Period size: 68 Copynumber: 2.3 Consensus size: 70
41156084 CTAGCCAATT
* * *
41156094 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACA
**
41156159 TTTATC
65 CATATC
* * *
41156165 TCTCTCGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTACT
1 TATCTCGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC-
*
41156227 ACATA-G
64 ACATATC
*
41156233 TATCTCGTAGCTTTCTTGT
1 TATCTCGTAGCTCTCTTGT
41156252 ACACATGATG
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
68 40 0.54
69 4 0.05
70 1 0.01
71 29 0.39
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (70 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACAC
ATATC
Found at i:41160765 original size:28 final size:28
Alignment explanation
Indices: 41160725--41160788 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
41160715 TGGGAAGTAG
* *
41160725 TTGGGCCTGATGGGCCATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAACGAGA
*
41160753 TTGGGCCTGATGGGCCATGTGAACGAGA
1 TTGGGCCTGATGGGCCATATGAACGAGA
41160781 TTGGGCCT
1 TTGGGCCT
41160789 AAAGGGGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.38, T:0.27
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATGAACGAGA
Found at i:41161135 original size:27 final size:27
Alignment explanation
Indices: 41161105--41161335 Score: 249
Period size: 27 Copynumber: 8.6 Consensus size: 27
41161095 TAATAAAGAG
41161105 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
41161132 AAATTACCGAAATA-CCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
41161158 AAATTACCGAAACACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
41161185 AAATTACCGAAACACACTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
41161212 AAATTA-TCAAA-ACACCATCGATTTGTA
1 AAATTACTGAAATAC-CC-TCGATTTGTA
** * **
41161239 AAATTACCAAAATACCTTTAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
41161266 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
41161293 AAATTA-TCGAAACACCC-CTGATTTGTA
1 AAATTACT-GAAATACCCTC-GATTTGTA
41161320 AAATTA-TCGAAATACC
1 AAATTACT-GAAATACC
41161336 ATTGTAGTGT
Statistics
Matches: 179, Mismatches: 18, Indels: 14
0.85 0.09 0.07
Matches are distributed among these distances:
25 2 0.01
26 31 0.17
27 140 0.78
28 4 0.02
29 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:41161264 original size:81 final size:80
Alignment explanation
Indices: 41161105--41161335 Score: 318
Period size: 81 Copynumber: 2.9 Consensus size: 80
41161095 TAATAAAGAG
* *
41161105 AAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCTCGATTTGTAAAATTACCGAAA
1 AAATTACTGAAATACCCTCGATTTGTAAAATTATCGAAACACCTCGATTTGTAAAATTACCGAAA
* *
41161170 CACCCTCGATTTGTA
66 TACCCTCAATTTGTA
* * * * *
41161185 AAATTACCGAAACACACTCGATTTGTAAAATTATCAAAACACCATCGATTTGTAAAATTACCAAA
1 AAATTACTGAAATACCCTCGATTTGTAAAATTATCGAAACACC-TCGATTTGTAAAATTACCGAA
* *
41161250 ATACCTTTAATTTGTA
65 ATACCCTCAATTTGTA
* * *
41161266 AAATTACTAAAATACCCTCGATTTGTAAAATTATCGAAACACCCCTGATTTGTAAAATTATCGAA
1 AAATTACTGAAATACCCTCGATTTGTAAAATTATCGAAACACCTC-GATTTGTAAAATTACCGAA
41161331 ATACC
65 ATACC
41161336 ATTGTAGTGT
Statistics
Matches: 130, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
80 38 0.29
81 92 0.71
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (80 bp):
AAATTACTGAAATACCCTCGATTTGTAAAATTATCGAAACACCTCGATTTGTAAAATTACCGAAA
TACCCTCAATTTGTA
Found at i:41161346 original size:27 final size:27
Alignment explanation
Indices: 41161289--41161404 Score: 110
Period size: 27 Copynumber: 4.3 Consensus size: 27
41161279 ACCCTCGATT
* * *
41161289 TGTAAAATTATCGAAACACCCCTG-ATT
1 TGTAAAATTATCGAAATACCCTTGTA-G
*
41161316 TGTAAAATTATCGAAATACCATTGTAG
1 TGTAAAATTATCGAAATACCCTTGTAG
* *
41161343 TGTAAAATTACCAAAATACCCTTGTAG
1 TGTAAAATTATCGAAATACCCTTGTAG
* * *
41161370 TGTAAAATGA-CTGACATACCCCTGTAG
1 TGTAAAATTATC-GAAATACCCTTGTAG
*
41161397 GGTAAAAT
1 TGTAAAAT
41161405 GACTATTTCC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 1 0.01
27 73 0.97
28 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (27 bp):
TGTAAAATTATCGAAATACCCTTGTAG
Found at i:41161377 original size:81 final size:81
Alignment explanation
Indices: 41161105--41161364 Score: 305
Period size: 81 Copynumber: 3.2 Consensus size: 81
41161095 TAATAAAGAG
** * * *
41161105 AAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCTC-GATTTGTAAAATTACCGAA
1 AAATTACCAAAATACCCTCGATTTGTAAAATTATCGAAACACCCCTGATTTGTAAAATTACCGAA
* *
41161169 ACACCCTCG-ATTTGTA
66 ATA-CCTTGTATTTGTA
* * * * * *
41161185 AAATTACCGAAACACACTCGATTTGTAAAATTATCAAAACA-CCATCGATTTGTAAAATTACCAA
1 AAATTACCAAAATACCCTCGATTTGTAAAATTATCGAAACACCCCT-GATTTGTAAAATTACCGA
41161249 AATACCTT-TAATTTGTA
65 AATACCTTGT-ATTTGTA
* *
41161266 AAATTACTAAAATACCCTCGATTTGTAAAATTATCGAAACACCCCTGATTTGTAAAATTATCGAA
1 AAATTACCAAAATACCCTCGATTTGTAAAATTATCGAAACACCCCTGATTTGTAAAATTACCGAA
*
41161331 ATACCATTGTA-GTGTA
66 ATACC-TTGTATTTGTA
41161347 AAATTACCAAAATACCCT
1 AAATTACCAAAATACCCT
41161365 TGTAGTGTAA
