Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014380.1 Corchorus capsularis cultivar CVL-1 contig14401, 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: 16958
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1414 original size:17 final size:17
Alignment explanation
Indices: 1392--1424 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1382 TTTTATGGAT
1392 ATTTAT-ATTATTAATTA
1 ATTTATAATT-TTAATTA
1409 ATTTATAATTTTAATT
1 ATTTATAATTTTAATT
1425 GATGTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAATTA
Found at i:6352 original size:2 final size:2
Alignment explanation
Indices: 6345--6371 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6335 CGACAATTAA
6345 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6372 ATGTAACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7130 original size:2 final size:2
Alignment explanation
Indices: 7125--7150 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7115 TATATTCTCT
7125 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
7151 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:7236 original size:21 final size:21
Alignment explanation
Indices: 7193--7275 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
7183 TGCACAACTT
* * * *
7193 GTTAGTTTTCTCGGGACCCTC
1 GTTAATTTTCTCAGGATCATC
7214 GTTAATTTTCTCAGGATCATC
1 GTTAATTTTCTCAGGATCATC
* *
7235 GTCATTAATTTTCTAAGGATCGTC
1 G---TTAATTTTCTCAGGATCATC
*
7259 GTTAATTTTCACAGGAT
1 GTTAATTTTCTCAGGAT
7276 AATCCTCGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 32 0.63
24 19 0.37
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (21 bp):
GTTAATTTTCTCAGGATCATC
Found at i:7246 original size:24 final size:24
Alignment explanation
Indices: 7194--7388 Score: 111
Period size: 24 Copynumber: 8.5 Consensus size: 24
7184 GCACAACTTG
* *
7194 TTAGTTTTCTCGGGA-C--CCTCG
1 TTAGTTTTCTCAGGATCATCCTCA
* *
7215 TTAATTTTCTCAGGATCATCGTCA
1 TTAGTTTTCTCAGGATCATCCTCA
* * * *
7239 TTAATTTTCTAAGG---ATCGTCG
1 TTAGTTTTCTCAGGATCATCCTCA
* * * *
7260 TTAATTTTCACAGGATAATCCTCG
1 TTAGTTTTCTCAGGATCATCCTCA
* * *
7284 TTGGTTATCTCAGG---ATCGTCA
1 TTAGTTTTCTCAGGATCATCCTCA
*
7305 TTAGTTTTCACAGGATCATCCTCA
1 TTAGTTTTCTCAGGATCATCCTCA
* * * *
7329 TTGGTTTTCTCAGAATAATCCTCG
1 TTAGTTTTCTCAGGATCATCCTCA
* * *
7353 TTTGTTTTCTCAGGATCATTCTCG
1 TTAGTTTTCTCAGGATCATCCTCA
*
7377 TTGGTTTTCTCA
1 TTAGTTTTCTCA
7389 AGAACGTAGA
Statistics
Matches: 136, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
21 47 0.35
22 1 0.01
24 88 0.65
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (24 bp):
TTAGTTTTCTCAGGATCATCCTCA
Found at i:7320 original size:21 final size:21
Alignment explanation
Indices: 7232--7321 Score: 65
Period size: 21 Copynumber: 4.1 Consensus size: 21
7222 TCTCAGGATC
7232 ATCGTCATTAATTTTCTA-AGG
1 ATCGTCATTAATTTTC-ACAGG
*
7253 ATCGTCGTTAATTTTCACAGG
1 ATCGTCATTAATTTTCACAGG
* * ** * *
7274 ATAATCCTCGTTGGTTATCTCAGG
1 ---ATCGTCATTAATTTTCACAGG
*
7298 ATCGTCATTAGTTTTCACAGG
1 ATCGTCATTAATTTTCACAGG
7319 ATC
1 ATC
7322 ATCCTCATTG
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.02
21 37 0.69
24 16 0.30
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (21 bp):
ATCGTCATTAATTTTCACAGG
Found at i:7333 original size:45 final size:45
Alignment explanation
Indices: 7197--7341 Score: 164
Period size: 45 Copynumber: 3.2 Consensus size: 45
7187 CAACTTGTTA
* * * * * * *
7197 GTTTTCTCGGGACCCTCGTTAATTTTCTCAGGATCATCGTCATTA
1 GTTTTCTCAGGATCGTCATTAATTTTCACAGGATCATCCTCATTG
* * * * *
7242 ATTTTCTAAGGATCGTCGTTAATTTTCACAGGATAATCCTCGTTG
1 GTTTTCTCAGGATCGTCATTAATTTTCACAGGATCATCCTCATTG
* *
7287 GTTATCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTG
1 GTTTTCTCAGGATCGTCATTAATTTTCACAGGATCATCCTCATTG
