Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001966.1 Hibiscus syriacus cultivar Beakdansim tig00003973_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 458221
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:385457 original size:22 final size:22
Alignment explanation
Indices: 385429--385472 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
385419 CACTCTCTCA
385429 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
385451 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
385473 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:385761 original size:20 final size:20
Alignment explanation
Indices: 385736--385773 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
385726 CGATTCTCTC
385736 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
385756 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
385774 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:387106 original size:21 final size:21
Alignment explanation
Indices: 387080--387119 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
387070 CCGTTGAACA
387080 GGGGGGAATCGGTACCCTCTT
1 GGGGGGAATCGGTACCCTCTT
*
387101 GGGGGGAATCGGTTCCCTC
1 GGGGGGAATCGGTACCCTC
387120 CGAGCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.40, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCTCTT
Found at i:387413 original size:30 final size:30
Alignment explanation
Indices: 387379--387439 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
387369 AAATCGTTTG
387379 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
387409 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
387439 G
1 G
387440 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:389880 original size:20 final size:20
Alignment explanation
Indices: 389826--389888 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
389816 AACAGAACCC
* *
389826 CAGGGGGGTATCGATTCCCCC
1 CAGGGGGGAATCGATT-CCCT
* *
389847 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
389868 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
389888 C
1 C
389889 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 17 0.50
21 5 0.15
22 12 0.35
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:393719 original size:22 final size:21
Alignment explanation
Indices: 393677--393716 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
393667 GAGTTTGTTT
*
393677 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
393698 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
393717 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:395659 original size:21 final size:21
Alignment explanation
Indices: 395633--395672 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
395623 CCGTTGAACA
395633 GGGGGGAATCGGTACCCTCTT
1 GGGGGGAATCGGTACCCTCTT
*
395654 GGGGGGAATCGGTTCCCTC
1 GGGGGGAATCGGTACCCTC
395673 CGAGCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.40, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCTCTT
Found at i:395968 original size:30 final size:30
Alignment explanation
Indices: 395934--395994 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
395924 AAATCGTTTG
395934 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
395964 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
395994 G
1 G
395995 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:396752 original size:18 final size:18
Alignment explanation
Indices: 396731--396793 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
396721 TCCACTTCGG
396731 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCGCCCA
*
396749 GAGCTATCACCTCGCCCA
1 GAGCCATCACCTCGCCCA
* *
396767 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCGCCCA
*
396785 AAGCCATCA
1 GAGCCATCA
396794 TCTGATCGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.27, C:0.44, G:0.14, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCGCCCA
Found at i:397313 original size:20 final size:19
Alignment explanation
Indices: 397274--397339 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
397264 TAGTTTACTT
* *
397274 TCGCAACACAAAATGACTA
1 TCGCAACGCGAAATGACTA
*
397293 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
397313 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
397332 TCGCAACG
1 TCGCAACG
397340 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:397426 original size:19 final size:19
Alignment explanation
Indices: 397400--397466 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
397390 GCGATTTTGT
**
397400 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
397419 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
397439 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
397458 CGTTGCGAT
1 CGTTGCGAT
397467 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:397446 original size:20 final size:19
Alignment explanation
Indices: 397412--397466 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
397402 TTGCGATTTT
*
397412 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
397431 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
397451 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
397467 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:399324 original size:14 final size:14
Alignment explanation
Indices: 399305--399340 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
399295 ATTGTTTAAT
399305 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