Statistics
Matches: 152, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 38 0.25
81 106 0.70
82 6 0.04
83 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
AAATTACCAAAATACCCTCGATTTGTAAAATTATCGAAACACCCCTGATTTGTAAAATTACCGAA
ATACCTTGTATTTGTA
Found at i:41169499 original size:26 final size:26
Alignment explanation
Indices: 41169464--41169526 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
41169454 GTCATAGCCA
41169464 AATT-TAACATTTCATAACAGCATTT
1 AATTATAACATTTCATAACAGCATTT
41169489 AATTATAACATTTCATAACAGCATTT
1 AATTATAACATTTCATAACAGCATTT
41169515 AATTATAACATT
1 AATTATAACATT
41169527 AAACTATCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.11
26 33 0.89
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (26 bp):
AATTATAACATTTCATAACAGCATTT
Found at i:41169500 original size:13 final size:13
Alignment explanation
Indices: 41169484--41169526 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
41169474 TTCATAACAG
41169484 CATTTAATTATAA
1 CATTTAATTATAA
* * * *
41169497 CATTTCATAACAG
1 CATTTAATTATAA
41169510 CATTTAATTATAA
1 CATTTAATTATAA
41169523 CATT
1 CATT
41169527 AAACTATCAA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (13 bp):
CATTTAATTATAA
Found at i:41173077 original size:43 final size:43
Alignment explanation
Indices: 41172953--41173109 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 43
41172943 TGTGTTATCG
* * *
41172953 TGTAAGACCATGACTGGGACATTGGCATCGACT-TATGATTTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGA-TATTTGATTT-CA
* * * *
41172997 TGTGAGACCACGTTTGAGACATTGGCATCG-TACTTGATTTCA
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTCA
** * * **
41173039 TGTAAGACCTTGTCTAGGACAGTGGCATCGATATTTGATGACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTCA
41173082 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
41173110 TGTATGAGCT
Statistics
Matches: 90, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
42 26 0.29
43 39 0.43
44 25 0.28
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTCA
Found at i:41177488 original size:22 final size:22
Alignment explanation
Indices: 41177446--41177489 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41177436 AATTATTTAC
* *
41177446 GACTAAAGTATAGCGTTCATAT
1 GACTAAAGAATAGCGTGCATAT
41177468 GACTAAATGAATAGC-TGCATAT
1 GACTAAA-GAATAGCGTGCATAT
41177490 ATGCATATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (22 bp):
GACTAAAGAATAGCGTGCATAT
Found at i:41177790 original size:40 final size:40
Alignment explanation
Indices: 41177716--41177936 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
41177706 AACCCAAGTA
* *
41177716 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* * *
41177755 CCTTCGAGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
41177795 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
41177835 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
41177875 -CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
41177914 CCTTCGGGACTTAGCCCAGATAT
1 CCTTCGGGACTTAGCCCGGATAT
41177937 CATTCGAATA
Statistics
Matches: 166, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 48 0.29
40 115 0.69
41 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:41177919 original size:79 final size:80
Alignment explanation
Indices: 41177716--41177936 Score: 349
Period size: 79 Copynumber: 2.8 Consensus size: 80
41177706 AACCCAAGTA
* * * *
41177716 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGAGTCTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
41177779 GTCAATAGCACAAAAG
65 GTCAATAGCACAAAAG
41177795 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
41177860 TCAATAGCACAAATG
66 TCAATAGCACAAAAG
* *
41177875 -CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAAGCCTTCGGGACTTAGCCCAGATAT
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
41177937 CATTCGAATA
Statistics
Matches: 133, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
79 73 0.55
80 59 0.44
81 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCAATAGCACAAAAG
Found at i:41177927 original size:119 final size:119
Alignment explanation
Indices: 41177716--41177936 Score: 356
Period size: 119 Copynumber: 1.9 Consensus size: 119
41177706 AACCCAAGTA
* * *
41177716 CCTTCGGGATTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGAGTCTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGCAACTAGCACAAATGCCTTCGAGACTTAGCCCGGATATAGT
*
41177781 CAATAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
66 CAATAGCACAAAAGCCTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATG
*
41177835 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG-CTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAG-CCGGATATAG-CAACTAGCACAAATGCCTTCGAGACTTAGCCCGGATATA
*
41177898 GTCACTAGCACAAAAGCCTTCGGGACTTAGCCCAGATAT
64 GTCAATAGCACAAAAGCCTTCGGGACTTAGCCCAGATAT
41177937 CATTCGAATA
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
119 71 0.76
120 20 0.21
