Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017098.1 Corchorus olitorius cultivar O-4 contig17131, 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: 3024
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Found at i:231 original size:31 final size:31
Alignment explanation
Indices: 160--231 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
150 GTCTATCAGC
*
160 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
191 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
221 GTTTTAATTTG
1 -TTTTAATTTG
232 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:568 original size:16 final size:16
Alignment explanation
Indices: 547--636 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
537 CCTACCCGAG
547 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
563 CCCGAACCCG-ACATAA
1 CCCGAACCCGAAAAT-A
* * *
579 CCCGAGCCTGAAAATG
1 CCCGAACCCGAAAATA
**
595 CCCGAACCCG-ACTTAA
1 CCCGAACCCGAAAAT-A
* *
611 CCCGAGCCTGAAAATA
1 CCCGAACCCGAAAATA
627 CCCGAACCCG
1 CCCGAACCCG
637 CCCGAGCCCG
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
15 5 0.09
16 44 0.81
17 5 0.09
ACGTcount: A:0.34, C:0.40, G:0.17, T:0.09
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:573 original size:6 final size:6
Alignment explanation
Indices: 510--558 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
500 TATCAAATCA
* * * *
510 AACCCA AACCCG AGCCCG AACCCG AACCC- TACCCG AGCCCG AACCCG
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
557 AA
1 AA
559 AATACCCGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
AACCCG
Found at i:592 original size:32 final size:32
Alignment explanation
Indices: 547--636 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
537 CCTACCCGAG
* *
547 CCCGAACCCGAAAATACCCGAACCCGACATAA
1 CCCGAGCCTGAAAATACCCGAACCCGACATAA
* *
579 CCCGAGCCTGAAAATGCCCGAACCCGACTTAA
1 CCCGAGCCTGAAAATACCCGAACCCGACATAA
611 CCCGAGCCTGAAAATACCCGAACCCG
1 CCCGAGCCTGAAAATACCCGAACCCG
637 CCCGAGCCCG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.34, C:0.40, G:0.17, T:0.09
Consensus pattern (32 bp):
CCCGAGCCTGAAAATACCCGAACCCGACATAA
Found at i:1067 original size:103 final size:102
Alignment explanation
Indices: 945--1161 Score: 346
Period size: 103 Copynumber: 2.1 Consensus size: 102
935 TTTGGTAAAT
*
945 ATTTGTAAT-AAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTGTAATAAAA
1 ATTTGTAATAAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTATAATAAAA
* **
1009 ATGTAATCTTTAAACTAAAAGATGAGGATTTTTGTTTG
66 ATGTAATCTTTAAACAAAAAGATGA-GACCTTTGTTTG
1047 ATTTGTAATAAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTATAATAAAA
1 ATTTGTAATAAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTATAATAAAA
* *
1112 ATGTGATCTTTAAGCAAAAAGATGAGACCTTTGTTTG
66 ATGTAATCTTTAAACAAAAAGATGAGACCTTTGTTTG
* *
1149 ATTTATGATAAAA
1 ATTTGTAATAAAA
1162 TTATAATCTT
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 30 0.28
103 76 0.72
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (102 bp):
ATTTGTAATAAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTATAATAAAA
ATGTAATCTTTAAACAAAAAGATGAGACCTTTGTTTG
Found at i:1083 original size:52 final size:51
Alignment explanation
Indices: 945--1173 Score: 343
Period size: 51 Copynumber: 4.5 Consensus size: 51
935 TTTGGTAAAT
945 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
*
996 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGGATTTTTGTTTG
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
1047 ATTTGTAATAAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
1 ATTTGTAAT-AAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
* * * * **
1099 ATTTATAATAAAAATGTGATCTTTAAGCAAAAAGATGAG-ACCTTTGTTTG
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
* * * *
1149 ATTTATGATAAAATTATAATCTTTA
1 ATTTGTAATAAAAATGTAATCTTTA
1174 TTAAAAGATT
Statistics
Matches: 165, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
50 30 0.18
51 86 0.52
52 49 0.30
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (51 bp):
ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
Found at i:1210 original size:50 final size:47
Alignment explanation
Indices: 1156--1713 Score: 429
Period size: 50 Copynumber: 11.1 Consensus size: 47
1146 TTGATTTATG
*
1156 ATAAAATTATAATCTTT-ATTAAAAGATTGAACCTTTTAAACAATTTGTAA
1 ATAAAATT-GAAT-TTTAATTAAAAGATTGAA-CTTTTAAA-AATTTGTAA
* *
1206 ATAAAGGTTGGACTTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAA
1 ATAAA-ATT-GAATTTTAATTAAAAGATTGAACTTTTAA-AAATTTGTAA
*
1256 ATAAATGTTGAACTTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAA
1 ATAAA-ATTGAA-TTTTAATTAAAAGATTGAACTTTTAA-AAATTTGTAA
* * *
1306 ATAAAGGTTGTACTTTTAATTAAAAGATTCAACTTTTAAGAAATTTGTAA
1 ATAAA-ATTG-AATTTTAATTAAAAGATTGAACTTTTAA-AAATTTGTAA
* * *
1356 ATAAAGGTTGGACTTTTAATAAAAAGATTGAA-TTTCTAAGAAATTTGTAA
1 ATAAA-ATT-GAATTTTAATTAAAAGATTGAACTTT-TAA-AAATTTGTAA
** * ** * *
1406 ATGAAGGTTGAACTTTCAATTAAAAGATCAAACCTTTAAGCAATTTGTAA
1 AT-AAAATTGAA-TTTTAATTAAAAGATTGAACTTTTAA-AAATTTGTAA
*
1456 ATAAAAGTTGAACTTTTAATTAAAAGATTGAACTTTTAAGAAATTGGTAA
1 ATAAAA-TTGAA-TTTTAATTAAAAGATTGAACTTTTAA-AAATTTGTAA
* ** * * *
1506 ATGGAGGTTGGACTTTTAATTAAAAGATTGAAGCTTTTAAGTAGTTTGTAA
1 AT-AAAATT-GAATTTTAATTAAAAGATTGAA-CTTTTAA-AAATTTGTAA
** ** *
1557 ATAAAGATTGGGTTTTAGATTAAAAGATCAAACTTTTAAGTAATTTGTAA
1 ATAAA-ATTGAATTTTA-ATTAAAAGATTGAACTTTTAA-AAATTTGTAA
* * *
1607 ATAAAGATTGGATTTTTAATGAAAAG-TTGAAACCTTTTAAGCAATTTGTAA
1 ATAAA-ATT-GAATTTTAATTAAAAGATTG-AA-CTTTTAA-AAATTTGTAA
* * *
1658 ATAAAAATGAAATCTTTAAGTTAAAATATTGAACTTTTAACTAATTTGTAA
1 ATAAAATTG-AAT-TTTAA-TTAAAAGATTGAACTTTTAA-AAATTTGTAA
1709 ATAAA
1 ATAAA
1714 GATGAAATTT
Statistics
Matches: 431, Mismatches: 54, Indels: 45
0.81 0.10 0.08
Matches are distributed among these distances:
49 11 0.03
50 297 0.69
51 113 0.26
52 7 0.02
53 3 0.01
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.38
Consensus pattern (47 bp):
ATAAAATTGAATTTTAATTAAAAGATTGAACTTTTAAAAATTTGTAA
