Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014746.1 Kokia drynarioides strain JFW-HI SEQ_129785, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 188894
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:7048 original size:18 final size:18
Alignment explanation
Indices: 7025--7067 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
7015 GTTCAAGGGG
7025 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
7043 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
7061 TAATTAA
1 TAATTAA
7068 AAATCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:7226 original size:14 final size:15
Alignment explanation
Indices: 7195--7240 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
7185 ATAAAATGAT
7195 AACGTAAATAATTAA
1 AACGTAAATAATTAA
* *
7210 AACGT-AATATTTTA
1 AACGTAAATAATTAA
*
7224 AACATAAATAATTAA
1 AACGTAAATAATTAA
7239 AA
1 AA
7241 TATAATATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (15 bp):
AACGTAAATAATTAA
Found at i:7245 original size:15 final size:15
Alignment explanation
Indices: 7199--7245 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
7189 AATGATAACG
*
7199 TAAATAATTAAAACG
1 TAAATAATTAAAACA
* *
7214 T-AATATTTTAAACA
1 TAAATAATTAAAACA
*
7228 TAAATAATTAAAATA
1 TAAATAATTAAAACA
7243 TAA
1 TAA
7246 TATGAGACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (15 bp):
TAAATAATTAAAACA
Found at i:30100 original size:3 final size:3
Alignment explanation
Indices: 30069--30190 Score: 165
Period size: 3 Copynumber: 40.0 Consensus size: 3
30059 CAATTTCTTT
* * * * *
30069 TTA TTA ATA TTA ATA TTAA TTA ATA TTA TTA TCAA TTA TTA -TA CCTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA TTA TTA -TTA
30116 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30164 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
30191 ATGTTCATTC
Statistics
Matches: 106, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.02
3 97 0.92
4 7 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:30860 original size:14 final size:14
Alignment explanation
Indices: 30822--30864 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
30812 CAATTTGTAA
*
30822 TTGGACCTTTGTAT
1 TTGGACCTTTATAT
* *
30836 TGGGACTTTTATAT
1 TTGGACCTTTATAT
30850 TTGGACCTTTA-AT
1 TTGGACCTTTATAT
30863 TT
1 TT
30865 TATTTTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.51
Consensus pattern (14 bp):
TTGGACCTTTATAT
Found at i:30891 original size:17 final size:17
Alignment explanation
Indices: 30866--30936 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
30856 CTTTAATTTT
*
30866 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
30883 ATTTAAATTTAATGA-AA
1 ATTTAAATTTAA-AATAA
* * * *
30900 ATTCAAACTCAAAATGA
1 ATTTAAATTTAAAATAA
*
30917 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
30934 ATT
1 ATT
30937 CAAACTTATT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
16 1 0.03
17 38 0.95
18 1 0.03
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:30920 original size:34 final size:34
Alignment explanation
Indices: 30876--30942 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
30866 ATTTTAATTT
*
30876 AAAATAAATTTAAATTTAATGA-AAATTCAAACTC
1 AAAATAAATTTAAATTTAA-AATAAATTCAAACTC
* *
30910 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
30943 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:31500 original size:39 final size:39
Alignment explanation
Indices: 31392--31668 Score: 159
Period size: 39 Copynumber: 7.1 Consensus size: 39
31382 TCAAGGTAGG
* * * * *
31392 AGATTGGTTAATGGTGATCTGCCCCAAGCTCGGGGTAAG
1 AGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAA
* ** * * * * * * * *
31431 AGATCGAATGGCTATAATCTACCACTGGCTCGGGATAAG
1 AGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAA
* *
31470 AGATTGGTTGACGATGATTTGCCCCAGGCTCGAGGTAAA
1 AGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAA
* *
31509 AGATCAAATGGTTG-C-A--ATCTGCCCCAAGCTCGGGGTAAG
1 AGAT----TGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAA
* * * *
31548 AGACTGGTTGATGATGATTTGCCCCAGGCTCAGGGTAAA
1 AGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAA
* **** * * * * *
31587 ATATCAAATG-GGTTCAATCTGCCCTAGGCTCGGGGTAAG
1 AGATTGGTTGACGAT-GATCTGCCCCAGGCTCGGGGTAAA
*
31626 AGATTGGTTGACGATGATCTGCCTCAGGCTCGGGGTAAA
1 AGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAA
31665 AGAT
1 AGAT
31669 CAAATGGCTG
Statistics
Matches: 167, Mismatches: 61, Indels: 20
0.67 0.25 0.08
Matches are distributed among these distances:
35 6 0.04
37 1 0.01
38 2 0.01
39 148 0.89
40 2 0.01
41 1 0.01
42 1 0.01
43 6 0.04
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (39 bp):
AGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAA
Found at i:31501 original size:78 final size:78
Alignment explanation
Indices: 31367--31709 Score: 398
Period size: 78 Copynumber: 4.4 Consensus size: 78
31357 TGGGTAACCA
* ** * * * * * *
31367 CAATCTACCTCAGGCTCAAGGTAGGAGATTGGTTAATGGTGATCTGCCCCAAGCTCGGGGTAAGA
1 CAATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAAA
* *
31432 GATCGAATGGCTA
66 GATCAAATGGCTG
* * * * * *
31445 TAATCTACCACTGGCTCGGGATAAGAGATTGGTTGACGATGATTTGCCCCAGGCTCGAGGTAAAA
1 CAATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAAA
*
31510 GATCAAATGGTTG
66 GATCAAATGGCTG
* * * * * *
31523 CAATCTGCCCCAAGCTCGGGGTAAGAGACTGGTTGATGATGATTTGCCCCAGGCTCAGGGTAAAA
1 CAATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAAA
* * *
31588 TATCAAATGGGTT
66 GATCAAATGGCTG
* * *
31601 CAATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCTCAGGCTCGGGGTAAAA
1 CAATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAAA
31666 GATCAAATGGCTG
66 GATCAAATGGCTG
* *
31679 CAATCTACCCCAGGCTCGAGGTAAAAGATTG
1 CAATCTACCCCAGGCTCGGGGTAAGAGATTG
31710 ATGATGTAAC
Statistics
Matches: 221, Mismatches: 44, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
78 221 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
CAATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAGGCTCGGGGTAAAA
GATCAAATGGCTG
Found at i:31693 original size:39 final size:39
Alignment explanation
Indices: 31489--31707 Score: 177
Period size: 39 Copynumber: 5.6 Consensus size: 39
31479 GACGATGATT
*
31489 TGCCCCAGGCTCGAGGTAAAAGATCAAATGGTTGCAATC
1 TGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTGCAATC
* * * *
31528 TGCCCCAAGCTCGGGGTAAGAGA-C---TGGTTGATGATGATT
1 TGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTG--CA--ATC
* *
31567 TGCCCCAGGCTCAGGGTAAAATATCAAATGGGTT-CAATC
1 TGCCCCAGGCTCGGGGTAAAAGATCAAAT-GGTTGCAATC
* *
31606 TGCCCTAGGCTCGGGGTAAGAGAT----TGGTTGACGATGATC
1 TGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTG-C-A--ATC
* *
31645 TGCCTCAGGCTCGGGGTAAAAGATCAAATGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTGCAATC
* *
31684 TACCCCAGGCTCGAGGTAAAAGAT
1 TGCCCCAGGCTCGGGGTAAAAGAT
31708 TGATGATGTA
Statistics
Matches: 140, Mismatches: 22, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
34 4 0.03
35 7 0.05
36 1 0.01
37 2 0.01
38 1 0.01
39 111 0.79
40 1 0.01
41 2 0.01
42 1 0.01
43 6 0.04
44 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (39 bp):
TGCCCCAGGCTCGGGGTAAAAGATCAAATGGTTGCAATC
Found at i:32050 original size:48 final size:48
Alignment explanation
Indices: 31991--32470 Score: 577
Period size: 48 Copynumber: 9.9 Consensus size: 48
31981 TCCCTTCAAA
* * ** * *
31991 TCTTCGTGGTACTTGATCCACCGTTATGGGTTATATCTTTCCCTTGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG
* *
32039 TCTTCATGGTACTGGATCCGCCGTTGCGACTTAGATCTTTCCCTTGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG
* * * *
32087 TCTTCATGGTACTGGATCCGCCGTTGCGACTTAGATATTTCCCTTGCG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG
* **
32135 TCTTCGTGGTACTGGATCCGTCGTTGCGGCTTAGATCTTTCCCTTACG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG
* *
32183 TCTTCGAGGTACTGGATCC-CCTGTTGCGGGTTAGATCTTTCCCTTGTG
1 TCTTCGTGGTACTGGATCCGCC-GTTGCGGCTTAGATCTTTCCCTTGTG
* * *
32231 TCTTCGTGGTACTGGATCCGCCATTGCAGCTTAGATCTTTCCCTTGCG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG
* * * *
32279 TCTTCGTGGTATTGGATCCGTCGTTGCAGCTTAGATATTTCCCTTGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG
* * *
32327 TCTTCGTGGTACTGGATTCACCGTTGCGGCTTAGATCTTTCCCTTCATG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTT-GTG
* * * * * *
32376 TCTTTTCGTGGTATTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTGTG
1 TC--TTCGTGGTACT-GGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG
* * *
32426 TCTTCGTGGTACTGGATCCGTCGTTGCGACTTAGAACTTTCCCTT
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTT
32471 CATGTCTTTG
Statistics
Matches: 375, Mismatches: 50, Indels: 14
0.85 0.11 0.03
Matches are distributed among these distances:
47 3 0.01
48 326 0.87
49 6 0.02
50 4 0.01
51 34 0.09
52 2 0.01
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (48 bp):
TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTG
Found at i:32505 original size:49 final size:49
Alignment explanation
Indices: 32363--32519 Score: 194
Period size: 49 Copynumber: 3.2 Consensus size: 49
32353 CGGCTTAGAT
32363 CTTTCCCTTCATGTCTTTTCGTGGTATTAGGTTCGCCATTGCGACTTAAAC
1 CTTTCCCTTCATGTC-TTT-GTGGTATTAGGTTCGCCATTGCGACTTAAAC
* * * * * *
32414 CTTTCCCTT-GTGTCTTCGTGGTACT-GGATCCGTCGTTGCGACTTAGAA-
1 CTTTCCCTTCATGTCTTTGTGGTATTAGG-TTCGCCATTGCGACTTA-AAC
*
32462 CTTTCCCTTCATGTCTTTGGGGTATTAGGTTCGCCATTGCGACTTAAAC
1 CTTTCCCTTCATGTCTTTGTGGTATTAGGTTCGCCATTGCGACTTAAAC
32511 CTTTCCCTT
1 CTTTCCCTT
32520 GAAATCTTCA
Statistics
Matches: 88, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
47 2 0.02
48 32 0.36
49 39 0.44
50 6 0.07
51 9 0.10
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (49 bp):
CTTTCCCTTCATGTCTTTGTGGTATTAGGTTCGCCATTGCGACTTAAAC
Found at i:33489 original size:14 final size:14
Alignment explanation
Indices: 33469--33549 Score: 53
Period size: 13 Copynumber: 5.7 Consensus size: 14
33459 CGACCTCTCC
33469 CTTTTTCTATTTTTG
1 CTTTTTCT-TTTTTG
33484 -TTTTTCTTGTTTTTG
1 CTTTTTC-T-TTTTTG
33499 CTTTTTC-TTTTTG
1 CTTTTTCTTTTTTG
* *
33512 -TCTCTCTTTTTT-
1 CTTTTTCTTTTTTG
* *
33524 CTTCTTCTTCTTTTT
1 CTTTTTCTT-TTTTG
33539 CTTTTTTCTTT
1 C-TTTTTCTTT