399319 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
399333 TGATTTGT
1 TGATTTGT
399341 TTGATGTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:399449 original size:18 final size:18
Alignment explanation
Indices: 399421--399465 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
399411 GCAAAATAGA
* *
399421 CTATCGCAACGTGAAATGG
1 CTAT-GCAACGAGAAATCG
399440 CTATGCAACGAGAAATCG
1 CTATGCAACGAGAAATCG
*
399458 CAATGCAA
1 CTATGCAA
399466 AATGAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (18 bp):
CTATGCAACGAGAAATCG
Found at i:399476 original size:19 final size:19
Alignment explanation
Indices: 399452--399498 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
399442 ATGCAACGAG
399452 AAATCGCAATGCAAAATGA
1 AAATCGCAATGCAAAATGA
*
399471 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCAAAATGA
399490 AAATCGCAA
1 AAATCGCAA
399499 CGAGAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (19 bp):
AAATCGCAATGCAAAATGA
Found at i:399505 original size:19 final size:19
Alignment explanation
Indices: 399452--399505 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
399442 ATGCAACGAG
399452 AAATCGCAATGCA-AAATGA
1 AAATCGCAATG-AGAAATGA
*
399471 AAATCGCAATGCGAAATGA
1 AAATCGCAATGAGAAATGA
*
399490 AAATCGCAACGAGAAA
1 AAATCGCAATGAGAAA
399506 ATCGCAATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.52, C:0.17, G:0.19, T:0.13
Consensus pattern (19 bp):
AAATCGCAATGAGAAATGA
Found at i:399582 original size:20 final size:20
Alignment explanation
Indices: 399536--399592 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
399526 TCGCATTGCG
* * *
399536 ATTTTCTCGTTACGATAACC
1 ATTTTCGCGTTGCGATAGCC
399556 A-TTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
399575 ATTTTCGCATTGCGATAG
1 ATTTTCGCGTTGCGATAG
399593 TCAAATGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:399972 original size:14 final size:14
Alignment explanation
Indices: 399953--399988 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
399943 GATTGTTAAT
399953 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
399967 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
399981 TGATTTGT
1 TGATTTGT
399989 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:400111 original size:14 final size:14
Alignment explanation
Indices: 400092--400145 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
400082 CGAAATGGCT
400092 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
400106 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
400125 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
400139 ATAGCAA
1 ATCGCAA
400146 TGCGATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.50, C:0.19, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:400118 original size:33 final size:33
Alignment explanation
Indices: 400073--400150 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
400063 AAAACAGACT
* ***
400073 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
400106 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
400139 ATAGCAATGCGA
1 ATCGCAATGCGA
400151 TTTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:400138 original size:19 final size:19
Alignment explanation
Indices: 400102--400138 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
400092 ATCGCAACGA
* *
400102 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
400121 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
400139 ATAGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:400213 original size:20 final size:20
Alignment explanation
Indices: 400169--400227 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
400159 TCGCATTGCG
* *
400169 ATTTTCTCGTTGCGATAACCC
1 ATTTTCGCGTTGCGAT-AGCC
400190 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
400210 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
400228 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:400581 original size:636 final size:640
Alignment explanation
Indices: 399065--401024 Score: 3189
Period size: 635 Copynumber: 3.1 Consensus size: 640
399055 TGGTAAGTCA
*
399065 AATGCAAGTTTTG-T-ACATATATACTCATTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
399128 CAATAATTTGATGTTTGTAGGTTTTAGAT-TGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTC
66 CAATAATTTGATGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTC
399192 TG-AGGTTAATCCTTAAGTGAGCTGCGTG-AATGGATGTAC-GGGTCACAAAGTTGTTGATTCAT
131 TGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCAT
399254 TGATTCAATAATTGATGAAG-AAT-AGAATTA-T-TTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTA-TTTTTGATTGTTTAATTGATTTGTAA
399315 AAGATGATTTGTAAATGTTGATTTG--T--TTGATGT-TACATAATTTGTGTTGAAATGTAATAG
260 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAA-TTGTGTTGAAATGTAATAG
* * *
399375 TTGATTTGTTGATTTTCAATATGCTTTATGTTGAAGGCAAAATAGACTATCGCAACGTGAAATGG
324 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
*
399440 CTATGCAACGAGAAATCGCAATGCAAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAA
389 C--T----------ATCGCAA--C--GA-GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
399505 AATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTACGATAACCA-TTTCGCGTTGCG
437 AATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCATTTTCGCGTTGCG
*
399569 ATAGCCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCA
502 ATAGCCATTTTCGCGTTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCA
399634 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAA
567 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAA
399699 AATACACAT
632 AATACACAT
399708 AATGCAAAG-TTTGTTAACATATATACTCCTTTGGTTTGAAAATGTTTGGTTAAGTA-CTA-AAT
1 AATGC-AAGTTTTGTTAACATATATACTCCTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
* * *
399770 TCAATAATTTGTTGTTTGTAGGTTTT-TATGTATAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
65 TCAATAATTTGATGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
*
399834 CTGCAGGTTAATCCTTAAGTGAGCTGCATGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCA
130 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCA
399899 TTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTG-TTAATTGATTTGTAA
195 TTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAA
399963 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATT-TGTTGAAATGTAATAGT
260 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTGTGTTGAAATGTAATAGT
400027 TGATTTGTTGATTTTCAATCTG-TTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGC
325 TGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGC
* *
400091 TATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATAGCAATGCGATTTTT
390 TATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGATTTTC
400156 ATTTCGCATTGCGATTTTCTCGTTGCGATAACCCATTTTCGCGTTGCGATAGCCATTTTCGCGTT
455 ATTTCGCATTGCGATTTTCTCGTTGCGATAA-CCATTTTCGCGTTGCGATAGCCATTTTCGCGTT
400221 GCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTC
519 GCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTC
400286 AAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACAT-AAATACACAT
584 AAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
400342 AATGCAAGTTTTGTTAACATATATACTCCTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
*
400407 CAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTT-GTTTC
66 CAATAATTTGATGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTC
*
400471 TGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTATTGATTCAT
131 TGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCAT
400536 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAAA
400601 AGATGATTTGTAAATGTTGATTTGTTTAA-TGATGTGTACAT-ATTGTGTTGAAA-GTAATAGTT
261 AGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTGTGTTGAAATGTAATAGTT
* *
400663 GATTTGTTGA-TTTCAATCTGCTTTATGTGGAAGGCAAGACAGACTATCGCAACGCGAAATGGCT
326 GATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCT
*
400727 ATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGAGAAAATCGCAATGCGATTTTCA
391 ATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGATTTTCA
400792 TTT--C---GC-A--------TTGCG------ATTTTCGCGTTGCGATAGCCATTTTCGCGTTGC
456 TTTCGCATTGCGATTTTCTCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGC
*
400837 GATAGTCAAATGAATGT-TAATAAGTGATGACAAATGAACAGATCATAGCAATGTTC-AACTCAA
521 GATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAA
400900 GTTACTAATACATG-CTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
586 GTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
400954 AATGCAAGTTTTGTTAACATATATACTCCTTTGGTTTGAAAATG-TTGGTTAAGTACCTAGAATT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
401018 CAATAAT
66 CAATAAT
401025 AATTGTTAAA
Statistics
Matches: 1267, Mismatches: 24, Indels: 84
0.92 0.02 0.06
Matches are distributed among these distances:
611 56 0.04
612 75 0.06
613 38 0.03
614 50 0.04
621 5 0.00
629 1 0.00
630 2 0.00
633 86 0.07
634 76 0.06
635 270 0.21
636 165 0.13
637 76 0.06
638 7 0.01
642 2 0.00
643 73 0.06
644 32 0.03
645 50 0.04
646 43 0.03
647 3 0.00
648 48 0.04
649 11 0.01
650 44 0.03
651 38 0.03
652 9 0.01
653 7 0.01
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (640 bp):
AATGCAAGTTTTGTTAACATATATACTCCTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
CAATAATTTGATGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTC
TGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCAT
TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAAA
AGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTGTGTTGAAATGTAATAGTT
GATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCT
ATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGATTTTCA
TTTCGCATTGCGATTTTCTCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGC
GATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAA
GTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
Found at i:400609 original size:14 final size:14
Alignment explanation
Indices: 400590--400625 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
400580 ATTGTTTAAT
400590 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
400604 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
400618 TGATTTGT
1 TGATTTGT
400626 TTAATGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:400759 original size:19 final size:19
Alignment explanation
Indices: 400737--400773 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
400727 ATCGCAACGA
*
400737 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGAGAAAT
400756 GAAAATCGCAATGAGAAA
1 GAAAATCGCAATGAGAAA
400774 ATCGCAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGAGAAAT
Found at i:400781 original size:14 final size:14
Alignment explanation
Indices: 400727--400782 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