Found at i:1260 original size:100 final size:99
Alignment explanation
Indices: 1156--1714 Score: 621
Period size: 100 Copynumber: 5.6 Consensus size: 99
1146 TTGATTTATG
*
1156 ATAAAATTATAATCTTT-ATTAAAAGATTGAACCTTTTAA-ACAATTTGTAAATAAAGGTTGGAC
1 ATAAAATT-GAATCTTTAATTAAAAGATTGAA-CTTTTAAGA-AATTTGTAAATAAAGGTTGGAC
1219 TTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAA
63 TTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAA
* *
1256 ATAAATGTTGAA-CTTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGTACT
1 ATAAA-ATTGAATC-TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGGACT
*
1320 TTTAATTAAAAGATTCAACTTTTAAGAAATTTGTAA
64 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAA
* * * * *
1356 ATAAAGGTTGGA-CTTTTAATAAAAAGATTGAA-TTTCTAAGAAATTTGTAAATGAAGGTTGAAC
1 ATAAA-ATTGAATC-TTTAATTAAAAGATTGAACTTT-TAAGAAATTTGTAAATAAAGGTTGGAC
* ** * *
1419 TTTCAATTAAAAGATCAAACCTTTAAGCAATTTGTAA
63 TTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAA
* **
1456 ATAAAAGTTGAA-CTTTTAATTAAAAGATTGAACTTTTAAGAAATTGGTAAATGGAGGTTGGACT
1 ATAAAA-TTGAATC-TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGGACT
* *
1520 TTTAATTAAAAGATTGAAGCTTTTAAGTAGTTTGTAA
64 TTTAATTAAAAGATTGAA-CTTTTAAGAAATTTGTAA
** ** * * *
1557 ATAAAGATTGGGT-TTTAGATTAAAAGATCAAACTTTTAAGTAATTTGTAAATAAAGATTGGATT
1 ATAAA-ATTGAATCTTTA-ATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGGACT
* *
1621 TTTAATGAAAAG-TTGAAACCTTTTAAGCAATTTGTAA
64 TTTAATTAAAAGATTG-AA-CTTTTAAGAAATTTGTAA
* * **
1658 ATAAAAATGAAATCTTTAAGTTAAAATATTGAACTTTTAACTAATTTGTAAATAAAG
1 ATAAAATTG-AATCTTTAA-TTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAG
1715 ATGAAATTTT
Statistics
Matches: 397, Mismatches: 47, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
99 4 0.01
100 238 0.60
101 117 0.29
102 38 0.10
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.38
Consensus pattern (99 bp):
ATAAAATTGAATCTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGGACTTT
TAATTAAAAGATTGAACTTTTAAGAAATTTGTAA
Found at i:1267 original size:30 final size:29
Alignment explanation
Indices: 1228--1374 Score: 87
Period size: 30 Copynumber: 5.6 Consensus size: 29
1218 CTTTTAATTA
1228 AAAGATTGAACTTTTAAGAAATTTGTAAAT
1 AAAG-TTGAACTTTTAAGAAATTTGTAAAT
1258 AAATGTTGAACTTTT----AA--T-TAAA-
1 AAA-GTTGAACTTTTAAGAAATTTGTAAAT
*
1280 AGA-TTGAACTTTTAAGAAATTTGTAAAT
1 AAAGTTGAACTTTTAAGAAATTTGTAAAT
*
1308 AAAGGTTGTACTTTT----AA--T-TAAA-
1 AAA-GTTGAACTTTTAAGAAATTTGTAAAT
* *
1330 AGA-TTCAACTTTTAAGAAATTTGTAAAT
1 AAAGTTGAACTTTTAAGAAATTTGTAAAT
*
1358 AAAGGTTGGACTTTTAA
1 AAA-GTTGAACTTTTAA
1375 TAAAAAGATT
Statistics
Matches: 87, Mismatches: 9, Indels: 42
0.63 0.07 0.30
Matches are distributed among these distances:
20 18 0.21
22 4 0.05
23 8 0.09
24 6 0.07
26 6 0.07
27 8 0.09
28 4 0.05
30 32 0.37
31 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (29 bp):
AAAGTTGAACTTTTAAGAAATTTGTAAAT
Found at i:1310 original size:150 final size:149
Alignment explanation