33550 GTTCATTGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
12 4 0.08
13 16 0.31
14 10 0.19
15 9 0.17
16 13 0.25
ACGTcount: A:0.01, C:0.17, G:0.05, T:0.77
Consensus pattern (14 bp):
CTTTTTCTTTTTTG
Found at i:33503 original size:16 final size:16
Alignment explanation
Indices: 33469--33507 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
33459 CGACCTCTCC
33469 CTTTTTC-TATTTTTG
1 CTTTTTCTTATTTTTG
*
33484 -TTTTTCTTGTTTTTG
1 CTTTTTCTTATTTTTG
33499 CTTTTTCTT
1 CTTTTTCTT
33508 TTTGTCTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.77
Consensus pattern (16 bp):
CTTTTTCTTATTTTTG
Found at i:33519 original size:28 final size:28
Alignment explanation
Indices: 33469--33538 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
33459 CGACCTCTCC
* *
33469 CTTTTTCTATTTTTGTTTTTCTTGTTTT-TG
1 CTTTTTC--TTTTTGTCTCTCTT-TTTTCTG
*
33499 CTTTTTCTTTTTGTCTCTCTTTTTTCTT
1 CTTTTTCTTTTTGTCTCTCTTTTTTCTG
*
33527 CTTCTTCTTTTT
1 CTTTTTCTTTTT
33539 CTTTTTTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.11
28 24 0.69
30 7 0.20
ACGTcount: A:0.01, C:0.17, G:0.06, T:0.76
Consensus pattern (28 bp):
CTTTTTCTTTTTGTCTCTCTTTTTTCTG
Found at i:33528 original size:22 final size:22
Alignment explanation
Indices: 33503--33548 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
33493 TTTTTGCTTT
* *
33503 TTCTTTTTGTCTCTCTTTTTTC
1 TTCTTCTTCTCTCTCTTTTTTC
* *
33525 TTCTTCTTCTTTTTCTTTTTTC
1 TTCTTCTTCTCTCTCTTTTTTC
33547 TT
1 TT
33549 TGTTCATTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (22 bp):
TTCTTCTTCTCTCTCTTTTTTC
Found at i:34424 original size:17 final size:18
Alignment explanation
Indices: 34394--34428 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
34384 TTCATCTTGA
34394 CTTTTTCTTCCTTTTTTT
1 CTTTTTCTTCCTTTTTTT
*
34412 CTTTTT-TTGCTTTTTTT
1 CTTTTTCTTCCTTTTTTT
34429 ATTGGGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (18 bp):
CTTTTTCTTCCTTTTTTT
Found at i:38923 original size:97 final size:97
Alignment explanation
Indices: 38738--38931 Score: 220
Period size: 97 Copynumber: 2.0 Consensus size: 97
38728 AACTTTCGAA
* * *
38738 AAGGATATTTGATTATCTCGATTTGAAGAAAATTCGCACTTAGTGAGTTAAAGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAATTCGCACCTAGTAAGTTAAAGCACAAATTTTCA
*
38803 GAATCAGAGATAAAGAAACATTGCCTCGATTT
66 GAATCAGAAATAAAGAAACATTGCCTCGATTT
* * *
38835 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATT-GCACCTAGTAAGTT-AAG-ACGAAAATTT
1 AAGGATATTCGATTATCTCGATTTGAAG-AAAATTCGCACCTAGTAAGTTAAAGCAC--AAATTT
*
38897 TCA-ACACTC-GAAATAAA-AGAATATTGCCTCGATTT
63 TCAGA-A-TCAGAAATAAAGA-AACATTGCCTCGATTT
38932 TAAAGTTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
95 2 0.02
96 5 0.06
97 68 0.82
98 8 0.10
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAATTCGCACCTAGTAAGTTAAAGCACAAATTTTCA
GAATCAGAAATAAAGAAACATTGCCTCGATTT
Found at i:39321 original size:59 final size:58
Alignment explanation
Indices: 39196--39632 Score: 395
Period size: 59 Copynumber: 7.4 Consensus size: 58
39186 TGGTCACTCG
* * ** * * * * *
39196 GGGGGAAAAATGGTAATTTTAGGAAAGTTAGGGGTCAAAAAACGGAATTTTTAGACA-TCC
1 GGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGT--AAAAATGGAATTTTTGGA-AGTTC
* * * * *
39256 GAGGGTAAAATGATACTTTTTGGAAGAATC-AGCATCAAAAATGGAATTTTTGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAAAATCGAG-GT-AAAAATGGAATTTTTGGAAGTTC
** * *
39315 GGGGGTAAAATGGTTCTTTTTTGGAAAAATCGGGGTTAAAAATGAAATTTTTGGAAGTT-
1 GGGGGTAAAATGG-TAATTTTTGGAAAAATCGAGG-TAAAAATGGAATTTTTGGAAGTTC
* * *
39374 TGGGGTAGAATGGTAATTTTGTGAAAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTT-
1 GGGGGTAAAATGGTAATTTT-TG-GAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTTC
39433 GGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAATGGAA-TTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGG-AAGTTC
* ** ***
39491 GAGGCAAAAAT-GTAATTTTTGGGAAAAATCGAGGTCAAAAATGGAATTTTAAAAAGTTC
1 GGGGGTAAAATGGTAATTTTT-GGAAAAATCGAGGT-AAAAATGGAATTTTTGGAAGTTC
* *
39550 GGGGGTAAAATGGTAATTTTTAGAAAAATCGAGGTTAAAAATAGAA-TTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAAAATCGAGG-TAAAAATGGAATTTTTGG-AAGTTC
** *
39609 AAGGGTAAAAAT-ATAATTTTTGGA
1 GGGGGT-AAAATGGTAATTTTTGGA
39633 TAGTTTAAGG
Statistics
Matches: 310, Mismatches: 51, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
56 6 0.02
57 36 0.12
58 33 0.11
59 148 0.48
60 85 0.27
61 2 0.01
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTTC
Found at i:39570 original size:117 final size:118
Alignment explanation
Indices: 39290--39632 Score: 444
Period size: 117 Copynumber: 2.9 Consensus size: 118
39280 AGAATCAGCA
** *
39290 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTTCTTTTTTGGAAAAATCGGGGTTAAA
1 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGG-TAATTTTTGGAAAAATCGAGGTTAAA
* * ** * *
39355 AATGAAATTTTTGG-AAGTTTG-GGGTAGAATGGTAATTTTGTGAAAAAAATCGAGG
65 AATGGAA-TTTTGGAAAGTTCGAGGCAAAAAT-GTAATTTT-TGGAAAAAATCGAGG
39410 T-AAAAATGGAATTTTTGGAAGTT-GGGGGTAAAATGGTAATTTTTGGAAAAATCGAGG-TAAAA
1 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAA
*
39472 ATGGAATTTTGGAAAGTTCGAGGCAAAAATGTAATTTTTGGGAAAAATCGAGG
66 ATGGAATTTTGGAAAGTTCGAGGCAAAAATGTAATTTTTGGAAAAAATCGAGG
*** *
39525 TCAAAAATGGAATTTTAAAAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAAATCGAGGTTAAAA
1 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAA
* * * *
39590 ATAGAATTTTGGAAAGTTCAAGGGTAAAAATATAATTTTTGGA
66 ATGGAATTTTGGAAAGTTCGA-GGCAAAAATGTAATTTTTGGA
39633 TAGTTTAAGG
Statistics
Matches: 198, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
115 20 0.10
116 43 0.22
117 57 0.29
118 37 0.19
119 40 0.20
120 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (118 bp):
TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAA
ATGGAATTTTGGAAAGTTCGAGGCAAAAATGTAATTTTTGGAAAAAATCGAGG
Found at i:39604 original size:29 final size:28
Alignment explanation
Indices: 39333--39604 Score: 171
Period size: 28 Copynumber: 9.3 Consensus size: 28
39323 AATGGTTCTT
* *
39333 TTTTGGAAAAATCGGGGTTAAAAATGAAA
1 TTTTGGAAAAATCGAGG-TAAAAATGGAA
** * * *
39362 TTTTTGG-AAGTTTGGGGT-AGAATGGTAA
1 -TTTTGGAAAAATCGAGGTAAAAATGG-AA
39390 TTTTGTGAAAAAAATCGAGGTAAAAATGGAA
1 TTTTG-G--AAAAATCGAGGTAAAAATGGAA
** * *
39421 TTTTTGG-AAGTTGGGGGT-AAAATGGTAA
1 -TTTTGGAAAAATCGAGGTAAAAATGG-AA
39449 TTTTTGGAAAAATCGAGGTAAAAATGGAA
1 -TTTTGGAAAAATCGAGGTAAAAATGGAA
** * *
39478 TTTTGGAAAGTTCGAGGCAAAAATGTAA
1 TTTTGGAAAAATCGAGGTAAAAATGGAA
39506 TTTTTGGGAAAAATCGAGGTCAAAAATGGAA
1 -TTTT-GGAAAAATCGAGGT-AAAAATGGAA
*
39537 TTTT--AAAAAGTTCGGGGGT-AAAATGGTAA
1 TTTTGGAAAAA--TC-GAGGTAAAAATGG-AA
* *
39566 TTTTTAGAAAAATCGAGGTTAAAAATAGAA
1 -TTTTGGAAAAATCGAGG-TAAAAATGGAA
39596 TTTTGGAAA
1 TTTTGGAAA
39605 GTTCAAGGGT
Statistics
Matches: 190, Mismatches: 30, Indels: 45
0.72 0.11 0.17
Matches are distributed among these distances:
27 22 0.12
28 51 0.27
29 35 0.18
30 41 0.22
31 25 0.13
32 16 0.08
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (28 bp):
TTTTGGAAAAATCGAGGTAAAAATGGAA
Found at i:39632 original size:30 final size:30
Alignment explanation
Indices: 39292--39637 Score: 213
Period size: 30 Copynumber: 11.8 Consensus size: 30
39282 AATCAGCATC
*
39292 AAAAATGGAATTTTTGG-AAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
** **
39321 -AAAATGGTTCTTTTTTGGAAAAATCG-GGGTT
1 AAAAATGG--AATTTTTGGAAAGTTCGAGGG-T
* *
39352 AAAAATGAAATTTTTGG-AAGTTTG-GGGT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
* * **
39380 -AGAATGGTAATTTTGTGAAAAAAATCGA-GGT
1 AAAAATGG-AATTTT-TG-GAAAGTTCGAGGGT
*
39411 AAAAATGGAATTTTTGG-AAGTT-GGGGGT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
**
39439 -AAAATGGTAATTTTTGGAAAAATCGA-GGT
1 AAAAATGG-AATTTTTGGAAAGTTCGAGGGT
*
39468 AAAAATGGAA-TTTTGGAAAGTTCGA-GGC
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
* **
39496 AAAAATGTAATTTTTGGGAAAAATCGA-GGT
1 AAAAATGGAATTTTT-GGAAAGTTCGAGGGT
** *
39526 CAAAAATGGAA-TTTTAAAAAGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAAAGTTCGAGGGT
* ** *
39556 -AAAATGGTAATTTTTAGAAAAATCGAGGTT
1 AAAAATGG-AATTTTTGGAAAGTTCGAGGGT
* *
39586 AAAAATAGAA-TTTTGGAAAGTTCAAGGGT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
** *
39615 AAAAATATAATTTTTGGATAGTT
1 AAAAATGGAATTTTTGGAAAGTT
39638 TAAGGACCTA
Statistics
Matches: 243, Mismatches: 50, Indels: 47
0.71 0.15 0.14
Matches are distributed among these distances:
27 13 0.05
28 60 0.25
29 52 0.21
30 72 0.30
31 34 0.14
32 12 0.05
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAAGTTCGAGGGT
Found at i:40706 original size:3 final size:3
Alignment explanation
Indices: 40675--40776 Score: 89
Period size: 3 Copynumber: 33.0 Consensus size: 3
40665 CACTTTCTTT
* * * * *
40675 TTA TTA ATA TTA ATA TTAA TTA ATA TTA TTA TCAA TTA TTA -TA CCTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA TTA TTA -TTA
* *
40722 TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TGTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
40768 TCA TTA TTA
1 TTA TTA TTA
40777 ATAATAATGT
Statistics
Matches: 79, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
2 2 0.03
3 67 0.85
4 10 0.13
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:41476 original size:17 final size:17
Alignment explanation
Indices: 41451--41521 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
41441 CTTTAATTTT
*
41451 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
41468 ATTTAAATTTAAAGA-AA
1 ATTTAAATTTAAA-ATAA
* * *
41485 ATTCAAACTTAAAATGA
1 ATTTAAATTTAAAATAA
*
41502 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
41519 ATT
1 ATT
41522 CAAACTTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.02
17 42 0.95
18 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:41497 original size:34 final size:34
Alignment explanation
Indices: 41459--41551 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 34
41449 TTATTTTAAT
41459 TTAAAATAAATTTAAATTTAAAGA-AAATTCAAAC
1 TTAAAATAAATTTAAATTTAAA-ATAAATTCAAAC
* *
41493 TTAAAATGAATTTGAATTTAAAATAAATTCAAAC
1 TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
* *
41527 TTATTTAA-AAATTAAAATTTAAAAT
1 TTA--AAATAAATTTAAATTTAAAAT
41552 TTGGACTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
