Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2064
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: 44040
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:5779 original size:47 final size:47
Alignment explanation
Indices: 5721--5843 Score: 210
Period size: 47 Copynumber: 2.6 Consensus size: 47
5711 CGGTTTTGCT
* * *
5721 TGGTTGTTGCTTCGATTGTTGATGCTGCTGGTGTTGGTTTCGAGTGC
1 TGGTTGCTGCTTTGATTGTTGCTGCTGCTGGTGTTGGTTTCGAGTGC
*
5768 TGGTTGCTGCTTTGATTGTTGCTGCTGCTGGTGTTGGTTTCGAGTGT
1 TGGTTGCTGCTTTGATTGTTGCTGCTGCTGGTGTTGGTTTCGAGTGC
5815 TGGTTGCTGCTTTGATTGTTGCTGCTGCT
1 TGGTTGCTGCTTTGATTGTTGCTGCTGCT
5844 CCTCCTTTCT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.05, C:0.14, G:0.35, T:0.46
Consensus pattern (47 bp):
TGGTTGCTGCTTTGATTGTTGCTGCTGCTGGTGTTGGTTTCGAGTGC
Found at i:6026 original size:17 final size:18
Alignment explanation
Indices: 5993--6033 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
5983 TTTCAGCTTG
*
5993 TTGCTTTGCTGTTCCACT
1 TTGCTTTGCTCTTCCACT
6011 TTGCTTTG-TCTTCCACT
1 TTGCTTTGCTCTTCCACT
6028 TT-CTTT
1 TTGCTTT
6034 ATTGTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 8 0.36
ACGTcount: A:0.05, C:0.27, G:0.12, T:0.56
Consensus pattern (18 bp):
TTGCTTTGCTCTTCCACT
Found at i:6040 original size:45 final size:45
Alignment explanation
Indices: 5990--6203 Score: 338
Period size: 45 Copynumber: 4.8 Consensus size: 45
5980 ATTTTTCAGC
*
5990 TTGTTGCTTTGCTGTTCCACTTTGCTTTGTCTTCCACTTTCTTTA
1 TTGTTGCTTTGCTGTTCCACGTTGCTTTGTCTTCCACTTTCTTTA
* *
6035 TTGTTGCTTTGTTATTCCACGTTGCTTTGTCTTCCACTTTCTTTA
1 TTGTTGCTTTGCTGTTCCACGTTGCTTTGTCTTCCACTTTCTTTA
* * *
6080 TTGTTGCTTTGTTATTCCACGTTGCTTTGTCTTCCACTTTCTTTC
1 TTGTTGCTTTGCTGTTCCACGTTGCTTTGTCTTCCACTTTCTTTA
* * *
6125 TTGTTACTTTGCTGTTCCACGTTGCTTTATCTTCTACTTTCTTTA
1 TTGTTGCTTTGCTGTTCCACGTTGCTTTGTCTTCCACTTTCTTTA
*
6170 TTATTGCTTTGCTGTTCCACGTTGCTTTGTCTTC
1 TTGTTGCTTTGCTGTTCCACGTTGCTTTGTCTTC
6204 ATCATTGCTG
Statistics
Matches: 156, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 156 1.00
ACGTcount: A:0.08, C:0.23, G:0.14, T:0.55
Consensus pattern (45 bp):
TTGTTGCTTTGCTGTTCCACGTTGCTTTGTCTTCCACTTTCTTTA
Found at i:6071 original size:17 final size:17
Alignment explanation
Indices: 6037--6116 Score: 66
Period size: 18 Copynumber: 5.0 Consensus size: 17
6027 TTTCTTTATT
6037 GTTGCTTTGTTATTCCAC
1 GTTGCTTTG-TATTCCAC
*
6055 GTTGCTTTGTCTTCCAC
1 GTTGCTTTGTATTCCAC
*
6072 -TTTC-TT-TATT----
1 GTTGCTTTGTATTCCAC
6082 GTTGCTTTGTTATTCCAC
1 GTTGCTTTG-TATTCCAC
*
6100 GTTGCTTTGTCTTCCAC
1 GTTGCTTTGTATTCCAC
6117 TTTCTTTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
11 3 0.06
12 2 0.04
14 7 0.14
15 2 0.04
16 3 0.06
17 14 0.29
18 18 0.37
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.53
Consensus pattern (17 bp):
GTTGCTTTGTATTCCAC
Found at i:6376 original size:16 final size:17
Alignment explanation
Indices: 6346--6379 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6336 GTGCTGCACG
6346 TTATCTATTTATTTTAT
1 TTATCTATTTATTTTAT
*
6363 TTAT-TATTTTTTTTAT
1 TTATCTATTTATTTTAT
6379 T
1 T
6380 CCAGTACTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATCTATTTATTTTAT
Found at i:7003 original size:17 final size:17
Alignment explanation
Indices: 6952--6993 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
6942 GAAATGCATT
6952 TATGCATGAAATGAACA
1 TATGCATGAAATGAACA
6969 TATGCATGAAATGAACA
1 TATGCATGAAATGAACA
6986 TATGCATG