Indices: 1166--1724 Score: 641
Period size: 150 Copynumber: 3.7 Consensus size: 149
1156 ATAAAATTAT
1166 AATCTTT-ATTAAAAGATTGAACCTTTTAA-ACAATTTGTAAATAAAGGTTGGACTTTTAATTAA
1 AATCTTTAATTAAAAGATTGAA-CTTTTAAGA-AATTTGTAAATAAAGGTTGGACTTTTAATTAA
**
1229 AAGATTGAACTTTTAAGAAATTTGTAAATAAATGTTGAACTTTTAATTAAAAGATTGAACTTTTA
64 AAGATTGAACTTTTAAGAAATTTGTAAATAAA-GTTGAACTTTTAATTAAAAGATCAAACTTTTA
*
1294 AGAAATTTGTAAATAAAGGTTG
128 AGAAATTTGTAAATAAAGATTG
* * *
1316 TA-CTTTTAATTAAAAGATTCAACTTTTAAGAAATTTGTAAATAAAGGTTGGACTTTTAATAAAA
1 AATC-TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGGACTTTTAATTAAA
* * *
1380 AGATTGAA-TTTCTAAGAAATTTGTAAATGAAGGTTGAACTTTCAATTAAAAGATCAAACCTTTA
65 AGATTGAACTTT-TAAGAAATTTGTAAAT-AAAGTTGAACTTTTAATTAAAAGATCAAACTTTTA
*
1444 AGCAATTTGTAAATAAA-AGTTG
128 AGAAATTTGTAAATAAAGA-TTG
* **
1466 AA-CTTTTAATTAAAAGATTGAACTTTTAAGAAATTGGTAAATGGAGGTTGGACTTTTAATTAAA
1 AATC-TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGGACTTTTAATTAAA
* * **
1530 AGATTGAAGCTTTTAAGTAGTTTGTAAATAAAGATTG-GGTTTTAGATTAAAAGATCAAACTTTT
65 AGATTGAA-CTTTTAAGAAATTTGTAAATAAAG-TTGAACTTTTA-ATTAAAAGATCAAACTTTT
*
1594 AAGTAATTTGTAAATAAAGATTG
127 AAGAAATTTGTAAATAAAGATTG
* * * * ** * *
1617 GATTTTTAATGAAAAG-TTGAAACCTTTTAAGCAATTTGTAAATAAA-AATGAAATCTTTAAGTT
1 AATCTTTAATTAAAAGATTG-AA-CTTTTAAGAAATTTGTAAATAAAGGTTGGACT-TTTAA-TT
* ** * *
1680 AAAATATTGAACTTTTAACTAATTTGTAAATAAAGATGAAATTTT
62 AAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGTTGAACTTTT
1725 TGATGGGCTT
Statistics
Matches: 351, Mismatches: 41, Indels: 32
0.83 0.10 0.08
Matches are distributed among these distances:
149 4 0.01
150 190 0.54
151 91 0.26
152 54 0.15
153 12 0.03
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.38
Consensus pattern (149 bp):
AATCTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGGACTTTTAATTAAAA
GATTGAACTTTTAAGAAATTTGTAAATAAAGTTGAACTTTTAATTAAAAGATCAAACTTTTAAGA
AATTTGTAAATAAAGATTG
Found at i:1481 original size:19 final size:20
Alignment explanation
Indices: 1457--1494 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1447 AATTTGTAAA
1457 TAAAAG-TTGAACTTTTAAT
1 TAAAAGATTGAACTTTTAAT
1476 TAAAAGATTGAACTTTTAA
1 TAAAAGATTGAACTTTTAA
1495 GAAATTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (20 bp):
TAAAAGATTGAACTTTTAAT
Found at i:2374 original size:48 final size:48
Alignment explanation
Indices: 2316--2704 Score: 492
Period size: 48 Copynumber: 8.1 Consensus size: 48
2306 TTTATTGCAT
* *
2316 GTTTTACCCTTCCCAGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
* * * * *
2364 GTTTGGCCCTTCCCAGTCGAAAGGTGTTGTTTTCAACATTTTATTTCT
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
* * * *
2412 GTTTTGCCCTTCCCGATCGGAAGGTGTTGTCTTCAATATTTTATTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
* * * **
2460 GTTTTGCCCTTCCCGGTCGAAAGGTGTTCTTTTCAACAATTTATTCAT
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
* * * * *
2508 GTTTTGCCCTTCCCGGTTGGAAGGGGTTGTATTCAATACTTTTATTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACA-TTTTATTCCC