33 1 0.02
34 33 0.66
35 14 0.28
36 2 0.04
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
Found at i:42695 original size:20 final size:20
Alignment explanation
Indices: 42657--42695 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42647 GCTCCGCCCT
* **
42657 ATCCTCGCCCGCCTTGCATC
1 ATCCTCGCCCACCCCGCATC
42677 ATCCTCGCCCACCCCGCAT
1 ATCCTCGCCCACCCCGCAT
42696 AATATAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.54, G:0.13, T:0.21
Consensus pattern (20 bp):
ATCCTCGCCCACCCCGCATC
Found at i:45529 original size:16 final size:18
Alignment explanation
Indices: 45508--45540 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
45498 ATTCACAAAG
45508 GAAAGTT-GTA-TTTTAA
1 GAAAGTTAGTACTTTTAA
45524 GAAAGTTAGTACTTTTA
1 GAAAGTTAGTACTTTTA
45541 GCATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.42
Consensus pattern (18 bp):
GAAAGTTAGTACTTTTAA
Found at i:51031 original size:28 final size:30
Alignment explanation
Indices: 50856--51033 Score: 113
Period size: 28 Copynumber: 6.1 Consensus size: 30
50846 AATAAAAGGG
*
50856 AAATTTTAAAAAAATAAAA-ATAAAGGATT-
1 AAATTTAAAAAAAATAAAATA-AAAGGATTA
** * * * *
50885 TGATTAAATAAAAAATAGAATATAAGG-GT-
1 AAATTTAA-AAAAAATAAAATAAAAGGATTA
* * *
50914 GAATTTAAAAGAAATAAAATAAAAGGGTTA
1 AAATTTAAAAAAAATAAAATAAAAGGATTA
* *
50944 AATTTTAATAAAAATAAAAATAAAAGGATT-
1 AAATTTAAAAAAAAT-AAAATAAAAGGATTA
* * *
50974 TAA-TTAAAAAAAATAAAATAAATGG-GTA
1 AAATTTAAAAAAAATAAAATAAAAGGATTA
**
51002 AAATTTAAAAGGAA-AAAATAAAA-GATTA
1 AAATTTAAAAAAAATAAAATAAAAGGATTA
51030 AAAT
1 AAAT
51034 CAAATTAAAA
Statistics
Matches: 112, Mismatches: 29, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
27 2 0.02
28 41 0.37
29 29 0.26
30 26 0.23
31 14 0.12
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (30 bp):
AAATTTAAAAAAAATAAAATAAAAGGATTA
Found at i:51924 original size:8 final size:8
Alignment explanation
Indices: 51911--51936 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
51901 TTTACTTTCG
51911 AAAAATAA
1 AAAAATAA
51919 AAAAATAA
1 AAAAATAA
51927 AAAAATAA
1 AAAAATAA
51935 AA
1 AA
51937 TAAAAGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:55726 original size:17 final size:18
Alignment explanation
Indices: 55704--55737 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55694 TAAATGAGTT
55704 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
55721 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
55738 ATAGAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:62938 original size:74 final size:74
Alignment explanation
Indices: 62817--62966 Score: 300
Period size: 74 Copynumber: 2.0 Consensus size: 74
62807 ACCATATGAA
62817 AATAATTTTGATGAAAACAAATACTAACAAAAGTAAGGCCAATACAAATGAGCAAAGAAATGAAA
1 AATAATTTTGATGAAAACAAATACTAACAAAAGTAAGGCCAATACAAATGAGCAAAGAAATGAAA
62882 GAATTTTGT
66 GAATTTTGT
62891 AATAATTTTGATGAAAACAAATACTAACAAAAGTAAGGCCAATACAAATGAGCAAAGAAATGAAA
1 AATAATTTTGATGAAAACAAATACTAACAAAAGTAAGGCCAATACAAATGAGCAAAGAAATGAAA
62956 GAATTTTGT
66 GAATTTTGT
62965 AA
1 AA
62967 AAAAAAAAAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (74 bp):
AATAATTTTGATGAAAACAAATACTAACAAAAGTAAGGCCAATACAAATGAGCAAAGAAATGAAA
GAATTTTGT
Found at i:64982 original size:29 final size:29
Alignment explanation
Indices: 64943--65501 Score: 320
Period size: 29 Copynumber: 19.1 Consensus size: 29
64933 CAGAGTAAAA
**
64943 AAAAT-GTAATTTTTGGATGCCCGAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* *
64971 AAAATGGTAATTTTTGGACGTTCAAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* * *
65000 AAAACGATAATTTTTGGATGTTCAAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* ** * * *
65029 AAAACGGTAATTTTCAGATGCTCGA-CGA
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* *
65057 AAAATGGTAATTTTGGGATGATT-AAGGGGT
1 AAAATGGTAATTTTTGGATG-TTCGA-GGGT
*** *** * *
65087 AAAACAATAATTTTTGGACACTCAAGGGA
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
*
65116 AAAATGGTAATTTTTGGACGTTCGAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
*** * *
65145 AAAATGGTAA-TTTTGGACACTCGGGGGA
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* *
65173 AAAATGGTAATTTTTGAAAAGTTCGA-GGT
1 AAAATGGTAATTTTTG-GATGTTCGAGGGT
* *** ** * *
65202 AAAAAAT-GTAAGTTTCAAACATTCAAAGGT
1 --AAAATGGTAATTTTTGGATGTTCGAGGGT
*
65232 AAAATGGTAATTTTTGAATGTTCGAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
*
65261 AAAAAGGTAATTTTTGGATGTT-GAAGGGT
1 AAAATGGTAATTTTTGGATGTTCG-AGGGT
* * *
65290 AAAATGGTAA-TTTTGGAAAGTT-TATGGT
1 AAAATGGTAATTTTTGG-ATGTTCGAGGGT
** *
65318 CAAAAAAT-GTAATTTTTGGACATCCGAGGGT
1 ---AAAATGGTAATTTTTGGATGTTCGAGGGT
*
65349 AAAATGGTAATTTTTGGATGTTCAAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* * * * *
65378 AAAATGATAATTTTTAGAAGTTTGAGGGC
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* *
65407 AAAACT-GTAATTTTTGGAAGATT-AAGGGTT
1 AAAA-TGGTAATTTTTGGATG-TTCGAGGG-T
* *
65437 AAAAT-GTAATTTTTTGTGAAAGTTCGAGTGT
1 AAAATGGTAA-TTTTTG-G-ATGTTCGAGGGT
*
65468 CAAAAT-GTAA-TTTTGGAATGTTCAAGGGT
1 -AAAATGGTAATTTTTGG-ATGTTCGAGGGT
65497 CAAAA
1 -AAAA
65502 CATGATTTTT
Statistics
Matches: 415, Mismatches: 89, Indels: 53
0.75 0.16 0.10
Matches are distributed among these distances:
28 69 0.17
29 252 0.61
30 55 0.13
31 24 0.06
32 15 0.04
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATGTTCGAGGGT
Found at i:65175 original size:116 final size:114
Alignment explanation
Indices: 64968--65501 Score: 382
Period size: 116 Copynumber: 4.6 Consensus size: 114
64958 GATGCCCGAG
** * * *
64968 GGTAAAATGGTAATTTTTGGACGTTCAAGGGTAAAACGATAATTTTTGGATGTTCAAGGGTAAAA
1 GGTAAAAAAGTAATTTTTGGACATTCAAGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAAA
* * * ** * *
65033 CGGTAATTTTCAGATGCTC-GACGAAAAATGGTAATTTTGGGATGATTAAGG
66 TGGTAATTTT-GGA-ACTCGGGGGAAAAATGGTAATTTTGGGAAGATT-AGA
* * * *
65084 GGTAAAACAA-TAATTTTTGGACACTCAAGGGAAAAATGGTAATTTTTGGACGTTCGAGGGTAAA
1 GGTAAAA-AAGTAATTTTTGGACATTCAAGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAA
* * *
65148 ATGGTAATTTTGGACACTCGGGGGAAAAATGGTAATTTT-TGAAAAGTTCGA
65 ATGGTAATTTTGGA-ACTCGGGGGAAAAATGGTAATTTTGGGAAGA-TTAGA
* *** * * *
65199 GGTAAAAAATGTAAGTTTCAAACATTCAAAGGTAAAATGGTAATTTTTGAATGTTCGAGGGTAAA
1 GGTAAAAAA-GTAATTTTTGGACATTCAAGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAA
* ** * * * * * *
65264 AAGGTAATTTTTGGATGTTGAAGGGTAAAATGGTAATTTTGGAAAGTTTA-T
65 ATGGTAA-TTTTGGAACTCG-GGGGAAAAATGGTAATTTTGGGAAGATTAGA
* *
65315 GGTCAAAAAATGTAATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAA
1 GGT-AAAAAA-GTAATTTTTGGACATTCAAGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAA
* * * * * * *
65380 AATGATAATTTTTAGAAGTTTGAGGGCAAAACT-GTAATTTTTGGAAGATTA-A
64 AATGGTAA-TTTTGGAA-CTCG-GGGGAAAAATGGTAATTTTGGGAAGATTAGA
* * * * *
65432 GGGTTAAAATGTAATTTTTTGTGAAAGTTCGAGTGTCAAAAT-GTAA-TTTTGGAATGTTCAAGG
1 -GGTAAAAAAGTAA-TTTTTG-GACA-TTCAAGGGT-AAAATGGTAATTTTTGG-ATGTTCAAGG
65495 GTCAAAA
60 GT-AAAA
65502 CATGATTTTT
Statistics
Matches: 333, Mismatches: 68, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
114 2 0.01
115 16 0.05
116 143 0.43
117 116 0.35
118 24 0.07
119 23 0.07
120 9 0.03
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (114 bp):
GGTAAAAAAGTAATTTTTGGACATTCAAGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAAA
TGGTAATTTTGGAACTCGGGGGAAAAATGGTAATTTTGGGAAGATTAGA
Found at i:65399 original size:88 final size:87
Alignment explanation
Indices: 65254--65424 Score: 247
Period size: 88 Copynumber: 2.0 Consensus size: 87
65244 TTTGAATGTT
* * * *
65254 CGAGGGTAAAAAGGTAATTTTTGGATGTTGAAGGGTAAAATGGTAATTTTGGAAAGTTT-ATGGT
1 CGAGGGTAAAAAGGTAATTTTTGGATGTTCAAGGGTAAAATGATAATTTTAGAAAGTTTGA-GGG
65318 CAAAAAATGTAATTTTTGGACATC
65 C-AAAAATGTAATTTTTGGACATC
*
65342 CGAGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAAATGATAATTTTTAG-AAGTTTGAGGG
1 CGAGGGTAAAAAGGTAATTTTTGGATGTTCAAGGGTAAAATGATAA-TTTTAGAAAGTTTGAGGG
*
65406 CAAAACTGTAATTTTTGGA
65 CAAAAATGTAATTTTTGGA
65425 AGATTAAGGG
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
87 17 0.23
88 52 0.69
89 6 0.08
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (87 bp):
CGAGGGTAAAAAGGTAATTTTTGGATGTTCAAGGGTAAAATGATAATTTTAGAAAGTTTGAGGGC
AAAAATGTAATTTTTGGACATC
Found at i:65440 original size:88 final size:88
Alignment explanation
Indices: 65256--65450 Score: 238
Period size: 88 Copynumber: 2.2 Consensus size: 88
65246 TGAATGTTCG
* * * * *
65256 AGGGTAAAAAGGTAATTTTTGGATGTTGAAGGGTAAAATGGTAATTTTGGAAAGTTTATGGTCAA
1 AGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAAATGATAATTTTAGAAAGTTTATGGGCAA
*
65321 AAAATGTAATTTTTGGACATCCG
66 AAAATGTAATTTTTGGACATCCA
65344 AGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAAATGATAATTTTTAG-AAGTTTGA-GGGC
1 AGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAAATGATAA-TTTTAGAAAGTTT-ATGGGC
* * *
65407 -AAAACTGTAATTTTTGGAAGAT-TA
64 AAAAAATGTAATTTTTGG-ACATCCA
65431 AGGGTTAAAAT-GTAATTTTT
1 AGGG-TAAAATGGTAATTTTT
65451 TGTGAAAGTT
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
87 29 0.31
88 59 0.63
89 6 0.06
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (88 bp):
AGGGTAAAATGGTAATTTTTGGATGTTCAAGGGTAAAATGATAATTTTAGAAAGTTTATGGGCAA
AAAATGTAATTTTTGGACATCCA
Found at i:66614 original size:14 final size:14
Alignment explanation
Indices: 66595--66628 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
66585 TTGGTTATTA
*
66595 TTAATATTATTTAT
1 TTAATATTACTTAT
66609 TTAATATTACTTAT
1 TTAATATTACTTAT
66623 TTAATA
1 TTAATA
66629 CGTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATATTACTTAT
Found at i:67290 original size:17 final size:17
Alignment explanation
Indices: 67270--67385 Score: 144
Period size: 17 Copynumber: 6.7 Consensus size: 17
67260 AATTAAATTC
67270 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
67287 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
*
67304 TAAATTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
*
67321 TAAATTTAAACTCGAAAAA
1 TAAATTTAAATTC--AAAA
* *
67340 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
*
67357 TAAATTTACATGT-AAAA
1 TAAATTTAAAT-TCAAAA
*
67374 TAAATTAAAATT
1 TAAATTTAAATT
67386 TAGAATTTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.01