7332 GTTTTCTCAG
1 GTTTTCTCAG
7342 AATAATCCTC
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (45 bp):
GTTTTCTCAGGATCGTCATTAATTTTCACAGGATCATCCTCATTG
Found at i:7785 original size:24 final size:23
Alignment explanation
Indices: 7753--7813 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
7743 GACCTCTTTG
7753 TTAATTTTCTCAGGATTATCGTCA
1 TTAATTTTCTCAGGA-TATCGTCA
* *
7777 TTAATTTTCTAAGG--ATCGTCG
1 TTAATTTTCTCAGGATATCGTCA
*
7798 TTAATTTTCACAGGAT
1 TTAATTTTCTCAGGAT
7814 CATCCTCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 18 0.58
24 13 0.42
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (23 bp):
TTAATTTTCTCAGGATATCGTCA
Found at i:7883 original size:45 final size:44
Alignment explanation
Indices: 7782--7883 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 44
7772 CGTCATTAAT
* *
7782 TTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGG
1 TTTCTCAGGATCGTCATTAATTTTCACAGGATCATCCTCGTTGG
* *
7826 TTATCTCGGGATCGTCATTAGTTTTCACAGGATCATCCTCAG-TGG
1 TT-TCTCAGGATCGTCATTAATTTTCACAGGATCATCCTC-GTTGG
7871 ATTTCTCAGGATC
1 -TTTCTCAGGATC
7884 ATTCTCGTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 2 0.04
45 45 0.90
46 3 0.06
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (44 bp):
TTTCTCAGGATCGTCATTAATTTTCACAGGATCATCCTCGTTGG
Found at i:8190 original size:538 final size:535
Alignment explanation
Indices: 7164--10245 Score: 3673
Period size: 538 Copynumber: 5.7 Consensus size: 535
7154 ATATATATAT
* *
7164 ATATATATAGTCAATACCTTGCACAACTTGTTAGTTTTCTCGGGACCCTC---GTTAATTTTCTC
1 ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTCTTTGTTAATTTTCTC
*
7226 AGGATCATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATAATCCTCGTTGGTTA
66 AGGATCATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTTA
* * *
7291 TCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGAATAATCCTCGTTT
131 TCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTCGTTA
* * * * *
7356 GTTTTCTCAGGATCATTCTCGTTGGTTTTCTCAAGAACGTAGAAATAGCCAATAGTTACACTCAA
196 GTTTTATCAGGATCA-TCTCGTTGGTTTTCTCAGGACCGTTGAAATAGTCAATAGTTACACTCAA
* *
7421 TCCCCAACAACAATCTCTCTTCGAGGCATCAGTTCATCAAATATAGTATACCATCCTTCCTTCCA
260 TCCCCAACAACAATCTCTCTTCGAGGCATCAGTTCGTCAAATATATTATACCATCCTTCCTTCCA
* * *
7486 AGATACAAGCTGCAAAATTGACTCAGTTCTTCAATATTATACAGGATCATGCACATTAACCAAAA
325 AGATACAAGCTGCAAAATTGACTCAATTCTTCAATATTTTACAGAATCATGCACATTAACCAAAA
* * *
7551 ATGCCATAAATAATGTACACAAGCCTGATCCGAACCCGACCCAAACCCGCCCATGCACAGCTCTA
390 ATGCCATAAATCATGTACACAAGCTTGATCCGAACCC--CCCGAACCCG-CCATGCACAGCTCTA
* * * *
7616 CATGCGATCCTCATCATCCTATAGGCAAGCTAACATTAAGTCGTATTAATTGATACTGAAGAATA
452 CATGCGATCCTCATCAACCTGTAGACAAGATAACATTAAGTCGTATTAATTGATACTGAAGAATA
7681 TATTCTCTCTCACACATAC
517 TATTCTCTCTCACACATAC
*
7700 ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCAGGA-CCTCTTTGTTAATTTTCTC
1 ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTCTTTGTTAATTTTCTC
*
7764 AGGATTATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTTA
66 AGGATCATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTTA
* * * *
7829 TCTCGGGATCGTCATTAGTTTTCACAGGATCATCCTCAGTGGATTTCTCAGGATCATTCTCGTTA
131 TCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTCGTTA
* * *
7894 GTCTTATCAGGATCATCATCGTTGGTTTTCTCATGACCGTTGAAATAGACAATAGTTACACTCAA
196 GTTTTATCAGGATCATC-TCGTTGGTTTTCTCAGGACCGTTGAAATAGTCAATAGTTACACTCAA
* * *
7959 TCCCGAACAACAATCTCTATTCGAGGCATCAGTTCGTCATATATATTATACCATCCTTCCTTCCA
260 TCCCCAACAACAATCTCTCTTCGAGGCATCAGTTCGTCAAATATATTATACCATCCTTCCTTCCA
* * *
8024 AGATACAAGCTGCAAAATTGACTCAATTCTTCAATATTTTACAGAATCATGCAAATCAACAAAAA
325 AGATACAAGCTGCAAAATTGACTCAATTCTTCAATATTTTACAGAATCATGCACATTAACCAAAA
* *
8089 ATGCCAAAAATCACGTACACAAGCTTGATCCGAACCCGGCCCGAACCCGCCTATGCACAGCTCTA
