Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2788
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: 58606
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:418 original size:35 final size:35
Alignment explanation
Indices: 361--493 Score: 96
Period size: 35 Copynumber: 3.9 Consensus size: 35
351 TGAGAATTTT
* * *
361 TTTTTAAAAA-AAGAGAAA-TTTGAAACACGATTT
1 TTTTTAAAAACACGACAAATTTTGAAACACGATTA
* * **
394 TTTTTAAAAAACACGA-AAATTTTGAATCAAGAGAA
1 TTTTT-AAAAACACGACAAATTTTGAAACACGATTA
* * **
429 TTTTTGAAAACCCGA-AAATTTTTGGAAACACGAAGA
1 TTTTTAAAAACACGACAAA-TTTT-GAAACACGATTA
*
465 TTTTT-AAAACACGACAATTTTTGAAACAC
1 TTTTTAAAAACACGACAAATTTTGAAACAC
494 AAGAAATTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
33 5 0.06
34 26 0.32
35 34 0.43
36 15 0.19
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (35 bp):
TTTTTAAAAACACGACAAATTTTGAAACACGATTA
Found at i:450 original size:17 final size:17
Alignment explanation
Indices: 401--702 Score: 154
Period size: 17 Copynumber: 17.4 Consensus size: 17
391 TTTTTTTTAA
401 AAAACACGAAAATTTTG
1 AAAACACGAAAATTTTG
* * *
418 -AATCAAGAGAATTTTTG
1 AAAACACGA-AAATTTTG
*
435 AAAACCCGAAAATTTTTG
1 AAAACACGAAAA-TTTTG
* * *
453 GAAACACGAAGATTTTT
1 AAAACACGAAAATTTTG
*
470 AAAACACGACAATTTTTG
1 AAAACACGA-AAATTTTG
* * *
488 AAACACAAGAAATTTTTTT
1 AAA-ACACGAAA-ATTTTG
* ** *
507 TAAA-GTGCAAAATTTTT
1 AAAACACG-AAAATTTTG
524 AAAACACTG-AAATTTGTG
1 AAAACAC-GAAAATTT-TG
*
542 -AAACAC-AGAATTGTTG
1 AAAACACGAAAATT-TTG
558 -AAACACGAAAATTTTTG
1 AAAACACGAAAA-TTTTG
* *
575 AAAATATGAAAATATTTG
1 AAAACACGAAAAT-TTTG
*
593 AAAACGCGAAAATTTT-
1 AAAACACGAAAATTTTG
* *
609 TAAACACAAAAATTTTTAG
1 AAAACACGAAAA-TTTT-G
628 AAAACACGAAAACTTTTG
1 AAAACACGAAAA-TTTTG
* * *
646 -AATCACTAGAATTTTG
1 AAAACACGAAAATTTTG
*
662 AAAACACGTAAATTTTTG
1 AAAACACG-AAAATTTTG
* *
680 -AAACACCGGAATTTTTG
1 AAAACA-CGAAAATTTTG
697 AAAACA
1 AAAACA
703 TGTTGAGTTT
Statistics
Matches: 216, Mismatches: 46, Indels: 45
0.70 0.15 0.15
Matches are distributed among these distances:
16 32 0.15
17 83 0.38
18 74 0.34
19 27 0.12
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (17 bp):
AAAACACGAAAATTTTG
Found at i:450 original size:18 final size:18
Alignment explanation
Indices: 401--702 Score: 211
Period size: 18 Copynumber: 17.3 Consensus size: 18
391 TTTTTTTTAA
401 AAAACACGAAAA-TTTTG
1 AAAACACGAAAATTTTTG
* * *
418 -AATCAAGAGAATTTTTG
1 AAAACACGAAAATTTTTG
*
435 AAAACCCGAAAATTTTTG
1 AAAACACGAAAATTTTTG
* *
453 GAAACACGAAGATTTTT-
1 AAAACACGAAAATTTTTG
*
470 AAAACACGACAATTTTTG
1 AAAACACGAAAATTTTTG
* * *
488 AAACACAAGAAATTTTTTT
1 AAA-ACACGAAAATTTTTG
* **
507 TAAA-GTGCAAAATTTTT-
1 AAAACACG-AAAATTTTTG
*
524 AAAACACTG-AAATTTGTG
1 AAAACAC-GAAAATTTTTG
* *
542 -AAACAC-AGAATTGTTG
1 AAAACACGAAAATTTTTG
558 -AAACACGAAAATTTTTG
1 AAAACACGAAAATTTTTG
* * *
575 AAAATATGAAAATATTTG
1 AAAACACGAAAATTTTTG
*
593 AAAACGCGAAAATTTTT-
1 AAAACACGAAAATTTTTG
*
610 -AAACACAAAAATTTTTAG
1 AAAACACGAAAATTTTT-G
*
628 AAAACACGAAAACTTTTG
1 AAAACACGAAAATTTTTG
* * *
646 -AATCACTAGAA-TTTTG
1 AAAACACGAAAATTTTTG
*
662 AAAACACGTAAATTTTTG
1 AAAACACGAAAATTTTTG
*
680 -AAACACCG-GAATTTTTG
1 AAAACA-CGAAAATTTTTG
697 AAAACA
1 AAAACA
703 TGTTGAGTTT
Statistics
Matches: 218, Mismatches: 49, Indels: 35
0.72 0.16 0.12
Matches are distributed among these distances:
16 39 0.18
17 72 0.33
18 79 0.36
19 28 0.13
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (18 bp):
AAAACACGAAAATTTTTG
Found at i:638 original size:35 final size:33
Alignment explanation
Indices: 443--702 Score: 159
Period size: 35 Copynumber: 7.5 Consensus size: 33
433 TGAAAACCCG
* *
443 AAAATTTTTGGAAACACGAAGATTTTTAAAACAC
1 AAAATTTTTGAAAACACGAAAATTTTT-AAACAC
* * * **
477 GACAATTTTTGAAACACAAGAAATTTTTTTTAAAGTGC
1 -AAAATTTTTGAAA-ACACGAAA--ATTTTTAAA-CAC
*
515 AAAATTTTT-AAAACACTG-AAATTTGTGAAACAC
1 AAAATTTTTGAAAACAC-GAAAATTT-TTAAACAC
* * * *
548 AGAATTGTTG-AAACACGAAAATTTTTGAAAATATG
1 AAAATTTTTGAAAACACGAAAATTTTT--AAACA-C