17 70 0.81
18 1 0.01
19 14 0.16
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:67321 original size:7 final size:6
Alignment explanation
Indices: 67262--67393 Score: 67
Period size: 6 Copynumber: 22.3 Consensus size: 6
67252 AACTTTTTAA
* * * *
67262 TTAAAT TCTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TCAAA- ATAAAT
1 TTAAAT T-TAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* ** * * *
67309 TTAAAT TTAAA- ATAAAT TTAAACT CGAAAA ATAAGT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT
* * * * *
67356 ATAAAT TTACAT GTAAA- ATAAAT TAAAAT TTAGAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TT
67394 TAAAATTGGA
Statistics
Matches: 90, Mismatches: 28, Indels: 15
0.68 0.21 0.11
Matches are distributed among these distances:
5 18 0.20
6 57 0.63
7 15 0.17
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:67348 original size:53 final size:51
Alignment explanation
Indices: 67270--67379 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 51
67260 AATTAAATTC
* *
67270 TAAATTTAAATTCAAAATAAATTTAAATTCAAAATAAATTTAAATTTAAAA
1 TAAATTTAAACTCAAAATAAATTTAAATTCAAAATAAATTTAAATGTAAAA
* * *
67321 TAAATTTAAACTCGAAAAATAAGTTTAAATTTAAAATAAATTTACATGTAAAA
1 TAAATTTAAACTC--AAAATAAATTTAAATTCAAAATAAATTTAAATGTAAAA
67374 TAAATT
1 TAAATT
67380 AAAATTTAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
51 12 0.23
53 40 0.77
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (51 bp):
TAAATTTAAACTCAAAATAAATTTAAATTCAAAATAAATTTAAATGTAAAA
Found at i:68372 original size:210 final size:210
Alignment explanation
Indices: 67775--68372 Score: 917
Period size: 210 Copynumber: 2.8 Consensus size: 210
67765 TCTTGATCTT
* * * * ** * * *
67775 CTTCTCTGTATCTTACCAGGAAGATGACCATTTTATTGCGTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTCGACTTGCTTCTCAATATCTCATC
* * * *
67840 GGGAAGATGGGATTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTGATTTGGTCTACTTCTC
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTGACTTGGTCTACTTCTC
* * *
67905 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCATCTCTGTATCTCATTAGGAA
131 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCTTCTCTGTATCTCATCAGCAA
67970 GACGGATTTGGTCCA
196 GACGGATTTGGTCCA
* *
67985 CTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTCGACTTGCTTCTCAATATCTCATT
1 CTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTCGACTTGCTTCTCAATATCTCATC
*
68050 AGGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTGACTTGGTCTACTTCTC
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTGACTTGGTCTACTTCTC
* * *
68115 AGTATCTCATCAGGAAGATGACTGCATCGCTTGTTTTGATCCGCTTCTCTGTATCTCGTCAGCAA
131 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCTTCTCTGTATCTCATCAGCAA
* *
68180 GATGGATTTGGTCTA
196 GACGGATTTGGTCCA
*
68195 CTTCTCTGTATCTCATCAAGAAGACGATCGCTTTATTGCTTCGACTTGCTTCTCAATATCTCATC
1 CTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTCGACTTGCTTCTCAATATCTCATC
* * *
68260 AGGAAGCTGGGGCTCGAAGTTTCACTCACATCGACCTTTGGTTTCATTGACTTGGTCTACTTCTC
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTGACTTGGTCTACTTCTC
* * *
68325 AGTATCTCATCAGGAATATGACCGCATCACTTATTTTGATTCGCTTCT
131 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCTTCT
68373 TTGACCCATA
Statistics
Matches: 354, Mismatches: 34, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
210 354 1.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (210 bp):
CTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTCGACTTGCTTCTCAATATCTCATC
AGGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTGACTTGGTCTACTTCTC
AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCTTCTCTGTATCTCATCAGCAA
GACGGATTTGGTCCA
Found at i:73864 original size:13 final size:13
Alignment explanation
Indices: 73843--73878 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
73833 GCGGCCTTGA
*
73843 TGTTCTAGTGGCC
1 TGTTATAGTGGCC
73856 TGTTATAGTGGCC
1 TGTTATAGTGGCC
73869 TGTTATAGTG
1 TGTTATAGTG
73879 TCCTTATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.42
Consensus pattern (13 bp):
TGTTATAGTGGCC
Found at i:86031 original size:14 final size:14
Alignment explanation
Indices: 86012--86045 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
86002 TTTAAAAATG
*
86012 TATTAAATAAGTAA
1 TATTAAATAAATAA
86026 TATTAAATAAATAA
1 TATTAAATAAATAA
86040 TATTAA
1 TATTAA
86046 TAATAACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TATTAAATAAATAA
Found at i:87982 original size:28 final size:28
Alignment explanation
Indices: 87916--88044 Score: 107
Period size: 28 Copynumber: 4.5 Consensus size: 28
87906 GCCCGAAGGC
* *
87916 AAAATGGTAATTTTAAGATGTTCGAGGGT
1 AAAATGGTAATTTT-AGATGCTCAAGGGT
* *
87945 -AAACGATAATTTTAGATGCTCAAGGGT
1 AAAATGGTAATTTTAGATGCTCAAGGGT
* * *
87972 AAAATGGTAATTTTGGAATGATCGAGGGGT
1 AAAATGGTAATTTTAG-ATGCTC-AAGGGT
* * ** *
88002 AAAATAGTAATTTTTGGACACTCAAAGGT
1 AAAATGGTAA-TTTTAGATGCTCAAGGGT
88031 AAAATGGTAATTTT
1 AAAATGGTAATTTT
88045 TGGACGTTCG
Statistics
Matches: 80, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
27 12 0.15
28 27 0.34
29 18 0.22
30 17 0.21
31 6 0.08
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (28 bp):
AAAATGGTAATTTTAGATGCTCAAGGGT
Found at i:88041 original size:59 final size:59
Alignment explanation
Indices: 87911--88188 Score: 223
Period size: 58 Copynumber: 4.8 Consensus size: 59
87901 TGGATGCCCG
* ** * * * * **
87911 AAGGCAAAATGGTAATTTTAAGATGTTCGA-GGGT-AAACGATAA-TTTTAGATGCTCA
1 AAGGTAAAATGGTAATTTTTGGATGATCGAGGGGTAAAAAGGTAATTTTTGGACACTCA
*
87967 AGGGTAAAATGGTAA-TTTTGGAATGATCGAGGGGTAAAATA-GTAATTTTTGGACACTCA
1 AAGGTAAAATGGTAATTTTTGG-ATGATCGAGGGGTAAAA-AGGTAATTTTTGGACACTCA
* * * * *
88026 AAGGTAAAATGGTAATTTTTGGACGTTCGA-GGTTAAAACGATAATTTTTGGACACTCA
1 AAGGTAAAATGGTAATTTTTGGATGATCGAGGGGTAAAAAGGTAATTTTTGGACACTCA
* * ** ** * * *
88084 AGGGCAAAATGGTAATTTTT-GAAAAGTTTAGGGTTAAAAATGTAA-TTTTGGTACATTCA
1 AAGGTAAAATGGTAATTTTTGGATGA-TCGAGGGGTAAAAAGGTAATTTTTGG-ACACTCA
* *
88143 GAGGTAAAATGGTAATTTTTGGATGTTCG-GGGGTAAAAAGGTAATT
1 AAGGTAAAATGGTAATTTTTGGATGATCGAGGGGTAAAAAGGTAATT
88189 CGAGGGTAAA
Statistics
Matches: 173, Mismatches: 37, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
55 4 0.02
56 20 0.12
57 6 0.03
58 69 0.40
59 66 0.38
60 8 0.05
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (59 bp):
AAGGTAAAATGGTAATTTTTGGATGATCGAGGGGTAAAAAGGTAATTTTTGGACACTCA
Found at i:88129 original size:117 final size:116
Alignment explanation
Indices: 87887--88180 Score: 326
Period size: 117 Copynumber: 2.5 Consensus size: 116
87877 AAACGGAGTC
* ** * * * **
87887 AAAAATGCAATTTTTGGATGCCCGAAGGCAAAATGGTAATTTTAAGATGTTCGAGGGT-AAACGA
1 AAAAATGTAATTTTTGGACACTCAAAGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAACGA
** * * *
87951 TAATTTTAGATGCTCAAGGGTAAAATGGTAATTTTGGAATGATCGAGGGGT
66 TAATTTTAGACACTCAAGGGCAAAATGGTAATTTTGAAAAGATCGAGGGGT
* *
88002 -AAAATAGTAATTTTTGGACACTCAAAGGTAAAATGGTAATTTTTGGACGTTCGAGGTTAAAACG
1 AAAAAT-GTAATTTTTGGACACTCAAAGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAACG
* ** *
88066 ATAATTTTTGGACACTCAAGGGCAAAATGGTAATTTTTGAAAAG-TTTAGGGTT
65 ATAA-TTTTAGACACTCAAGGGCAAAATGGTAA-TTTTGAAAAGATCGAGGGGT
* * *
88119 AAAAATGTAA-TTTTGGTACATTCAGAGGTAAAATGGTAATTTTTGGATGTTCGGGGGTAAAA
1 AAAAATGTAATTTTTGG-ACACTCAAAGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAA
88181 AGGTAATTCG
Statistics
Matches: 149, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
114 5 0.03
115 42 0.28
116 15 0.10
117 74 0.50
118 13 0.09
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (116 bp):
AAAAATGTAATTTTTGGACACTCAAAGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAACGA
TAATTTTAGACACTCAAGGGCAAAATGGTAATTTTGAAAAGATCGAGGGGT
Found at i:88177 original size:29 final size:29
Alignment explanation
Indices: 87916--88390 Score: 160
Period size: 29 Copynumber: 16.6 Consensus size: 29
87906 GCCCGAAGGC
** * *
87916 AAAATGGTAATTTTAAGATGTTCGAGGGT
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* * * * *
87945 -AAACGATAA-TTTTAGATGCTCAAGGGT
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* * *
87972 AAAATGGTAA-TTTTGGAATGATCGAGGGGT
1 AAAATGGTAATTTTTGG-ACGTTC-AAGGGT
* ** *
88002 AAAATAGTAATTTTTGGACACTCAAAGGT
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* *
88031 AAAATGGTAATTTTTGGACGTTCGAGGTT
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* * ** *
88060 AAAACGATAATTTTTGGACACTCAAGGGC
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* * *
88089 AAAATGGTAATTTTTGAAAAGTT-TAGGGTT
1 AAAATGGTAATTTTTG-GACGTTCAAGGG-T
*
88119 AAAAAT-GTAA-TTTTGGTACATTC-AGAGGT
1 -AAAATGGTAATTTTTGG-ACGTTCAAG-GGT
* **
88148 AAAATGGTAATTTTTGGATGTTCGGGGGT
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* * * *
88177 AAAAAGGTAA---TTCGAGGGT-AA----
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* ** * * * * * **
88198 AATA-GTAATTTTTGGAAAGTTCGAGGTCAA
1 AAAATGGTAATTTTTGGACGTTCAAGG--GT
* * * ***
88228 AAAAT-ATATTTTTTGGACATTTTGGGGT
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* * **
88256 AAAATGGTAATTTTTGAAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* * *
88285 AAAATGGTAATTTTTGGAAGTTCGAGGGC
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
* * *
88314 AAAACGATAATTTTTGGAAGTTCAAGGGT
1 AAAATGGTAATTTTTGGACGTTCAAGGGT
*
88343 AAAAAT-GTAATTTTTGAGAAGTTCAAGGGTT
1 -AAAATGGTAATTTTTG-GACGTTCAAGGG-T
88374 AAAAT-GTAATTTTTGGA
1 AAAATGGTAATTTTTGGA
88391 AAGTTCGAGG
Statistics
Matches: 331, Mismatches: 87, Indels: 56
0.70 0.18 0.12
Matches are distributed among these distances:
20 2 0.01
21 3 0.01
23 4 0.01
24 1 0.00
26 6 0.02
27 15 0.05
28 29 0.09
29 181 0.55
30 78 0.24
31 12 0.04
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGACGTTCAAGGGT
Found at i:88221 original size:30 final size:30
Alignment explanation
Indices: 88187--88407 Score: 201
Period size: 29 Copynumber: 7.4 Consensus size: 30
88177 AAAAAGGTAA
88187 TTCGAGGGTAAAATAGTAATTTTTGGAAAG
1 TTCGAGGGTAAAATAGTAATTTTTGGAAAG
* * *
88217 TTCGA-GGTCAAAAAATA-TATTTTTTGGACAT
1 TTCGAGGGT---AAAATAGTAATTTTTGGAAAG
* *
88248 TTTG-GGGTAAAATGGTAATTTTT-GAAAG
1 TTCGAGGGTAAAATAGTAATTTTTGGAAAG
* *
88276 TTTGAGGGTAAAATGGTAATTTTTGG-AAG