121 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (119 bp):
CCTTCGGGACTTAGCCGGATATAGCAACTAGCACAAATGCCTTCGAGACTTAGCCCGGATATAGT
CAATAGCACAAAAGCCTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATG
Found at i:41186113 original size:22 final size:22
Alignment explanation
Indices: 41186071--41186114 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41186061 AATTATTTAC
* *
41186071 GACTAAAGTATAGCGTTCATAT
1 GACTAAAGAATAGCGTGCATAT
41186093 GACTAAATGAATAGC-TGCATAT
1 GACTAAA-GAATAGCGTGCATAT
41186115 ACGCATATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (22 bp):
GACTAAAGAATAGCGTGCATAT
Found at i:41186414 original size:40 final size:40
Alignment explanation
Indices: 41186340--41186559 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
41186330 AACCCAAGTA
* *
41186340 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
41186379 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
41186419 CCTTCGGGACTTA-CCCAGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
41186458 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
41186498 CCTTCGGGACTTAGCCCGGATATAGTCACTAG-ACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
41186537 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
41186560 CATTCGAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
39 77 0.46
40 86 0.52
41 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:41186471 original size:79 final size:79
Alignment explanation
Indices: 41186340--41186559 Score: 345
Period size: 79 Copynumber: 2.8 Consensus size: 79
41186330 AACCCAAGTA
* * * *
41186340 CCTTCGGGATTTAGCCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CCTTCGGGACTTACCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
41186404 TCAATAGCACAAAAG
65 TCAATAGCACAAAAG
*
41186419 CCTTCGGGACTTACCCAGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTACCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
*
41186484 CAATAGCACAAATG
66 CAATAGCACAAAAG
*
41186498 CCTTCGGGACTTAGCCCGGATATAGTCACTAG-ACAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTA-CCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
41186560 CATTCGAATA
Statistics
Matches: 131, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
79 113 0.86
80 18 0.14
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTACCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CAATAGCACAAAAG
Found at i:41191671 original size:17 final size:19
Alignment explanation
Indices: 41191629--41191672 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41191619 ATGAAATTTT
*
41191629 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
41191648 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
41191666 AA-TATTA
1 AATTATTA
41191673 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:41191703 original size:12 final size:12
Alignment explanation
Indices: 41191686--41191710 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41191676 TATGTATGTT
41191686 TGAAAATTTTTA
1 TGAAAATTTTTA
41191698 TGAAAATTTTTA
1 TGAAAATTTTTA
41191710 T
1 T
41191711 TATTATTTAC
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGAAAATTTTTA
Found at i:41192843 original size:25 final size:25
Alignment explanation
Indices: 41192789--41192859 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
41192779 CTACTTCCTT
* *
41192789 TTTTCTTCTTCTTTTC-CTTCTTGTC
1 TTTTCTT-TTCTTTTCTCTTCATCTC
41192814 TTTTCTTTTCTTTTCTCTTCATCTAC
1 TTTTCTTTTCTTTTCTCTTCATCT-C
*
41192840 -TTTCTCTTCTTTT-T-TTCATC
1 TTTTCTTTTCTTTTCTCTTCATC
41192860 CATAGCTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.15
24 9 0.22
25 25 0.61
26 1 0.02
ACGTcount: A:0.04, C:0.27, G:0.01, T:0.68
Consensus pattern (25 bp):
TTTTCTTTTCTTTTCTCTTCATCTC
Found at i:41192844 original size:20 final size:18
Alignment explanation
Indices: 41192760--41192837 Score: 50
Period size: 20 Copynumber: 4.2 Consensus size: 18
41192750 TATTTTCTTT
**
41192760 TCTTTTCTCCTCTCTTCA
1 TCTTTTCTTTTCTCTTCA
* * *
41192778 TCTACTTCCTTTTTTCTTCT
1 TCT--TTTCTTTTCTCTTCA
* *
41192798 TCTTTTCCTTCTTGTCTT-T
1 TCTTTT-CTT-TTCTCTTCA
41192817 TCTTTTCTTTTCTCTTCA
1 TCTTTTCTTTTCTCTTCA
41192835 TCT
1 TCT
41192838 ACTTTCTCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
17 6 0.13
18 11 0.24
19 10 0.22
20 19 0.41
ACGTcount: A:0.04, C:0.31, G:0.01, T:0.64
Consensus pattern (18 bp):
TCTTTTCTTTTCTCTTCA
Found at i:41192852 original size:62 final size:62
Alignment explanation
Indices: 41192738--41192856 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
41192728 AGGATTCAGT
* *
41192738 TTTTTCTTCTTCTATTTTCTTTTCTTTTCTCCTCTCTTCATCTACTTCCTTTTTTCTTCTTC
1 TTTTCCTTCTTCTATTTTCTTTTCTTTTCTCCTCTCTACATCTACTTCCTTTTTTCTTCTTC
* * * * *
41192800 TTTTCCTTCTTGTCTTTTCTTTTCTTTTCTCTTCATCTACTTTCT-CTTCTTTTTTTC
1 TTTTCCTTCTTCTATTTTCTTTTCTTTTCTCCTC-TCTAC-ATCTACTTCCTTTTTTC
41192857 ATCCATAGCT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 30 0.62
63 15 0.31