400717 CGAAATGGCT
*
400727 ATCGCAACGAGAAA
1 ATCGCAATGAGAAA
400741 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G--A-GAAA
400760 ATCGCAATGAGAAA
1 ATCGCAATGAGAAA
400774 ATCGCAATG
1 ATCGCAATG
400783 CGATTTTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 12 0.33
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (14 bp):
ATCGCAATGAGAAA
Found at i:400798 original size:33 final size:33
Alignment explanation
Indices: 400708--400785 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
400698 AAGACAGACT
* ***
400708 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
400741 ATCGCAATGCGAAATGAAAATCGCAATGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
400774 ATCGCAATGCGA
1 ATCGCAATGCGA
400786 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:400829 original size:20 final size:20
Alignment explanation
Indices: 400804--400841 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
400794 TCGCATTGCG
400804 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
400824 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
400842 TCAAATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:401874 original size:24 final size:24
Alignment explanation
Indices: 401823--401876 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
401813 GTATTCAAAA
* * *
401823 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGAAC
*
401847 TTTGATATTGGTCAATACACGAAT
1 TTTGATATTGGTCAATACACGAAC
401871 TTTGAT
1 TTTGAT
401877 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGAAC
Found at i:402065 original size:12 final size:12
Alignment explanation
Indices: 402048--402072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
402038 ATATAATCCT
402048 GAAGAAGAAAAA
1 GAAGAAGAAAAA
402060 GAAGAAGAAAAA
1 GAAGAAGAAAAA
402072 G
1 G
402073 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:404328 original size:19 final size:19
Alignment explanation
Indices: 404306--404436 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
404296 GGAAATTACT
404306 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
404325 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
404339 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
404358 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
404372 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
404391 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
404405 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
404424 ATCGCAACGCGAA
1 ATCGCAATGCGAA
404437 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:404348 original size:33 final size:33
Alignment explanation
Indices: 404306--404432 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
404296 GGAAATTACT
404306 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
404339 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
404371 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
404405 ATTGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
404433 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:404413 original size:66 final size:66
Alignment explanation
Indices: 404307--404439 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
404297 GAAATTACTA
*
404307 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
404372 T
66 T
* *
404373 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATTGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
404438 T
66 T
404439 T
1 T
404440 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:404454 original size:19 final size:20
Alignment explanation
Indices: 404432--404474 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
404422 AAATCGCAAC
404432 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
404451 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
404471 GCGA
1 GCGA
404475 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:404634 original size:14 final size:14
Alignment explanation
Indices: 404615--404651 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
404605 CATCAATTAA
404615 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
404629 ACAAATCACCTTTT
1 ACAAATCAACTTTT
404643 ACAAATCAA
1 ACAAATCAA
404652 TTAAACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:406077 original size:21 final size:21
Alignment explanation
Indices: 406011--406077 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
406001 GTGAATCGTG
*
406011 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
406031 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
406053 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
406074 CTCT
1 CTCT
406078 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:406096 original size:42 final size:41
Alignment explanation
Indices: 406011--406133 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
406001 GTGAATCGTG
* * * * *
406011 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
406053 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
406095 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
406134 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:408180 original size:20 final size:20
Alignment explanation
Indices: 408135--408195 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
408125 TCTTTTGGTT
408135 GAAATGAAAATCGCAA-CGA
1 GAAATGAAAATCGCAACCGA
*
408154 GATAATGAGAATCGCAACTCG-
1 GA-AATGAAAATCGCAAC-CGA
**
408175 GAAATGACTATCGCAA-CGA