390 ATGCCATAAATCATGTACACAAGCTTGATCCGAACCC--CCCGAACCCGCC-ATGCACAGCTCTA
* * * * *
8154 CATGTGATCCTCATCAACTTGTAGACAAGTTAACATTAAGTCATATTAATTGGTACTGAAGAATA
452 CATGCGATCCTCATCAACCTGTAGACAAGATAACATTAAGTCGTATTAATTGATACTGAAGAATA
8219 TATTCTCTCTCACACATAC
517 TATTCTCTCTCACACATAC
* *
8238 ATACATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTCATTGTTAATTTTCTC
1 ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTCTTTGTTAATTTTCTC
* *
8303 AGGATCATCGTCATTAATTTTCTAAGGATTGTCGTTAATTTTCACAGAATCATCCTCGTTGGTTA
66 AGGATCATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTTA
* *
8368 TCTCATGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCAATACTCGTT
131 TCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATC-ATCCTCGTT
*
8433 AGTTTTCTCAGGATCGATGTTGGTTTTCTCAAGATCGTCCTCGTTAGTTTTCTCAGGACCGTTGA
195 AGTTTTATCAGGATC-A-----------TC----TCGT--T-G---GTTTTCTCAGGACCGTTGA
* * * *
8498 AATAGTCGATAGTTACACTCAATCTCCAACAACAATCTCTCTTCGAGGCGTCAATTCGTCAAATA
238 AATAGTCAATAGTTACACTCAATCCCCAACAACAATCTCTCTTCGAGGCATCAGTTCGTCAAATA
* * *
8563 TAATATACCATCCTTCCATCCAAGATACAAGCTGCAAAAATGACT-AAGTTCTTCAATATTTTAC
303 TATTATACCATCCTTCCTTCCAAGATACAAGCTGCAAAATTGACTCAA-TTCTTCAATATTTTAC
8627 AGAATCATGCACATTAACCAAAAATGCCATAAATCATGTACACAAGCCTT-ATCCGAA---CCCG
367 AGAATCATGCACATTAACCAAAAATGCCATAAATCATGTACACAAG-CTTGATCCGAACCCCCCG
* *
8688 ----C-CCATGCACAGCTCAACATGCGATCCTCATCAACCTGTAGGCAAGATAACATTAAGTCGT
431 AACCCGCCATGCACAGCTCTACATGCGATCCTCATCAACCTGTAGACAAGATAACATTAAGTCGT
* * *
8748 ATTAATTAATACTGAACAATATATTCTCTCTTACACATAC
496 ATTAATTGATACTGAAGAATATATTCTCTCTCACACATAC
*
8788 ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTACTTT-TTAATGTTCT
1 ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCT-CTTTGTTAATTTTCT
** *
8852 CAGGATCATCGTCATTAATTTTCTAAATATCGTTGTTAATTTTCACAGGATCATCCTCGTTGGTT
65 CAGGATCATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTT
* *
8917 ATCTCATGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTTGTT
130 ATCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTCGTT
*
8982 AGTTTTCTCAGGATCGATGTTGGTTTTCTCAGGATCATCCTCGTTGGTTTTCTCAGGGCCGTTGA
195 AG--TT-T-----T--A-----------TCAGGATCAT-CTCGTTGGTTTTCTCAGGACCGTTGA
* *
9047 AATAGTCGATAGTTACACTCAATCCCCAACAACAATCTCTCTTCGAGGCGTCAGTTCGTCAAATA
238 AATAGTCAATAGTTACACTCAATCCCCAACAACAATCTCTCTTCGAGGCATCAGTTCGTCAAATA
* *
9112 TAATATACCATCCTTCCTTCCAAGATACAAGCTGCAAAAATGACTCAATTCTTCAATATTTTACA
303 TATTATACCATCCTTCCTTCCAAGATACAAGCTGCAAAATTGACTCAATTCTTCAATATTTTACA
* * *
9177 GAATCATGCACATTAACCAAAAATGACATAAATCATATACACAAGCCTT-ATTCGAA---CCCG-
368 GAATCATGCACATTAACCAAAAATGCCATAAATCATGTACACAAG-CTTGATCCGAACCCCCCGA
* * * *
9237 ---C-CCATGCACAGTTCAACATGCGATCCTCATCAACCTGTAGTCAAGATAACATTAGGTCGTA
432 ACCCGCCATGCACAGCTCTACATGCGATCCTCATCAACCTGTAGACAAGATAACATTAAGTCGTA
* *
9298 TTAATTGATACTGAACAATATATTCTCTCTCATACATAC
497 TTAATTGATACTGAAGAATATATTCTCTCTCACACATAC
*
9337 ATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTCGGGA-CCTGCTTT-TTAATTTTCT
1 ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCT-CTTTGTTAATTTTCT
* **
9400 CAGGATCATCGTCATTAATTTTCCAAATATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTT
65 CAGGATCATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTT
* * *
9465 ATTTCAGGATCGTCATTAGTTTTCATCA-AATCA-CCTTCATTGGTTTTCTCAGTATCATCCTCG
130 ATCTCAGGATCGTCATTAGTTTTCA-CAGGATCATCC-TCATTGGTTTTCTCAGGATCATCCTCG
* * ** **
9528 TTAGTTTTCTCAGGATCGT-T-GTTGGTTTTCTCAGGATCATCCTCGTT-AGTTTTCTCAGGATC
193 TTAGTTTTATCAGGATCATCTCGTTGGTTTTCTCAGG---A--C-CGTTGA-AATAGTCA--AT-
* * * *
9590 AGTTACATTCAATCCCCAACAACAATCTCTATTCGAGGTATCAGTTCATCAAATATAGTATACTA
248 AGTTACACTCAATCCCCAACAACAATCTCTCTTCGAGGCATCAGTTCGTCAAATATA-T-TA-TA
