Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004227.1 Kokia drynarioides strain JFW-HI SEQ_117483, 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: 43108
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Warning! 202 characters in sequence are not A, C, G, or T
Found at i:53 original size:3 final size:3
Alignment explanation
Indices: 1--33 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34 ATAAATGGGT
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:1280 original size:29 final size:28
Alignment explanation
Indices: 1241--1633 Score: 307
Period size: 29 Copynumber: 13.6 Consensus size: 28
1231 TCCCTAAACT
**
1241 TTCCAAAAATTCTGTTTTTACTCTCGAAC
1 TTCCAAAAATTCCATTTTTAC-CTCGAAC
1270 TTCCAAAAATTCCATTTTTTGACCTCGAAAC
1 TTCCAAAAATTCCA-TTTTT-ACCTCG-AAC
* ** *
1301 ATCCAAAAATTCTGTTTTTACCCTTGAAC
1 TTCCAAAAATTCCATTTTTA-CCTCGAAC
* *
1330 TTCCAAAAATCCCATTTTAACCTCGAAAC
1 TTCCAAAAATTCCATTTTTACCTCG-AAC
* *
1359 TTCCAAAAATTCCATTTTTAACCCCAAAAC
1 TTCCAAAAATTCCATTTTT-ACCTC-GAAC
* *
1389 TTCCAAAAATTCCATTTTTAACCCCAAAAC
1 TTCCAAAAATTCCATTTTT-ACCTC-GAAC
**
1419 TTCCAAAAATTCCATTTTTACCCTTAAAC
1 TTCCAAAAATTCCATTTTTA-CCTCGAAC
* * *
1448 TTCCAAAAATCCCATTTTTGACCCCAAAAC
1 TTCCAAAAATTCCATTTTT-ACCTC-GAAC
* * * *
1478 TTACAAAAGTTCCATTTTTACCCCTAAAC
1 TTCCAAAAATTCCATTTTTACCTC-GAAC
*
1507 TTCCAAAAA-TCCAATTTT---T-G-AC
1 TTCCAAAAATTCCATTTTTACCTCGAAC
* *
1529 -CCCAAAACTTCCATTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTA-CCTCGAAC
* *
1557 TTCCAAAAATGCCATTTTTAACCACGAAAC
1 TTCCAAAAATTCCATTTTT-ACCTCG-AAC
*
1587 TTCCAAAAATTCCATTTTTGCCCTCGAAC
1 TTCCAAAAATTCCATTTTT-ACCTCGAAC
*
1616 ATCC-AAAATCTCCATTTT
1 TTCCAAAAAT-TCCATTTT
1634 CGACCTCAAA
Statistics
Matches: 301, Mismatches: 42, Indels: 42
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.02
22 10 0.03
26 1 0.00
27 1 0.00
28 19 0.06
29 125 0.42
30 123 0.41
31 16 0.05
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (28 bp):
TTCCAAAAATTCCATTTTTACCTCGAAC
Found at i:1420 original size:89 final size:87
Alignment explanation
Indices: 1232--1646 Score: 409
Period size: 89 Copynumber: 4.8 Consensus size: 87
1222 CCTTGGAGGT
** * *
1232 CCCTAAACTTTCCAAAAATTCTGTTTTTACTCTCGAACTTCCAAAAATTCCATTTTTTGACCTCG
1 CCCTAAAC-TTCCAAAAATTCCATTTTTAC-CTCGAACTTCCAAAAATTCCA-TTTTTGACCCCA
* **
1297 AAACATCCAAAAATTCTGTTTTTAC
63 AAACTTCCAAAAATTCCATTTTTAC
* * * * *
1322 CCTTGAACTTCCAAAAATCCCATTTTAACCTCGAAACTTCCAAAAATTCCATTTTTAACCCCAAA
1 CCCTAAACTTCCAAAAATTCCATTTTTACCTCG-AACTTCCAAAAATTCCATTTTTGACCCCAAA
1387 ACTTCCAAAAATTCCATTTTTAAC
65 ACTTCCAAAAATTCCATTTTT-AC
* ** *
1411 CCCAAAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCAAA
1 CCCTAAACTTCCAAAAATTCCATTTTTA-CCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAA
* *
1476 ACTTACAAAAGTTCCATTTTTAC
65 ACTTCCAAAAATTCCATTTTTAC
* * * *
1499 CCCTAAACTTCCAAAAA-TCCAATTTT---T-G-AC-CCCAAAACTTCCATTTTT-ACCCTC-GA
1 CCCTAAACTTCCAAAAATTCCATTTTTACCTCGAACTTCCAAAAATTCCATTTTTGACCC-CAAA
*
1555 ACTTCCAAAAATGCCATTTTTAAC