** * *
2557 GTTTTGCATTTCCTGGTCGAAAGGTGTTG-TTTCAACATTTTATTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
*
2604 GTTTTGCCTTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
* * * *
2652 ATTTTGCCCTTCCCGGTCGGAAGGTGTTCTTTTCAATATTTTATTCCT
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
2700 GTTTT
1 GTTTT
2705 CAATATTTCA
Statistics
Matches: 291, Mismatches: 48, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
47 35 0.12
48 226 0.78
49 30 0.10
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (48 bp):
GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCC
Found at i:2706 original size:20 final size:20
Alignment explanation
Indices: 2681--2724 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2671 GAAGGTGTTC
*
2681 TTTTCAATATTTTATTCCTG
1 TTTTCAATATTTCATTCCTG
2701 TTTTCAATATTTCATTCCTG
1 TTTTCAATATTTCATTCCTG
2721 TTTT
1 TTTT
2725 ACCCTTCCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTCAATATTTCATTCCTG
Found at i:2740 original size:68 final size:68
Alignment explanation
Indices: 2631--2772 Score: 203
Period size: 68 Copynumber: 2.1 Consensus size: 68
2621 CGGAAGGTGT
* * *
2631 TGTTTTCAACATTTTATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTCTTTTCAATATTTTAT
1 TGTTTTCAACATTTCATTCCCATTTTACCCTTCCCGGTCGGAAGGTGTTCTTTTCAATATTTCAT
2696 TCC
66 TCC
* ** * * *
2699 TGTTTTCAATATTTCATTCCTGTTTTACCCTTCCTGGTCGGAAGGTGTTGTTTTCAATCTTTCAT
1 TGTTTTCAACATTTCATTCCCATTTTACCCTTCCCGGTCGGAAGGTGTTCTTTTCAATATTTCAT
2764 TCC
66 TCC
2767 TGTTTT
1 TGTTTT
2773 GCCCTTCCCG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.15, C:0.22, G:0.14, T:0.49
Consensus pattern (68 bp):
TGTTTTCAACATTTCATTCCCATTTTACCCTTCCCGGTCGGAAGGTGTTCTTTTCAATATTTCAT
TCC
Found at i:2770 original size:48 final size:48
Alignment explanation
Indices: 2699--2816 Score: 182
Period size: 48 Copynumber: 2.5 Consensus size: 48
2689 ATTTTATTCC
* * *
2699 TGTTTTCAATATTTCATTCCTGTTTTACCCTTCCTGGTCGGAAGGTGT
1 TGTTTTCAATATTTCATTCCTGTTTTACCCTTCCCGATCAGAAGGTGT
* *
2747 TGTTTTCAATCTTTCATTCCTGTTTTGCCCTTCCCGATCAGAAGGTGT
1 TGTTTTCAATATTTCATTCCTGTTTTACCCTTCCCGATCAGAAGGTGT
*
2795 TGTTTTCAATATTTTATTCCTG
1 TGTTTTCAATATTTCATTCCTG
2817 CTTTCAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.47
Consensus pattern (48 bp):
TGTTTTCAATATTTCATTCCTGTTTTACCCTTCCCGATCAGAAGGTGT
Found at i:2791 original size:116 final size:116
Alignment explanation
Indices: 2586--2898 Score: 457
Period size: 116 Copynumber: 2.7 Consensus size: 116
2576 AAAGGTGTTG
* * * * *
2586 TTTCAACATTTTATTCCCGTTTTGCCTTTCCCGGTCGGAAGGTGTTGTTTTCAA-CATTTTATTC
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATC-TTTCATTC
* * * *
2650 CCATTTTGCCCTTCCCGGTCGGAAGGTGTTCTTTTCAATATTTTATTCCTGT
65 CCGTTTTGCCCTTCCCGATCAGAAGGTGTTCTTTTCAATATTTTATTCCTGC
* *
2702 TTTCAATATTTCATTCCTGTTTTACCCTTCCTGGTCGGAAGGTGTTGTTTTCAATCTTTCATTCC
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATCTTTCATTCC
* *