* * * * * * * *
9655 TCCTTCCTTCCTTCCTATATACAAGCTACAAAATTTACTTAGTTCTTCAATATTTTACAAAATCA
310 -CCATCCTTCCTTCCAAGATACAAGCTGCAAAATTGACTCAATTCTTCAATATTTTACAGAATCA
* * * *
9720 TGCACATTAACCAAAAATGTCATAAATCATGTACGCAAGCCTGATTCGAACCCAGCCCGAAACCC
374 TGCACATTAACCAAAAATGCCATAAATCATGTACACAAGCTTGATCCGAACCC--CCCG-AACCC
* *
9785 GCCATGTACAGCTCTACAT--G-----C-T--A----T--AC----T--CATTAAGTCATATTAA
436 GCCATGCACAGCTCTACATGCGATCCTCATCAACCTGTAGACAAGATAACATTAAGTCGTATTAA
* ** * *
9828 TTGAAACTTTAGAATATATTTTCTCTCACATATAC
501 TTGATACTGAAGAATATATTCTCTCTCACACATAC
* ** *
9863 ATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTTAGGACCCTCCTTGTTAATTTTCTC
1 ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTCTTTGTTAATTTTCTC
* ** *
9928 AGGATTATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCATGGGAACATCCTCGTTGGTTA
66 AGGATCATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTTA
* * * * *
9993 TCTCAGGATCGTCTTTAGTTTTAATAGGATCATCCTCATTGGTTTTCTTAGGATCATCCTCTTTA
131 TCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTCGTTA
* * * ** *
10058 GTTTTATCAGAATCATCCTCGTTGGTTTTCTTAGTACCGTTGAAATAACCAACAGTTACACTCAA
196 GTTTTATCAGGATCAT-CTCGTTGGTTTTCTCAGGACCGTTGAAATAGTCAATAGTTACACTCAA
* ** * * ** *
10123 TCCCCAACAACAATCTCTCTTTGAGTTAGCAGTTCGTCAAAT-TTTGTATAATATCCTTCCTTAC
260 TCCCCAACAACAATCTCTCTTCGAGGCATCAGTTCGTCAAATATAT-TATACCATCCTTCCTTCC
* * * * * * *
10187 AAGATATAAGCTGGAAAATTAACTAAATTCTT-ATATATTTTACAAAATAATACACATTA
324 AAGATACAAGCTGCAAAATTGACTCAATTCTTCA-ATATTTTACAGAATCATGCACATTA
10246 TGACATAAAG
Statistics
Matches: 2247, Mismatches: 208, Indels: 201
0.85 0.08 0.08
Matches are distributed among these distances:
516 1 0.00
517 57 0.03
518 2 0.00
519 3 0.00
520 1 0.00
521 48 0.02
522 1 0.00
524 22 0.01
525 3 0.00
526 89 0.04
527 147 0.07
528 3 0.00
529 3 0.00
530 20 0.01
532 3 0.00
533 52 0.02
534 1 0.00
535 6 0.00
536 46 0.02
537 102 0.05
538 484 0.22
539 131 0.06
540 23 0.01
541 2 0.00
542 4 0.00
545 1 0.00
546 3 0.00
547 3 0.00
548 150 0.07
549 348 0.15
550 262 0.12
551 7 0.00
552 5 0.00
553 1 0.00
555 9 0.00
556 4 0.00
557 2 0.00
558 2 0.00
559 1 0.00
560 2 0.00
561 181 0.08
562 3 0.00
569 1 0.00
570 8 0.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (535 bp):
ATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTCTTTGTTAATTTTCTC
AGGATCATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTTA
TCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTCGTTA
GTTTTATCAGGATCATCTCGTTGGTTTTCTCAGGACCGTTGAAATAGTCAATAGTTACACTCAAT
CCCCAACAACAATCTCTCTTCGAGGCATCAGTTCGTCAAATATATTATACCATCCTTCCTTCCAA
GATACAAGCTGCAAAATTGACTCAATTCTTCAATATTTTACAGAATCATGCACATTAACCAAAAA
TGCCATAAATCATGTACACAAGCTTGATCCGAACCCCCCGAACCCGCCATGCACAGCTCTACATG
CGATCCTCATCAACCTGTAGACAAGATAACATTAAGTCGTATTAATTGATACTGAAGAATATATT
CTCTCTCACACATAC
Found at i:8443 original size:25 final size:24
Alignment explanation
Indices: 8263--8490 Score: 109
Period size: 24 Copynumber: 9.8 Consensus size: 24
8253 ACCTTGTACA
* * *
8263 ACTCGTTAGTTTTCTCGGGACCCT
1 ACTCGTTAGTTTTCTCAGGATCAT
* *
8287 -CATTGTTAATTTTCTCAGGATCAT
1 AC-TCGTTAGTTTTCTCAGGATCAT
* * *
8311 -CGTCATTAATTTTCTAAGGAT--T
1 AC-TCGTTAGTTTTCTCAGGATCAT
* * * *
8333 -GTCGTTAATTTTCACAGAATCAT
1 ACTCGTTAGTTTTCTCAGGATCAT
* * * *
8356 CCTCGTTGGTTATCTCATGATC--
1 ACTCGTTAGTTTTCTCAGGATCAT
* * *
8378 -GTCATTAGTTTTCACAGGATCAT
1 ACTCGTTAGTTTTCTCAGGATCAT
* * *
8401 CCTCATTGGTTTTCTCAGGATCAAT
1 ACTCGTTAGTTTTCTCAGGATC-AT
*
8426 ACTCGTTAGTTTTCTCAGGATC-G
1 ACTCGTTAGTTTTCTCAGGATCAT
* * *
8449 A-T-GTTGGTTTTCTCAAGATCGT
1 ACTCGTTAGTTTTCTCAGGATCAT
*
8471 CCTCGTTAGTTTTCTCAGGA
1 ACTCGTTAGTTTTCTCAGGA
8491 CCGTTGAAAT
Statistics
Matches: 153, Mismatches: 40, Indels: 22
0.71 0.19 0.10