65 ACTTCCAAAAATTCCATTTTT-AC
* * * * * *
1579 CACGAAACTTCCAAAAATTCCATTTTTGCCCTCGAACATCC-AAAATCTCCATTTTCGACCTCAA
1 CCCTAAACTTCCAAAAATTCCATTTTT-ACCTCGAACTTCCAAAAAT-TCCATTTTTGACCCCAA
1643 AACT
64 AACT
1647 CTCAAAATTA
Statistics
Matches: 268, Mismatches: 41, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
79 23 0.09
80 33 0.12
81 10 0.04
83 1 0.00
85 1 0.00
86 1 0.00
87 14 0.05
88 62 0.23
89 114 0.43
90 9 0.03
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (87 bp):
CCCTAAACTTCCAAAAATTCCATTTTTACCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAA
CTTCCAAAAATTCCATTTTTAC
Found at i:1448 original size:59 final size:59
Alignment explanation
Indices: 1236--1721 Score: 400
Period size: 59 Copynumber: 8.3 Consensus size: 59
1226 GGAGGTCCCT
** * * * *
1236 AAACTTTCCAAAAATTCTGTTTTTACTCTCGAACTTCCAAAAATTCCATTTTTTGACCTCG
1 AAAC-TTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTTAACCCCA
* ** * * * *
1297 AAACATCCAAAAATTCTGTTTTTACCCTTGAACTTCCAAAAATCCCA-TTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
*
1355 AAACTTCCAAAAATTCCATTTTTAACCC-CAAAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC-GAACTTCCAAAAATTCCATTTTTAACCCCA
** * *
1415 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
* * * *
1474 AAACTTACAAAAGTTCCATTTTTACCC-CTAAACTTCCAAAAA-TCCAATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCC-ATTTTTAACCCCA
* * *
1533 AAA----C-----TTCCATTTTTACCCTCGAACTTCCAAAAATGCCATTTTTAACCACG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
* * ** *
1583 AAACTTCCAAAAATTCCATTTTTGCCCTCGAACATCC-AAAATCTCCATTTTCGACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAT-TCCATTTTTAACCCCA
* * *
1642 AAAC-TCTC-AAAATTACC-CTTTTACACC-CGAA-TGTCTAAAAATTCCATTTTTAAACCCTA
1 AAACTTC-CAAAAATT-CCATTTTTAC-CCTCGAACT-TCCAAAAATTCCATTTTT-AACCCCA
*
1701 AAATTTCTC-AAAATTACCATT
1 AAACTTC-CAAAAATT-CCATT
1722 CTACCCCCGG
Statistics
Matches: 357, Mismatches: 42, Indels: 52
0.79 0.09 0.12
Matches are distributed among these distances:
50 39 0.11
51 3 0.01
54 1 0.00
55 1 0.00
58 64 0.18
59 160 0.45
60 84 0.24
61 5 0.01
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
Found at i:1558 original size:50 final size:50
Alignment explanation
Indices: 1480--1591 Score: 147
Period size: 50 Copynumber: 2.2 Consensus size: 50
1470 CCCAAAACTT
* *
1480 ACAAAAGTTCCATTTTTACCCCTAAACTTCCAAAAAT-CCAATTTTTGACC
1 ACAAAACTTCCATTTTTACCCCTAAACTTCCAAAAATGCC-ATTTTTAACC
* *
1530 CCAAAACTTCCATTTTTA-CCCTCGAACTTCCAAAAATGCCATTTTTAACC
1 ACAAAACTTCCATTTTTACCCCT-AAACTTCCAAAAATGCCATTTTTAACC
*
1580 ACGAAACTTCCA
1 ACAAAACTTCCA
1592 AAAATTCCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
49 4 0.07
50 48 0.89
51 2 0.04
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.30
Consensus pattern (50 bp):
ACAAAACTTCCATTTTTACCCCTAAACTTCCAAAAATGCCATTTTTAACC
Found at i:1621 original size:109 final size:109
Alignment explanation
Indices: 1421--1646 Score: 285
Period size: 109 Copynumber: 2.1 Consensus size: 109
1411 CCCAAAACTT