64 3 0.06
ACGTcount: A:0.04, C:0.28, G:0.01, T:0.67
Consensus pattern (62 bp):
TTTTCCTTCTTCTATTTTCTTTTCTTTTCTCCTCTCTACATCTACTTCCTTTTTTCTTCTTC
Found at i:41193831 original size:15 final size:14
Alignment explanation
Indices: 41193811--41193855 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
41193801 CCATACGGGT
41193811 TAATAAATAAAATAA
1 TAATAAATAAAA-AA
41193826 TAAT-AATAAAAAA
1 TAATAAATAAAAAA
*
41193839 TTATAATATAAAAAA
1 TAATAA-ATAAAAAA
41193854 TA
1 TA
41193856 GGCAATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 13 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAAATAAAAAA
Found at i:41193844 original size:16 final size:15
Alignment explanation
Indices: 41193819--41193855 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
41193809 GTTAATAAAT
41193819 AAAATAATAATAATAA
1 AAAATAATAAT-ATAA
*
41193835 AAAATTATAATATAA
1 AAAATAATAATATAA
41193850 AAAATA
1 AAAATA
41193856 GGCAATAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAATAATATAA
Found at i:41198259 original size:31 final size:31
Alignment explanation
Indices: 41198216--41198294 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
41198206 TTTAACGATT
*
41198216 ACTGCGCCAAAGCCTTTTCATAAATCATATC
1 ACTGGGCCAAAGCCTTTTCATAAATCATATC
*
41198247 ACTGGGCCAAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCAAAGCCTTTTCATAAATCATATC
*
41198278 ACTGGGCCGAAGCCTTT
1 ACTGGGCCAAAGCCTTT
41198295 ACTATAAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
ACTGGGCCAAAGCCTTTTCATAAATCATATC
Found at i:41198376 original size:41 final size:41
Alignment explanation
Indices: 41198318--41198407 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
41198308 TGACCCATAG
* ** *
41198318 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCA-TTCAATATCACATGAAATACCAATGAATGTATGCAA
41198360 GCCCATTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTCAATATCACATGAAATACCAATGAATGTATGCAA
41198401 GCCCATT
1 GCCCATT
41198408 TGGGGAGACT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 39 0.89
42 5 0.11
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (41 bp):
GCCCATTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:41198597 original size:26 final size:26
Alignment explanation
Indices: 41198553--41198650 Score: 153
Period size: 26 Copynumber: 3.8 Consensus size: 26
41198543 CCTCTTTAAT
*
41198553 AACTAGGGCA-AAGCCCTTTTCAGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
*
41198578 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAGTA
* *
41198604 AAGTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
41198630 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
41198651 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
25 9 0.14
26 57 0.86
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAGTA
Found at i:41200449 original size:31 final size:31
Alignment explanation
Indices: 41200406--41200484 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
41200396 TTTAACGATT
*
41200406 ACTGCGCCAAAGCCTTTTCATAAATCATATC
1 ACTGGGCCAAAGCCTTTTCATAAATCATATC
*
41200437 ACTGGGCCAAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCAAAGCCTTTTCATAAATCATATC
*
41200468 ACTGGGCCGAAG-CTTTT
1 ACTGGGCCAAAGCCTTTT
41200485 ACTATAAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 5 0.11
31 40 0.89
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (31 bp):
ACTGGGCCAAAGCCTTTTCATAAATCATATC
Found at i:41200580 original size:42 final size:42
Alignment explanation
Indices: 41200512--41200599 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
41200502 CCATAGGCCT
* ** *
41200512 ATTTCAATATCACATGTAATGTCAATGGATGTATGCAAGCCC
1 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
41200554 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
1 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
41200596 ATTT
1 ATTT
41200600 GGGGAGACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (42 bp):
ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
Found at i:41200788 original size:26 final size:26
Alignment explanation
Indices: 41200744--41200893 Score: 239
Period size: 26 Copynumber: 5.8 Consensus size: 26
41200734 CCTCTTTAAT
*
41200744 AACTAGGGCA-AAGCCCTTTTCAGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
*
41200769 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAGTA
* *
41200795 AAGTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
*
41200821 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAGTA
*
41200847 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
41200873 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
41200894 GCACTTCCTC
Statistics
Matches: 114, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
25 9 0.08
26 105 0.92
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAGTA
Found at i:41200822 original size:52 final size:52
Alignment explanation
Indices: 41200744--41200893 Score: 266
Period size: 52 Copynumber: 2.9 Consensus size: 52
