Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004247.1 Hibiscus syriacus cultivar Beakdansim tig00009315_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: 73020
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:852 original size:9 final size:9
Alignment explanation
Indices: 836--874 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
826 TGGTAATAAT
836 TAAT-TTAA
1 TAATATTAA
844 TAATATTAA
1 TAATATTAA
*
853 TAATATAAA
1 TAATATTAA
862 TAATA-TAA
1 TAATATTAA
870 TAATA
1 TAATA
875 AAATAGTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 11 0.39
9 17 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TAATATTAA
Found at i:1550 original size:46 final size:45
Alignment explanation
Indices: 1077--1747 Score: 1116
Period size: 45 Copynumber: 14.9 Consensus size: 45
1067 AAAGCTCCCA
* * *
1077 AAGG-TTTAAAAACATCATGAACTGAAGGGCTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
1121 AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
1166 AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1211 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA-CCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
1255 AAGGTTTTGATAACATCATGCACTGAAGGGCTTACAGATGACCC-
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
1299 AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
1344 GAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1389 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1434 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
1479 AAGATTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
1524 AAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCG
1 AAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
1570 AAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCC-
1 AAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
1615 ATAGGTTTTGAAAACATCATGCATTGAACGACTTACAGATGACCCG
1 A-AGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
1661 AAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCTG
1 AAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1707 AAGGTTTTGAAAAACATCATGCACTGAAGGACTTACAGATG
1 AAGGTTTTG-AAAACATCATGCACTGAAGGACTTACAGATG
1748 TTGGAAATAG
Statistics
Matches: 597, Mismatches: 22, Indels: 14
0.94 0.03 0.02
Matches are distributed among these distances:
44 89 0.15
45 348 0.58
46 160 0.27
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (45 bp):
AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
Found at i:2427 original size:22 final size:22
Alignment explanation
Indices: 2402--2487 Score: 90
Period size: 22 Copynumber: 3.9 Consensus size: 22
2392 AAATCCAATA
*
2402 AATCTTTCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
2424 AATCTATCATCTTT--AAAGAG
1 AATCTATCATCTTTGAAAAGAG
2444 ATAGGT-TATCATCTTTGAAGAA-AG
1 A-A--TCTATCATCTTTGAA-AAGAG
*
2468 AGTCTATCATCTTTGAAAAG
1 AATCTATCATCTTTGAAAAG
2488 TGTAGATGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
20 7 0.13
21 4 0.07
22 36 0.67
23 1 0.02
24 4 0.07
25 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:3544 original size:75 final size:75
Alignment explanation
Indices: 3420--3593 Score: 240
Period size: 75 Copynumber: 2.3 Consensus size: 75
3410 TGATATAGGG
* * * * *
3420 TTTCAGCATACCCCAACATTTGCTAATACAAACGTTCAAAATGCGTCAACATTCCTCATTCTGAT
1 TTTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTGAT
3485 TGAAAGGGGC
66 TGAAAGGGGC
* * * * *
3495 TTTCAGCATGCCCCAGCATTTGCTGATATAAATATTCAAAATACATCAACATTCATGATTCTGAT
1 TTTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTGAT
*
3560 TGAGAGGGGC
66 TGAAAGGGGC
*
3570 TTTCAGTATGCCCCAACATTTGCT
1 TTTCAGCATGCCCCAACATTTGCT
3594 TCTTGTTAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 86 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (75 bp):
TTTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTGAT
TGAAAGGGGC
Found at i:4569 original size:21 final size:20
Alignment explanation
Indices: 4520--4571 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
4510 GCTTGGAGCG
*
4520 TGGGGGGAATCGGTACCCCC
1 TGGGGGGAATCGGTACCCAC
*
4540 TGAGGGGAATCGGTACCCAC
1 TGGGGGGAATCGGTACCCAC
4560 TGGGGGGGAATC
1 T-GGGGGGAATC
4572 AGTTCCCTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.15
Consensus pattern (20 bp):
TGGGGGGAATCGGTACCCAC
Found at i:10202 original size:22 final size:21
Alignment explanation
Indices: 10160--10199 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10150 GAGTTTATTT