* * * *
1421 CCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTACAAAA
1 CCAAAACTTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCACAAAACTTACAAAA
* * *
1486 GTTCCATTTTTACCCCTAAACTTCCAAAAATC-CAATTTTTGACC
66 ATTCCATTTTTACCCCTAAACATCC-AAAATCTCAATTTTCGACC
* * * *
1530 CCAAAACTTCCATTTTTACCCTCGAACTTCCAAAAATGCCATTTTTAACCACGAAACTTCCAAAA
1 CCAAAACTTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCACAAAACTTACAAAA
* * *
1595 ATTCCATTTTT-GCCCTCGAACATCCAAAATCTCCATTTTCGACC
66 ATTCCATTTTTACCCCT-AAACATCCAAAATCTCAATTTTCGACC
*
1639 TCAAAACT
1 CCAAAACT
1647 CTCAAAATTA
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
108 10 0.10
109 90 0.90
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (109 bp):
CCAAAACTTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCACAAAACTTACAAAA
ATTCCATTTTTACCCCTAAACATCCAAAATCTCAATTTTCGACC
Found at i:13724 original size:196 final size:195
Alignment explanation
Indices: 13433--13818 Score: 621
Period size: 196 Copynumber: 2.0 Consensus size: 195
13423 GCAAGCAAAT
* * *
13433 TCTTCGAACCCCAGCTTCCTGATGAGATACGAAGAAGCAGGGTGAAGCAATGAAAGGTTAGCTTC
1 TCTTCGAACCCCAGCTTCCTAATGAGACACGAAGAAGCAGGGTGAAGCAATAAAAGGTTAGCTTC
* *
13498 CTGATGAGATACTGAGAAGTGGACCAAATTCTTCTTCCTAATGAGATACAGAGAAGCGAATTGAA
66 CTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGAATTGAA
*
13563 ACAAGCGATGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCGA
131 ACAAGCGATGCGGTCATCTTCCTGATAAGATACTAAGAAGAAGACCAAATCAAACCCACGTTCGA
* * * *
13628 TCTTCGAACTCCAGCTTCTTAATGCGACACTG-AGAAGCAGGTTGAAGCAATAAAATGGTTAGCT
1 TCTTCGAACCCCAGCTTCCTAATGAGACAC-GAAGAAGCAGGGTGAAGCAATAAAA-GGTTAGCT
* *
13692 TCCTGATGAGATACTGAGAAGTGAATCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTG
64 TCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGAATTG
* *
13757 AAACAAGCGATGCGGTCATCTTCTTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACG
129 AAACAAGCGATGCGGTCATCTTCCTGATAAGATACTAAGAAGAAGACCAAATCAAACCCACG
13819 CTCAAAGCGT
Statistics
Matches: 175, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
195 46 0.26
196 129 0.74
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (195 bp):
TCTTCGAACCCCAGCTTCCTAATGAGACACGAAGAAGCAGGGTGAAGCAATAAAAGGTTAGCTTC
CTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGAATTGAA
ACAAGCGATGCGGTCATCTTCCTGATAAGATACTAAGAAGAAGACCAAATCAAACCCACGTTCGA
Found at i:15428 original size:30 final size:29
Alignment explanation
Indices: 15365--15598 Score: 274
Period size: 29 Copynumber: 8.0 Consensus size: 29
15355 GTCCCTAAAC
*
15365 CTTCCAAAAATTCTATTTTTACCCCCGAA
1 CTTCCAAAAATTCTATTTTTACCCCCAAA
* *
15394 CTTCCAAAAA-TCTCATTTTTGACCTCAAAA
1 CTTCCAAAAATTCT-ATTTTT-ACCCCCAAA
*
15424 CTTCCAAAAATTCTATTTTTACCCTCAAA
1 CTTCCAAAAATTCTATTTTTACCCCCAAA
***
15453 CTTCCAAAAA-TCTCATTTTTAACCTGGAAA
1 CTTCCAAAAATTCT-ATTTTT-ACCCCCAAA
15483 CTTCCAAAAATTCTATTTTTACCCCCAAA
1 CTTCCAAAAATTCTATTTTTACCCCCAAA
* * *
15512 CTACTAAAAATTCAATTTTTACCCCCAAA
1 CTTCCAAAAATTCTATTTTTACCCCCAAA
* * **
15541 CTTCTAAAAATTCCATTTTTAACCCTAAAA