1 GAAATGAAAATCGCAACCGA
408194 GA
1 GA
408196 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 25 0.71
21 2 0.06
22 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAATGAAAATCGCAACCGA
Found at i:408217 original size:33 final size:33
Alignment explanation
Indices: 408160--408257 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 33
408150 ACGAGATAAT
* *
408160 GAGAATCGCAACTCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
408194 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
408227 GACAATCGCAACGCGAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
408258 TGCGAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:408252 original size:19 final size:19
Alignment explanation
Indices: 408135--408319 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
408125 TCTTTTGGTT
*
408135 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
408154 GATAATGAGAATCGCAACTC
1 GA-AATGAAAATCGCAACGC
**
408174 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
408192 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
408208 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
408226 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
408241 GAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAAC-GC
*
408261 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
408280 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
408299 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
408318 GA
1 GA
408320 TTTTGGTTTC
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 44 0.32
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:408284 original size:39 final size:38
Alignment explanation
Indices: 408230--408319 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
408220 GCGACCAGAC
408230 AATCGCAACGCGAAATGAAAATCGCAACTGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAAC-GCGAAATAAA
*
408269 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
408307 AATCGCAATGCGA
1 AATCGCAACGCGA
408320 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:408337 original size:19 final size:19
Alignment explanation
Indices: 408315--408360 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
408305 AAAATCGCAA
*
408315 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
408334 TGCGAATTTTTATTTCGCGT
1 TGCG-ATTTTGATTTCGCGT
408354 TGCGATT
1 TGCGATT
408361 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.11, C:0.15, G:0.26, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:408941 original size:20 final size:20
Alignment explanation
Indices: 408916--408968 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
408906 GCGCTATGTA
408916 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
408936 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
408956 TATCTCGTTGCGA
1 AATCGCGTTGCGA
408969 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:409002 original size:20 final size:20
Alignment explanation
Indices: 408977--409030 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
408967 GATTTTGTAT
408977 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
408997 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
409017 TATCGCATTGCGAT
1 TATCGCATTGCGAT
409031 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:409015 original size:61 final size:61
Alignment explanation
Indices: 408917--409033 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
408907 CGCTATGTAA
* * * * *
408917 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
408978 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
409034 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:409049 original size:61 final size:61
Alignment explanation
Indices: 408917--409051 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
408907 CGCTATGTAA
* * * * * ** *
408917 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
408978 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
409040 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
409052 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:417416 original size:20 final size:20
Alignment explanation
Indices: 417373--417420 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
417363 AGACTGGGGT
**
417373 TATCAATATCAAGGGTTCGG
1 TATCAATATCAAGGGTTCAA
417393 TATCAATATCGAAGGG-TCAA
1 TATCAATATC-AAGGGTTCAA
417413 TATCAATA
1 TATCAATA
417421 CCCACGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (20 bp):
TATCAATATCAAGGGTTCAA
Found at i:418520 original size:60 final size:59
Alignment explanation
Indices: 418420--418583 Score: 159
Period size: 60 Copynumber: 2.7 Consensus size: 59
418410 GGAGTTGATA
* * * *
418420 CTAAATTTAGTCCTCAAACTTTTAAATATATTAATATCATCCTTAAACTATGA-CTATCAAT
1 CTAAA-TTAGTCCTCAAACTTTTGAATAT-TCAATTTCATCCTCAAACTATGATCT-TCAAT
* * *
418481 CTAAATTAGTCCTCAAACTTTTGAATATTCCATTTTCATCCCCAAACTATGATCTTCATT
1 CTAAATTAGTCCTCAAACTTTTGAATATT-CAATTTCATCCTCAAACTATGATCTTCAAT
* * * * *
418541 TTGAATTGGTCCCCAAACTTTTAGAATATTTCAGTTTCATCCT
1 CTAAATTAGTCCTCAAACTTTT-GAATA-TTCAATTTCATCCT
418584 AAATTATACG
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 61 0.71
61 22 0.26
62 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (59 bp):
CTAAATTAGTCCTCAAACTTTTGAATATTCAATTTCATCCTCAAACTATGATCTTCAAT
Found at i:424048 original size:9 final size:9
Alignment explanation
Indices: 424034--424060 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