*
10160 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
10181 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
10200 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:17531 original size:14 final size:14
Alignment explanation
Indices: 17514--17543 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17504 AAATGTAATT
*
17514 ATGCAAATATGAAA
1 ATGCAAAAATGAAA
17528 ATGCAAAAATGAAA
1 ATGCAAAAATGAAA
17542 AT
1 AT
17544 ATAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (14 bp):
ATGCAAAAATGAAA
Found at i:17593 original size:12 final size:13
Alignment explanation
Indices: 17569--17597 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
17559 AAAATGAAAA
17569 AAATGCAAAATGT
1 AAATGCAAAATGT
17582 AAATGC-AAATGT
1 AAATGCAAAATGT
17594 AAAT
1 AAAT
17598 ATGTGAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:17596 original size:36 final size:34
Alignment explanation
Indices: 17499--17596 Score: 90
Period size: 36 Copynumber: 2.8 Consensus size: 34
17489 GAATAGTTTG
* * *
17499 AAAT-AAAATGTAATTATGCAAATATGAAAATGCAA
1 AAATGAAAATGTAA--ATGCAAATGTAAAAATGAAA
* ** *
17534 AAATGAAAATATAAATATAAACGTAAAAATGAAAA
1 AAATGAAAATGTAAATGCAAATGTAAAAATG-AAA
17569 AAATGCAAAATGTAAATGCAAATGTAAA
1 AAATG-AAAATGTAAATGCAAATGTAAA
17597 TATGTGAATG
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
34 12 0.24
35 11 0.22
36 26 0.53
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.22
Consensus pattern (34 bp):
AAATGAAAATGTAAATGCAAATGTAAAAATGAAA
Found at i:17606 original size:20 final size:19
Alignment explanation
Indices: 17569--17609 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
17559 AAAATGAAAA
17569 AAATGCAAAATGTAAATGC
1 AAATGCAAAATGTAAATGC
* *
17588 AAATGTAAATATGTGAATGC
1 AAATGCAAA-ATGTAAATGC
17608 AA
1 AA
17610 CAATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.24
Consensus pattern (19 bp):
AAATGCAAAATGTAAATGC
Found at i:21051 original size:2 final size:2
Alignment explanation
Indices: 21044--21075 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21034 TTTTAAGATA
21044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21076 TATTAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21388 original size:2 final size:2
Alignment explanation
Indices: 21377--21411 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
21367 ACTTAGATAA
21377 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21412 TGACATAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:22825 original size:3 final size:3
Alignment explanation
Indices: 22810--22873 Score: 101
Period size: 3 Copynumber: 20.7 Consensus size: 3
22800 ATATTTAATT
*
22810 TAA TAA TAT TAA TAA TATA TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
22857 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
22874 TAGTGAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 51 0.88
4 7 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:23145 original size:45 final size:45
Alignment explanation
Indices: 23081--23855 Score: 1156
Period size: 45 Copynumber: 17.0 Consensus size: 45
23071 TCAAAAAGCT
* *
23081 CCCGAAGGTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
23126 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * * *
23171 CCCAAATGTTTTGAAAACATCATGCACTGATGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
23216 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
23261 CCTGAAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
23307 CCCTAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
23352 CCCGGAGGTTTTGAAAACATCATGCACTGAATGACTTACAAATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
23397 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
23442 ACCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
23487 CCTGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
23532 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
23578 CCCGAAGGTCTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGT-TTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
23624 CCC-AGAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGA
1 CCCGA-AGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * * *
23669 TCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTAGAGATTA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
23715 CCTGAAGGTTTTGAAAAAAACATCATGCACTGAAGGACTTACAAATGA
1 CCCGAAGGTTTTG---AAAACATCATGCACTGAAGGACTTACAGATGA
* * * *