1 TTCGAGGGTAAAATAGTAATTTTTGGAAAG
* *
88305 TTCGAGGGCAAAA-CGATAATTTTTGG-AAG
1 TTCGAGGGTAAAATAG-TAATTTTTGGAAAG
*
88334 TTCAAGGGTAAAA-ATGTAATTTTT-GAGAAG
1 TTCGAGGGTAAAATA-GTAATTTTTGGA-AAG
*
88364 TTCAAGGGTTAAAAT-GTAATTTTTGGAAAG
1 TTCGAGGG-TAAAATAGTAATTTTTGGAAAG
88394 TTCGAGGGTCAAAA
1 TTCGAGGGT-AAAA
88408 CATGATTTAT
Statistics
Matches: 161, Mismatches: 15, Indels: 30
0.78 0.07 0.15
Matches are distributed among these distances:
28 14 0.09
29 76 0.47
30 41 0.25
31 24 0.15
32 6 0.04
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (30 bp):
TTCGAGGGTAAAATAGTAATTTTTGGAAAG
Found at i:88327 original size:166 final size:165
Alignment explanation
Indices: 88028--88354 Score: 389
Period size: 166 Copynumber: 2.0 Consensus size: 165
88018 GACACTCAAA
* * * *
88028 GGTAAAATGGTAATTTTTGGACGTTCGAGGTTAAAACGATAATTTTTGGACACTCAAGGGCAAAA
1 GGTAAAATAGTAATTTTTGGAAGTTCGAGGTCAAAACAATAATTTTTGGACACTCAAGGGCAAAA
* * *
88093 TGGTAATTTTTGAAAAGTTTAGGGTTAAAAATGTAATTTTGGTACATTCAGAGGTAAAATGGTAA
66 TGGTAATTTTTGAAAAGTTTAGGGTTAAAAATGTAATTTTGGTACATTCAGAGGCAAAACGATAA
* **
88158 TTTTTGGATGTTCGGGGGTAAAAAGGTAATTCGAG
131 TTTTTGGAAGTTCAAGGGTAAAAAGGTAATTCGAG
* *** *
88193 GGTAAAATAGTAATTTTTGGAAAGTTCGAGGTCAAAA-AATATATTTTTTGGACATTTTGGGGTA
1 GGTAAAATAGTAATTTTTGG-AAGTTCGAGGTCAAAACAATA-A-TTTTTGGACACTCAAGGGCA
88257 AAATGGTAATTTTTG-AAAGTTTGAGGG-T-AAAATGGTAATTTTTGG-A-AGTTC-GAGGGCAA
63 AAATGGTAATTTTTGAAAAGTTT-AGGGTTAAAAAT-GTAA-TTTTGGTACA-TTCAGA-GGCAA
*
88316 AACGATAATTTTTGGAAGTTCAAGGGTAAAAATGTAATT
123 AACGATAATTTTTGGAAGTTCAAGGGTAAAAAGGTAATT
88355 TTTGAGAAGT
Statistics
Matches: 138, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
165 30 0.22
166 68 0.49
167 40 0.29
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (165 bp):
GGTAAAATAGTAATTTTTGGAAGTTCGAGGTCAAAACAATAATTTTTGGACACTCAAGGGCAAAA
TGGTAATTTTTGAAAAGTTTAGGGTTAAAAATGTAATTTTGGTACATTCAGAGGCAAAACGATAA
TTTTTGGAAGTTCAAGGGTAAAAAGGTAATTCGAG
Found at i:90233 original size:17 final size:18
Alignment explanation
Indices: 90213--90287 Score: 84
Period size: 17 Copynumber: 4.3 Consensus size: 18
90203 TTTTAATTAA
90213 AAAATAAGTTTAAA-TTT
1 AAAATAAGTTTAAACTTT
* *
90230 AAAATAAATTTAAACTTAA
1 AAAATAAGTTTAAACTT-T
90249 AAAATAAGTTTAAA-TTT
1 AAAATAAGTTTAAACTTT
* *
90266 AAAATAA-ATTAAATTTT
1 AAAATAAGTTTAAACTTT
90283 AAAAT
1 AAAAT
90288 TGGGTTCAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
16 5 0.10
17 28 0.56
18 4 0.08
19 13 0.26
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAATAAGTTTAAACTTT
Found at i:90233 original size:19 final size:19
Alignment explanation
Indices: 90209--90269 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
90199 AACTTTTTAA
90209 TTAAAAAATAAGTTTAAAT
1 TTAAAAAATAAGTTTAAAT
* *
90228 TT--AAAATAAATTTAAAC
1 TTAAAAAATAAGTTTAAAT
90245 TTAAAAAATAAGTTTAAAT
1 TTAAAAAATAAGTTTAAAT
90264 TTAAAA
1 TTAAAA
90270 TAAATTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 15 0.42
19 21 0.58
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (19 bp):
TTAAAAAATAAGTTTAAAT
Found at i:98451 original size:23 final size:22
Alignment explanation
Indices: 98419--98521 Score: 107
Period size: 23 Copynumber: 4.5 Consensus size: 22
98409 GCTGGGGAAA
*
98419 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
98441 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * **
98464 CAGTAGGCGCACATAGCACAAAT
1 CAGTAGGCACACACAGTGC-AAT
* *
98487 CAGTAGGCACACAAAGTGCGAAA
1 CAGTAGGCACACACAGTGC-AAT
*
98510 CAGTAAGCACAC
1 CAGTAGGCACAC
98522 GAAGTGCGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
22 15 0.22
23 52 0.78
ACGTcount: A:0.40, C:0.27, G:0.21, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:98526 original size:23 final size:23
Alignment explanation
Indices: 98487--98563 Score: 127
Period size: 23 Copynumber: 3.3 Consensus size: 23
98477 TAGCACAAAT
* *
98487 CAGTAGGCACACAAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
98510 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
98533 CAGTAAGCGCACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
98556 CAGTAAGC
1 CAGTAAGC
98564 GCGCTAGCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.42, C:0.22, G:0.27, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:100257 original size:24 final size:25
Alignment explanation
Indices: 100201--100275 Score: 98
Period size: 24 Copynumber: 2.9 Consensus size: 25
100191 ACTTACGCAG
*
100201 GTCCGCATGGACTATCTTTCAAGTAA
1 GTCCACATGGACTATCTTTCAAG-AA
*
100227 GAATCCACATGGACTATTTTTCAAG-A
1 G--TCCACATGGACTATCTTTCAAGAA
100253 GTCCACATGGACTATCTTTCAAG
1 GTCCACATGGACTATCTTTCAAG
100276 CAATAGTTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
24 21 0.48
26 3 0.07
28 20 0.45
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (25 bp):
GTCCACATGGACTATCTTTCAAGAA
Found at i:104667 original size:20 final size:19
Alignment explanation
Indices: 104628--104667 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
104618 AGATGCGATA
* *
104628 AAAGAAGAGTAAAAGTTTT
1 AAAGAAAAGTAAAAATTTT
104647 AAAGAAAAGTAAAAATATTT
1 AAAGAAAAGTAAAAAT-TTT
104667 A
1 A
104668 GAAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (19 bp):
AAAGAAAAGTAAAAATTTT
Found at i:107771 original size:29 final size:29
Alignment explanation
Indices: 107728--107854 Score: 157
Period size: 30 Copynumber: 4.3 Consensus size: 29
107718 AATAAAGGAC
* *
107728 AAAAATGGAATTTTTAGAAGTTTCAAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
*
107757 AAAAAATGGAATTTTTGGAAG-TTCGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTC-GAGGT
* *
107787 AAAAATGGAATTTTTGAAAGTCTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGG-T
* *
107817 AAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
107846 AAAAATGGA
1 AAAAATGGA
107855 GTAAAAATGG
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
29 35 0.42
30 49 0.58
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGT
Found at i:107799 original size:59 final size:59
Alignment explanation
Indices: 107728--107854 Score: 202
Period size: 59 Copynumber: 2.2 Consensus size: 59
107718 AATAAAGGAC
*
107728 AAAAATGGAATTTTT-AGAAGTTTCAAGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGA-AAGTCTCAAGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGT
* * *
107787 AAAAATGGAATTTTTGAAAGTCTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGAAAGTCTCAAGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGT
107846 AAAAATGGA
1 AAAAATGGA
107855 GTAAAAATGG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
59 62 0.98
60 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (59 bp):
AAAAATGGAATTTTTGAAAGTCTCAAGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:107860 original size:40 final size:39
Alignment explanation
Indices: 107816--107893 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
107806 GTCTCGAGGT
*
107816 TAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAG
1 TAAAAATGGAATTTTTGGAAGTTTAGGGGT-AAAATGGAG
* *
107856 TAAAAATGGATTTTTTGGAAGTTTAGGTGTAAAATGGA
1 TAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGA
107894 ATTTTTGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 8 0.23
40 27 0.77
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.33
Consensus pattern (39 bp):
TAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGAG
Found at i:107897 original size:68 final size:71
Alignment explanation
Indices: 107785--107923 Score: 205
Period size: 68 Copynumber: 2.0 Consensus size: 71
107775 AAGTTCGGGG
107785 GTAAAAATGGAATTTTTGAAAGTCTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGT-AAA
1 GTAAAAATGGAATTTTTGAAAGTCTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTCAAA
107849 AATGGA
66 AATGGA
* * * *
107855 GTAAAAATGGATTTTTTGGAAGT-T-TAGGTGT-AAAATGGAATTTTTGGAAGTTTTGGGGTCAA
1 GTAAAAATGGAATTTTTGAAAGTCTCGAGGT-TAAAAATGGAATTTTTGGAAGTTTGGGGGTCAA
107917 AAATGGA
65 AAATGGA
107924 ATTTTTGGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
68 31 0.49
69 11 0.17
70 21 0.33
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (71 bp):
GTAAAAATGGAATTTTTGAAAGTCTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTCAAA
AATGGA
Found at i:107919 original size:98 final size:99
Alignment explanation
Indices: 107758--107947 Score: 274
Period size: 98 Copynumber: 1.9 Consensus size: 99
107748 TTTCAAGGTA
* *
107758 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGTCTCGAGGTTAAAAAT
1 AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGAAAGTCTCGAGGTCAAAAAT
**
107823 GGAATTTTTGGAAGTTTGGGGGTAAAAATGGAGT
66 GGAATTTTTGGAAGTTCAGGGGTAAAAATGGAGT
* * * * * * *
107857 AAAAATGGATTTTTTGGAAGTTTAGGTGT-AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAAT
1 AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGAAAGTCTCGAGGTCAAAAAT
107921 GGAATTTTTGGAAGTTCAGGGGTAAAA
66 GGAATTTTTGGAAGTTCAGGGGTAAAA
107948 TATAATTTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
98 55 0.69
99 25 0.31
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (99 bp):
AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGAAAGTCTCGAGGTCAAAAAT
GGAATTTTTGGAAGTTCAGGGGTAAAAATGGAGT
Found at i:107922 original size:30 final size:29
Alignment explanation
Indices: 107855--107970 Score: 148
Period size: 28 Copynumber: 4.0 Consensus size: 29
107845 TAAAAATGGA
* *
107855 GTAAAAATGGATTTTTTGGAAGTTTAGGT
1 GTAAAAATGGAATTTTTGGAAGTTTAGGG
*
107884 GT-AAAATGGAATTTTTGGAAGTTTTGGG
1 GTAAAAATGGAATTTTTGGAAGTTTAGGG
*
107912 GTCAAAAATGGAATTTTTGGAAGTTCAGGG
1 GT-AAAAATGGAATTTTTGGAAGTTTAGGG
107942 GTAAAATAT--AATTTTTGGATAGTTTAGGG
1 GTAAAA-ATGGAATTTTTGGA-AGTTTAGGG
107971 AACTCGAGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
28 35 0.45
29 14 0.18
30 28 0.36
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (29 bp):
GTAAAAATGGAATTTTTGGAAGTTTAGGG
Found at i:109724 original size:28 final size:30
Alignment explanation
Indices: 109662--109724 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
109652 ATAGTAGCAG
* *
109662 ATTTGGGTCTTCTGTTTGGGTTAAATTGTA
1 ATTTGGGTCATCTGTTTGGGTTAAATTGAA
*
109692 A--TGGGTCAT-TGTTTGGG-TCAATTGAA
1 ATTTGGGTCATCTGTTTGGGTTAAATTGAA
109718 ATTTGGG
1 ATTTGGG