41200734 CCTCTTTAAT
* *
41200744 AACTAGGGCA-AAGCCCTTTTCAGTAAACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
*
41200795 AAGTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
41200847 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
41200894 GCACTTCCTC
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 8 0.09
52 86 0.91
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (52 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
Found at i:41206465 original size:51 final size:49
Alignment explanation
Indices: 41206285--41206480 Score: 230
Period size: 50 Copynumber: 3.9 Consensus size: 49
41206275 TAGCCAAAGC
* * *
41206285 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* * * * *
41206334 TATCTGCTACACGTAGTAGTCTGCACTTAGTACTACACACATGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* * * * *
41206384 CATCTGATACACGTAGTAGCCTGCAGTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-T
* *
41206435 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
41206481 TCACAATAGA
Statistics
Matches: 122, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
49 39 0.32
50 44 0.36
51 39 0.32
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:41206480 original size:101 final size:99
Alignment explanation
Indices: 41206298--41206481 Score: 260
Period size: 101 Copynumber: 1.8 Consensus size: 99
41206288 CTGGTACGCA
* * * *
41206298 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGCTACACGTAGTAGTCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCGGCTACACATAGTAGCCTGCACTTA
41206363 GTACTACACACATGACCTAACCATCTGATACACG
66 GTACTACACACATGACCTAACCATCTGATACACG
* * * * *
41206397 TAGTAGCCTGCAGTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCGGCTACACATAGTAGCCTGCACT
*
41206462 TAGTACTACACACGTGACCT
64 TAGTACTACACACATGACCT
41206482 CACAATAGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 28 0.38
100 3 0.04
101 42 0.58
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCGGCTACACATAGTAGCCTGCACTTA
GTACTACACACATGACCTAACCATCTGATACACG
Found at i:41209319 original size:43 final size:43
Alignment explanation
Indices: 41209256--41209343 Score: 142
Period size: 43 Copynumber: 2.0 Consensus size: 43
41209246 CGTTTTACCA
**
41209256 AAATTAACCTTTTTTGCTAACTG-GAATGTTGCGAAAATTAAAC
1 AAATTAACCTTTTTCACTAACTGCG-ATGTTGCGAAAATTAAAC
41209299 AAATTAACCTTTTTCACTAACTGCGATGTTGCGAAAATTAAAC
1 AAATTAACCTTTTTCACTAACTGCGATGTTGCGAAAATTAAAC
41209342 AA
1 AA
41209344 TCTTTCGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 41 0.98
44 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (43 bp):
AAATTAACCTTTTTCACTAACTGCGATGTTGCGAAAATTAAAC
Found at i:41211730 original size:51 final size:49
Alignment explanation
Indices: 41211562--41211801 Score: 237
Period size: 49 Copynumber: 4.8 Consensus size: 49
41211552 AAAGCAATTT
* * ** * *
41211562 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAAACAATTATCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCG
* * * * * ** *
41211611 AGTACACGTAGTAGCCTGCAATTAGTGCTACACACGTAACCTAACCATCT
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCG
* * * **
41211661 GATACACGTAGTAGCCTGCACTTAGTACTATACACGTGATTGAAGTTATCG
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCG
* * * *
41211712 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCT
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCG
*
41211761 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
41211802 TCACAATAGA
Statistics
Matches: 153, Mismatches: 35, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
49 75 0.49
50 42 0.27
51 36 0.24
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (49 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCG
Found at i:41211796 original size:100 final size:100
Alignment explanation
Indices: 41211561--41211799 Score: 277
Period size: 100 Copynumber: 2.4 Consensus size: 100
41211551 CAAAGCAATT
* * *
41211561 TGGTACGCATAGTAGCCTGCACTTAGTACTACACA--TGCAAACAATTATCCAGTACACGTAGTA
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTG-AAACAATTATCCAGTACACATAGTA
* *
41211624 GCCTGCAATTAGTGCTACACACGTAACCTAACCATC
65 GCCTGCAATTAGTACTACACACGCAACCTAACCATC
* * *** ** *
41211660 TGATACACGTAGTAGCCTGCACTTAGTACTATACACGTGATTGAAGTTATCGGGTACGCATAGTA
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAAACAA-TTATCCAGTACACATAGTA
* * * **
41211725 GCCTGCACTTAGTACTACACATGCGACC-AATTATC
65 GCCTGCAATTAGTACTACACACGCAACCTAACCATC
41211760 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA
41211800 CCTCACAATA
Statistics
Matches: 117, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
99 31 0.26
100 46 0.39
101 40 0.34
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (100 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAAACAATTATCCAGTACACATAGTAG
CCTGCAATTAGTACTACACACGCAACCTAACCATC
Found at i:41214574 original size:28 final size:28
Alignment explanation