1 CTTCCAAAAATTCTATTTTT-ACCCCCAAA
*
15571 CTTCCAAAAATTCCATTTTTACCCCCAA
1 CTTCCAAAAATTCTATTTTTACCCCCAA
15599 CGAAACTTCC
Statistics
Matches: 176, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.03
29 94 0.53
30 70 0.40
31 6 0.03
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
CTTCCAAAAATTCTATTTTTACCCCCAAA
Found at i:15457 original size:59 final size:58
Alignment explanation
Indices: 15365--15651 Score: 301
Period size: 59 Copynumber: 4.8 Consensus size: 58
15355 GTCCCTAAAC
* *
15365 CTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCAAAA
1 CTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCTCATTTTT-ACCTCAAAA
**
15424 CTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTAACCTGGAAA
1 CTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCTCATTTTT-ACCTCAAAA
* * * * *
15483 CTTCCAAAAATTCTATTTTTACCCCCAAACTACTAAAAAT-TCAATTTTTACCCCCAAA
1 CTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCTC-ATTTTTACCTCAAAA
* * * *
15541 CTTCTAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAAT-TCCATTTTTACCCCCAACGAAA
1 CTTCCAAAAATTCTATTTTT-ACCCTCAAACTTCCAAAAATCT-CATTTTTA-CCTC-A--AAA
* ** * *
15604 CTTCCAAAAGTTCCGTGTTTACCCTCGAACTTCCAAAAA-CTCCATTTT
1 CTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCT-CATTTT
15652 CGACCTCGAA
Statistics
Matches: 196, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
58 26 0.13
59 121 0.62
60 5 0.03
62 25 0.13
63 19 0.10
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (58 bp):
CTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTACCTCAAAA
Found at i:15710 original size:29 final size:29
Alignment explanation
Indices: 15365--15711 Score: 220
Period size: 29 Copynumber: 11.7 Consensus size: 29
15355 GTCCCTAAAC
* *
15365 CTTCCAAAAATTCTATTTTTACCCCCGAA
1 CTTCTAAAAATTCCATTTTTACCCCCGAA
* * **
15394 CTTCCAAAAA-TCTCATTTTTGACCTCAAAA
1 CTTCTAAAAATTC-CATTTTT-ACCCCCGAA
* * * *
15424 CTTCCAAAAATTCTATTTTTACCCTCAAA
1 CTTCTAAAAATTCCATTTTTACCCCCGAA
* * **
15453 CTTCCAAAAA-TCTCATTTTTAACCTGGAAA
1 CTTCTAAAAATTC-CATTTTTACCCCCG-AA
* * *
15483 CTTCCAAAAATTCTATTTTTACCCCCAAA
1 CTTCTAAAAATTCCATTTTTACCCCCGAA
* * *
15512 CTACTAAAAATTCAATTTTTACCCCCAAA
1 CTTCTAAAAATTCCATTTTTACCCCCGAA
***
15541 CTTCTAAAAATTCCATTTTTAACCCTAAAA
1 CTTCTAAAAATTCCATTTTT-ACCCCCGAA
*
15571 CTTCCAAAAATTCCATTTTTACCCCCAACGAAA
1 CTTCTAAAAATTCCATTTTTA-CCCC--CG-AA
* * * * *
15604 CTTCCAAAAGTTCCGTGTTTACCCTCGAA
1 CTTCTAAAAATTCCATTTTTACCCCCGAA
* * * *
15633 CTTCCAAAAACTCCATTTTCGA-CCTCGAAA
1 CTTCTAAAAATTCCATTTT-TACCCCCG-AA
* *
15663 C-TCTCAAAATTACC-CTTTTACCCCCGAA
1 CTTCTAAAAATT-CCATTTTTACCCCCGAA
15691 -TGTCTAAAAATTCCATTTTTA
1 CT-TCTAAAAATTCCATTTTTA
15712 AACCCTAGAT
Statistics
Matches: 255, Mismatches: 45, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
28 9 0.04
29 139 0.55
30 80 0.31
31 4 0.02
32 3 0.01
33 20 0.08
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
CTTCTAAAAATTCCATTTTTACCCCCGAA
Found at i:17791 original size:17 final size:17
Alignment explanation