1 TATGCATG
6994 CATGAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (17 bp):
TATGCATGAAATGAACA
Found at i:7111 original size:15 final size:14
Alignment explanation
Indices: 7091--7142 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 14
7081 ACGTTTTCTC
*
7091 TTTTTTTTCTTTGA
1 TTTTTTTTTTTTGA
7105 TTTTTTTTGTTTTGA
1 TTTTTTTT-TTTTGA
*
7120 TTTCTTTGATTTTTGA
1 TTT-TTT-TTTTTTGA
7136 TTTTTTT
1 TTTTTTT
7143 AAATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
16 12 0.38
17 1 0.03
ACGTcount: A:0.08, C:0.04, G:0.10, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTTTGA
Found at i:7141 original size:24 final size:24
Alignment explanation
Indices: 7096--7142 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
7086 TTCTCTTTTT
*
7096 TTTCTTTGATTTTTTTTGTTTTGA
1 TTTCTTTGATTTTTATTGTTTTGA
*
7120 TTTCTTTGATTTTTGATTTTTTT
1 TTTCTTTGATTTTT-ATTGTTTT
7143 AAATTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.09, C:0.04, G:0.11, T:0.77
Consensus pattern (24 bp):
TTTCTTTGATTTTTATTGTTTTGA
Found at i:10441 original size:481 final size:481
Alignment explanation
Indices: 9340--10785 Score: 2525
Period size: 482 Copynumber: 3.0 Consensus size: 481
9330 AAAAACTCAC
*
9340 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATTTAACAAGTTGTTTAGTCTATTAGGA
1 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
9405 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
66 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
9470 CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
131 CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
*
9535 AAGTAAAAGAGCACATTTTACTGCCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCTA
196 AAGTAAAAGAGCACATTTTACTACCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCT-
9600 CTTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCT
260 CTTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCT
*
9665 ACCATTTGTCATACAAAAATAACATGACCAATTTAGATATATTTAAAATACTTATTTTATAAAAA
325 ACCATTTGTCATACAAAAATAACATGACCAATTTAGTTATATTTAAAATACTTATTTTATAAAAA
*
9730 TAAGTTAATTAGTACATAGTATAGAATATATTAGTCAGTGTATAATATATATTTATATACAATAA
390 TAAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGTGTATAATATATATTTATATACAATAA
9795 AAATATCAAAAACAAGATTTATCAAAA
455 AAATATCAAAAACAAGATTTATCAAAA
9822 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
1 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
9887 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
66 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
* * *
9952 CCGTTTCTCATTCCATAAGAACTAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
131 CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
* * *
10017 AAATAAAAAAGCACATTTTACTACCATTTTTTTAAATTCACACCACTGAGTTTCTCAGATCTCTC
196 AAGTAAAAGAGCACATTTTACTACCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCTC
*
10082 TTCATGCATCGCATATGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCTA
261 TTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCTA
* *
10147 CCATTTGTCATACAAAGATAACATGACCAATTTAGTTATATTTAAAATACTTATTTTATAGAAAT
326 CCATTTGTCATACAAAAATAACATGACCAATTTAGTTATATTTAAAATACTTATTTTATAAAAAT
10212 AAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGGTGTATAATATATATTTATATACAATAA
391 AAGTTAATTAGTACATAGTTTAGAATATATTAGTCA-GTGTATAATATATATTTATATACAATAA
10277 AAATATCAAAAACAAGATTTATCAAAA
455 AAATATCAAAAACAAGATTTATCAAAA
*