2767 TGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCCTGC
66 CGTTTTGCCCTTCCCGATCAGAAGGTGTTCTTTTCAATATTTTATTCCTGC
* * * *
2818 TTTCAATATTTCATTCCCATTTCGCCCTTCCTGGTCGGAAGATGTTGTTTTCAATATTTCATTCC
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATCTTTCATTCC
2883 CGTTTTGCCCTTCCCG
66 CGTTTTGCCCTTCCCG
2899 GTCGGAAGTT
Statistics
Matches: 176, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
116 175 0.99
117 1 0.01
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.45
Consensus pattern (116 bp):
TTTCAATATTTCATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATCTTTCATTCC
CGTTTTGCCCTTCCCGATCAGAAGGTGTTCTTTTCAATATTTTATTCCTGC
Found at i:2822 original size:68 final size:68
Alignment explanation
Indices: 2750--2882 Score: 185
Period size: 68 Copynumber: 2.0 Consensus size: 68
2740 AAGGTGTTGT
* ** * * *
2750 TTTCAATCTTTCATTCCTGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCC
1 TTTCAATATTTCATTCCCATTTCGCCCTTCCCGATCAGAAGATGTTGTTTTCAATATTTCATTCC
2815 TGC
66 TGC
* * *
2818 TTTCAATATTTCATTCCCATTTCGCCCTTCCTGGTCGGAAGATGTTGTTTTCAATATTTCATTCC
1 TTTCAATATTTCATTCCCATTTCGCCCTTCCCGATCAGAAGATGTTGTTTTCAATATTTCATTCC
2883 CGTTTTGCCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (68 bp):
TTTCAATATTTCATTCCCATTTCGCCCTTCCCGATCAGAAGATGTTGTTTTCAATATTTCATTCC
TGC
Found at i:2893 original size:48 final size:47
Alignment explanation
Indices: 2818--2971 Score: 178
Period size: 48 Copynumber: 3.4 Consensus size: 47
2808 TTATTCCTGC
* *
2818 TTTCAATATTTCATTCCCATTTCGCCCTTCCTGGTCGGAAGATGTTGT
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCC-GGTCGGAAGATGTTGT
2866 TTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGG-A-A----G-
1 TTTCAATATTTCATTCCCGTTTTGCCCTT-CCGGTCGGAAGATGTTGT
* *
2907 TTTCAATATTTCATTCCCGTTTTGCCCTTTCCGATCGGAAGGTGTTGT
1 TTTCAATATTTCATTCCCGTTTTGCCC-TTCCGGTCGGAAGATGTTGT
* *
2955 TTTCATTATTTTATTCC
1 TTTCAATATTTCATTCC
2972 TGCTTTCAAT
Statistics
Matches: 91, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
41 34 0.37
42 4 0.04
46 1 0.01
47 2 0.02
48 48 0.53
49 2 0.02
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.44
Consensus pattern (47 bp):
TTTCAATATTTCATTCCCGTTTTGCCCTTCCGGTCGGAAGATGTTGT
Found at i:2911 original size:41 final size:41
Alignment explanation
Indices: 2866--2947 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
2856 AAGATGTTGT
*
2866 TTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGGAAG
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAAG
*
2907 TTTCAATATTTCATTCCCGTTTTGCCCTTTCCGATCGGAAG
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAAG
2948 GTGTTGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (41 bp):
TTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAAG
Found at i:2937 original size:116 final size:115
Alignment explanation
Indices: 2586--2937 Score: 335
Period size: 116 Copynumber: 3.0 Consensus size: 115
2576 AAAGGTGTTG
* * * * * *
2586 TTTCAACATTTTATTCCCGTTTTGCCTTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCC
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTCATTCC
* * ** * *
2651 CATTTTGCCCTTCCCGGTCGGAAGGTGTTC--T-TTTCAATATTTTATTCCTGT
66 CGTTTTGCCCTTCCCGGTCGGAAGGT-TTCAATATTTCATTCCTTT-TGCC--C
* * *
2702 TTTCAATATTTCATTCCTGTTTTACCCTTCCTGGTCGGAAGGTGTTGTTTTCAATCTTTCATTCC
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTCATTCC
* * * *
2767 TGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCC---TG--C
66 CGTTTTGCCCTTCCCGGTCGGAA---G--G-TTTCAATATTTCATTCCTTTTGCCC
* * *
2818 TTTCAATATTTCATTCCCATTTCGCCCTTCCTGGTCGGAAGATGTTGTTTTCAATATTTCATTCC
1 TTTCAATATTTCATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTCATTCC
2883 CGTTTTGCCCTTCCCGGTCGGAA-GTTTCAATATTTCATTCCCGTTTTGCCC
66 CGTTTTGCCCTTCCCGGTCGGAAGGTTTCAATATTTCATT-CC-TTTTGCCC
2934 TTTC
1 TTTC
2938 CGATCGGAAG
Statistics
Matches: 191, Mismatches: 29, Indels: 32
0.76 0.12 0.13
Matches are distributed among these distances:
109 14 0.07
110 3 0.02
114 2 0.01
116 159 0.83
119 1 0.01
120 1 0.01
121 4 0.02
122 1 0.01
123 1 0.01
124 5 0.03
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.45
Consensus pattern (115 bp):
TTTCAATATTTCATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTCATTCC
CGTTTTGCCCTTCCCGGTCGGAAGGTTTCAATATTTCATTCCTTTTGCCC
Found at i:2984 original size:20 final size:20
Alignment explanation
Indices: 2955--2993 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2945 AAGGTGTTGT
*
2955 TTTCATTATTTTATTCCTGC
1 TTTCAATATTTTATTCCTGC
*
2975 TTTCAATATTTTTTTCCTG
1 TTTCAATATTTTATTCCTG
2994 TTTTGCCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTCAATATTTTATTCCTGC
Found at i:3022 original size:157 final size:159
Alignment explanation
Indices: 2699--3009 Score: 428
Period size: 157 Copynumber: 1.9 Consensus size: 159
2689 ATTTTATTCC
* * *
2699 TGTTTTCAATATTTCATTCCTGTTTTACCCTTCCTGGTCGGAAGGTGTTGTTTTCAATCTTTCAT
1 TGTTTTCAATATTTCATTCCCGTTTTACCCTTCCCGGTCGGAA---G--GTTTTCAATATTTCAT
*
2764 TCCTGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCCTGCTTTCAATATTT
61 TCCCGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCCTGCTTTCAATATTT
* *
2829 CATTCCCATTTCGCCCTTCCTGGTCGGAAGATGT
126 CATTCCCATTTCGCCCTTCCCGGTCGGAAGAGGT
*
2863 TGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGGAA-G-TTTCAATATTTCATTCCCG
1 TGTTTTCAATATTTCATTCCCGTTTTACCCTTCCCGGTCGGAAGGTTTTCAATATTTCATTCCCG
* * * **
2926 TTTTGCCCTTTCCGATCGGAAGGTGTTGTTTTCATTATTTTATTCCTGCTTTCAATATTTTTTTC
66 TTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCCTGCTTTCAATATTTCATTC
** *
2991 CTGTTTTGCCCTTCCCGGT
131 CCATTTCGCCCTTCCCGGT
3010 TGGTAGGGGT
Statistics
Matches: 133, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
157 92 0.69
158 1 0.01
164 40 0.30
ACGTcount: A:0.14, C:0.24, G:0.15, T:0.46
Consensus pattern (159 bp):
TGTTTTCAATATTTCATTCCCGTTTTACCCTTCCCGGTCGGAAGGTTTTCAATATTTCATTCCCG
TTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCCTGCTTTCAATATTTCATTC
CCATTTCGCCCTTCCCGGTCGGAAGAGGT
Done.