424024 AACCCTAATT
424034 CACCATTGA
1 CACCATTGA
424043 CACCATTGA
1 CACCATTGA
424052 CACCATTGA
1 CACCATTGA
424061 AGGTAACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.22
Consensus pattern (9 bp):
CACCATTGA
Found at i:428107 original size:23 final size:23
Alignment explanation
Indices: 428081--428128 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
428071 ATAAAGTACA
*
428081 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
428104 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
428127 AT
1 AT
428129 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:428381 original size:29 final size:29
Alignment explanation
Indices: 428333--428398 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
428323 TCATTTGCAC
* * *
428333 AAAAAATTATTTGATTATTTGATATTTTAT
1 AAAATATTATTTGATAATTTGA-ATTTAAT
*
428363 AAAATATTATTT-ATAATTTTAATTTAAT
1 AAAATATTATTTGATAATTTGAATTTAAT
428391 AATAATAT
1 AA-AATAT
428399 ATATCGTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 8 0.26
29 12 0.39
30 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTGATAATTTGAATTTAAT
Found at i:428580 original size:23 final size:23
Alignment explanation
Indices: 428554--428616 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
428544 ATATAACCAC
428554 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
428577 TACCCATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
428600 TACCTATTACATCATAT
1 TACCTATTACATTATAT
428617 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:429093 original size:39 final size:39
Alignment explanation
Indices: 429039--429124 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
429029 CAAGTTGTAG
*
429039 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
429078 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
429117 ATTTTGAT
1 ATTTTGAT
429125 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:429177 original size:35 final size:35
Alignment explanation
Indices: 429133--429225 Score: 177
Period size: 35 Copynumber: 2.7 Consensus size: 35
429123 ATGAGCATCG
*
429133 GAAGTATTTCGGACTTATGATTTGGGTGGTACTCA
1 GAAGCATTTCGGACTTATGATTTGGGTGGTACTCA
429168 GAAGCATTTCGGACTTATGATTTGGGTGGTACTCA
1 GAAGCATTTCGGACTTATGATTTGGGTGGTACTCA
429203 GAAGCATTTCGGACTTATGATTT
1 GAAGCATTTCGGACTTATGATTT
429226 TAGTTGCTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.37
Consensus pattern (35 bp):
GAAGCATTTCGGACTTATGATTTGGGTGGTACTCA
Found at i:429442 original size:18 final size:18
Alignment explanation
Indices: 429419--429455 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
429409 CGAAATATAT
429419 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
429437 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
429455 A
1 A
429456 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:429915 original size:23 final size:23
Alignment explanation
Indices: 429889--429951 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
429879 ATATAACCAC
429889 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
429912 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
429935 TACCTATTACATCATAT
1 TACCTATTACATTATAT
429952 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:430354 original size:25 final size:25
Alignment explanation
Indices: 430297--430362 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
430287 CACTCAAAAG
*
430297 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*** *
430322 ACAAACATACCTAAATATGTATTTA
1 ATGTACATACCTAAATATGTAGTTA
*
430347 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
430363 TTAATGATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:433358 original size:183 final size:183
Alignment explanation
Indices: 432833--433325 Score: 907
Period size: 183 Copynumber: 2.7 Consensus size: 183
432823 TTAAAATTAC
*
432833 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
432897 TATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
432962 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
433016 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
433081 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
433146 ATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
433199 CGACACTTTTTAACAATGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
433264 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCG
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
433326 ATAGCATTGC
Statistics
Matches: 301, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
183 298 0.99
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:434835 original size:3 final size:3
Alignment explanation
Indices: 434827--434907 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
434817 ACTTGTTTGG
* * * **
434827 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
434875 AAC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
434908 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:434844 original size:12 final size:12
Alignment explanation
Indices: 434831--434919 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
434821 GTTTGGATCA
* *
434831 TCATCTTCATCA
1 TCATCGTCATCT
* *
434843 TCATCATCATCA
1 TCATCGTCATCT
* *
434855 TCGTCATCATCT
1 TCATCGTCATCT
* *
434867 TCATCGCCAACT
1 TCATCGTCATCT
*
434879 TCATCGTCATCA
1 TCATCGTCATCT
434891 TCATCGTCATCT
1 TCATCGTCATCT
*
434903 TCATCGTCAGCT
1 TCATCGTCATCT
