Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold604
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: 18044
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Found at i:3336 original size:28 final size:29
Alignment explanation
Indices: 3293--3358 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
3283 TTGTAGGCTT
* *
3293 TTTGAAAAGATTCCACTGACTTAT-AGGC
1 TTTGAAAAGATGCCACTGACTTATGAAGC
* *
3321 TTTGAAAAGCTGCCACTGACTTGTGAAGC
1 TTTGAAAAGATGCCACTGACTTATGAAGC
3350 TTTGAAAAG
1 TTTGAAAAG
3359 GGTTTGCCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (29 bp):
TTTGAAAAGATGCCACTGACTTATGAAGC
Found at i:3387 original size:31 final size:30
Alignment explanation
Indices: 3293--3409 Score: 111
Period size: 31 Copynumber: 4.0 Consensus size: 30
3283 TTGTAGGCTT
*
3293 TTTGAAAA-GA-TT-CCACTGACTTATAGGC
1 TTTGAAAAGGATTTGCCACTGACTTGT-GGC
*
3321 TTTGAAAA-G--CTGCCACTGACTTGTGAAGC
1 TTTGAAAAGGATTTGCCACTGACTTGTG--GC
* *
3350 TTTGAAAAGGGTTTGCCACTTACTTGTGGTC
1 TTTGAAAAGGATTTGCCACTGACTTGTGG-C
*
3381 TTTGAAAATGATTTGCCACTGACTTGTGG
1 TTTGAAAAGGATTTGCCACTGACTTGTGG
3410 GTGCTTGAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
27 2 0.03
28 20 0.27
29 10 0.13
30 2 0.03
31 27 0.36
32 14 0.19
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (30 bp):
TTTGAAAAGGATTTGCCACTGACTTGTGGC
Found at i:3532 original size:28 final size:28
Alignment explanation
Indices: 3498--3579 Score: 112
Period size: 28 Copynumber: 3.0 Consensus size: 28
3488 CTAAAACCTA
*
3498 TGGGCTTTGAAGATATGCCACTAACTTC
1 TGGGCTTTGAAGAGATGCCACTAACTTC
* *
3526 TGGGCTTTGAA-AGATGCCACTGACTTG
1 TGGGCTTTGAAGAGATGCCACTAACTTC
* *
3553 TGGGCTGTGAAGAGGTGCCACTAACTT
1 TGGGCTTTGAAGAGATGCCACTAACTT
3580 GTTGGACCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 23 0.49
28 24 0.51
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (28 bp):
TGGGCTTTGAAGAGATGCCACTAACTTC
Found at i:3580 original size:28 final size:28
Alignment explanation
Indices: 3498--3703 Score: 135
Period size: 30 Copynumber: 7.4 Consensus size: 28
3488 CTAAAACCTA
** *
3498 TGGGCTTTGAAGATATGCCACTAACTTC
1 TGGGCTTTGAAGAGGTGCCACTAACTTG
* *
3526 TGGGCTTTGAA-AGATGCCACTGACTTG
1 TGGGCTTTGAAGAGGTGCCACTAACTTG
*
3553 TGGGCTGTGAAGAGGTGCCACTAACTTG
1 TGGGCTTTGAAGAGGTGCCACTAACTTG
*
3581 TTGGACCTTTGAA-AGGATG-CATCTATACTTG
1 -TGG-GCTTTGAAGAGG-TGCCA-CTA-ACTTG
* *
3612 TGGGCTCTGAAGAGGT-TC-C--AC-TG
1 TGGGCTTTGAAGAGGTGCCACTAACTTG
* *
3635 CGGGCTTTGAA-AGGATGCCACTGACTATTG
1 TGGGCTTTGAAGAGG-TGCCACTAAC--TTG
*
3665 TGGGCTTTGAAG-GATTGCCACTAACTTTG
1 TGGGCTTTGAAGAG-GTGCCACTAAC-TTG
*
3694 TGGACTTTGA
1 TGGGCTTTGA
3704 CAGGCATGCC
Statistics
Matches: 142, Mismatches: 18, Indels: 35
0.73 0.09 0.18
Matches are distributed among these distances:
22 3 0.02
23 12 0.08
24 3 0.02
25 1 0.01
27 26 0.18
28 25 0.18
29 28 0.20
30 39 0.27
31 5 0.04
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (28 bp):
TGGGCTTTGAAGAGGTGCCACTAACTTG
Found at i:3623 original size:59 final size:55
Alignment explanation
Indices: 3498--3691 Score: 150
Period size: 55 Copynumber: 3.5 Consensus size: 55
3488 CTAAAACCTA
* ** *
3498 TGGGCTTTGAAGATATGCCACTAACTTCTGGGCTTTGAAAGATGCCACTGACTTG
1 TGGGCTCTGAAGAGGTGCCACTAACTTCTGGCCTTTGAAAGATGCCACTGACTTG
* * *
3553 TGGGCTGTGAAGAGGTGCCACTAACTTGTTGGACCTTTGAAAGGATG-CATCTATACTTG
1 TGGGCTCTGAAGAGGTGCCACTAACTT-CTGG-CCTTTGAAA-GATGCCA-CT-GACTTG