Matches are distributed among these distances:
21 46 0.30
22 2 0.01
23 4 0.03
24 80 0.52
25 21 0.14
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (24 bp):
ACTCGTTAGTTTTCTCAGGATCAT
Found at i:8460 original size:21 final size:23
Alignment explanation
Indices: 8357--8490 Score: 89
Period size: 21 Copynumber: 5.8 Consensus size: 23
8347 CAGAATCATC
* *
8357 CTCGTTGGTTATCTCATGATCG-
1 CTCGTTGGTTTTCTCAGGATCGA
* * *
8379 -TCATTAGTTTTCACAGGATC-A
1 CTCGTTGGTTTTCTCAGGATCGA
* *
8400 TCCTCATTGGTTTTCTCAGGATCAATA
1 --CTCGTTGGTTTTCTCAGGATC--GA
*
8427 CTCGTTAGTTTTCTCAGGATCGA
1 CTCGTTGGTTTTCTCAGGATCGA
* *
8450 -T-GTTGGTTTTCTCAAGATCGTC
1 CTCGTTGGTTTTCTCAGGATCG-A
*
8472 CTCGTTAGTTTTCTCAGGA
1 CTCGTTGGTTTTCTCAGGA
8491 CCGTTGAAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
21 32 0.37
22 1 0.01
23 2 0.02
24 32 0.37
25 19 0.22
27 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (23 bp):
CTCGTTGGTTTTCTCAGGATCGA
Found at i:8929 original size:45 final size:45
Alignment explanation
Indices: 8887--8972 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
8877 AATATCGTTG
* *
8887 TTAATTTTCACAGGATCATCCTCGTTGGTTATCTCATGATCGTCA
1 TTAATTTTCACAGGATCATCCTCATTGGTTATCTCAGGATCGTCA
* *
8932 TTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATC
1 TTAATTTTCACAGGATCATCCTCATTGGTTATCTCAGGATC
8973 ATCCTTGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (45 bp):
TTAATTTTCACAGGATCATCCTCATTGGTTATCTCAGGATCGTCA
Found at i:8962 original size:24 final size:24
Alignment explanation
Indices: 8891--9038 Score: 148
Period size: 24 Copynumber: 6.4 Consensus size: 24
8881 TCGTTGTTAA
*
8891 TTTTCACAGGATCATCCTCGTTGG
1 TTTTCTCAGGATCATCCTCGTTGG
* * * * *
8915 TTATCTC---ATGATCGTCATTAG
1 TTTTCTCAGGATCATCCTCGTTGG
* *
8936 TTTTCACAGGATCATCCTCATTGG
1 TTTTCTCAGGATCATCCTCGTTGG
* *
8960 TTTTCTCAGGATCATCCTTGTTAG
1 TTTTCTCAGGATCATCCTCGTTGG
8984 TTTTCTCAGGATCGA---T-GTTGG
1 TTTTCTCAGGATC-ATCCTCGTTGG
9005 TTTTCTCAGGATCATCCTCGTTGG
1 TTTTCTCAGGATCATCCTCGTTGG
9029 TTTTCTCAGG
1 TTTTCTCAGG
9039 GCCGTTGAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.01
21 32 0.32
22 1 0.01
23 1 0.01
24 64 0.64
25 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (24 bp):
TTTTCTCAGGATCATCCTCGTTGG
Found at i:8970 original size:69 final size:69
Alignment explanation
Indices: 8891--9038 Score: 199
Period size: 69 Copynumber: 2.1 Consensus size: 69
8881 TCGTTGTTAA
* * *
8891 TTTTCACAGGATCATCCTCGTTGGTTATCTCATGATCG-TCATTAGTTTTCACAGGATCATCCTC
1 TTTTCTCAGGATCATCCTCGTTAGTTATCTCAGGATCGAT-ATTAGTTTTCACAGGATCATCCTC
8955 ATTGG
65 ATTGG
* * * * * *
8960 TTTTCTCAGGATCATCCTTGTTAGTTTTCTCAGGATCGATGTTGGTTTTCTCAGGATCATCCTCG
1 TTTTCTCAGGATCATCCTCGTTAGTTATCTCAGGATCGATATTAGTTTTCACAGGATCATCCTCA
9025 TTGG
66 TTGG
9029 TTTTCTCAGG
1 TTTTCTCAGG
9039 GCCGTTGAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 68 0.99
70 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (69 bp):
TTTTCTCAGGATCATCCTCGTTAGTTATCTCAGGATCGATATTAGTTTTCACAGGATCATCCTCA
TTGG
Found at i:9239 original size:549 final size:547
Alignment explanation
Indices: 7900--10067 Score: 2867
Period size: 549 Copynumber: 4.0 Consensus size: 547
7890 GTTAGTCTTA
* * * * * *
7900 TCAGGATCATCATCGTTGGTTTTCTCATGACCGTTGAAATAGACAATAGTTACACTCAATCCCGA
1 TCAGGATCATCCTCGTTAGTTTTCTCAGGACCGTTGAAATAGTCGATAGTTACACTCAATCCCCA
* *
7965 ACAACAATCTCTATTCGAGGCATCAGTTCGTCATATATATTATACCATCCTTCCTTCCAAGATAC
66 ACAACAATCTCTATTCGAGGCATCAGTTCGTCAAATATAATATACCATCCTTCCTTCCAAGATAC
* * * *
8030 AAGCTGCAAAATTGACTCAATTCTTCAATATTTTACAGAATCATGCAAATCAACAAAAAATGCCA
131 AAGCTGCAAAAATGACTCAATTCTTCAATATTTTACAGAATCATGCACATTAACCAAAAATGCCA
* * * *
8095 AAAATCACGTACACAAG-CTTGATCCGAACCCGGCCCGAACCCGCCTATGCACAGCTCTACATGT