434915 TCATC
1 TCATC
434920 CTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:434883 original size:36 final size:36
Alignment explanation
Indices: 434843--434919 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
434833 ATCTTCATCA
*
434843 TCATCATCATCATCGTCATCATCTTCATCGCCAACT
1 TCATCATCATCATCATCATCATCTTCATCGCCAACT
* * * *
434879 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAACT
434915 TCATC
1 TCATC
434920 CTCTGCGACC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAACT
Found at i:436742 original size:198 final size:198
Alignment explanation
Indices: 436385--437550 Score: 2169
Period size: 198 Copynumber: 5.9 Consensus size: 198
436375 TTTAAATTAG
436385 TATCGACACAAACTATA--ACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
*
436448 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
436513 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
436578 AAAA
195 AAAA
436582 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
436647 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
436712 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
436776 AAAA
195 AAAA
436780 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
436845 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
436910 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
436975 AAA
196 AAA
* *
436978 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
437043 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
437108 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
437172 AAA
196 AAA
437175 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
437240 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
437305 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
437370 AAAA
195 AAAA
* *
437374 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGATAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* * *
437439 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
437504 TTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
437551 GGCCATATTG
Statistics
Matches: 947, Mismatches: 15, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
197 227 0.24
198 527 0.56
199 133 0.14
200 60 0.06
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:437684 original size:19 final size:19
Alignment explanation
Indices: 437660--437699 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
437650 CATTCATAAA
437660 TATAAATCGAATACAAAAT
1 TATAAATCGAATACAAAAT
**
437679 TATAAATCTTATACAAAAT
1 TATAAATCGAATACAAAAT
437698 TA
1 TA
437700 ACCCTACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
TATAAATCGAATACAAAAT
Found at i:439523 original size:33 final size:33
Alignment explanation
Indices: 439486--439551 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
439476 CATCTTAATA
*
439486 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
439519 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
439552 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:439610 original size:21 final size:21
Alignment explanation
Indices: 439585--439649 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
439575 CCCCTTATGC
* *
439585 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
439606 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
439627 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
439648 CT
1 CT
439650 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:441928 original size:21 final size:19
Alignment explanation
Indices: 441881--441928 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
441871 TCCGGTATCA
441881 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
441900 TTGATACCGGTTTTTATCATAT
1 TT-TTACCGG-TTTTATCAT-T
441922 TTTTACC
1 TTTTACC
441929 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 6 0.25
21 13 0.54
22 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:442080 original size:17 final size:18
Alignment explanation
Indices: 442058--442100 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
442048 ATATATCCGG
442058 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
442075 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
442095 TATCAT
1 TATCAT
442101 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:442108 original size:20 final size:19
Alignment explanation
Indices: 442063--442108 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
442053 TCCGGTATCA
442063 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
442082 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
442103 TTTTAC
1 TTTTAC
442109 ATGGTATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:442175 original size:181 final size:182
Alignment explanation
Indices: 441848--442321 Score: 700
Period size: 182 Copynumber: 2.6 Consensus size: 182
441838 CGTACTTACG
*
441848 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGG-TT
* * *
441913 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTA
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
* *
441978 TAGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
442030 AAAGTATCGACACTTTTAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
442095 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
442160 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * ** * *
442212 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGATTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