* *
583 AAAATATTTGAAAACGCGAAAATTTTTAAACAC
1 AAAATTTTTGAAAACACGAAAATTTTTAAACAC
* *
616 AAAAATTTTTAGAAAACACGAAAACTTTTGAATCAC
1 -AAAATTTTT-GAAAACACGAAAA-TTTTTAAACAC
* *
652 TAGAA-TTTTGAAAACACGTAAATTTTTGAAACACC
1 -AAAATTTTTGAAAACACGAAAATTTTT-AAACA-C
**
687 GGAATTTTTGAAAACA
1 AAAATTTTTGAAAACA
703 TGTTGAGTTT
Statistics
Matches: 173, Mismatches: 34, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
32 2 0.01
33 27 0.16
34 39 0.23
35 51 0.29
36 37 0.21
37 11 0.06
38 6 0.03
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (33 bp):
AAAATTTTTGAAAACACGAAAATTTTTAAACAC
Found at i:914 original size:16 final size:17
Alignment explanation
Indices: 875--916 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
865 ACACGAGAAA
*
875 AAAAATTTTGAAGACAT
1 AAAAATTTTGAAGACAC
892 AAAAATTTTGAA-ACAC
1 AAAAATTTTGAAGACAC
*
908 AAGAATTTT
1 AAAAATTTT
917 TTTTGAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (17 bp):
AAAAATTTTGAAGACAC
Found at i:922 original size:20 final size:20
Alignment explanation
Indices: 897--937 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
887 GACATAAAAA
897 TTTTGAAACACAAG-AATTTT
1 TTTTGAAA-ACAAGAAATTTT
*
917 TTTTGAAAACACGAAATTTT
1 TTTTGAAAACAAGAAATTTT
937 T
1 T
938 GAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTGAAAACAAGAAATTTT
Found at i:936 original size:19 final size:20
Alignment explanation
Indices: 897--937 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
887 GACATAAAAA
*
897 TTTTGAAACACAAGAATTTT
1 TTTTGAAACACAAGAAATTT
*
917 TTTTGAAA-ACACGAAATTT
1 TTTTGAAACACAAGAAATTT
936 TT
1 TT
938 GAATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTGAAACACAAGAAATTT
Found at i:1125 original size:16 final size:16
Alignment explanation
Indices: 1096--1150 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1086 AAATTAAATT
1096 AAAAATAT--AAATAC
1 AAAAATATAAAAATAC
1110 AAAAATATAAAAATAC
1 AAAAATATAAAAATAC
* * *
1126 ATAAAGTACTAATAATAT
1 A-AAAATA-TAAAAATAC
1144 AAAAATA
1 AAAAATA
1151 CGAGTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 8 0.24
16 7 0.21
17 10 0.30
18 8 0.24
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAATATAAAAATAC
Found at i:1264 original size:15 final size:15
Alignment explanation
Indices: 1241--1294 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1231 TTGAAACCTT
*
1241 TTCTCTTTTTTCTTC
1 TTCTTTTTTTTCTTC
1256 TTCTTTTTTTT-TTC
1 TTCTTTTTTTTCTTC
* * *
1270 TTTCTTTCTCTTCTTT
1 -TTCTTTTTTTTCTTC
1286 TTCTTTTTT
1 TTCTTTTTT
1295 GGCCTGTTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 3 0.10
15 26 0.84
16 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTCTTTTTTTTCTTC
Found at i:1271 original size:24 final size:24
Alignment explanation
Indices: 1239--1293 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
1229 AATTGAAACC
*
1239 TTTTCTCTTT-TTTCTTCTTCTTTT
1 TTTTTTCTTTCTTTC-TCTTCTTTT
1263 TTTTTTCTTTCTTTCTCTTCTTTT
1 TTTTTTCTTTCTTTCTCTTCTTTT
1287 TCTTTTT
1 T-TTTTT
1294 TGGCCTGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTCTTTCTTTCTCTTCTTTT
Found at i:1294 original size:27 final size:26
Alignment explanation
Indices: 1239--1293 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
1229 AATTGAAACC
1239 TTTTCTCTTTTTTCTTCTTCTTTTTT
1 TTTTCTCTTTTTTCTTCTTCTTTTTT
*
1265 TTTTCT-TTCTTTC-TCTTCTTTTTCT
1 TTTTCTCTTTTTTCTTCTTCTTTTT-T
1290 TTTT
1 TTTT
1294 TGGCCTGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 10 0.37
25 11 0.41
26 6 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTCTCTTTTTTCTTCTTCTTTTTT
Found at i:1568 original size:3 final size:3
Alignment explanation
Indices: 1560--1651 Score: 55
Period size: 3 Copynumber: 29.0 Consensus size: 3
1550 CTGTTCATTT
*
1560 TTC TTC TTC TTTC TTC TTC CTC TT- TTC TTC TTTC TTC TTTC TTC TTTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC -TTC TTC -TTC TTC -TTC
* * *
1608 TTTC TTTC TTC TT- TTT TTC TTTC TTTC TTT TTC -TC TTC TCC TTC