196 TAAATCATGTACACAAGCCTT-ATCCGAA-----CCCG----C-CC-ATGCACAGCTCAACATGC
* * ** *
8159 GATCCTCATCAACTTGTAGACAAGTTAACATTAAGTCATATTAATTGGTACTGAAGAATATATTC
249 GATCCTCATCAACCTGTAG-CAAGATAACATTAAGTCATATTAATTAATACTGAACAATATATTC
* *
8224 TCTCTCACACATACATACATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTCA
313 TCTCTCACACATACATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTC-
* * *
8289 TTGTTAATTTTCTCAGGATCATCGTCATTAATTTTCTAAGGATTGTCGTTAATTTTCACAGAATC
377 TTGTTAATTTTCTCAGGATCATCGTCATTAATTTTCTAAAGATCGTCGTTAATTTTCACAGGATC
*
8354 ATCCTCGTTGGTTATCTCATGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAG
442 ATCCTCGTTGGTTATCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAG
*
8419 GATCAATACTCGTTAGTTTTCTCAGGATCGATGTTGGTTTTC
507 GATC-ATCCTCGTTAGTTTTCTCAGGATCGATGTTGGTTTTC
* * *
8461 TCAAGATCGTCCTCGTTAGTTTTCTCAGGACCGTTGAAATAGTCGATAGTTACACTCAATCTCCA
1 TCAGGATCATCCTCGTTAGTTTTCTCAGGACCGTTGAAATAGTCGATAGTTACACTCAATCCCCA
* * * *
8526 ACAACAATCTCTCTTCGAGGCGTCAATTCGTCAAATATAATATACCATCCTTCCATCCAAGATAC
66 ACAACAATCTCTATTCGAGGCATCAGTTCGTCAAATATAATATACCATCCTTCCTTCCAAGATAC
8591 AAGCTGCAAAAATGACT-AAGTTCTTCAATATTTTACAGAATCATGCACATTAACCAAAAATGCC
131 AAGCTGCAAAAATGACTCAA-TTCTTCAATATTTTACAGAATCATGCACATTAACCAAAAATGCC
8655 ATAAATCATGTACACAAGCCTTATCCGAACCCGCCCATGCACAGCTCAACATGCGATCCTCATCA
195 ATAAATCATGTACACAAGCCTTATCCGAACCCGCCCATGCACAGCTCAACATGCGATCCTCATCA
* *
8720 ACCTGTAGGCAAGATAACATTAAGTCGTATTAATTAATACTGAACAATATATTCTCTCTTACACA
260 ACCTGTA-GCAAGATAACATTAAGTCATATTAATTAATACTGAACAATATATTCTCTCTCACACA
* * *
8785 TACATATATATAGTCAATACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTACTTTTTAATGTT
324 TACATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTCGGGACCCT-CTTGTTAATTTT
* *
8850 CTCAGGATCATCGTCATTAATTTTCTAAATATCGTTGTTAATTTTCACAGGATCATCCTCGTTGG
388 CTCAGGATCATCGTCATTAATTTTCTAAAGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGG
* *
8915 TTATCTCATGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTTG
453 TTATCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTCG
8980 TTAGTTTTCTCAGGATCGATGTTGGTTTTC
518 TTAGTTTTCTCAGGATCGATGTTGGTTTTC
* *
9010 TCAGGATCATCCTCGTTGGTTTTCTCAGGGCCGTTGAAATAGTCGATAGTTACACTCAATCCCCA
1 TCAGGATCATCCTCGTTAGTTTTCTCAGGACCGTTGAAATAGTCGATAGTTACACTCAATCCCCA
* *
9075 ACAACAATCTCTCTTCGAGGCGTCAGTTCGTCAAATATAATATACCATCCTTCCTTCCAAGATAC
66 ACAACAATCTCTATTCGAGGCATCAGTTCGTCAAATATAATATACCATCCTTCCTTCCAAGATAC
*
9140 AAGCTGCAAAAATGACTCAATTCTTCAATATTTTACAGAATCATGCACATTAACCAAAAATGACA
131 AAGCTGCAAAAATGACTCAATTCTTCAATATTTTACAGAATCATGCACATTAACCAAAAATGCCA
* * *
9205 TAAATCATATACACAAGCCTTATTCGAACCCGCCCATGCACAGTTCAACATGCGATCCTCATCAA
196 TAAATCATGTACACAAGCCTTATCCGAACCCGCCCATGCACAGCTCAACATGCGATCCTCATCAA
* * * *
9270 CCTGTAGTCAAGATAACATTAGGTCGTATTAATTGATACTGAACAATATATTCTCTCTCATACAT
261 CCTGTAG-CAAGATAACATTAAGTCATATTAATTAATACTGAACAATATATTCTCTCTCACACAT
*
9335 ACATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTCGGGA-CCTGCTTTTTAATTTTC
325 ACATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTCGGGACCCT-CTTGTTAATTTTC
* *
9399 TCAGGATCATCGTCATTAATTTTCCAAATATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGT
389 TCAGGATCATCGTCATTAATTTTCTAAAGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGT
* * *
9464 TATTTCAGGATCGTCATTAGTTTTCATCA-AATCA-CCTTCATTGGTTTTCTCAGTATCATCCTC
454 TATCTCAGGATCGTCATTAGTTTTCA-CAGGATCATCC-TCATTGGTTTTCTCAGGATCATCCTC
*
9527 GTTAGTTTTCTCAGGATCGTTGTTGGTTTTC
517 GTTAGTTTTCTCAGGATCGATGTTGGTTTTC
*
9558 TCAGGATCATCCTCGTTAGTTTTCTC---A--G--G----A-TC---AGTTACATTCAATCCCCA
1 TCAGGATCATCCTCGTTAGTTTTCTCAGGACCGTTGAAATAGTCGATAGTTACACTCAATCCCCA
* * * * *
9608 ACAACAATCTCTATTCGAGGTATCAGTTCATCAAATATAGTATACTATCCTTCCTTCCTTCCTAT