* * *
3612 TGGGCTCTGAAGAGGT-TC-C--ACTGC-GGGCTTTGAAAGGATGCCACTGACTATTG
1 TGGGCTCTGAAGAGGTGCCACTAACTTCTGGCCTTTGAAA-GATGCCACTGAC--TTG
* *
3665 TGGGCTTTGAAG-GATTGCCACTAACTT
1 TGGGCTCTGAAGAG-GTGCCACTAACTT
3692 TGTGGACTTT
Statistics
Matches: 110, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
51 2 0.02
52 16 0.15
53 19 0.17
54 1 0.01
55 28 0.25
56 3 0.03
57 14 0.13
58 7 0.06
59 20 0.18
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (55 bp):
TGGGCTCTGAAGAGGTGCCACTAACTTCTGGCCTTTGAAAGATGCCACTGACTTG
Found at i:3672 original size:30 final size:29
Alignment explanation
Indices: 3293--3718 Score: 128
Period size: 30 Copynumber: 14.7 Consensus size: 29
3283 TTGTAGGCTT
* * * *
3293 TTTGAAAAGATTCCACTGAC-TTATAGGC
1 TTTGAAAGGATGCCACTGACTTTGTGGGC
* * *
3321 TTTGAAAAGCTGCCACTGAC-TTGTGAAGC
1 TTTGAAAGGATGCCACTGACTTTGTG-GGC
* * *
3350 TTTGAAAAGGGTTTGCCACTTAC-TTGTGGTC
1 TTTG-AAA-GG-ATGCCACTGACTTTGTGGGC
*
3381 TTTGAAAATGATTTGCCACTGAC-TTGTGGG-
1 TTTG-AAAGGA--TGCCACTGACTTTGTGGGC
* * * *
3411 TGCTTGAAAAGATGCCAATAAACCTTGTGGGC
1 T--TTGAAAGGATGCCACT-GACTTTGTGGGC
* * *
3443 TTTGAACGGATGCCACTGGAC-CT-TGGGA
1 TTTGAAAGGATGCCACT-GACTTTGTGGGC
* * * * * *
3471 TGTGAAGATGATTACCACTAAAAC-CTATGGGC
1 TTTGAA-AGGA-TGCCACT--GACTTTGTGGGC
* * *
3503 TTTG-AAGATATGCCACTAAC-TTCTGGGC
1 TTTGAAAG-GATGCCACTGACTTTGTGGGC
3531 TTTGAAA-GATGCCACTGAC-TTGTGGGC
1 TTTGAAAGGATGCCACTGACTTTGTGGGC
* * *
3558 TGTGAAGAGG-TGCCACTAAC-TTGTTGGACC
1 TTTGAA-AGGATGCCACTGACTTTG-TGG-GC
*
3588 TTTGAAAGGATG-CATCTATAC-TTGTGGGC
1 TTTGAAAGGATGCCA-CT-GACTTTGTGGGC
* *
3617 TCTGAAGAGG-TTCCACTG-C-----GGGC
1 TTTGAA-AGGATGCCACTGACTTTGTGGGC
3640 TTTGAAAGGATGCCACTGACTATTGTGGGC
1 TTTGAAAGGATGCCACTGACT-TTGTGGGC
* *
3670 TTTG-AAGGATTGCCACTAACTTTGTGGAC
1 TTTGAAAGGA-TGCCACTGACTTTGTGGGC
*
3699 TTTGACAGGCATGCCA-TGAC
1 TTTGAAAGG-ATGCCACTGAC
3719 CTATGGCTTT
Statistics
Matches: 306, Mismatches: 55, Indels: 73
0.71 0.13 0.17
Matches are distributed among these distances:
22 3 0.01
23 16 0.05
24 1 0.00
27 23 0.08
28 56 0.18
29 54 0.18
30 79 0.26
31 49 0.16
32 25 0.08
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (29 bp):
TTTGAAAGGATGCCACTGACTTTGTGGGC
Found at i:3686 original size:53 final size:52
Alignment explanation
Indices: 3587--3686 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 52
3577 CTTGTTGGAC
*
3587 CTTTGAAAGGATGCATCTATACTTGTGGGCTCTGAAGAGGTTCCACTGCGGG
1 CTTTGAAAGGATGCATCTATACTTGTGGGCTCTGAAGAGATTCCACTGCGGG
*
3639 CTTTGAAAGGATGCCA-CTGACTA-TTGTGGGCTTTGAAG-GATTGCCACT
1 CTTTGAAAGGATG-CATCT-A-TACTTGTGGGCTCTGAAGAGATT-CCACT
3687 AACTTTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
52 18 0.43
53 22 0.52
54 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (52 bp):
CTTTGAAAGGATGCATCTATACTTGTGGGCTCTGAAGAGATTCCACTGCGGG
Found at i:13482 original size:51 final size:51
Alignment explanation
Indices: 13360--13495 Score: 150
Period size: 51 Copynumber: 2.6 Consensus size: 51
13350 AAAATTAGTA
* * *
13360 TTTTAGAGATAACAACGGGGCTAGAGTATCCCCGATTATGGAAAAACGGTGC
1 TTTTAGAAATAA-AACGGGGTTAGAGTATCCCCGATTATGGAAAAACGATGC
* * * *
13412 TCTAAAAAATAAAATCGGGGTTAGAGTATCCCCGATTAT-GAAAAATTGATG-
1 TTTTAGAAATAAAA-CGGGGTTAGAGTATCCCCGATTATGGAAAAA-CGATGC
*
13463 TTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 TTTTAGAAATAAAA-CGGGGTTAGAGTATCCCC