1 -TTC -TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC TTC
1652 GTTCAACCCC
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
2 6 0.08
3 41 0.55
4 27 0.36
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:1575 original size:7 final size:7
Alignment explanation
Indices: 1563--1646 Score: 91
Period size: 7 Copynumber: 11.6 Consensus size: 7
1553 TTCATTTTTC
1563 TTCTTCT
1 TTCTTCT
1570 TTCTTC-
1 TTCTTCT
*
1576 TTCCTCTT
1 TTCTTC-T
1584 TTCTTCT
1 TTCTTCT
1591 TTCTTCT
1 TTCTTCT
1598 TTCTTCT
1 TTCTTCT
1605 TTCTTTCT
1 TTC-TTCT
1613 TTCTTCTT
1 TTCTTC-T
*
1621 TTTTTCT
1 TTCTTCT
1628 TTCTTTCT
1 TTC-TTCT
1636 TT-TTCT
1 TTCTTCT
1642 CTTCT
1 -TTCT
1647 CCTTCGTTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
6 9 0.14
7 32 0.48
8 25 0.38
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTCT
Found at i:1601 original size:4 final size:4
Alignment explanation
Indices: 1566--1637 Score: 75
Period size: 4 Copynumber: 19.5 Consensus size: 4
1556 ATTTTTCTTC
* *
1566 TTCT TTC- TTCT TCCT CT-T TTC- TTCT TTC- TTCT TTC- TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
1609 TTCT TTC- TTCT TTTT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1638 TTCTCTTCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
3 17 0.30
4 39 0.70
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:1612 original size:15 final size:15
Alignment explanation
Indices: 1566--1637 Score: 94
Period size: 15 Copynumber: 4.9 Consensus size: 15
1556 ATTTTTCTTC
*
1566 TTCTTTCTTCTTCCT
1 TTCTTTCTTCTTTCT
*
1581 CT-TTTCTTCTTTC-
1 TTCTTTCTTCTTTCT
1594 TTCTTTCTTCTTTCT
1 TTCTTTCTTCTTTCT
*
1609 TTCTTTCTTCTTTTT
1 TTCTTTCTTCTTTCT
1624 TTCTTTCTTTCTTT
1 TTCTTTC-TTCTTT
1638 TTCTCTTCTC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
13 1 0.02
14 21 0.42
15 22 0.44
16 6 0.12
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTCTTTCT
Found at i:1638 original size:15 final size:15
Alignment explanation
Indices: 1547--1644 Score: 67
Period size: 15 Copynumber: 6.1 Consensus size: 15
1537 AAAAATAATT
*
1547 TTTCTGTTCATTTTTC
1 TTTCT-TTCTTTTTTC
*
1563 TTCTTCTTTCTTCTTCCTC
1 -T-TTCTTTCTT-TT-TTC
*
1582 TTT-TCTTCTTTCTTC
1 TTTCT-TTCTTTTTTC
1597 TTTC-TTCTTTCTTTC
1 TTTCTTTCTTT-TTTC
1612 TTTC-TTCTTTTTTTC
1 TTTCTTTC-TTTTTTC
1627 TTTCTTTCTTTTTCTC
1 TTTCTTTCTTTTT-TC
1643 TT
1 TT
1645 CTCCTTCGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
14 6 0.09
15 28 0.42
16 12 0.18
17 12 0.18
18 7 0.10
19 2 0.03
ACGTcount: A:0.01, C:0.26, G:0.01, T:0.72
Consensus pattern (15 bp):
TTTCTTTCTTTTTTC
Found at i:1999 original size:30 final size:30
Alignment explanation
Indices: 1963--2021 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1953 AATTGCAGCA
* * *
1963 AAAATTTTGGGGCCAAAGTGTAATTTTGAG
1 AAAATTTAGGGGCCAAAATATAATTTTGAG
*
1993 AAAATTTAGGGGTCAAAATATAATTTTGA
1 AAAATTTAGGGGCCAAAATATAATTTTGA
2022 AACAGAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (30 bp):
AAAATTTAGGGGCCAAAATATAATTTTGAG
Found at i:8584 original size:502 final size:499
Alignment explanation
Indices: 7615--8619 Score: 1947
Period size: 502 Copynumber: 2.0 Consensus size: 499
7605 GAACGGTGCG
7615 TTTAGGGGGTATGGGGATAATTTCCTAGGTCCCTGTCCATTTTCACGCATTTAATTTTAGTCCTT
1 TTTAGGGGGTATGGGGATAATTTCCTAGGTCCCTGTCCATTTTCACGCATTTAATTTTAGTCCTT
7680 TATTCTGTTTTATTGTTTAATTTATTTATTTTATTATGATTTATACTTTTAATTTCACTTAAATT
66 TATTCTGTTTTATTGTTTAATTTATTTATTTTATTATGATTTATACTTTTAATTTCACTTAAATT
7745 TCGATTCACTCCCTTATTTATTTAATTTCAGCCTTTCATGAATTTTATTTATTTATTACTTCTTT
131 TCGATTCACTCCCTTATTTATTTAATTTCAGCCTTTCATGAATTTTATTTATTTATTACTTCTTT
7810 ATTTTCATATACTTAAAAATTGGATTGTTTACATTCTTTTATTTGTGCATTTTTTTGCTCATTTA
196 ATTTTCATATACTTAAAAATTGGATTGTTTACATTCTTTTATTTGTGCATTTTTTTGCTCATTTA
7875 TTTTATTTACTTAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAAAGAAATGAAATTA
261 TTTTATTTACTTAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAAAGAAATGAAATTA
7940 TACCTGTCAATTTGTTACTCTGAAGAGAAAGCATTTGAAGAGAAGTCAAGTTTCCAATTACAAGA