10304 ACAACTCTCTTACTATCTTATTCAAACTATACAGGTTATATAACAAGTTGTTTAGTCTATT-GGA
1 ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
10368 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
66 ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
*
10433 CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCTATAAAAACTTGGCCAAATTCAATGTAGTC
131 CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
*
10498 TAAGTAAAAGAGCACATTTTACTATCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCT
196 -AAGTAAAAGAGCACATTTTACTACCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCT
* * * * *
10563 CTTCATGCATCGCATGTGGAAGTAACCATGCAATAAACACACTAATATAATTAATTCTCGATTCT
260 CTTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCT
* * *** * **
10628 ATCATTTGTCATACAAATATAATGCGATCAATTTAGTTACGTTTAAAATACTTATTTTATAAAAA
325 ACCATTTGTCATACAAAAATAACATGACCAATTTAGTTATATTTAAAATACTTATTTTATAAAAA
* * * * * *
10693 TAAGTTAACTAGCACACAATTTAAAATATATTAGTCAGTGTATAATATATATTTATATATAATAA
390 TAAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGTGTATAATATATATTTATATACAATAA
* *
10758 AAATATCAAAATCAAGATTTATTAAAA
455 AAATATCAAAAACAAGATTTATCAAAA
10785 A
1 A
10786 GTATTGTTCC
Statistics
Matches: 917, Mismatches: 45, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
481 344 0.38
482 573 0.62
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (481 bp):
ACAACTCTCTTACTATCTTATTCAAACTATACATGTTATATAACAAGTTGTTTAGTCTATTAGGA
ATGTAATTTTTGGATAGGAAGTCAAAGTACTTCCAAGCTTTTATCCGAAGCCATAATAGTAGCAT
CTGTTTCTCATTCCCTAAGAACCAAAGCTTCTTCCGATAAAAACTTGGCCAAATTCAATGTAGTC
AAGTAAAAGAGCACATTTTACTACCATTTTTTTAAATTCACACCACTGAATTTCTCAGATCTCTC
TTCATGCATCGCATGTGGAGGTAACTACGCAATAAACACACTAGTATAACTAATTCTCGATTCTA
CCATTTGTCATACAAAAATAACATGACCAATTTAGTTATATTTAAAATACTTATTTTATAAAAAT
AAGTTAATTAGTACATAGTTTAGAATATATTAGTCAGTGTATAATATATATTTATATACAATAAA
AATATCAAAAACAAGATTTATCAAAA
Found at i:11342 original size:2 final size:2
Alignment explanation
Indices: 11335--11369 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11325 CACATTAACA
*
11335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11370 AACAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17204 original size:28 final size:28
Alignment explanation
Indices: 17164--17224 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
17154 AAAGGTCAAC
17164 AAATGAAATCTATCTTTGACGATGAGTT
1 AAATGAAATCTATCTTTGACGATGAGTT
17192 AAATGAAATCTATCTTTGACGATGAGTT
1 AAATGAAATCTATCTTTGACGATGAGTT
17220 AAATG
1 AAATG
17225 TATCTCAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (28 bp):
AAATGAAATCTATCTTTGACGATGAGTT
Found at i:22302 original size:5 final size:5
Alignment explanation
Indices: 22248--22329 Score: 52
Period size: 5 Copynumber: 17.6 Consensus size: 5
22238 AATTTTAAAA
* * * *
22248 ATAAT AAAAT ATAAA AT-AT A-AAT AT-AT -TAAT TTAAT A-AAT ATAAAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT
* *
22294 ATAAT ATAAT ATAAT -TAAA ATAAT -TAAT ATGAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
22330 TACAACACAT
Statistics
Matches: 58, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
3 1 0.02
4 20 0.34
5 33 0.57
6 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:22323 original size:34 final size:32
Alignment explanation
Indices: 22245--22323 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 32
22235 GATAATTTTA
*
22245 AAAATAA-TAAAATATAAAATATAAATATATT
1 AAAATAATTAATATATAAAATATAAATATATT
** *
22276 AATTTAATAAATATA-AAAATAATATAATATAATT