Indices: 41214542--41214610 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
41214532 TGTGAATCTT
* * * *
41214542 GCACTAAGTGTGTGAATGTGATTATTGA
1 GCACTAAGTGTGCGAATGTAAATATCGA
* *
41214570 GCACTAAGTGTGCGAGTTTAAATATCGA
1 GCACTAAGTGTGCGAATGTAAATATCGA
41214598 GCACTAAGTGTGC
1 GCACTAAGTGTGC
41214611 AAACTATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAATGTAAATATCGA
Found at i:41220979 original size:38 final size:38
Alignment explanation
Indices: 41220937--41221047 Score: 123
Period size: 38 Copynumber: 2.9 Consensus size: 38
41220927 ATGCTGGAAT
*
41220937 TATATCCGGGTTAAATCCCACAGGCTTCGTGCTAGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGTAA
* * * * *
41220975 TATATCCGGGTTAAATCCTGCAGGCCTGGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGTAA
* * *
41221013 TATATCTGAGTTTAAAGTCCCGTAGGCTTCGTGCT
1 TATATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCT
41221048 GGTGTTATGC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 39 0.66
39 6 0.10
40 14 0.24
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGTAA
Found at i:41229179 original size:40 final size:40
Alignment explanation
Indices: 41229124--41229228 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
41229114 TATTCGGATG
* *
41229124 ATATCCGGACTAAGATCTGAAGGCATTTGTGCTAGTTACT
1 ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTACT
*
41229164 ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTATT
1 ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTACT
* **
41229204 ATAACCGGGTTAAG-TCCCGAAGGCA
1 ATATCCGGACTAAGAT-CCGAAGGCA
41229229 TTCGTGCGGG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (40 bp):
ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTACT
Found at i:41229242 original size:40 final size:40
Alignment explanation
Indices: 41229142--41229280 Score: 174
Period size: 40 Copynumber: 3.5 Consensus size: 40
41229132 ACTAAGATCT
* * * * **
41229142 GAAGGCATTTGTGCTAGTTACTATATCCGGACTAAGAT-CC
1 GAAGGCATTCGTGCTGGTTATTATAACCGGGTTAAG-TCCC
*
41229182 GAAGGCAATT-GTGCTAGTTATTATAACCGGGTTAAGTCCC
1 GAAGGC-ATTCGTGCTGGTTATTATAACCGGGTTAAGTCCC
*
41229222 GAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCC
1 GAAGGCATTCGTGCTGGTTATTATAACCGGGTTAAGTCCC
41229262 GAAGGCATTCGTGCTGGTT
1 GAAGGCATTCGTGCTGGTT
41229281 GTTACATCCG
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
39 4 0.04
40 82 0.92
41 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (40 bp):
GAAGGCATTCGTGCTGGTTATTATAACCGGGTTAAGTCCC
Found at i:41236261 original size:15 final size:15
Alignment explanation
Indices: 41236243--41236277 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41236233 TGTTTGATGC
41236243 TAATGCTGAATATGA
1 TAATGCTGAATATGA
41236258 TAATGCTGAATATGA
1 TAATGCTGAATATGA
*
41236273 AAATG
1 TAATG
41236278 TTGTACTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (15 bp):
TAATGCTGAATATGA
Found at i:41237274 original size:40 final size:39
Alignment explanation
Indices: 41237225--41237371 Score: 152
Period size: 40 Copynumber: 3.7 Consensus size: 39
41237215 GATGATATCT
* * *
41237225 GGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCC
1 GGACTAAG-TCCGAAGGCATTCGTGCTAGTTATTATAACC
*
41237265 GGACTAAGATCTGAAGGCAATT-GTGCTAGTTATTATAACC
1 GGACTAAG-TCCGAAGGC-ATTCGTGCTAGTTATTATAACC
** **
41237305 GGGTTAAGTCTCGAAGGCATTCGTGCGGGTTATTATAACC
1 GGACTAAGTC-CGAAGGCATTCGTGCTAGTTATTATAACC
**
41237345 GGGTTAAGTCCCGAAGGCATTCGTGCT
1 GGACTAAGT-CCGAAGGCATTCGTGCT
41237372 GGTTGTTACA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 5 0.05
40 85 0.90
41 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (39 bp):
GGACTAAGTCCGAAGGCATTCGTGCTAGTTATTATAACC
Found at i:41240711 original size:39 final size:39
Alignment explanation
Indices: 41240657--41240734 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
41240647 ATCCTCGATG
41240657 TTAGCTCAAAAATATGTGAGAAAGGGGTGTGAAGTGTAT
1 TTAGCTCAAAAATATGTGAGAAAGGGGTGTGAAGTGTAT
41240696 TTAGCTCAAAAATATGTGAGAAAGGGGTGTGAAGTGTAT
1 TTAGCTCAAAAATATGTGAGAAAGGGGTGTGAAGTGTAT
41240735 CTTGCATACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.28
Consensus pattern (39 bp):
TTAGCTCAAAAATATGTGAGAAAGGGGTGTGAAGTGTAT
Found at i:41244418 original size:15 final size:15
Alignment explanation
Indices: 41244400--41244434 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41244390 TGTTTGATGC
41244400 TAATGCTGAATATGA
1 TAATGCTGAATATGA
41244415 TAATGCTGAATATGA
1 TAATGCTGAATATGA
*
41244430 AAATG
1 TAATG
41244435 TTGTACTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (15 bp):
TAATGCTGAATATGA
Found at i:41245493 original size:39 final size:40
Alignment explanation
Indices: 41245386--41245527 Score: 182
Period size: 40 Copynumber: 3.6 Consensus size: 40
41245376 ATATCCGGAC
* * * **
41245386 TAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCGGAC
1 TAAGATCCGAAGGCATTCGTGCTAGTTATTATAACCGGGT
41245426 TAAGATCCGAAGGCAATT-GTGCTAGTTATTATAACCGGGT
1 TAAGATCCGAAGGC-ATTCGTGCTAGTTATTATAACCGGGT