326 TACCTGTCAATTTGTTACTCTGAAGAGAAAGCATTTGAAGAGAAGTCAAGTTTCCAATTACAAGA
8005 GGAATTTCACCTGAAACATATAATTAAATCAGTAAAAATTATAAATATTTTCCTAGCAAAACCTT
391 GGAATTTCACCTGAAACATATAATTAAATCAGTAAAAATTATAAATATTTTCCTAGCAAAACCTT
8070 AATTTATTTGTTGAGCATATTAGTGTCCATTTGATTTATTTATT
456 AATTTATTTGTTGAGCATATTAGTGTCCATTTGATTTATTTATT
*
8114 TTTAGGGGGTATGTGGATAATTTCCTAGTTGGTCCCTGTCCATTTTCACGCATTTAATTTTAGTC
1 TTTAGGGGGTATGGGGATAATTTCCTA---GGTCCCTGTCCATTTTCACGCATTTAATTTTAGTC
8179 CTTTATTCTGTTTTATTGTTTAATTTATTTATTTTATTATGATTTATACTTTTAATTTCACTTAA
63 CTTTATTCTGTTTTATTGTTTAATTTATTTATTTTATTATGATTTATACTTTTAATTTCACTTAA
* *
8244 ATTTTGATTCAGTCCCTTATTTATTTAATTTCAGCCTTTCATGAATTTTATTTATTTATTACTTC
128 ATTTCGATTCACTCCCTTATTTATTTAATTTCAGCCTTTCATGAATTTTATTTATTTATTACTTC
8309 TTTATTTTCATATACTTAAAAATTGGATTGTTTACATTCTTTTATTTGTGCATTTTTTTGCTCAT
193 TTTATTTTCATATACTTAAAAATTGGATTGTTTACATTCTTTTATTTGTGCATTTTTTTGCTCAT
8374 TTATTTTATTTACTTAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAAAGAAATGAAA
258 TTATTTTATTTACTTAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAAAGAAATGAAA
8439 TTATACCTGTCAATTTGTTACTCTGAAGAGAAAGCATTTGAAGAGAAGTCAAGTTTCCAATTACA
323 TTATACCTGTCAATTTGTTACTCTGAAGAGAAAGCATTTGAAGAGAAGTCAAGTTTCCAATTACA
*
8504 AGAGGAATTTCACCTGAAACATATAATTAAATTAGTAAAAATTATAAATATTTTCCTAGCAAAAC
388 AGAGGAATTTCACCTGAAACATATAATTAAATCAGTAAAAATTATAAATATTTTCCTAGCAAAAC
8569 CTTAATTTATTTGTTGAGCATATTAGTGTCCATTTGATTTATTTATT
453 CTTAATTTATTTGTTGAGCATATTAGTGTCCATTTGATTTATTTATT
8616 TTTA
1 TTTA
8620 AATATGCAAG
Statistics
Matches: 499, Mismatches: 4, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
499 26 0.05
502 473 0.95
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (499 bp):
TTTAGGGGGTATGGGGATAATTTCCTAGGTCCCTGTCCATTTTCACGCATTTAATTTTAGTCCTT
TATTCTGTTTTATTGTTTAATTTATTTATTTTATTATGATTTATACTTTTAATTTCACTTAAATT
TCGATTCACTCCCTTATTTATTTAATTTCAGCCTTTCATGAATTTTATTTATTTATTACTTCTTT
ATTTTCATATACTTAAAAATTGGATTGTTTACATTCTTTTATTTGTGCATTTTTTTGCTCATTTA
TTTTATTTACTTAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAAAGAAATGAAATTA
TACCTGTCAATTTGTTACTCTGAAGAGAAAGCATTTGAAGAGAAGTCAAGTTTCCAATTACAAGA
GGAATTTCACCTGAAACATATAATTAAATCAGTAAAAATTATAAATATTTTCCTAGCAAAACCTT
AATTTATTTGTTGAGCATATTAGTGTCCATTTGATTTATTTATT
Found at i:10349 original size:15 final size:16
Alignment explanation
Indices: 10323--10352 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10313 ATAAAAGTAC
10323 ATATTTTAAATCAAAA
1 ATATTTTAAATCAAAA
10339 ATATTTT-AATCAAA
1 ATATTTTAAATCAAA
10353 TCATCTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTTTAAATCAAAA
Found at i:16841 original size:20 final size:19
Alignment explanation
Indices: 16809--16846 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
16799 AAATTGTTTA
16809 AAATATAAAAAATTAAAAAT
1 AAATATAAAAAA-TAAAAAT
16829 AAATA-AAAGAAATAAAAA
1 AAATATAAA-AAATAAAAA
16847 GGAATTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AAATATAAAAAATAAAAAT
Found at i:17932 original size:8 final size:8
Alignment explanation
Indices: 17916--17946 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
17906 CAAGAAGTAT
*
17916 TTTACATA
1 TTTATATA
17924 TTTATATA
1 TTTATATA
17932 TTTATATA
1 TTTATATA
17940 TTTATAT
1 TTTATAT
17947 TCATGGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTATATA
Found at i:20579 original size:20 final size:20
Alignment explanation
Indices: 20551--20589 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20541 CTCTTCTAGC
20551 TTTCATCTTCT-TTTTCATCT
1 TTTCATCTT-TGTTTTCATCT
*
20571 TTTCTTCTTTGTTTTCATC
1 TTTCATCTTTGTTTTCATC
20590 CCCTATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTCATCTTTGTTTTCATCT
Found at i:32893 original size:24 final size:24
Alignment explanation
Indices: 32858--32907 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
32848 ATCAGCAAAC
*
32858 ACACACACATATCTGCACATATAG
1 ACACACACATATCTGCACATACAG
* *
32882 ACACACATATATCTGTACATACAG
1 ACACACACATATCTGCACATACAG
32906 AC
1 AC