1 AAAATAATTAATATATAAAAT-ATA-AATAT-ATT
22310 AAAATAATTAATAT
1 AAAATAATTAATAT
22324 GATATATACA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
31 10 0.27
32 8 0.22
33 5 0.14
34 14 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAATAATTAATATATAAAATATAAATATATT
Found at i:22622 original size:12 final size:13
Alignment explanation
Indices: 22604--22633 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
22594 TTCTTTGGTT
22604 TATTAATTAATTA
1 TATTAATTAATTA
22617 -ATTAATTAATTA
1 TATTAATTAATTA
22629 TATTA
1 TATTA
22634 GATAAGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTAATTAATTA
Found at i:22920 original size:52 final size:55
Alignment explanation
Indices: 22826--22956 Score: 137
Period size: 53 Copynumber: 2.4 Consensus size: 55
22816 TTAATTTTGA
* *
22826 TAAAATTAAAAATAATAATAATAGTATATCAATAAGATTAAATAT-T-ATAATAG
1 TAAAATTAAAATTAATAACAATAGTATATCAATAAGATTAAATATATGATAATAG
** *
22879 TAAAATTAAAATTAATAACAATA-TATAT-TTTTAGATTTAAATATAATGATAATAG
1 TAAAATTAAAATTAATAACAATAGTATATCAATAAGA-TTAAATAT-ATGATAATAG
* *
22934 T-AAAGTAAATTATAATAACAATA
1 TAAAATTAAAAT-TAATAACAATA
22957 AAAAATAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
51 4 0.06
52 13 0.20
53 21 0.32
54 9 0.14
55 19 0.29
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (55 bp):
TAAAATTAAAATTAATAACAATAGTATATCAATAAGATTAAATATATGATAATAG
Found at i:31300 original size:19 final size:19
Alignment explanation
Indices: 31237--31310 Score: 76
Period size: 19 Copynumber: 3.6 Consensus size: 19
31227 TGTAAGGTTT
31237 TGGTTTTATACTATATGGA
1 TGGTTTTATACTATATGGA
**
31256 TGGTTGTCATTGATTTTATAATGGA
1 TGG-T-T--TT-ATACTAT-ATGGA
31281 TGGTTTTATACTATATGGA
1 TGGTTTTATACTATATGGA
31300 TGGTTTTATAC
1 TGGTTTTATAC
31311 AAATAAATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
19 19 0.42
20 6 0.13
21 3 0.07
23 3 0.07
24 6 0.13
25 8 0.18
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (19 bp):
TGGTTTTATACTATATGGA
Found at i:32880 original size:12 final size:12
Alignment explanation
Indices: 32858--32891 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
32848 GAAGATGAAG
32858 AAGAAAGAAAAAA
1 AAGAAA-AAAAAA
32871 AAGAAAAAAAAA
1 AAGAAAAAAAAA
*
32883 GAGAAAAAA
1 AAGAAAAAA
32892 TATGAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:40429 original size:17 final size:17
Alignment explanation
Indices: 40407--40452 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
40397 AAGAAGATAC
*
40407 AAATATGATATAT-TAAT
1 AAATAT-ATAAATATAAT
40424 AAATATATAAATATAAT
1 AAATATATAAATATAAT
*
40441 AAATAAATAAAT
1 AAATATATAAAT
40453 TTTAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AAATATATAAATATAAT
Found at i:40489 original size:20 final size:20
Alignment explanation
Indices: 40419--40490 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 20
40409 ATATGATATA
40419 TTAATA-AA-TATATAAA-T
1 TTAATATAATTATATAAATT
* *
40436 ATAATA-AA-TAAATAAATT
1 TTAATATAATTATATAAATT
40454 TTAATATAATTATATAATATT
1 TTAATATAATTATATAA-ATT
40475 TTATATATAATTATAT
1 TTA-ATATAATTATAT
40491 TCATATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
17 14 0.30
18 6 0.13
19 2 0.04
20 6 0.13
21 6 0.13
22 12 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATATAATTATATAAATT
Found at i:40499 original size:22 final size:22
Alignment explanation
Indices: 40453--40524 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
40443 ATAAATAAAT