109725 CCCAATTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 8 0.29
27 8 0.29
28 11 0.39
30 1 0.04
ACGTcount: A:0.19, C:0.06, G:0.30, T:0.44
Consensus pattern (30 bp):
ATTTGGGTCATCTGTTTGGGTTAAATTGAA
Found at i:109850 original size:17 final size:16
Alignment explanation
Indices: 109824--109887 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
109814 CTTTTTAATT
*
109824 AATTTTAATTTACAATG
1 AATTTAAATTTA-AATG
*
109841 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAA-TG
**
109858 AATTTAAACTCAAAAATG
1 AATTTAAA-T-TTAAATG
109876 AATTTAAATTTA
1 AATTTAAATTTA
109888 GAACAAATTC
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
16 3 0.08
17 21 0.57
18 10 0.27
19 3 0.08
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (16 bp):
AATTTAAATTTAAATG
Found at i:110801 original size:39 final size:39
Alignment explanation
Indices: 110687--110896 Score: 151
Period size: 39 Copynumber: 5.4 Consensus size: 39
110677 CTGTGATCGA
* * *
110687 GGTAAGAGTTTGGTTGACGATGATCTACCCCAAGCTCGG
1 GGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGG
* * * * * ****
110726 GGTAAGAGATCGAATAGCT-ATAATCTGCCTTTGGCTCGG
1 GGTAAGAGATTG-GTTGATGATGATCTGCCCCAAGCTCGG
* *
110765 GGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCAG
1 GGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGG
* * * *
110804 GGTAAAAGATCAAATGGCT--TCA--ATCTGCCCCAAGCTCGA
1 GGTAAGAGAT----TGGTTGATGATGATCTGCCCCAAGCTCGG
* * *
110843 GGTAAGAGACTAGTTGATGACGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGG
110882 GGTAAGAGATTGGTT
1 GGTAAGAGATTGGTT
110897 AACGATGTCG
Statistics
Matches: 126, Mismatches: 35, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
35 3 0.02
37 2 0.02
38 3 0.02
39 110 0.87
40 2 0.02
41 2 0.02
43 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (39 bp):
GGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGG
Found at i:110807 original size:78 final size:78
Alignment explanation
Indices: 110683--110891 Score: 258
Period size: 78 Copynumber: 2.7 Consensus size: 78
110673 TACCCTGTGA
* * * *
110683 TCGAGGTAAGAGTTTGGTTGACGATGATCTACCCCAAGCTCGGGGTAAGAGATCGAATAGCTAT-
1 TCGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATAGCT-TC
****
110747 AATCTGCCTTTGGC
65 AATCTGCCCCAAGC
* * * * *
110761 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCAGGGTAAAAGATCAAATGGCTTCA
1 TCGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATAGCTTCA
110826 ATCTGCCCCAAGC
66 ATCTGCCCCAAGC
* * *
110839 TCGAGGTAAGAGACTAGTTGATGACGATCTGCCCCAAGCTCGGGGTAAGAGAT
1 TCGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGAT
110892 TGGTTAACGA
Statistics
Matches: 110, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 109 0.99
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
TCGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATAGCTTCA
ATCTGCCCCAAGC
Found at i:111102 original size:101 final size:101
Alignment explanation
Indices: 110978--111159 Score: 287
Period size: 101 Copynumber: 1.8 Consensus size: 101
110968 ACTTCGCTGT
* *
110978 AACTTCAAGAAGGTAGGATTTGATGTTGAAGCTTCATCTTGCTCTTACTACAACTTC-AGAAAGA
1 AACTTCAAGAAGGTAGGAATTGATGTTAAAGCTTCATCTTGCTCTTACTACAACTTCAAG-AAGA
*
111042 TAAAGACTTGCTATTGTTTTTAATCTGACTTTACTGC
65 TAAAGACTTGCCATTGTTTTTAATCTGACTTTACTGC
* *
111079 AACTTCAAG-AGGATAGGAATTGATGTTAAAGCTTCATCTTGCTCTTGCTACAACTTCAAGGAGA
1 AACTTCAAGAAGG-TAGGAATTGATGTTAAAGCTTCATCTTGCTCTTACTACAACTTCAAGAAGA
111143 TAAAGACTTGCCATTGT
65 TAAAGACTTGCCATTGT
111160 AGTTTTGATC
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
100 3 0.04
101 69 0.93
102 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (101 bp):
AACTTCAAGAAGGTAGGAATTGATGTTAAAGCTTCATCTTGCTCTTACTACAACTTCAAGAAGAT
AAAGACTTGCCATTGTTTTTAATCTGACTTTACTGC
Found at i:111494 original size:48 final size:48
Alignment explanation
Indices: 111284--111564 Score: 194
Period size: 49 Copynumber: 5.7 Consensus size: 48
111274 AATCTTCAAT
* * * * * *
111284 GTACTGGATTCGCTGTTGCGGCTTAAATCTTTTCCTTCTTGTCTTCTGAAG
1 GTACTGGATCCGCCGTTGCGACTTAGATCTTTCCCTT-TTGTCTT-TG-TG
* * * * *
111335 TTCAC-GG-TCCGCTGTTACGACTTAAAGCTTTCCCTTTTGTATCTTTGTG
1 GT-ACTGGATCCGCCGTTGCGACTTAGATCTTTCCCTTTTG--TCTTTGTG
* * *
111384 GTACAGGATCCGCCGTTGCG-GTCTAGATCTTTCCCTTTATGTCTCTAG-G
1 GTACTGGATCCGCCGTTGCGACT-TAGATCTTTCCCTTT-TGTCT-TTGTG
* * *
111433 GTACTAGG-TCCGCCATTGCGACTTAAACCTTTCCCTTTTGTCTTTGTG
1 GTACT-GGATCCGCCGTTGCGACTTAGATCTTTCCCTTTTGTCTTTGTG
* * * * * **
111481 GTACTGGGTCCGCCGTTACGACTTAGATTTTTCCCTTCATGTCTTCGCA
1 GTACTGGATCCGCCGTTGCGACTTAGATCTTTCCCTT-TTGTCTTTGTG
* *
111530 GTACTGGATCCGCCTTTGCGGCTTAGATCTTTCCC
1 GTACTGGATCCGCCGTTGCGACTTAGATCTTTCCC
111565 CTCATGTCTC
Statistics
Matches: 183, Mismatches: 34, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
47 4 0.02
48 37 0.20
49 77 0.42
50 54 0.30
51 9 0.05
52 2 0.01
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.39
Consensus pattern (48 bp):
GTACTGGATCCGCCGTTGCGACTTAGATCTTTCCCTTTTGTCTTTGTG
Found at i:111534 original size:97 final size:98
Alignment explanation
Indices: 111352--111564 Score: 245
Period size: 97 Copynumber: 2.2 Consensus size: 98
111342 TCCGCTGTTA
* * *
111352 CGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTACAGGATCCGCCGTTGCGGTCTAGATCTTTC
1 CGACTTAAACCTTTCCCTTTTG-ATCTTTGTGGTACAGGATCCGCCGTTACGCTCTAGATCTTTC
* *
111417 CCTTTATGTCTCTAGGGTACTAGG-TCCGCCATTG
65 CCTTCATGTCTCTAGAGTACT-GGATCCGCCATTG
* * *
111451 CGACTTAAACCTTTCCCTTTTG-TCTTTGTGGTACTGGGTCCGCCGTTACGACT-TAGATTTTTC
1 CGACTTAAACCTTTCCCTTTTGATCTTTGTGGTACAGGATCCGCCGTTACG-CTCTAGATCTTTC
* *
111514 CCTTCATGTCT-TCGCAGTACTGGATCCGCCTTTG
65 CCTTCATGTCTCTAG-AGTACTGGATCCGCCATTG
* * *
111548 CGGCTTAGATCTTTCCC
1 CGACTTAAACCTTTCCC
111565 CTCATGTCTC
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
96 4 0.04
97 72 0.73
98 1 0.01
99 21 0.21
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (98 bp):
CGACTTAAACCTTTCCCTTTTGATCTTTGTGGTACAGGATCCGCCGTTACGCTCTAGATCTTTCC
CTTCATGTCTCTAGAGTACTGGATCCGCCATTG
Found at i:111684 original size:97 final size:97
Alignment explanation
Indices: 111568--111759 Score: 253
Period size: 97 Copynumber: 2.0 Consensus size: 97
111558 CTTTCCCCTC
*
111568 ATGTCTCTGAGGTACAAGGTTCACTGA-TACGACTTAAA-CTCTTCCCTTTCGTATCTTTGCGGT
1 ATGTCTCTGAGGTACAAGGTTC-CTCATTACGACTTAAATC-CTTCCCTTTCGTATCTTTGCGGT
111631 ACTGGATCCACCATTGCAGTCTTAAATCTTTCTA
64 ACTGGATCCACCATTGCAGTCTTAAATCTTTCTA
* * * * *
111665 ATGTCTCTGAGGTATAAGGTTCGTCATTACGACTTAAATCCTTCCTTTTTGTATCTTTGTGGTAC
1 ATGTCTCTGAGGTACAAGGTTCCTCATTACGACTTAAATCCTTCCCTTTCGTATCTTTGCGGTAC
** * * *
111730 TGGATCTGCCGTTGCGGTCTTAGATCTTTC
66 TGGATCCACCATTGCAGTCTTAAATCTTTC
111760 CCGTCATGTT
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 2 0.02
97 79 0.96
98 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (97 bp):
ATGTCTCTGAGGTACAAGGTTCCTCATTACGACTTAAATCCTTCCCTTTCGTATCTTTGCGGTAC
TGGATCCACCATTGCAGTCTTAAATCTTTCTA
Found at i:111724 original size:245 final size:246
Alignment explanation
Indices: 111284--111768 Score: 565
Period size: 245 Copynumber: 2.0 Consensus size: 246
111274 AATCTTCAAT
* * * * * * *
111284 GTACTGGATTCGCTGTTGCGGCTTAAATCTTTTCCTTCTTGTCTTCTGAAGTTCACGGTCCGCTG
1 GTACTGGATCCGCTGTTGCGGCTTAAATCTTTCCCCTCATGTCTTCTGAAGTACAAGGTCCACTG
* * * * * * *
111349 TTACGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTACAGGATCCGCCGTTGCGGTCTAGATCT
66 ATACGACTTAAAGCTTTCCCTTTCGTATCTTTGCGGTACAGGATCCACCATTGCAGTCTAAATCT
* *
111414 TTCCCTTTATGTCTCTAGGGTACTAGGTCCGCCATTGCGACTTAAACCTTTCCCTTTTGTCTTTG
131 TT-CCTTAATGTCTCTAGGGTACTAGGTCCGCCATTACGACTTAAACCTTTCCCTTTTGTCTTTG
* * *
111479 TGGTACTGGGTCCGCCGTTAC-GACTTAGATTTTTCCCTTCATGTCTTCGCA
195 TGGTACTGGATCCGCCGTTACGGACTTAGATCTTTCCCGTCATGTCTTCGCA
* * *
111530 GTACTGGATCCGCCT-TTGCGGCTTAGATCTTTCCCCTCATGTC-TCTGAGGTACAAGGTTCACT
1 GTACTGGATCCG-CTGTTGCGGCTTAAATCTTTCCCCTCATGTCTTCTGAAGTACAAGGTCCACT
*
111593 GATACGACTTAAA-CTCTTCCCTTTCGTATCTTTGCGGTACTGGATCCACCATTGCAGTCTTAAA
65 GATACGACTTAAAGCT-TTCCCTTTCGTATCTTTGCGGTACAGGATCCACCATTGCAGTC-TAAA
* * *
111657 TCTTT-C-TAATGTCTCT-GAGGTA-TAAGGTTCGTCATTACGACTTAAATCC-TTCCTTTTTGT
128 TCTTTCCTTAATGTCTCTAG-GGTACT-AGGTCCGCCATTACGACTTAAA-CCTTTCCCTTTTG-
* * *
111717 ATCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCATGT
189 -TCTTTGTGGTACTGGATCCGCCGTTACGGACTTAGATCTTTCCCGTCATGT
111769 TTCATGGTGC
Statistics
Matches: 201, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
242 2 0.01
243 41 0.20
244 5 0.02
245 88 0.44
246 63 0.31
247 2 0.01
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (246 bp):
GTACTGGATCCGCTGTTGCGGCTTAAATCTTTCCCCTCATGTCTTCTGAAGTACAAGGTCCACTG
ATACGACTTAAAGCTTTCCCTTTCGTATCTTTGCGGTACAGGATCCACCATTGCAGTCTAAATCT
TTCCTTAATGTCTCTAGGGTACTAGGTCCGCCATTACGACTTAAACCTTTCCCTTTTGTCTTTGT
GGTACTGGATCCGCCGTTACGGACTTAGATCTTTCCCGTCATGTCTTCGCA
Found at i:113756 original size:17 final size:18
Alignment explanation
Indices: 113734--113767 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
113724 TAGTGTCCAT
113734 GCTTC-ACATAGAAAGAG
1 GCTTCAACATAGAAAGAG
*
113751 GCTTCAACATGGAAAGA
1 GCTTCAACATAGAAAGA
113768 TGATGGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (18 bp):
GCTTCAACATAGAAAGAG
Found at i:118730 original size:30 final size:30
Alignment explanation
Indices: 118669--119081 Score: 458
Period size: 29 Copynumber: 14.1 Consensus size: 30
118659 TTCGAAATCG
* ** *
118669 AAAATGGAGTTTTT-GAACATTCGAGAGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
* * *
118698 AAAATGAAATTTTTGAAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
*
118728 AAAATGGAATTTTTAGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
* *
118757 AAAATGGAATTATTGGAAGTTTCG-GGTTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-A
*
118787 AAAATGGAATTTTTGGAAGTTTTG-GGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-A
* *
118817 AAAATGGAATTTTTAGAAGTTT-GGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
*
118846 AAAATTGAATTTTTGGAAGTTTCG-GGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
* * *
118875 AAAATAGAATTTTTGAAAGTTTAG-GGGT-
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
**
118903 AAAATGGAATTTTTGGAAGTTTCGA-GAAA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
* *