Indices: 17755--17794 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17745 AGTTGTCATT
**
17755 GCATTTTACTTGTCTTC
1 GCATTTTACTTGTCAAC
*
17772 GCATTTTATTTGTCAAC
1 GCATTTTACTTGTCAAC
17789 GCATTT
1 GCATTT
17795 ACATTGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.50
Consensus pattern (17 bp):
GCATTTTACTTGTCAAC
Found at i:21099 original size:12 final size:12
Alignment explanation
Indices: 21082--21106 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21072 TCAGAACACT
21082 CCAACCTACGTC
1 CCAACCTACGTC
21094 CCAACCTACGTC
1 CCAACCTACGTC
21106 C
1 C
21107 TCCTACTTTG
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:0.24, C:0.52, G:0.08, T:0.16
Consensus pattern (12 bp):
CCAACCTACGTC
Found at i:21743 original size:7 final size:7
Alignment explanation
Indices: 21731--21768 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
21721 TTATGCTTAA
21731 ATTTATT
1 ATTTATT
21738 ATTTATT
1 ATTTATT
21745 ATTTATT
1 ATTTATT
21752 ATTTATT
1 ATTTATT
*
21759 CTTT-TT
1 ATTTATT
21765 ATTT
1 ATTT
21769 GATTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTATT
Found at i:23446 original size:32 final size:32
Alignment explanation
Indices: 23378--23445 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
23368 CCAACTCAAG
23378 AAAAAGTGTCAAGTTTTAGGTATCAAATTAGA
1 AAAAAGTGTCAAGTTTTAGGTATCAAATTAGA
* *
23410 AAAAAGTGTTAAG-TTTGGGTATCAAATT-GA
1 AAAAAGTGTCAAGTTTTAGGTATCAAATTAGA
23440 ACAAAA
1 A-AAAA
23446 AAAAATTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 3 0.09
31 18 0.55
32 12 0.36
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (32 bp):
AAAAAGTGTCAAGTTTTAGGTATCAAATTAGA
Found at i:26308 original size:15 final size:17
Alignment explanation
Indices: 26270--26310 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
26260 TTATATTAAG
*
26270 TATAAATATGTTTTGTA
1 TATAAATATGATTTGTA
*
26287 TAAAAATATGATTT-TA
1 TATAAATATGATTTGTA
26303 -ATAAATAT
1 TATAAATAT
26311 ATATTATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
TATAAATATGATTTGTA
Found at i:27621 original size:18 final size:18
Alignment explanation
Indices: 27598--27638 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
27588 ATCTCCGATC
* *
27598 GAATTAGATCGATTAATT
1 GAATTAAATCGAGTAATT
27616 GAATTAAATCGAGTAATT
1 GAATTAAATCGAGTAATT
*
27634 CAATT
1 GAATT
27639 TTAATTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (18 bp):
GAATTAAATCGAGTAATT
Found at i:34844 original size:9 final size:9
Alignment explanation
Indices: 34751--34850 Score: 66
Period size: 9 Copynumber: 11.2 Consensus size: 9
34741 TTTTTAGTAA
34751 TTATATATAT
1 TTATATAT-T
34761 TTATATATT
1 TTATATATT
*
34770 TTAAAT-TT
1 TTATATATT
*
34778 TTATAAATT
1 TTATATATT
*
34787 GTATATATT
1 TTATATATT
* * *
34796 TCA-AAATA
1 TTATATATT
34804 TTATA-AGCTTT
1 TTATATA---TT
34815 TTATATATT
1 TTATATATT
34824 TT-TA-ATT
1 TTATATATT
*
34831 GTATATATT
1 TTATATATT
34840 TTATATATT
1 TTATATATT
34849 TT
1 TT
34851 TCAAAATAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