32908 TACTAGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (24 bp):
ACACACACATATCTGCACATACAG
Found at i:37040 original size:24 final size:24
Alignment explanation
Indices: 37005--37054 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
36995 ATCAGCAAAC
*
37005 ACACACACATATCTGCACATATAG
1 ACACACACATATCTGCACATACAG
* *
37029 ACACACATATATCTGTACATACAG
1 ACACACACATATCTGCACATACAG
37053 AC
1 AC
37055 TACTAGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (24 bp):
ACACACACATATCTGCACATACAG
Found at i:41493 original size:285 final size:291
Alignment explanation
Indices: 40972--41540 Score: 925
Period size: 285 Copynumber: 2.0 Consensus size: 291
40962 GAAATGTGAC
* * *
40972 GGATCAAAAGGGACGAATAAGCTAATTTCTGCCATAAGGTAGATGGTGAACTTAGGATGTGGAGT
1 GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGATAAATGGTGAACTTAGGATGTGGAGT
*
41037 TCCAATAAATACCTAAACATACCTAAACTTTTGGCCATTCAAATAGATTAGACTAATTTTTAATT
66 TCC----AATA-CTAAACATACCTAAACTTTTGGCAATTCAAATAGATTAGACTAATTTTTAATT
*
41102 ACTTAAAAATATTGCATAAATTTAATAACAAAATGGAGAATAAAAGAAACATGAAATTATACCTG
126 ACTTAAAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTG
* * ***
41167 TCAATTTGTTATTGTTAAGATAAAGCTCTCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATT
191 TCAAATTGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATT
41232 TCACCTGAAACGTATAATTAAATCGGTCAAAATTAT
256 TCACCTGAAACGTATAATTAAATCGGTCAAAATTAT
41268 GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGATAAATGGT-AACTTAGGATGTGGAGT
1 GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGATAAATGGTGAACTTAGGATGTGGAGT
*
41332 TCC-A-A-T-AA-ATACCTAAACTTTTGGCAATTCAAATAGATTATACTAATTTTTAATTACTTA
66 TCCAATACTAAACATACCTAAACTTTTGGCAATTCAAATAGATTAGACTAATTTTTAATTACTTA
*
41392 AAAATATTGCATAAATTTAATAACAAATTAGAGAATAAAAGAAACATGAAATTATACCTGTCAAA
131 AAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGTCAAA
* *
41457 TTGTTATTGCTAAGATAAAGAAATTGGAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCACC
196 TTGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCACC
41522 TGAAACGTATAATTAAATC
261 TGAAACGTATAATTAAATC
41541 ATCACTTTAG
Statistics
Matches: 259, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
285 190 0.73
286 2 0.01
287 1 0.00
289 1 0.00
290 1 0.00
295 20 0.08
296 44 0.17
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (291 bp):
GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGATAAATGGTGAACTTAGGATGTGGAGT
TCCAATACTAAACATACCTAAACTTTTGGCAATTCAAATAGATTAGACTAATTTTTAATTACTTA
AAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGTCAAA
TTGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCACC
TGAAACGTATAATTAAATCGGTCAAAATTAT
Found at i:45277 original size:15 final size:16
Alignment explanation
Indices: 45251--45280 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
45241 ATAAAAGTAC
45251 ATATTTTAAATCAAAA
1 ATATTTTAAATCAAAA
45267 ATATTTT-AATCAAA
1 ATATTTTAAATCAAA
45281 TCATCTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTTTAAATCAAAA
Found at i:46711 original size:285 final size:291
Alignment explanation
Indices: 46190--46758 Score: 943
Period size: 285 Copynumber: 2.0 Consensus size: 291
46180 GAAATGTGAC
* *
46190 GGATCAAAAGGGACGAATAAGCTAATTTCTGCCATAAGGTAGATGGTGAACTTAGGATGTGGAGT
1 GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGGTAAATGGTGAACTTAGGATGTGGAGT
*
46255 TCCAATAAATACCTAAACATACCTAAACTTTTGGCCATTCAAATAGATTAGACTAATTTTTAATT
66 TCC----AATA-CTAAACATACCTAAACTTTTGGCAATTCAAATAGATTAGACTAATTTTTAATT
*
46320 ACTTAAAAATATTGCATAAATTTAATAACAAAATGGAGAATAAAAGAAACATGAAATTATACCTG
126 ACTTAAAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTG
* * ***
46385 TCAATTTGTTATTGTTAAGATAAAGCTCTCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATT
191 TCAAATTGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATT
46450 TCACCTGAAACGTATAATTAAATCGGTCAAAATTAT
256 TCACCTGAAACGTATAATTAAATCGGTCAAAATTAT
46486 GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGGTAAATGGT-AACTTAGGATGTGGAGT