**
41245466 TAAG-TCCGAAGGCATTCGTGCGGGTTATTATAACCGGGT
1 TAAGATCCGAAGGCATTCGTGCTAGTTATTATAACCGGGT
41245505 TAAG-TCCCGAAGGCATTCGTGCT
1 TAAGAT-CCGAAGGCATTCGTGCT
41245528 GTTGTTACAT
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
38 3 0.03
39 34 0.37
40 52 0.57
41 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (40 bp):
TAAGATCCGAAGGCATTCGTGCTAGTTATTATAACCGGGT
Found at i:41246954 original size:1 final size:1
Alignment explanation
Indices: 41246948--41247020 Score: 146
Period size: 1 Copynumber: 73.0 Consensus size: 1
41246938 CGATTCCGGC
41246948 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41247013 AAAAAAAA
1 AAAAAAAA
41247021 TAAGTTTTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41249446 original size:27 final size:27
Alignment explanation
Indices: 41249416--41249725 Score: 366
Period size: 27 Copynumber: 11.7 Consensus size: 27
41249406 TTAGTTTACC
41249416 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
41249443 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
41249470 AAATTACC-AAATA-CCCTGGATTTGTA
1 AAATTACCAAAATACCCCTGG-TTTGTA
41249496 AAATTACC-AAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
41249522 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
41249549 AAATTACCAAAATACCCCTGG-TTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
41249575 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
41249602 AAATTACC-AAATAACCCTTGATTTGTG
1 AAATTACCAAAAT-ACCCCTGGTTTGTA
* * * * *
41249629 AAATTATCGAAATA-CCTTAGTTTGCA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
41249655 AAATTACTAAAATA-CCCTCGATTTGCA
1 AAATTACCAAAATACCCCT-GGTTTGTA
* * *
41249682 AAATTACTAAAATA-CCCTCGATTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
41249708 AAATTACCAAAGTACCCC
1 AAATTACCAAAATACCCC
41249726 GATTTACAGA
Statistics
Matches: 249, Mismatches: 26, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
25 5 0.02
26 103 0.41
27 137 0.55
28 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:41249494 original size:53 final size:53
Alignment explanation
Indices: 41249416--41249724 Score: 365
Period size: 53 Copynumber: 5.8 Consensus size: 53
41249406 TTAGTTTACC
*
41249416 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATA-CCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGCA
* *
41249470 AAATTACC-AAATACCCTGGATTTGTAAAATTACC-AAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTGG-TTTGTAAAATTACCAAAATACCCTTGGTTTGCA
* *
41249522 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGG-TTGTA
1 AAATTACCAAAATA-CCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGCA
* **
41249575 AAATTACCAAAATACCCTTGGTTTGTAAAATTACC-AAATAACCCTTGATTTGTG
1 AAATTACCAAAATACCC-TGGTTTGTAAAATTACCAAAAT-ACCCTTGGTTTGCA
* * * * * * * *
41249629 AAATTATCGAAATACCTTAGTTTGCAAAATTACTAAAATACCCTCGATTTGCA
1 AAATTACCAAAATACCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGCA
* * * *
41249682 AAATTACTAAAATACCCTCGATTGTAAAATTACCAAAGTACCC
1 AAATTACCAAAATACCCTGGTTTGTAAAATTACCAAAATACCC
41249725 CGATTTACAG
Statistics
Matches: 223, Mismatches: 24, Indels: 17
0.84 0.09 0.06
Matches are distributed among these distances:
52 36 0.16
53 139 0.62
54 48 0.22
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (53 bp):
AAATTACCAAAATACCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGCA
Found at i:41249776 original size:27 final size:26
Alignment explanation
Indices: 41249442--41249778 Score: 125
Period size: 27 Copynumber: 12.7 Consensus size: 26
41249432 CCTGGTTTGT
* * *
41249442 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTA-CGAAATACCCTCGATTTAC
* * **
41249469 AAAATTACCAAATACCCTGGATTTGT
1 AAAATTACGAAATACCCTCGATTTAC
* * **
41249495 AAAATTACCAAATACCC-CTGGTTTGT
1 AAAATTACGAAATACCCTC-GATTTAC
* * **
41249521 AAAATTACCAAAATACCC-CTGGTTTGT
1 AAAATTA-CGAAATACCCTC-GATTTAC
* *
41249548 AAAATTACCAAAATACCC-CTGGTTGT--
1 AAAATTA-CGAAATACCCTC-GATT-TAC
* * * **
41249574 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTA-CGAAATACCCTCGATTTAC
* * **
41249601 AAAATTACCAAATAACCCTTGATTTGT
1 AAAATTACGAAAT-ACCCTCGATTTAC
* * * *
41249628 GAAATTATCGAAATACCTTAG-TTTGC
1 AAAATTA-CGAAATACCCTCGATTTAC
* *
41249654 AAAATTACTAAAATACCCTCGATTTGC
1 AAAATTAC-GAAATACCCTCGATTTAC
*
41249681 AAAATTACTAAAATACCCTCGATTGT--
1 AAAATTAC-GAAATACCCTCGATT-TAC
*
41249707 AAAATTACCAAAGTACCC-CGATTTAC
1 AAAATTACGAAA-TACCCTCGATTTAC
* ***
41249733 AGAATTATCGTTTTACCCTCGATTTAC
1 AAAATTA-CGAAATACCCTCGATTTAC
41249760 AAAATTATCGAAATACCCT
1 AAAATTA-CGAAATACCCT
41249779 TGTAAGGTAG
Statistics
Matches: 264, Mismatches: 30, Indels: 32
0.81 0.09 0.10
Matches are distributed among these distances:
24 1 0.00
25 10 0.04
26 114 0.43
27 132 0.50
28 7 0.03
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (26 bp):
AAAATTACGAAATACCCTCGATTTAC
Found at i:41249792 original size:27 final size:27
Alignment explanation
Indices: 41249769--41250010 Score: 324