7 4 0.06
8 16 0.23
9 34 0.49
10 8 0.12
11 6 0.09
12 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (9 bp):
TTATATATT
Found at i:35141 original size:30 final size:30
Alignment explanation
Indices: 35075--35152 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
35065 TAATATGCTC
* *
35075 TAATTTCTTATACTTTTTATATATTCGGAATT
1 TAATTT-TTATA-TTTTTATATATTCAGAATA
*
35107 TAATTTTTATATTTTTA-ATTTTCAAGAATA
1 TAATTTTTATATTTTTATATATTC-AGAATA
* *
35137 TAATTATTCTATTTTT
1 TAATTTTTATATTTTT
35153 TAAATTTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.12
30 24 0.60
31 5 0.12
32 6 0.15
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (30 bp):
TAATTTTTATATTTTTATATATTCAGAATA
Found at i:35701 original size:30 final size:29
Alignment explanation
Indices: 35636--35703 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
35626 ATAATATAGT
35636 ATTAAATTGATAAAAGATATATTTTTTAA
1 ATTAAATTGATAAAAGATATATTTTTTAA
* *
35665 AGTTAAATTGATAAGA-ATATAATTTTTTTTA
1 A-TTAAATTGATAAAAGATAT-A-TTTTTTAA
35696 ATTAAATT
1 ATTAAATT
35704 AATTTTCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 5 0.15
30 21 0.62
31 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (29 bp):
ATTAAATTGATAAAAGATATATTTTTTAA
Found at i:35923 original size:176 final size:176
Alignment explanation
Indices: 35625--36160 Score: 936
Period size: 176 Copynumber: 3.1 Consensus size: 176
35615 TAAACATTAG
* * *
35625 CATAATATAGTATTAAATTGAT--AAAAGA-TATATTTTTTAAAGTTAAATTGATAAGAATATAA
1 CATAATTTAGTATTAAATTGATAAAAAAAATTATATTTTTCAAAGTTAAATTGATAAGAATATAA
** *
35687 TTTTTTTTAATTAAATTAATTTTCAAATATATTATTAAATATTAATTTTAAAATATAATAAATTC
66 AATTTCTTAATTAAATTAATTTTCAAATATATTATTAAATATTAATTTTAAAATATAATAAATTC
35752 GTGCATCACAGAAAATAAAATAATAATAAATTATTATTTTTGTGTA
131 GTGCATCACAGAAAATAAAATAATAATAAATTATTATTTTTGTGTA
35798 CATAATTTAGTATTAAATTGATAAAAAAAATTATATTTTTCAAAGTTAAATTGATAAGAATATAA
1 CATAATTTAGTATTAAATTGATAAAAAAAATTATATTTTTCAAAGTTAAATTGATAAGAATATAA
35863 AATTTCTTAATTAAATTAATTTTCAAATATATTATTAAATATTAATTTTAAAATATAATAAATTC
66 AATTTCTTAATTAAATTAATTTTCAAATATATTATTAAATATTAATTTTAAAATATAATAAATTC
35928 GTGCATCACAGAAAATAAAATAATAATAAATTATTATTTTTGTGTA
131 GTGCATCACAGAAAATAAAATAATAATAAATTATTATTTTTGTGTA
*
35974 CATAATTTAGTATTAAATTGATAAAAAAATTTATATTTTTCAAAGTTAAATTGATAAGAATATAA
1 CATAATTTAGTATTAAATTGATAAAAAAAATTATATTTTTCAAAGTTAAATTGATAAGAATATAA
36039 AATTTCTTAATTAAATTAATTTTCAAATATATTATTAAAATATTAATTTTAAAATATAATAAATT
66 AATTTCTTAATTAAATTAATTTTCAAATATATTATT-AAATATTAATTTTAAAATATAATAAATT
* *
36104 CGTGCATCACATAAAATAAAAAAAATAATAAATTATCTATTTTTGTGTA
130 CGTGCATCACAGAAAAT-AAAATAATAATAAATTAT-TATTTTTGTGTA
36153 CAT-ATTTA
1 CATAATTTA
36161 CAAATCATTG
Statistics
Matches: 348, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
173 21 0.06
175 5 0.01
176 241 0.69
177 44 0.13
178 22 0.06
179 15 0.04
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (176 bp):
CATAATTTAGTATTAAATTGATAAAAAAAATTATATTTTTCAAAGTTAAATTGATAAGAATATAA
AATTTCTTAATTAAATTAATTTTCAAATATATTATTAAATATTAATTTTAAAATATAATAAATTC