1 GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGGTAAATGGTGAACTTAGGATGTGGAGT
*
46550 TCC-A-A-T-AA-ATACCTAAACTTTTGGCAATTCAAATAGATTATACTAATTTTTAATTACTTA
66 TCCAATACTAAACATACCTAAACTTTTGGCAATTCAAATAGATTAGACTAATTTTTAATTACTTA
46610 AAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGTCAAA
131 AAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGTCAAA
* *
46675 TTGTTATTGCTAAGATAAAGAAATTGGAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCACC
196 TTGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCACC
46740 TGAAACGTATAATTAAATC
261 TGAAACGTATAATTAAATC
46759 ATCACTTTAG
Statistics
Matches: 261, Mismatches: 12, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
285 191 0.73
286 2 0.01
287 1 0.00
289 1 0.00
290 1 0.00
295 20 0.08
296 45 0.17
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (291 bp):
GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGGTAAATGGTGAACTTAGGATGTGGAGT
TCCAATACTAAACATACCTAAACTTTTGGCAATTCAAATAGATTAGACTAATTTTTAATTACTTA
AAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGTCAAA
TTGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCACC
TGAAACGTATAATTAAATCGGTCAAAATTAT
Found at i:53465 original size:15 final size:15
Alignment explanation
Indices: 53430--53479 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
53420 AAATAATTAA
53430 AATAA-AACTAATAAT
1 AATAATAAC-AATAAT
53445 AATAATAACAATAAT
1 AATAATAACAATAAT
** *
53460 AATAATGGCAATGAT
1 AATAATAACAATAAT
53475 AATAA
1 AATAA
53480 CATTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 28 0.90
16 3 0.10
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAATAACAATAAT
Found at i:54831 original size:43 final size:43
Alignment explanation
Indices: 54737--54837 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 43
54727 TCCAATGCGT
* * *
54737 CTTGTTGCTTCAATCTACTCCACTGCACATCAAAGAGATACGG
1 CTTGTAGCTTCAATCCACTCCACTGCACATCAAAGAGATACGA
* * *
54780 CTTTTAGCTTCAATCCACTTCACTGCACTTCAGAA-AGAT-CTGA
1 CTTGTAGCTTCAATCCACTCCACTGCACATCA-AAGAGATAC-GA
*
54823 CTTGTAGCTTTAATC
1 CTTGTAGCTTCAATC
54838 TTCTTCGCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 1 0.02
43 45 0.94
44 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (43 bp):
CTTGTAGCTTCAATCCACTCCACTGCACATCAAAGAGATACGA
Found at i:55245 original size:44 final size:43
Alignment explanation
Indices: 55200--55358 Score: 153
Period size: 44 Copynumber: 3.6 Consensus size: 43
55190 TTGTTTTAAT
*
55200 CTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAGGATTAAT-GCTTCAAC
** * ** *
55244 CTGCTCTGCTGCAACTTCAGGGAGATAAGATTGGTGTCTTTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAGGATTAATG-CTTCAAC
* * *
55288 CTACTCCACTGCAACTTCAGCGAGATAAGGTTTGCAAT--TTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGAT-AGGATT--AATGCTTCAAC
55332 CTGCTCCACTGCAACTTCAAGGG-GATA
1 CTGCTCCACTGCAACTTC-AGGGAGATA
55359 ATGTTTGATA
Statistics
Matches: 92, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
43 2 0.02
44 82 0.89
45 7 0.08
47 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (43 bp):
CTGCTCCACTGCAACTTCAGGGAGATAGGATTAATGCTTCAAC
Found at i:55330 original size:88 final size:86
Alignment explanation
Indices: 55194--55359 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 86
55184 CATTCATTGT
* * * * **
55194 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCTGCTGCAAC
1 TTTAACCTACTCCACTGCAACTTCAGCGAGATAGGATTAATA--TTCAACCTGCTCCACTGCAAC
55259 TTC-AGGGAGATAAGATTGGTGTC
64 TTCAAGGG-GATAAGATTGGTGTC
*
55282 TTTAACCTACTCCACTGCAACTTCAGCGAGATAAGGTTTGCAAT-TTCAACCTGCTCCACTGCAA
1 TTTAACCTACTCCACTGCAACTTCAGCGAGAT-AGGATT--AATATTCAACCTGCTCCACTGCAA
55346 CTTCAAGGGGATAA
63 CTTCAAGGGGATAA
55360 TGTTTGATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
88 55 0.82
89 9 0.13
91 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (86 bp):
TTTAACCTACTCCACTGCAACTTCAGCGAGATAGGATTAATATTCAACCTGCTCCACTGCAACTT
CAAGGGGATAAGATTGGTGTC