118932 AAAATGGAATTTTTAGAAGTTT-GGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
*
118961 AAAATGGAATTTTTGGAAGTTT-TAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGG-TA
118991 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
*
119020 AAAATGGAATTTTTTGAAGTTTCGA-GGTAA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-A
** *
119050 AAAATAAAATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
119079 AAA
1 AAA
119082 TATAATTTCT
Statistics
Matches: 330, Mismatches: 41, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.07
29 173 0.52
30 134 0.41
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGGTA
Found at i:118734 original size:59 final size:59
Alignment explanation
Indices: 118669--119081 Score: 445
Period size: 59 Copynumber: 7.1 Consensus size: 59
118659 TTCGAAATCG
* ** * * *
118669 AAAATGGAGTTTTT-GAACATTCGAGAGTAAAAATGAAATTTTTGAAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCG-GGGTA
* * * *
118728 AAAATGGAATTTTTAGAAG-TTCGAGGGTAAAAATGGAATTATTGGAAGTTTCGGGTTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCGGGGT-A
* *
118787 AAAATGGAATTTTTGGAAGTTTTG-GGGTCAAAAATGGAATTTTT-AGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-AAAAATGGAATTTTTGA-AAGTTTCGGGGTA
* * *
118846 AAAATTGAATTTTTGGAAGTTTCG-GGGTAAAAATAGAATTTTTGAAAGTTTAGGGGT-
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTA
** *
118903 AAAATGGAATTTTTGGAAGTTTCGA-GAAAAAAATGGAATTTTT-AGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGA-AAGTTTCGGGGTA
* *
118961 AAAATGGAATTTTTGGAAGTTT-TAGGGTTAAAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGG-TAAAAATGGAATTTTTGAAAGTTTCG-GGGTA
* ** *
119020 AAAATGGAATTTTTTGAAGTTTCGA-GGTAAAAAATAAAATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-AAAAATGGAATTTTTGAAAGTTTC-GGGGTA
119079 AAA
1 AAA
119082 TATAATTTCT
Statistics
Matches: 308, Mismatches: 30, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
56 1 0.00
57 50 0.16
58 56 0.18
59 169 0.55
60 32 0.10
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTA
Found at i:120941 original size:17 final size:17
Alignment explanation
Indices: 120916--121016 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
120906 TTGGACTTTT
* *
120916 TAATTAATTTTAATTTA
1 TAATAAATTTAAATTTA
120933 TAATAAATTTAAATTTA
1 TAATAAATTTAAATTTA
**
120950 -AAGTAAATTTAAACTCAA
1 TAA-TAAATTTAAA-TTTA
*
120968 AAATAAATTTAAATTTA
1 TAATAAATTTAAATTTA
* * * *
120985 AAACAAATTCAAACTTA
1 TAATAAATTTAAATTTA
* *
121002 AAATAAATTAAAATT
1 TAATAAATTTAAATT
121017 AAAAAATTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
16 2 0.03
17 53 0.77
18 12 0.17
19 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (17 bp):
TAATAAATTTAAATTTA
Found at i:120945 original size:6 final size:6
Alignment explanation
Indices: 120936--120986 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
120926 TAATTTATAA
* * * **
120936 TAAATT TAAATT TAAA-G TAAATT TAAACT CAAAAA TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
120983 TAAA
1 TAAA
120987 ACAAATTCAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (6 bp):
TAAATT
Found at i:120973 original size:35 final size:33
Alignment explanation
Indices: 120934--121030 Score: 110
Period size: 35 Copynumber: 2.9 Consensus size: 33
120924 TTTAATTTAT
120934 AATAAATTTAAATTTAAAGTAAATTTAAACTCAAA
1 AATAAATTTAAATTTAAA--AAATTTAAACTCAAA
* *
120969 AATAAATTTAAATTTAAAACAAATTCAAACT-TAA
1 AATAAATTTAAATTT-AAA-AAATTTAAACTCAAA
*
121003 AATAAA-TTAAAATTAAAAAA-TTAAACTC
1 AATAAATTTAAATTTAAAAAATTTAAACTC
121031 TAGGCCCAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
30 6 0.11
31 3 0.05
32 3 0.05
33 7 0.13
34 8 0.15
35 25 0.45
36 3 0.05
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (33 bp):
AATAAATTTAAATTTAAAAAATTTAAACTCAAA
Found at i:121022 original size:52 final size:52
Alignment explanation
Indices: 120921--121023 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
120911 CTTTTTAATT
* * * * * * * *
120921 AATTTTAATTTATAATAAATTTAAATTTAAAGTAAATTTAAACTCAAAAATA
1 AATTTAAATTTAAAACAAATTCAAACTTAAAATAAATTAAAACTAAAAAATA
*
120973 AATTTAAATTTAAAACAAATTCAAACTTAAAATAAATTAAAATTAAAAAAT
1 AATTTAAATTTAAAACAAATTCAAACTTAAAATAAATTAAAACTAAAAAAT
121024 TAAACTCTAG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (52 bp):
AATTTAAATTTAAAACAAATTCAAACTTAAAATAAATTAAAACTAAAAAATA
Found at i:122298 original size:7 final size:7
Alignment explanation
Indices: 122276--122310 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
122266 AATATAATTT
*
122276 TATTAAA
1 TATTATA
122283 TAGTTATA
1 TA-TTATA
122291 TATTATA
1 TATTATA
122298 TATTATA
1 TATTATA
122305 TATTAT
1 TATTAT
122311 TTACTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (7 bp):
TATTATA
Found at i:125698 original size:23 final size:23
Alignment explanation
Indices: 125659--125713 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
125649 ATTTTGCTTT
*
125659 TAATTTTTAGTAACTCTCCTACCA
1 TAATGTTT-GTAACTCTCCTACCA
* * *
125683 TTATGTTTGTAACTCTCTTGCCA
1 TAATGTTTGTAACTCTCCTACCA
125706 TAATGTTT
1 TAATGTTT
125714 TGTTTTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (23 bp):
TAATGTTTGTAACTCTCCTACCA
Found at i:126333 original size:15 final size:16
Alignment explanation
Indices: 126313--126348 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
126303 GTTTTCTTGT
126313 AACACCCA-AAATCCG
1 AACACCCAGAAATCCG
126328 AACA-CCAGAAATCCG
1 AACACCCAGAAATCCG
126343 AACACC
1 AACACC
126349 GTCGTCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.16
15 15 0.79
16 1 0.05
ACGTcount: A:0.47, C:0.39, G:0.08, T:0.06
Consensus pattern (16 bp):
AACACCCAGAAATCCG
Found at i:127337 original size:59 final size:61
Alignment explanation
Indices: 127259--127375 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 61
127249 CTCAACTCGT
* *
127259 ATTTGATACTCACAATGACACA-AGTCATCGGACC-CTTAATCCGTAATGGAATTCATTTC
1 ATTTAATACTCACAATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGAATTCATTTC
* * **
127318 ATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTAAAGGAATTCAT
1 ATTTAATACTCACAATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGAATTCAT
127376 ATACTCACGA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 19 0.38
60 12 0.24
61 19 0.38
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (61 bp):
ATTTAATACTCACAATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGAATTCATTTC
Found at i:127445 original size:52 final size:52
Alignment explanation
Indices: 127324--127509 Score: 241
Period size: 52 Copynumber: 3.6 Consensus size: 52
127314 TTTCATTTAA
** *
127324 TACTCACGATGACA-TATAGTCATCGGACCTCT-TGTTCCGTAAAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TATAATCCGTAAAGG-ATTCATG
* * *
127377 TACTCACGACGACACTTAGTCATCGGACCTTATAATCCATCAAGGATTCATG
1 TACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTAAAGGATTCATG
* * *
127429 TACTCATGATGACACTTAGTCATCAGACCTTATAATCCGTGAAGGATTCATG
1 TACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTAAAGGATTCATG
*
127481 TACTCACGATGACACTTAGTAATCGGACC
1 TACTCACGATGACACTTAGTCATCGGACC
127510 CTTTTTCATT
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
52 80 0.68
53 36 0.31
54 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (52 bp):
TACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTAAAGGATTCATG
Found at i:130408 original size:29 final size:28
Alignment explanation
Indices: 130371--130428 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
130361 AAACATGTGG
* *
130371 GAGGTGTCCTAGAACCACTTGGAAATGT
1 GAGGTGTCCTAAAACCACTTGAAAATGT
130399 GAGGATGTCCTAAAACCACTTGAAAATGT
1 GAGG-TGTCCTAAAACCACTTGAAAATGT
130428 G
1 G
130429 GGGGGTGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (28 bp):
GAGGTGTCCTAAAACCACTTGAAAATGT
Found at i:131625 original size:17 final size:17
Alignment explanation
Indices: 131603--131635 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
131593 TTTGTAACTC
*
131603 TCCTGTTATTATGTTTA
1 TCCTGTCATTATGTTTA
131620 TCCTGTCATTATGTTT
1 TCCTGTCATTATGTTT
131636 GTAACTCTCC
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:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (17 bp):
TCCTGTCATTATGTTTA
Found at i:131646 original size:23 final size:23
Alignment explanation
Indices: 131588--131681 Score: 87
Period size: 23 Copynumber: 4.4 Consensus size: 23
131578 ACCAATTATT
*
131588 ATTAT-TTTGTAACTCTCCTGTT
1 ATTATGTTTGTAACTCTCCTGTC
131610 ATTATG-TT-T-A---TCCTGTC
1 ATTATGTTTGTAACTCTCCTGTC
131627 ATTATGTTTGTAACTCTCCTG-C
1 ATTATGTTTGTAACTCTCCTGTC
* *
131649 GATTACGTTTGTAACTCTCCTGCC
1 -ATTATGTTTGTAACTCTCCTGTC
*
131673 ATAATGTTT
1 ATTATGTTT
131682 TGTTTTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
17 12 0.20
18 2 0.03
19 1 0.02
20 2 0.03
21 1 0.02
22 8 0.14
23 32 0.54
24 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (23 bp):
ATTATGTTTGTAACTCTCCTGTC
Found at i:132582 original size:31 final size:31
Alignment explanation
Indices: 132544--132607 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
132534 TGCTGGGAAC
*
132544 TTGAAGAGTCAAACTTATCCATTATTTTGAT
1 TTGAAGAGTCAAACTTATCCATTATTATGAT
132575 TTGAAGAGTCAAACTTATCCATTATTATGAT
1 TTGAAGAGTCAAACTTATCCATTATTATGAT
132606 TT
1 TT
132608 AAAATGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (31 bp):
TTGAAGAGTCAAACTTATCCATTATTATGAT
Found at i:136017 original size:15 final size:14
Alignment explanation
Indices: 135989--136023 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
135979 TATATATGTT
135989 TATTTTTTTAAAAG
1 TATTTTTTTAAAAG
*
136003 TATTTGTTTTTAAAG
1 TATTT-TTTTAAAAG
136018 TATTTT
1 TATTTT
136024 GTTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (14 bp):
TATTTTTTTAAAAG
Found at i:136026 original size:16 final size:16
Alignment explanation
Indices: 135993--136022 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
135983 TATGTTTATT
135993 TTTTTAAAAGTATTTG
1 TTTTTAAAAGTATTTG
136009 TTTTT-AAAGTATTT
1 TTTTTAAAAGTATTT
136023 TGTTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (16 bp):
TTTTTAAAAGTATTTG
Found at i:141723 original size:52 final size:52
Alignment explanation
Indices: 141629--141875 Score: 327
Period size: 52 Copynumber: 4.8 Consensus size: 52