66 ACAACAATCTCTATTCGAGGCATCAGTTCGTCAAATATA--ATA-TA-CCATCCTTCCTTCCAAG
* * * * * *
9673 ATACAAGCTACAAAATTTACTTAGTTCTTCAATATTTTACAAAATCATGCACATTAACCAAAAAT
127 ATACAAGCTGCAAAAATGACTCAATTCTTCAATATTTTACAGAATCATGCACATTAACCAAAAAT
* * * * * * *
9738 GTCATAAATCATGTACGCAAGCCTGATTCGAACCCAGCCC--G-A-AAC-C--C--GCCAT-GT-
192 GCCATAAATCATGTACACAAGCCTTATCCGAACCC-GCCCATGCACAGCTCAACATGCGATCCTC
* * * * ** * *
9792 A-C-AGCTCTA-CATGCTATACTCATTAAGTCATATTAATTGAA-ACTTTAGAATATATTTTCTC
256 ATCAACCTGTAGCAAG--ATA-ACATTAAGTCATATTAATT-AATACTGAACAATATATTCTCTC
* **
9853 TCACATATACATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTTAGGACCCTCCTTGT
317 TCACACATACATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTCGGGACCCT-CTTGT
* * ** *
9918 TAATTTTCTCAGGATTATCGTCATTAATTTTCTAAGGATCGTCGTTAATTTTCATGGGAACATCC
381 TAATTTTCTCAGGATCATCGTCATTAATTTTCTAAAGATCGTCGTTAATTTTCACAGGATCATCC
* * * *
9983 TCGTTGGTTATCTCAGGATCGTCTTTAGTTTTAATAGGATCATCCTCATTGGTTTTCTTAGGATC
446 TCGTTGGTTATCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATC
* *
10048 ATCCTCTTTAGTTTTATCAG
511 ATCCTCGTTAGTTTTCTCAG
10068 AATCATCCTC
Statistics
Matches: 1464, Mismatches: 123, Indels: 74
0.88 0.07 0.04
Matches are distributed among these distances:
523 3 0.00
525 8 0.01
526 85 0.06
527 138 0.09
528 3 0.00
529 4 0.00
531 1 0.00
533 53 0.04
534 1 0.00
535 4 0.00
536 5 0.00
537 105 0.07
538 4 0.00
541 1 0.00
543 1 0.00
547 2 0.00
548 186 0.13
549 388 0.27
550 263 0.18
551 4 0.00
552 1 0.00
556 4 0.00
560 2 0.00
561 195 0.13
562 3 0.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (547 bp):
TCAGGATCATCCTCGTTAGTTTTCTCAGGACCGTTGAAATAGTCGATAGTTACACTCAATCCCCA
ACAACAATCTCTATTCGAGGCATCAGTTCGTCAAATATAATATACCATCCTTCCTTCCAAGATAC
AAGCTGCAAAAATGACTCAATTCTTCAATATTTTACAGAATCATGCACATTAACCAAAAATGCCA
TAAATCATGTACACAAGCCTTATCCGAACCCGCCCATGCACAGCTCAACATGCGATCCTCATCAA
CCTGTAGCAAGATAACATTAAGTCATATTAATTAATACTGAACAATATATTCTCTCTCACACATA
CATATATATAGTCAACACCTTGTACAACTCGTTAGTTTTCTCGGGACCCTCTTGTTAATTTTCTC
AGGATCATCGTCATTAATTTTCTAAAGATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTTA
TCTCAGGATCGTCATTAGTTTTCACAGGATCATCCTCATTGGTTTTCTCAGGATCATCCTCGTTA
GTTTTCTCAGGATCGATGTTGGTTTTC
Found at i:9420 original size:24 final size:24
Alignment explanation
Indices: 9394--9590 Score: 137
Period size: 24 Copynumber: 8.6 Consensus size: 24
9384 TGCTTTTTAA
* *
9394 TTTTCTCAGGATCATCGTCATTAA
1 TTTTCTCAGGATCATCGTCGTTAG
* *
9418 TTTTC-CA-AAT-ATCGTCGTTAA
1 TTTTCTCAGGATCATCGTCGTTAG
* * *
9439 TTTTCACAGGATCATCCTCGTTGG
1 TTTTCTCAGGATCATCGTCGTTAG
*
9463 TTATT-TCAGG---ATCGTCATTAG
1 TT-TTCTCAGGATCATCGTCGTTAG
* * * * *
9484 TTTTCATCA-AATCACCTTCATTGG
1 TTTTC-TCAGGATCATCGTCGTTAG
* *
9508 TTTTCTCAGTATCATCCTCGTTAG
1 TTTTCTCAGGATCATCGTCGTTAG
* *
9532 TTTTCTCAGG---ATCGTTGTTGG
1 TTTTCTCAGGATCATCGTCGTTAG
*
9553 TTTTCTCAGGATCATCCTCGTTAG
1 TTTTCTCAGGATCATCGTCGTTAG
9577 TTTTCTCAGGATCA
1 TTTTCTCAGGATCA
9591 GTTACATTCA
Statistics
Matches: 134, Mismatches: 26, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.01
21 43 0.32
22 7 0.05
23 7 0.05
24 73 0.54
25 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (24 bp):
TTTTCTCAGGATCATCGTCGTTAG
Found at i:9553 original size:45 final size:45
Alignment explanation
Indices: 9504--9589 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
9494 ATCACCTTCA
*
9504 TTGGTTTTCTCAGTATCATCCTCGTTAGTTTTCTCAGGATCGTTG
1 TTGGTTTTCTCAGGATCATCCTCGTTAGTTTTCTCAGGATCGTTG
9549 TTGGTTTTCTCAGGATCATCCTCGTTAGTTTTCTCAGGATC
1 TTGGTTTTCTCAGGATCATCCTCGTTAGTTTTCTCAGGATC
9590 AGTTACATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (45 bp):
TTGGTTTTCTCAGGATCATCCTCGTTAGTTTTCTCAGGATCGTTG
Found at i:9557 original size:21 final size:23
Alignment explanation
Indices: 9363--9590 Score: 125