GTGCATCACAGAAAATAAAATAATAATAAATTATTATTTTTGTGTA
Found at i:36092 original size:14 final size:14
Alignment explanation
Indices: 36053--36095 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
36043 TCTTAATTAA
*
36053 ATTAATTTTCAAAT
1 ATTAATTTTAAAAT
36067 A-T-ATTATTAAAAT
1 ATTAATT-TTAAAAT
36080 ATTAATTTTAAAAT
1 ATTAATTTTAAAAT
36094 AT
1 AT
36096 AATAAATTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 3 0.12
13 8 0.32
14 11 0.44
15 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTAATTTTAAAAT
Found at i:36098 original size:13 final size:13
Alignment explanation
Indices: 36051--36098 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
36041 TTTCTTAATT
*
36051 AAAT-TAATTTTC
1 AAATATAATTTTA
36063 AAATAT-ATTATTA
1 AAATATAATT-TTA
36076 AAATATTAATTTTA
1 AAATA-TAATTTTA
36090 AAATATAAT
1 AAATATAAT
36099 AAATTCGTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.23
13 12 0.39
14 9 0.29
15 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATATAATTTTA
Found at i:36673 original size:12 final size:12
Alignment explanation
Indices: 36656--36695 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
36646 ATAACACCCA
36656 AACAACAAAAAT
1 AACAACAAAAAT
*
36668 AACAACCAAAAT
1 AACAACAAAAAT
* *
36680 AGCAGCAAAAAT
1 AACAACAAAAAT
36692 AACA
1 AACA
36696 TGAAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:36742 original size:28 final size:27
Alignment explanation
Indices: 36698--36750 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
36688 AAATAACATG
*
36698 AAACAACATTAAAAACAACAAAAATAGC
1 AAACAACATAAAAAAC-ACAAAAATAGC
*
36726 AAACAACA-AAAACAACACGAAAATA
1 AAACAACATAAAA-AACACAAAAATA
36751 ACAACGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.70, C:0.19, G:0.04, T:0.08
Consensus pattern (27 bp):
AAACAACATAAAAAACACAAAAATAGC
Found at i:36798 original size:24 final size:23
Alignment explanation
Indices: 36765--36810 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
36755 CGAAAACAGT
36765 AAAAAAAGCACCAAAACAATAAA
1 AAAAAAAGCACCAAAACAATAAA
36788 AAAAAATAGCACCAAAACAATAA
1 AAAAAA-AGCACCAAAACAATAA
36811 TATAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.72, C:0.17, G:0.04, T:0.07
Consensus pattern (23 bp):
AAAAAAAGCACCAAAACAATAAA
Found at i:38682 original size:20 final size:19
Alignment explanation
Indices: 38647--38695 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
38637 GGTTACTTTA
* *
38647 AATATTTACTTAATATTCC
1 AATATATACATAATATTCC
38666 AATAGTATACATAATATTCC
1 AATA-TATACATAATATTCC
38686 AATATATACA
1 AATATATACA
38696 AACCTGAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (19 bp):
AATATATACATAATATTCC
Found at i:41343 original size:97 final size:97
Alignment explanation
Indices: 41172--41362 Score: 301
Period size: 97 Copynumber: 2.0 Consensus size: 97
41162 GTCTACTGCA
** * * * *
41172 ACACTTTTTTTGACTTAAGATGACGCAAAAAAAGTTGGCATAGGTATTGCGACGCTTCTCCCGAT
1 ACACTTTTTTTGACTTAAGACAACACAAAAAAAGTTGACATAGGTATTGCGACACTTCTCCCGAC
* *