Found at i:55529 original size:45 final size:45
Alignment explanation
Indices: 55492--56155 Score: 868
Period size: 45 Copynumber: 14.9 Consensus size: 45
55482 CAAGATATGT
55492 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGA-C-GC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * * *
55535 TATCTTTAGTCTACTTTGCTGCCAATATAGGAAGACAAAACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* **
55580 TATCTT-TGATCTACTTCGCTGCCAATACAGGAAGACAAGATTTGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
*
55625 TATCTTCAGTCTAC-TCGCTGCTAATACAGGAAGACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* *
55669 TATATTC-GATCTACTTCGCTG-CAATACAGGAAGACAAGATCTGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * * * *
55713 TATCTTCAATCAACTTCGTTGACAATACAGGAAGACAAGACATGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * * **
55758 TATCTTC-GATCTACTTCGTTGCCAATATAGTAAGACAAGATATGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
*
55803 TATCTTCAGTCTACTTCGCTGCCAATATAGGAAGACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * *
55848 TATCTT-TGATCTACTTCACTGCCAATATAGGAAGACAAGACCTGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
55893 TATCTTCAGTCTACTTCGCTGCCAA-ACAAGGAA-ACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATAC-AGGAAGACAAGACCTGC
* *
55937 TATCTTCAGTCTTCTTCGCTGCCAATACAGGAAGACAAGACCTGT
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* *
55982 TATCTTTAATCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
*
56027 TATCTTC-GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* *
56072 TATCTTCAGTCTACTTCGCTACCAATACAGGAAGATAAGACCT-C
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* **
56116 TATCTT-TGATCTACTTCATTGCCAATACAGGAAGACAAGA
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGA
56156 TCTGTTATTT
Statistics
Matches: 548, Mismatches: 55, Indels: 35
0.86 0.09 0.05
Matches are distributed among these distances:
43 38 0.07
44 153 0.28
45 353 0.64
46 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
Found at i:55835 original size:90 final size:90
Alignment explanation
Indices: 55492--56159 Score: 958
Period size: 90 Copynumber: 7.5 Consensus size: 90
55482 CAAGATATGT
* *
55492 TATCTTC-AGTCTACTTCGCTGCCAATACAGGAAGACAAGA-C-GCTATCTTTAGTCTACTTTGC
1 TATCTTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
* *
55554 TGCCAATATAGGAAGACAAAACCTGC
65 TGCCAATACAGGAAGACAAGACCTGC
* *
55580 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATTTGCTATCTTCAGTCTAC-TCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
*
55644 GCTAATACAGGAAGACAAGACCTGC
66 GCCAATACAGGAAGACAAGACCTGC
* * * *
55669 TATATTCGATCTACTTCGCTG-CAATACAGGAAGACAAGATCTGCTATCTTCAATCAACTTCGTT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
* *
55733 GACAATACAGGAAGACAAGACATGC
66 GCCAATACAGGAAGACAAGACCTGC
* * * *
55758 TATCTTCGATCTACTTCGTTGCCAATATAGTAAGACAAGATATGCTATCTTCAGTCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
*
55823 GCCAATATAGGAAGACAAGACCTGC
66 GCCAATACAGGAAGACAAGACCTGC
* * * *
55848 TATCTTTGATCTACTTCACTGCCAATATAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
55913 GCCAA-ACAAGGAA-ACAAGACCTGC
66 GCCAATAC-AGGAAGACAAGACCTGC
* * * * *
55937 TATCTTC-AGTCTTCTTCGCTGCCAATACAGGAAGACAAGACCTGTTATCTTTAATCTACTTCGC
1 TATCTTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
56001 TGCCAATACAGGAAGACAAGACCTGC
65 TGCCAATACAGGAAGACAAGACCTGC
56027 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
* *
56092 ACCAATACAGGAAGATAAGACCT-C
66 GCCAATACAGGAAGACAAGACCTGC
* **
56116 TATCTTTGATCTACTTCATTGCCAATACAGGAAGACAAGATCTG
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG
56160 TTATTTTCTC
Statistics
Matches: 519, Mismatches: 51, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
88 72 0.14
89 211 0.41
90 235 0.45
91 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (90 bp):
TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
GCCAATACAGGAAGACAAGACCTGC
Found at i:55940 original size:179 final size:180