23763 TCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTAGAGATTA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
23809 CCTGAAGGTTTTGAAAAAAACATCATGCACTGAAGGACTTACAGATG
1 CCCGAAGGTTTTG---AAAACATCATGCACTGAAGGACTTACAGATG
23856 TTGGAAATAG
Statistics
Matches: 666, Mismatches: 51, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
45 397 0.60
46 202 0.30
48 62 0.09
49 5 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:24537 original size:22 final size:22
Alignment explanation
Indices: 24512--24597 Score: 88
Period size: 22 Copynumber: 3.9 Consensus size: 22
24502 AAATCCAATA
*
24512 AATCTTTCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
24534 AATCTATCATCTTT--AAAGAG
1 AATCTATCATCTTTGAAAAGAG
*
24554 ATAGGCTATCATCTTTGAAGAA-AG
1 A-A-TCTATCATCTTTGAA-AAGAG
* *
24578 AGTATATCATCTTTGAAAAG
1 AATCTATCATCTTTGAAAAG
24598 TGTAGATATG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
20 7 0.13
21 3 0.06
22 37 0.70
24 4 0.08
25 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:25665 original size:76 final size:75
Alignment explanation
Indices: 25526--25696 Score: 207
Period size: 76 Copynumber: 2.3 Consensus size: 75
25516 ATGTGGTTTT
* * * * * *
25526 AGCATACCCTAACATTTGCTAATACAAACGTTCAAAATGCGTCAACATTCCTCATTCTAATTGAA
1 AGCATCCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTAATTGAA
25591 AGGGGCTTTC
66 AGGGGCTTTC
* * * * *
25601 AGCATTCCCCCAGCATTTGCTGATATAAATATTCAAAATACATCAACATTCATCATTCTGATTGA
1 AGCA-TCCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTAATTGA
*
25666 GAGGGGCTTTC
65 AAGGGGCTTTC
* *
25677 AGTATGCCCCAACATTTGCT
1 AGCATCCCCCAACATTTGCT
25697 TCTTGTTAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
75 18 0.22
76 62 0.77
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (75 bp):
AGCATCCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTAATTGAA
AGGGGCTTTC
Found at i:26463 original size:12 final size:12
Alignment explanation
Indices: 26446--26470 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26436 GGTTTGATGC
26446 TTTCTCTTTGAT
1 TTTCTCTTTGAT
26458 TTTCTCTTTGAT
1 TTTCTCTTTGAT
26470 T
1 T
26471 CTAGTTGCTT
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:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTCTCTTTGAT
Found at i:29260 original size:20 final size:21
Alignment explanation
Indices: 29235--29304 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
29225 CCAGAACCCC
*
29235 AGGGGGTATCGATTCCCC-TG
1 AGGGGGAATCGATTCCCCATG
* * *
29255 AGGGGGGAATCGGTTCCCCTTCAA
1 A-GGGGGAATCGATTCCCCAT--G
29279 AGGGGGAATCGATTCCCTCATG
1 AGGGGGAATCGATTCCC-CATG
29301 AGGG
1 AGGG
29305 TATCGATTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
22 5 0.13
23 15 0.38
24 3 0.08
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.21
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCATG
Found at i:29266 original size:21 final size:22
Alignment explanation
Indices: 29236--29304 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
29226 CAGAACCCCA
*
29236 GGGGGTATCGATTCCCC-TGAG
1 GGGGGAATCGATTCCCCATGAG
* * * *
29257 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCAT-GAG
29280 GGGGGAATCGATTCCCTCATGAG
1 GGGGGAATCGATTCCC-CATGAG
29303 GG
1 GG
29305 TATCGATTCC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 15 0.41
22 1 0.03
23 19 0.51
24 2 0.05
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.22
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCATGAG
Found at i:35382 original size:12 final size:13
Alignment explanation
Indices: 35358--35386 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35348 AAATGAAAAA
35358 AAATGCAAAATGT
1 AAATGCAAAATGT
35371 AAATGC-AAATGT
1 AAATGCAAAATGT
35383 AAAT
1 AAAT
35387 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:38339 original size:11 final size:13
Alignment explanation
Indices: 38323--38362 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
38313 ATGTTAAGTT
38323 TATTAATATAAT-
1 TATTAATATAATA
*
38335 T-TTAAGATAATA
1 TATTAATATAATA
38347 TATTAATAT-ATA
1 TATTAATATAATA
38359 TATT
1 TATT
38363 TTATTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 9 0.38
13 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TATTAATATAATA
Found at i:38653 original size:2 final size:2
Alignment explanation
Indices: 38646--38704 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
38636 AAATATTATT
* * *
38646 TA TA TA TA TA TA TA TA TA TA TA -A GA CT- TA GA TA AA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