40453 TTTA-ATATAATTATA-TAATA
1 TTTATATATAATTATATTAATA
*
40473 TTTTATATATAATTATATTCATA
1 -TTTATATATAATTATATTAATA
* *
40496 TTTAATAATTTAATTA-ATTTATA
1 TTT-AT-ATATAATTATATTAATA
40519 TTTATA
1 TTTATA
40525 AAATTACTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
21 5 0.11
22 16 0.36
23 15 0.34
24 8 0.18
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATATATAATTATATTAATA
Found at i:40529 original size:24 final size:24
Alignment explanation
Indices: 40482--40529 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40472 ATTTTATATA
*
40482 TAATTATATTCATATTTAATAATT
1 TAATTATATTCATATTTAAAAATT
*
40506 TAATTA-ATTTATATTTATAAAATT
1 TAATTATATTCATATTTA-AAAATT
40530 ACTATAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TAATTATATTCATATTTAAAAATT
Found at i:42672 original size:21 final size:20
Alignment explanation
Indices: 42643--42701 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
42633 ATTTTAAATC
*
42643 AATTTAATATTAAAAATATTT
1 AATTAAATATT-AAAATATTT
42664 AATTAAATAATTAAAATA-TT
1 AATTAAAT-ATTAAAATATTT
*
42684 -ATTAAAAATTTAAAATAT
1 AATTAAATA-TTAAAATAT
42702 ATAAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 14 0.42
20 2 0.06
21 13 0.39
22 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTAAATATTAAAATATTT
Found at i:42689 original size:19 final size:20
Alignment explanation
Indices: 42655--42709 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
42645 TTTAATATTA
42655 AAAATATTTAATTAAATAA-TT
1 AAAATA-TT-ATTAAATAATTT
42676 AAAATATTATTAAA-AATTT
1 AAAATATTATTAAATAATTT
42695 AAAATA-TA-TAAATAA
1 AAAATATTATTAAATAA
42710 AAATATTACG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.12
18 6 0.19
19 14 0.44
20 2 0.06
21 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATATTATTAAATAATTT
Found at i:42703 original size:21 final size:21
Alignment explanation
Indices: 42655--42713 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
42645 TTTAATATTA
42655 AAAATAT-TTAATTAAATAA-TT
1 AAAATATATT-ATTAAA-AATTT
42676 -AAA-ATATTATTAAAAATTT
1 AAAATATATTATTAAAAATTT
* *
42695 AAAATATATAAATAAAAAT
1 AAAATATATTATTAAAAAT
42714 ATTACGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 10 0.31
20 8 0.25
21 12 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATATATTATTAAAAATTT
Found at i:42713 original size:33 final size:33
Alignment explanation
Indices: 42650--42717 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
42640 ATCAATTTAA
* * *
42650 TATTAAAAATATTTAATTAAATAATTAAAATAT
1 TATTAAAAATATTAAAATAAATAATAAAAATAT
*
42683 TATTAAAAAT-TTAAAATATATAAATAAAAATAT
1 TATTAAAAATATTAAAATAAAT-AATAAAAATAT
42716 TA
1 TA
42718 CGTATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
TATTAAAAATATTAAAATAAATAATAAAAATAT
Found at i:43066 original size:13 final size:13
Alignment explanation
Indices: 43048--43072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43038 CAAGTAAATT
43048 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
43061 AAAAAAAAAGAA
1 AAAAAAAAAGAA
43073 AGCATTTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:43133 original size:18 final size:17
Alignment explanation
Indices: 43101--43134 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43091 GCGAGCTTGT
*
43101 GTAATTATGAAGCGTAC
1 GTAATTATCAAGCGTAC
43118 GTAATTATACAAGCGTA
1 GTAATTAT-CAAGCGTA
43135 AAGAAAGCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (17 bp):
GTAATTATCAAGCGTAC
Done.