41237 GGTTTCAAAAAGGTTGTCTTTAGTACAGTGTG
66 GCTTCCAAAAAGGTTGTCTTTAGTACAGTGTG
*
41269 ACACTTTTTTTGACTTAAGACAACACAAAAAAGGTTGACATAGGTATTGCGACACTTCTCCCGAC
1 ACACTTTTTTTGACTTAAGACAACACAAAAAAAGTTGACATAGGTATTGCGACACTTCTCCCGAC
41334 GCTTCCAAAAAGGTTGTCTTTAGTACAGT
66 GCTTCCAAAAAGGTTGTCTTTAGTACAGT
41363 TGGCGTAGGT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 85 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (97 bp):
ACACTTTTTTTGACTTAAGACAACACAAAAAAAGTTGACATAGGTATTGCGACACTTCTCCCGAC
GCTTCCAAAAAGGTTGTCTTTAGTACAGTGTG
Found at i:41528 original size:38 final size:39
Alignment explanation
Indices: 41461--41538 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
41451 AATGTCGACC
* * * *
41461 TTTAAAAAAGGTTGGGATAGGTCTTGTCTAAAGCAACCT
1 TTTAAAAAAAGTTGGAATAGATCTCGTCTAAAGCAACCT
*
41500 TTTAAAAAAAGTTGGAATAGATC-CGTCTAAGGCAACCT
1 TTTAAAAAAAGTTGGAATAGATCTCGTCTAAAGCAACCT
41538 T
1 T
41539 AAAAAGATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 14 0.41
39 20 0.59
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (39 bp):
TTTAAAAAAAGTTGGAATAGATCTCGTCTAAAGCAACCT
Found at i:41651 original size:38 final size:37
Alignment explanation
Indices: 41599--41756 Score: 119
Period size: 38 Copynumber: 4.2 Consensus size: 37
41589 AAGTAACCTT
* * **
41599 AAAAAAGTTAAGATATACATTGTTTAAGGCAACCTTTA
1 AAAAAAGTTAAGATAAACA-TGTCTAAAACAACCTTTA
*
41637 AAAAAAGTTGAGATAAACATGTCTAAAACAACCTTT-
1 AAAAAAGTTAAGATAAACATGTCTAAAACAACCTTTA
* ** *
41673 GAAAAA-TTGGGATAAATCTTGTCTAATAA-AACCTTTTA
1 AAAAAAGTTAAGATAAA-CATGTCTAA-AACAACC-TTTA
* * *
41711 AAAAAA-TTAAAATAAACCTTGTC-AAAGACAACCTTTT
1 AAAAAAGTTAAGATAAA-CATGTCTAAA-ACAACCTTTA
41748 AAAAAAGTT
1 AAAAAAGTT
41757 GGAATAAATT
Statistics
Matches: 99, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
35 9 0.09
36 18 0.18
37 31 0.31
38 41 0.41
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (37 bp):
AAAAAAGTTAAGATAAACATGTCTAAAACAACCTTTA
Found at i:41763 original size:38 final size:36
Alignment explanation
Indices: 41628--41764 Score: 120
Period size: 38 Copynumber: 3.7 Consensus size: 36
41618 TTGTTTAAGG
* *
41628 CAACCTTTAAAAAAAGTT-GAGATAAACATGTCTAAAA
1 CAACCTTTTAAAAAAGTTGGA-ATAAACTTGTC-AAAA
* *
41665 CAACC-TTTGAAAAA-TTGGGATAAATCTTGTCTAATAA
1 CAACCTTTTAAAAAAGTTGGAATAAA-CTTGTC-AA-AA
* **
41702 -AACCTTTTAAAAAAATTAAAATAAACCTTGTCAAAGA
1 CAACCTTTTAAAAAAGTTGGAATAAA-CTTGTCAAA-A
41739 CAACCTTTTAAAAAAGTTGGAATAAA
1 CAACCTTTTAAAAAAGTTGGAATAAA
41765 TTCTTTTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
35 7 0.09
36 21 0.26
37 18 0.22
38 35 0.43
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (36 bp):
CAACCTTTTAAAAAAGTTGGAATAAACTTGTCAAAA
Found at i:41920 original size:18 final size:18
Alignment explanation
Indices: 41897--41933 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
41887 TAAATACAAC
41897 TAAAAATATAAAATTAAAT
1 TAAAAATA-AAAATTAAAT
41916 TAAAAATAAAAATTAAAT
1 TAAAAATAAAAATTAAAT
41934 ATTCACTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATAAAAATTAAAT
Done.