38686 TT TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
38705 TGATATAACT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39373 original size:22 final size:22
Alignment explanation
Indices: 39348--39400 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
39338 CGATCTCCGG
39348 CCGGCCACCGTCAAATCCGCCA
1 CCGGCCACCGTCAAATCCGCCA
** *
39370 CCGGCCACCGTCAAATTTGCCG
1 CCGGCCACCGTCAAATCCGCCA
39392 CCGGCCACC
1 CCGGCCACC
39401 ACATCTGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.49, G:0.21, T:0.11
Consensus pattern (22 bp):
CCGGCCACCGTCAAATCCGCCA
Found at i:40107 original size:9 final size:9
Alignment explanation
Indices: 40089--40141 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
40079 TTGTAATATT
40089 TAAT-TTAA
1 TAATATTAA
40097 TAATATTAA
1 TAATATTAA
40106 TAATATATATTA
1 TAATAT-TA--A
*
40118 TAATAATAA
1 TAATATTAA
*
40127 TAATAATAA
1 TAATATTAA
40136 TAATAT
1 TAATAT
40142 AGTGAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 4 0.10
9 25 0.64
10 2 0.05
11 2 0.05
12 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATATTAA
Found at i:40109 original size:3 final size:3
Alignment explanation
Indices: 40094--40140 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
40084 ATATTTAATT
* *
40094 TAA TAA TAT TAA TAA T-A TATA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
40139 TA
1 TA
40141 TAGTGAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:40110 original size:24 final size:24
Alignment explanation
Indices: 40094--40142 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
40084 ATATTTAATT
*
40094 TAATAATATTAATAATATATATTA
1 TAATAATAATAATAATATATATTA
*
40118 TAATAATAATAATAATA-ATAATA
1 TAATAATAATAATAATATATATTA
40141 TA
1 TA
40143 GTGAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAATAATAATAATAATATATATTA
Found at i:41849 original size:21 final size:20
Alignment explanation
Indices: 41825--41866 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
41815 GTCATGCAAC
*
41825 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
41846 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
41866 T
1 T
41867 TGTAAGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:44277 original size:20 final size:20
Alignment explanation
Indices: 44252--44290 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
44242 CAAGTGAGAG
44252 ATTATTAGTTGTCATGCAAA
1 ATTATTAGTTGTCATGCAAA
44272 ATTATTAGTTGTCATGCAA
1 ATTATTAGTTGTCATGCAA
44291 CTAATAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTATTAGTTGTCATGCAAA
Found at i:44316 original size:21 final size:20
Alignment explanation
Indices: 44292--44333 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
44282 GTCATGCAAC
*
44292 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
44313 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
44333 T
1 T
44334 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:45291 original size:95 final size:95
Alignment explanation
Indices: 45116--45338 Score: 302
Period size: 95 Copynumber: 2.3 Consensus size: 95
45106 ATCGTCTAGC
** * * *
45116 TGTAAGAGCATTTGCAACTGCCAAAGAAAGGTATAAGAGTGACTGCATATGAAACATATAAGAAT
1 TGTAAGAGCATTTGCAGTTGCCAATGGAAGGTATAAGAGTGACTGCATATGAAACATATAACAAT
* *
45181 TTAACGCACACATCCTTCATTCAGTTTAGT
66 TCAACACACACATCCTTCATTCAGTTTAGT
* * * *
45211 TGTAAGATCATTTGCAGTTGCCAATGGAAGGTTTAAGAGTGACTGTATGTGAAACATATAACAAT
1 TGTAAGAGCATTTGCAGTTGCCAATGGAAGGTATAAGAGTGACTGCATATGAAACATATAACAAT
* *
45276 TCAATACACATATCCTTCATTCAGTTTAGT
66 TCAACACACACATCCTTCATTCAGTTTAGT
* * *
45306 TGTAGGAGCATTTGCGGTTACCAATGGAAGGTA
1 TGTAAGAGCATTTGCAGTTGCCAATGGAAGGTA
45339 CAAGCCAGGG
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
95 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (95 bp):
TGTAAGAGCATTTGCAGTTGCCAATGGAAGGTATAAGAGTGACTGCATATGAAACATATAACAAT
TCAACACACACATCCTTCATTCAGTTTAGT
Found at i:51495 original size:5 final size:5
Alignment explanation
Indices: 51485--51602 Score: 236
Period size: 5 Copynumber: 23.6 Consensus size: 5
51475 AGACTAAATC
51485 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
51535 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
51585 TTATA TTATA TTATA TTA
1 TTATA TTATA TTATA TTA
51603 AACACCATAA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 113 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:52126 original size:2 final size:2