Period size: 24 Copynumber: 10.0 Consensus size: 23
9353 CCTTGTACAA
* *
9363 CTCGTTAGTTTTCTCGGGA-CCT
1 CTCGTTAGTTTTCTCAGGATCAT
** *
9385 GCTTTTTAATTTTCTCAGGATCAT
1 -CTCGTTAGTTTTCTCAGGATCAT
* * *
9409 CGTCATTAATTTTC-CA-AAT-AT
1 C-TCGTTAGTTTTCTCAGGATCAT
* *
9430 CGTCGTTAATTTTCACAGGATCAT
1 C-TCGTTAGTTTTCTCAGGATCAT
*
9454 CCTCGTTGGTTATT-TCAGGATC--
1 -CTCGTTAGTT-TTCTCAGGATCAT
* * * *
9476 GTCATTAGTTTTCATCA-AATCAC
1 CTCGTTAGTTTTC-TCAGGATCAT
* * *
9499 CTTCATTGGTTTTCTCAGTATCAT
1 C-TCGTTAGTTTTCTCAGGATCAT
*
9523 CCTCGTTAGTTTTCTCAGGATCGT
1 -CTCGTTAGTTTTCTCAGGATCAT
*
9547 -T-GTTGGTTTTCTCAGGATCAT
1 CTCGTTAGTTTTCTCAGGATCAT
9568 CCTCGTTAGTTTTCTCAGGATCA
1 -CTCGTTAGTTTTCTCAGGATCA
9591 GTTACATTCA
Statistics
Matches: 160, Mismatches: 28, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
20 2 0.01
21 43 0.27
22 8 0.05
23 24 0.15
24 79 0.49
25 4 0.03
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.43
Consensus pattern (23 bp):
CTCGTTAGTTTTCTCAGGATCAT
Found at i:9580 original size:69 final size:69
Alignment explanation
Indices: 9407--9590 Score: 182
Period size: 69 Copynumber: 2.7 Consensus size: 69
9397 TCTCAGGATC
* * * * * *
9407 ATCGTCATTAATTTTC--CAAAT-ATCGTCGTTAATTTTCACAGGATCATCCTCGTTGGTTATTT
1 ATCGTCATTAGTTTTCATCAAATCACCTTCGTTAGTTTTCTCAGGATCATCCTCGTTAGTTATTT
9469 CAGG
66 CAGG
* * *
9473 ATCGTCATTAGTTTTCATCAAATCACCTTCATTGGTTTTCTCAGTATCATCCTCGTTAGTT-TTC
1 ATCGTCATTAGTTTTCATCAAATCACCTTCGTTAGTTTTCTCAGGATCATCCTCGTTAGTTATT-
9537 TCAGG
65 TCAGG
** * *
9542 ATCGTTGTTGGTTTTC-TCAGGATCATCC-TCGTTAGTTTTCTCAGGATCA
1 ATCGTCATTAGTTTTCATCA-AATCA-CCTTCGTTAGTTTTCTCAGGATCA
9591 GTTACATTCA
Statistics
Matches: 96, Mismatches: 16, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
66 15 0.16
68 10 0.10
69 69 0.72
70 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (69 bp):
ATCGTCATTAGTTTTCATCAAATCACCTTCGTTAGTTTTCTCAGGATCATCCTCGTTAGTTATTT
CAGG
Found at i:9962 original size:24 final size:24
Alignment explanation
Indices: 9917--9962 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9907 ACCCTCCTTG
* *
9917 TTAATTTTCTCAGGATTATCGTCA
1 TTAATTTTCTAAGGATCATCGTCA
*
9941 TTAATTTTCTAAGGATCGTCGT
1 TTAATTTTCTAAGGATCATCGT
9963 TAATTTTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (24 bp):
TTAATTTTCTAAGGATCATCGTCA
Found at i:10001 original size:45 final size:45
Alignment explanation
Indices: 9952--10047 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
9942 TAATTTTCTA
* * *
9952 AGGATCGTCGTTAATTTTCATGGGAACATCCTCGTTGGTTATCTC
1 AGGATCGTCGTTAATTTTAATAGGAACATCCTCATTGGTTATCTC
* * * * *
9997 AGGATCGTCTTTAGTTTTAATAGGATCATCCTCATTGGTTTTCTT
1 AGGATCGTCGTTAATTTTAATAGGAACATCCTCATTGGTTATCTC
10042 AGGATC
1 AGGATC
10048 ATCCTCTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (45 bp):
AGGATCGTCGTTAATTTTAATAGGAACATCCTCATTGGTTATCTC
Found at i:10044 original size:24 final size:24
Alignment explanation
Indices: 10017--10091 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
10007 TTAGTTTTAA
10017 TAGGATCATCCTCATTGGTTTTCT
1 TAGGATCATCCTCATTGGTTTTCT
* * *
10041 TAGGATCATCCTCTTTAGTTTTAT
1 TAGGATCATCCTCATTGGTTTTCT
* * *
10065 CAGAATCATCCTCGTTGGTTTTCT
1 TAGGATCATCCTCATTGGTTTTCT
10089 TAG
1 TAG
10092 TACCGTTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (24 bp):
TAGGATCATCCTCATTGGTTTTCT
Found at i:10787 original size:18 final size:18
Alignment explanation
Indices: 10741--10787 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
10731 AGTTCATATT
10741 GTATCAGAG-CAGAACATG
1 GTATCAGAGCCA-AACATG
10759 GTATCAGAGCCAAACATG
1 GTATCAGAGCCAAACATG
*
10777 GTATTAGAGCC
1 GTATCAGAGCC
10788 GAATGTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (18 bp):
GTATCAGAGCCAAACATG
Done.