141619 TTTCATTTCG
* * ** ** *
141629 TTCATATACTCACGATGACACATT-GCCACCAAACCT-TATAATCCACAAGGGA
1 TTCATATACTCACGATGACAC-TTAGTCATCGGACCTCT-TAATCCGTAAAGGA
* *
141681 TTCATATACTCACGATGACATTTAGTCATCGGACCTCTTAATCTGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
*
141733 TTCATATACTCACGATGACACTTACTCATCGGACCTCTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* *
141785 TTCATATACTCATGATAACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* * *
141837 CTCATACACTCACGATGACACTTAGTCATTGGACCTCTT
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
141876 CGTTTATGGC
Statistics
Matches: 173, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
51 2 0.01
52 170 0.98
53 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (52 bp):
TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
Found at i:144947 original size:15 final size:16
Alignment explanation
Indices: 144924--144953 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
144914 TTTACATCAA
144924 TTTATTAAAAAATAAT
1 TTTATTAAAAAATAAT
144940 TTTA-TAAAAAATAA
1 TTTATTAAAAAATAA
144954 ATACATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTATTAAAAAATAAT
Found at i:145557 original size:25 final size:24
Alignment explanation
Indices: 145528--145578 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
145518 AAATTTAAGG
145528 ATCAAATTTAACTAAAAAA-ATAAAT
1 ATCAAA-TTAA-TAAAAAATATAAAT
*
145553 ATCAAATTGATAAAAAATATAAAT
1 ATCAAATTAATAAAAAATATAAAT
145577 AT
1 AT
145579 TAACAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 11 0.46
25 6 0.25
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
ATCAAATTAATAAAAAATATAAAT
Found at i:147170 original size:12 final size:12
Alignment explanation
Indices: 147153--147203 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
147143 ATCCAAGCAG
147153 CAAAAATAATAA
1 CAAAAATAATAA
*
147165 CAAAAATAACAA
1 CAAAAATAATAA
* *
147177 CAAAAACAA-CA
1 CAAAAATAATAA
*
147188 TAAAAATAATAA
1 CAAAAATAATAA
147200 -AAAA
1 CAAAA
147204 TAGCACAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 12 0.38
12 20 0.62
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (12 bp):
CAAAAATAATAA
Found at i:158056 original size:29 final size:29
Alignment explanation
Indices: 158023--158143 Score: 127
Period size: 30 Copynumber: 4.1 Consensus size: 29
158013 TTAAAGTGTA
* *
158023 TTTTAGAAAGTTTGGGGTTAAAATGAAAT
1 TTTTAGAAAGTTTGGGGTCAAAATCAAAT
* * *
158052 TTTTAGGAAGTTTGAGGTTAAAAATCAAAT
1 TTTTAGAAAGTTTG-GGGTCAAAATCAAAT
* * *
158082 TTTTGGAAAGTTTAGGGGTCAAAATTAGAT
1 TTTTAGAAAGTTT-GGGGTCAAAATCAAAT
* *
158112 TTTT-GGAAGTTTGGGGTCAAATTCAAAT
1 TTTTAGAAAGTTTGGGGTCAAAATCAAAT
158140 TTTT
1 TTTT
158144 GGATAAAACA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
28 17 0.22
29 20 0.26
30 38 0.50
31 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.40
Consensus pattern (29 bp):
TTTTAGAAAGTTTGGGGTCAAAATCAAAT
Found at i:158123 original size:59 final size:58
Alignment explanation
Indices: 158023--158146 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 58
158013 TTAAAGTGTA
* * *
158023 TTTTAGAAAGTTTGGGGTTAAAATGAAATTTTTAGGAAGTTTGAGGTTAAAAATCAAAT
1 TTTTGGAAAGTTTGGGGTCAAAATGAAATTTTTAGGAAGTTTG-GGGTAAAAATCAAAT
* * * *
158082 TTTTGGAAAGTTTAGGGGTCAAAATTAGATTTTT-GGAAGTTTGGGGTCAAATTCAAAT
1 TTTTGGAAAGTTT-GGGGTCAAAATGAAATTTTTAGGAAGTTTGGGGTAAAAATCAAAT
158140 TTTTGGA
1 TTTTGGA
158147 TAAAACAAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
58 19 0.33
59 21 0.37
60 17 0.30
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (58 bp):
TTTTGGAAAGTTTGGGGTCAAAATGAAATTTTTAGGAAGTTTGGGGTAAAAATCAAAT
Found at i:162180 original size:2 final size:2
Alignment explanation
Indices: 162169--162203 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
162159 GAAAAAAAAC
*
162169 AT AT AA 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 A
162204 AAGAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:162798 original size:25 final size:26
Alignment explanation
Indices: 162770--162826 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
162760 TAATATTTTG
* *
162770 AAAAATATATA-AAATAGAAATTTAT
1 AAAAATACATACAAATACAAATTTAT
* *
162795 AAAAATGCATACAATTACAAATTTAT
1 AAAAATACATACAAATACAAATTTAT
162821 AAAAAT
1 AAAAAT
162827 CTTATAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (26 bp):
AAAAATACATACAAATACAAATTTAT
Found at i:163066 original size:12 final size:12
Alignment explanation
Indices: 163049--163074 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
163039 AAATTTATGA
163049 ATTTATAAATAT
1 ATTTATAAATAT
163061 ATTTATAAATAT
1 ATTTATAAATAT
163073 AT
1 AT
163075 GAAATCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTATAAATAT
Found at i:166569 original size:13 final size:13
Alignment explanation
Indices: 166553--166607 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
166543 TATTTTTGAG
166553 AAGTACTTTTAAA
1 AAGTACTTTTAAA
* *
166566 AAGTGCTTTGAAA
1 AAGTACTTTTAAA
*
166579 AAGTGA-TTTTTAA
1 AAGT-ACTTTTAAA
*
166592 AAGTACTTTTGAA
1 AAGTACTTTTAAA
166605 AAG
1 AAG
166608 CTTGGTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 1 0.03
13 33 0.97
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.36
Consensus pattern (13 bp):
AAGTACTTTTAAA
Found at i:166607 original size:26 final size:26
Alignment explanation
Indices: 166546--166607 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
166536 TTAGCATTAT
* *
166546 TTTTGAGAAGTACTTTTAAAAAGTGC
1 TTTTGAAAAGTACTTTTAAAAAGTAC
*
166572 -TTTGAAAAAGTGA-TTTTTAAAAGTAC
1 TTTTG-AAAAGT-ACTTTTAAAAAGTAC
166598 TTTTGAAAAG
1 TTTTGAAAAG
166608 CTTGGTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 4 0.13
26 21 0.70
27 5 0.17
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (26 bp):
TTTTGAAAAGTACTTTTAAAAAGTAC
Found at i:166783 original size:12 final size:12
Alignment explanation
Indices: 166766--166798 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
166756 TAGAAAATAA
*
166766 TTTATTATATTT
1 TTTATTATATAT
166778 TTTATTA-ATAT
1 TTTATTATATAT
166789 TTTATTATAT
1 TTTATTATAT
166799 GAAATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATTATATAT
Found at i:168872 original size:3 final size:3
Alignment explanation
Indices: 168864--168895 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
168854 CACATACCTC
168864 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
168896 CCTTTCGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:169338 original size:16 final size:16
Alignment explanation
Indices: 169298--169342 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
169288 AGGTTTAGGT
*
169298 TTAAAAATTGTAATTAA
1 TTAAAAATT-TATTTAA
169315 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
169329 TTAAAAATTTATTT
1 TTAAAAATTTATTT
169343 TCATCTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 10 0.40
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:170164 original size:16 final size:18
Alignment explanation
Indices: 170129--170166 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
170119 ATTTATTTTT
170129 ATATTCTATTATTGTTAA
1 ATATTCTATTATTGTTAA
*
170147 ATATT-TATTCTT-TTAA
1 ATATTCTATTATTGTTAA
170163 ATAT
1 ATAT
170167 GTAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
ATATTCTATTATTGTTAA
Found at i:170734 original size:51 final size:52
Alignment explanation
Indices: 170658--170760 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 52
170648 TATTATAAAT
170658 TCTATTTTTAGATAATAATTAATTTAAG-TTTTTTTTTTTAACAAACATGTA
1 TCTATTTTTAGATAATAATTAATTTAAGTTTTTTTTTTTTAACAAACATGTA
170709 TCTATTTTTAGATAATAATTAATTTAAGTTTTTTTTTTTTAACAAACATGTA
1 TCTATTTTTAGATAATAATTAATTTAAGTTTTTTTTTTTTAACAAACATGTA
170761 GCATTCATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 28 0.55
52 23 0.45
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (52 bp):
TCTATTTTTAGATAATAATTAATTTAAGTTTTTTTTTTTTAACAAACATGTA
Found at i:173650 original size:99 final size:99
Alignment explanation
Indices: 173479--173675 Score: 385
Period size: 99 Copynumber: 2.0 Consensus size: 99
173469 ATGATTGATG
173479 TTAAAAAACATTACTACACGCTGTTAATGCCTCTAATTTTTAAATAAATTGAAAAATTGGAAATT
1 TTAAAAAACATTACTACACGCTGTTAATGCCTCTAATTTTTAAATAAATTGAAAAATTGGAAATT
173544 ACTTCAATGAAGACAAATTGAAAAATTTTAGTAA
66 ACTTCAATGAAGACAAATTGAAAAATTTTAGTAA
*
173578 TTAAAAAACATTACTACACGCTGTTAATGCCTCTAATTTTTAAATAAATTGAAAAATTGGTAATT
1 TTAAAAAACATTACTACACGCTGTTAATGCCTCTAATTTTTAAATAAATTGAAAAATTGGAAATT
173643 ACTTCAATGAAGACAAATTGAAAAATTTTAGTA
66 ACTTCAATGAAGACAAATTGAAAAATTTTAGTA
173676 GTGCAACACA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (99 bp):
TTAAAAAACATTACTACACGCTGTTAATGCCTCTAATTTTTAAATAAATTGAAAAATTGGAAATT
ACTTCAATGAAGACAAATTGAAAAATTTTAGTAA
Found at i:178377 original size:36 final size:36
Alignment explanation
Indices: 178326--178450 Score: 187
Period size: 36 Copynumber: 3.5 Consensus size: 36
178316 CCTTATGCTG
* *
178326 TAACCGAGACATAAGCAATCACTTAGCATTACGCTC
1 TAACCGAGACGTAAGCAATCACATAGCATTACGCTC
* * *
178362 TAATCGAGATGTAAGCAATCACATAGCATTACACTC
1 TAACCGAGACGTAAGCAATCACATAGCATTACGCTC
* *
178398 TAACCTAGACGTAAGCAATCACATAGCATTACGCTT
1 TAACCGAGACGTAAGCAATCACATAGCATTACGCTC
178434 TAACCGAGACGTAAGCA
1 TAACCGAGACGTAAGCA
178451 TTCCATCGAA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 78 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (36 bp):
TAACCGAGACGTAAGCAATCACATAGCATTACGCTC
Found at i:182228 original size:26 final size:26
Alignment explanation
Indices: 182172--182228 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
182162 ATACTATAAG
* * *
182172 ATTTTTATAAATTTGTAATTGTATGC
1 ATTTTTATAAATTTATAATTATATAC
182198 ATTTTTATAAATTTATAATTTATATAC
1 ATTTTTATAAATTTATAA-TTATATAC
182225 -TTTT
1 ATTTT
182229 CAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (26 bp):
ATTTTTATAAATTTATAATTATATAC
Found at i:182355 original size:18 final size:18
Alignment explanation
Indices: 182322--182356 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
182312 GGACACTCAA
* *
182322 AATGGGTTTATTATTGAC
1 AATGGGTTAATCATTGAC
182340 AATGGGTTAATCATTGA
1 AATGGGTTAATCATTGA
182357 TATTTTTGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (18 bp):
AATGGGTTAATCATTGAC
Done.