442276 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
442322 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
181 107 0.41
182 155 0.59
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:442788 original size:229 final size:228
Alignment explanation
Indices: 442387--442873 Score: 875
Period size: 229 Copynumber: 2.1 Consensus size: 228
442377 GACCTACTTT
*
442387 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
442452 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
442517 ATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* *
442582 CAAATATAATAATAAATATGTTTTCAACAGTGAA
196 CAAAGATAATAATAAATATATTTTC-ACAGTGAA
442616 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
* *
442681 ATTTTTTTAATATTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
442746 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
*
442811 TAAAGATAATAATAAATATATTTTCACAGTGAA
196 CAAAGATAATAATAAATATATTTTCACAGTGAA
* *
442844 ATAAGTATAGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
442874 GATAATTTAC
Statistics
Matches: 248, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
228 36 0.15
229 212 0.85
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:444260 original size:28 final size:28
Alignment explanation
Indices: 444207--444261 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
444197 ATTTATCATT
* * *
444207 GGATTGAATTATAATTTTACACTTTTAA
1 GGATTGAATAAAAATTATACACTTTTAA
444235 GGATTGAATAAAAATTATATCA-TTTTA
1 GGATTGAATAAAAATTATA-CACTTTTA
444262 GAGGGGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (28 bp):
GGATTGAATAAAAATTATACACTTTTAA
Found at i:444970 original size:12 final size:12
Alignment explanation
Indices: 444941--444990 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
444931 AATTATTAAC
444941 ATATTTAA-AAT
1 ATATTTAATAAT
*
444952 ATATTTATTAAT
1 ATATTTAATAAT
*
444964 ATTTTTAATAAT
1 ATATTTAATAAT
*
444976 ATAATATAATAAT
1 AT-ATTTAATAAT
444989 AT
1 AT
444991 TATTATTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 7 0.22
12 15 0.47
13 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:444970 original size:23 final size:23
Alignment explanation
Indices: 444923--444980 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
444913 CATTTTAATA
444923 AAAATATTAATTATTAACATATTT
1 AAAATA-TAATTATTAACATATTT
* * *
444947 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAACATATTT
444970 AATAATATAAT
1 AA-AATATAAT
444981 ATAATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAACATATTT
Found at i:445422 original size:23 final size:22
Alignment explanation
Indices: 445395--445452 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
445385 TAGTCTAATA
445395 ATATTATAA-AAATTCTTTAAAAT
1 ATATTATAATAAA-T-TTTAAAAT
445418 ATATTTATTAATAAATTTTAAAAT
1 ATA-TTA-TAATAAATTTTAAAAT
*
445442 ATAATATAATA
1 ATATTATAATA
445453 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.16
23 5 0.16
24 14 0.45
25 4 0.13
26 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTATAATAAATTTTAAAAT
Found at i:445622 original size:23 final size:23
Alignment explanation
Indices: 445583--445643 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
445573 AAATAGTATT
*
445583 AAATAAATTAT-TCTAATATTTTTA
1 AAATAAATAATAT-TAAT-TTTTTA
445607 AAAT-AATAATATTAATTTTTTA
1 AAATAAATAATATTAATTTTTTA
*
445629 TAATAAATAATATTA
1 AAATAAATAATATTA
445644 TTTATTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 9 0.27
23 19 0.58
24 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATAAATAATATTAATTTTTTA
Found at i:452655 original size:4 final size:4
Alignment explanation
Indices: 452646--452671 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
452636 TCGATACCGT
452646 AGGA AGGA AGGA AGGA AGGA AGGA AG
1 AGGA AGGA AGGA AGGA AGGA AGGA AG
452672 AAGAACCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (4 bp):
AGGA
Found at i:454274 original size:19 final size:19
Alignment explanation
Indices: 454250--454290 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
454240 AAATTAATAA
454250 AACCCTCAAATTCCGATTC
1 AACCCTCAAATTCCGATTC
* **
454269 AACCCTTATTTTCCGATTC
1 AACCCTCAAATTCCGATTC
454288 AAC
1 AAC
454291 GATTTGATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (19 bp):
AACCCTCAAATTCCGATTC
Found at i:457208 original size:21 final size:21
Alignment explanation
Indices: 457178--457232 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
457168 CGGTTCAACC
457178 TAAATATTTTTAAT-TTTTTAT
1 TAAAT-TTTTTAATATTTTTAT
**
457199 TAAATGTTTTTGGTATTTTTAT
1 TAAAT-TTTTTAATATTTTTAT
*
457221 TTAATTTTTTAA
1 TAAATTTTTTAA
457233 ATAATTATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TAAATTTTTTAATATTTTTAT
Found at i:457649 original size:53 final size:54
Alignment explanation
Indices: 457561--457668 Score: 130
Period size: 53 Copynumber: 2.0 Consensus size: 54
457551 CATAATCACC
* * *
457561 TTTAGAAATTATCAGTTTCCTGTCAATCGATACTTTGA-ATAAATTTCTTCGTT
1 TTTAAAAATTATCAGTTTCCTGTCAATCGAGACTTTGAGATAAACTTCTTCGTT
* * * *
457614 TTTAAAAATTATCAG-TTCTTTGTCAATTGAGACTTTTAGATAGACTTCTTCGTT
1 TTTAAAAATTATCAGTTTC-CTGTCAATCGAGACTTTGAGATAAACTTCTTCGTT
457668 T
1 T
457669 GCTGAAGTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
52 3 0.07
53 29 0.63
54 14 0.30
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (54 bp):
TTTAAAAATTATCAGTTTCCTGTCAATCGAGACTTTGAGATAAACTTCTTCGTT
Done.