Alignment explanation
Indices: 55492--56156 Score: 952
Period size: 179 Copynumber: 3.7 Consensus size: 180
55482 CAAGATATGT
* *
55492 TATCTTC-AGTCTACTTCGCTGCCAATACAGGAAGACAAGA-C-GCTATCTTTAGTCTACTTTGC
1 TATCTTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
* * *
55554 TGCCAATATAGGAAGACAAAACCTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAG
65 TGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAG
* *
55619 ATTTGCTATCTTCAGTCTAC-TCGCTGCTAATACAGGAAGACAAGACCTGC
130 ATATGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * * *
55669 TATATTCGATCTACTTCGCTG-CAATACAGGAAGACAAGATCTGCTATCTTCAATCAACTTCGTT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
* * * * *
55733 GACAATACAGGAAGACAAGACATGCTATCTTCGATCTACTTCGTTGCCAATATAGTAAGACAAGA
66 GCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA
*
55798 TATGCTATCTTCAGTCTACTTCGCTGCCAATATAGGAAGACAAGACCTGC
131 TATGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * * *
55848 TATCTTTGATCTACTTCACTGCCAATATAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
*
55913 GCCAA-ACAAGGAA-ACAAGACCTGCTATCTTC-AGTCTTCTTCGCTGCCAATACAGGAAGACAA
66 GCCAATAC-AGGAAGACAAGACCTGCTATCTTCGA-TCTACTTCGCTGCCAATACAGGAAGACAA
** * * *
55975 GACCTGTTATCTTTAATCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
129 GATATGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
56027 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
* * * **
56092 ACCAATACAGGAAGATAAGACCT-CTATCTTTGATCTACTTCATTGCCAATACAGGAAGACAAGA
66 GCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA
56156 T
131 T
56157 CTGTTATTTT
Statistics
Matches: 430, Mismatches: 48, Indels: 18
0.87 0.10 0.04
Matches are distributed among these distances:
176 18 0.04
177 19 0.04
178 94 0.22
179 241 0.56
180 58 0.13
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (180 bp):
TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
GCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA
TATGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
Found at i:57470 original size:6 final size:6
Alignment explanation
Indices: 57459--57516 Score: 68
Period size: 6 Copynumber: 10.0 Consensus size: 6
57449 TTTGCCTTTC
*
57459 CTTTTT CTTTTT C-TTTT CTTCTT CTTTTT CTTTTT -TTTTT CTTTGTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT-TT
*
57506 -TTTTT ATTTTT
1 CTTTTT CTTTTT
57517 TTGATTGATC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
5 12 0.26
6 32 0.70
7 2 0.04
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:57509 original size:17 final size:17
Alignment explanation
Indices: 57460--57516 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
57450 TTGCCTTTCC
*
57460 TTTTTCTTTTTCTTTTC
1 TTTTTCTTTTTCTTTTT
*
57477 TTCTTCTTTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
57494 TTTTTCTTTGTT-TTTTT
1 TTTTTCTTT-TTCTTTTT
57511 ATTTTT
1 -TTTTT
57517 TTGATTGATC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 28 0.80
18 7 0.20
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTT
Found at i:57509 original size:23 final size:23
Alignment explanation
Indices: 57459--57518 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
57449 TTTGCCTTTC
*
57459 CTTTTTCTTTTTCTTTTCTTCTT
1 CTTTTTCTTTTTTTTTTCTTCTT
57482 CTTTTTCTTTTTTTTTTCTT-TGT
1 CTTTTTCTTTTTTTTTTCTTCT-T
* *
57505 TTTTTTATTTTTTT
1 CTTTTTCTTTTTTT
57519 GATTGATCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (23 bp):
CTTTTTCTTTTTTTTTTCTTCTT
Found at i:57518 original size:11 final size:11
Alignment explanation
Indices: 57460--57518 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
57450 TTGCCTTTCC
57460 TTTTTCTTTTT
1 TTTTTCTTTTT
* *
57471 CTTTTCTTCTTC
1 TTTTTCTT-TTT
57483 TTTTTCTTTTT
1 TTTTTCTTTTT
57494 TTTTTCTTTGTT
1 TTTTTCTTT-TT
*
57506 TTTTTATTTTT
1 TTTTTCTTTTT
57517 TT
1 TT
57519 GATTGATCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
11 22 0.54
12 19 0.46
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTT
Done.