Period size: 27 Copynumber: 9.0 Consensus size: 27
41249759 CAAAATTATC
*
41249769 GAAATACCCTTGTAAGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* * *
41249796 AAAATACCCCTGTAGGGTAGAA-TACC
1 GAAATACCCCTGTAAGGTAGAATTACT
*
41249822 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* * *
41249849 GAAAACACCCCTATAAGGTACAATTACT
1 G-AAATACCCCTGTAAGGTAGAATTACT
* * *
41249877 AAAATACCCTTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
41249904 GAAATACCCCTGTAAGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* *
41249931 AAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
*
41249958 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* *
41249985 AAAATACCCCTGTAGGGTAGAATTAC
1 GAAATACCCCTGTAAGGTAGAATTAC
41250011 CAGATACCCT
Statistics
Matches: 188, Mismatches: 25, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
26 24 0.13
27 142 0.76
28 22 0.12
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAAGGTAGAATTACT
Found at i:41262856 original size:40 final size:40
Alignment explanation
Indices: 41262769--41262949 Score: 226
Period size: 40 Copynumber: 4.6 Consensus size: 40
41262759 TATTCGGATG
* *
41262769 ATATCCGGGCTAAGTCCAGAAGGCA-TGGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACT
*
41262808 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACT
* **
41262848 ATACCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACT
* *
41262888 ATATCCGGGCTAAGACCCGAAGGC-GTTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCAG-TTGTGCTAG-TGACT
* *
41262928 ATATCC-GGCTAAATCCCAAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
41262950 TACTTGGGTT
Statistics
Matches: 125, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 37 0.30
40 86 0.69
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACT
Found at i:41267326 original size:46 final size:45
Alignment explanation
Indices: 41267270--41267445 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
41267260 TGTTTGGGCA
41267270 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
41267316 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
* * *
41267361 CATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTCATGGATGGAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGG-AATG
* * *
41267409 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41267446 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:41267425 original size:93 final size:93
Alignment explanation
Indices: 41267266--41267438 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
41267256 AGGATGTTTG
* * *
41267266 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAACTCGTTGAG
41267331 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
41267359 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTCATGGATG-GAAACGCCCGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCG-AACGCCCGAACTCGTTGA
41267423 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
41267439 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:41274060 original size:40 final size:39
Alignment explanation
Indices: 41273973--41274193 Score: 268
Period size: 40 Copynumber: 5.6 Consensus size: 39
41273963 TATTCGGATG
* * *
41273973 ATATCCGGGCTAAGTCCCGAAGGCATGGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCGTTGTGCTATTGACT
41274012 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGC-GTTGTGCTATTGACT
* * *
41274052 ATACCCGGGCTAAGTCCCAAAGGCGTTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCG-TTGTGCTA-TTGACT
* *
41274092 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGC-GTTGTGCTATTGACT
* *
41274132 ATATCCGGGCTAAGACCCGAAGGCGTTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCG-TTGTGCTA-TTGACT
*
41274172 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
41274194 TACTTGGGTT
Statistics
Matches: 158, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
39 41 0.26
40 112 0.71
41 5 0.03
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCCGAAGGCGTTGTGCTATTGACT
Found at i:41274109 original size:80 final size:80
Alignment explanation
Indices: 41273977--41274193 Score: 314
Period size: 80 Copynumber: 2.7 Consensus size: 80
41273967 CGGATGATAT
* * *
41273977 CCGGGCTAAGTCCCGAAGGC-ATGGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGGCAGTT
1 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTG-CTATATCCGGGCTAAGTCCCGAAGGCAGTT
*
41274040 GTGCTATTGACTATAC
65 GTGCTAGTGACTATAC
* **
41274056 CCGGGCTAAGTCCCAAAGGCGTTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCTTTTG
1 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCAGTTG
*
41274121 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* *
41274136 CCGGGCTAAGACCCGAAGGCGTTTGTGCGAGTTGCTATATCC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGG
41274194 TACTTGGGTT
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 34 0.27
80 89 0.71
81 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCAGTTG
TGCTAGTGACTATAC
Done.