Alignment explanation
Indices: 52119--52151 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52109 AAGCTTAGAG
52119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52152 CAAATTAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53407 original size:11 final size:11
Alignment explanation
Indices: 53393--53429 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
53383 TTTAAAAATT
53393 AAAAAA-AATA
1 AAAAAATAATA
53403 AAAAAATAATA
1 AAAAAATAATA
53414 AAAAAATAATGA
1 AAAAAATAAT-A
53426 AAAA
1 AAAA
53430 TATATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.24
11 14 0.56
12 5 0.20
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:54284 original size:2 final size:2
Alignment explanation
Indices: 54279--54309 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54269 AAATAAAAAT
54279 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54310 TAAAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56814 original size:21 final size:22
Alignment explanation
Indices: 56778--56818 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
56768 AATCATTAAA
*
56778 ATAATTGAATTTAAATTATTCG
1 ATAATTGAAATTAAATTATTCG
56800 ATAATT-AAATTAAATTATT
1 ATAATTGAAATTAAATTATT
56819 TTTTTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (22 bp):
ATAATTGAAATTAAATTATTCG
Found at i:56858 original size:3 final size:3
Alignment explanation
Indices: 56850--56882 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
56840 TTTGTTCTCT
56850 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56883 ACTGCAACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:60394 original size:65 final size:65
Alignment explanation
Indices: 60264--60393 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
60254 AGTTGAACCC
60264 TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCATTTTTTGTCTGGCAATTGGCTTCATTTT
1 TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCATTTTTTGTCTGGCAATTGGCTTCATTTT
*
60329 TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCA-TTTTTGTCTGGCAATTGGCTTCTTTTT
1 TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCATTTTTTGTCTGGCAATTGGCTTCATTTT
60393 T
1 T
60394 TAATTTTAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 27 0.42
65 37 0.58
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (65 bp):
TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCATTTTTTGTCTGGCAATTGGCTTCATTTT
Found at i:65426 original size:31 final size:28
Alignment explanation
Indices: 65367--65433 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 28
65357 ATTAATATAT
* * *
65367 ATATATTATCTTAAATATATTTTTAAAA
1 ATATATTAACTTAAAAATATTTTAAAAA
65395 ATATATTAACTTAAAAAATACTTTTCAAAAA
1 ATATATTAACTT-AAAAATA-TTTT-AAAAA
65426 ATATATTA
1 ATATATTA
65434 CATTTTAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 11 0.33
29 6 0.18
30 4 0.12
31 12 0.36
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATATTAACTTAAAAATATTTTAAAAA
Found at i:65687 original size:144 final size:142
Alignment explanation
Indices: 65447--65706 Score: 310
Period size: 144 Copynumber: 1.8 Consensus size: 142
65437 TTTAAGAATA
* *
65447 AAATATATTGTAAGTTAAGATATTTTAAAAATATATTATTAAAAGCTAAGATAGGAATAAAATAT
1 AAATATATTGTAAGTTAAGATATTTTAAAAATATATTATTAAAAGCTAAAATAGGAAAAAAATAT
* * * *
65512 ATATTTTTATATTAAAATAAGAATAAAATATATATTTAAATGTATATATATTAAATCAAAAATAA
66 AAATTTATATATT-AAATAAGAATAAAATATATATATAAATATATATATATTAAATCAAAAATAA
65577 AAATAAAATACTT
130 AAATAAAATACTT
* * * *
65590 AAATATATTTTAAGTTAAGATATTTTAAAATATATATTTTTAAAAGTTAAAATA-TATAAAAAAT
1 AAATATATTGTAAGTTAAGATATTTTAAAA-ATATATTATTAAAAGCTAAAATAGGA-AAAAAA-
* * * * *
65654 TATAAATTTAATAGTATT-TAT-ATACTAAGATATATATATATATATATATATAT
63 TATAAATTT-ATA-TATTAAATAAGAATAAAATATATATATAAATATATATATAT
65707 GTTACTTGTC
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
143 30 0.31
144 51 0.53
145 10 0.10
146 2 0.02
147 4 0.04
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (142 bp):
AAATATATTGTAAGTTAAGATATTTTAAAAATATATTATTAAAAGCTAAAATAGGAAAAAAATAT
AAATTTATATATTAAATAAGAATAAAATATATATATAAATATATATATATTAAATCAAAAATAAA
AATAAAATACTT
Found at i:71456 original size:15 final size:15
Alignment explanation
Indices: 71436--71467 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
71426 GAACAAGGTT
71436 CCTAGCATTGAGCAG
1 CCTAGCATTGAGCAG
71451 CCTAGCATTGAGCAG
1 CCTAGCATTGAGCAG
71466 CC
1 CC
71468 AGGAGAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (15 bp):
CCTAGCATTGAGCAG
Done.