13496 TCAGAAATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
51 36 0.51
52 34 0.49
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (51 bp):
TTTTAGAAATAAAACGGGGTTAGAGTATCCCCGATTATGGAAAAACGATGC
Found at i:13558 original size:79 final size:79
Alignment explanation
Indices: 13427--13811 Score: 626
Period size: 79 Copynumber: 4.9 Consensus size: 79
13417 AAAATAAAAT
*
13427 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
13492 CCCCTCAGAAATAA
66 CCCCTCGGAAATAA
* * *
13506 CGGGGTTGGAGTATCCTCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGAGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
13571 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* * * * *
13585 TGGGGTTGGAGTATCCCCGATTGTGGAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
13650 CCCCTCGAAAATAA
66 CCCCTCGGAAATAA
* * * *
13664 CGGGGTTGGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAGATAAAACCAGGATTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
13729 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
*
13743 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
13808 CCCC
66 CCCC
13812 GATTAAAGGA
Statistics
Matches: 277, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 277 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGGAAATAA
Found at i:13809 original size:51 final size:51
Alignment explanation
Indices: 13743--14017 Score: 286
Period size: 51 Copynumber: 5.4 Consensus size: 51
13733 TCGGAAATAA
* *
13743 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTAGAAATAAAAC
* *
13794 CGGGGTTGGAGTATCCCCGATTAA-AGGAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAAGA-AAAATTGATGTTTTAG-AAATAAAAC
* * * *
13845 CGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTTGAAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-AAGAAAAATTGATGTTTT-AGAAATAAAAC
* * * * * * *
13898 CGGGTTTAGAGTATCCCCGATTATGGAAAGTT-AGTGTTCTAGAAATGAAAC
1 CGGGGTTGGAGTATCCCCGATTAAGAAAAATTGA-TGTTTTAGAAATAAAAC
* * ** * * *
13949 CGGGGTTGGAGTATCCCCCATTAAGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTAGAAATAAAAC
14000 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
14018 TCGGAGATAA
Statistics
Matches: 187, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
50 2 0.01
51 128 0.68
52 28 0.15
53 29 0.16
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTAGAAATAAAAC
Found at i:13920 original size:104 final size:103
Alignment explanation
Indices: 13743--14017 Score: 306
Period size: 104 Copynumber: 2.7 Consensus size: 103
13733 TCGGAAATAA
* * * *
13743 CGGGGTTGGAGTATCCCCGATT-ATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTAAAGAAAAATTGATGTTTTAAAAATAAAACCGGGGTTAGAGTA
* *
13807 TCCCCGATTAAAGGAAA-TTGGTGTT-TTGAAAATAAAAC
66 TCCCCGATT-AAGGAAAGTTAGTGTTCTAG-AAATAAAAC
* * * *
13845 CGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTTGAAAAATAAAACCGGGTTTAGAGT
1 CGGGGTTGGAGTATCCCCGATTAAAGAAAAATTGATGTTTT-AAAAATAAAACCGGGGTTAGAGT
* *
13910 ATCCCCGATTATGGAAAGTTAGTGTTCTAGAAATGAAAC
65 ATCCCCGATTAAGGAAAGTTAGTGTTCTAGAAATAAAAC
* * ** * ** * *
13949 CGGGGTTGGAGTATCCCCCATT-AAGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTAAAGAAAAATTGATGTTTTAAAAATAAAACCGGGGTTAGAGTA
14013 TCCCC
66 TCCCC
14018 TCGGAGATAA
Statistics
Matches: 144, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
102 46 0.32
103 31 0.22
104 65 0.45
105 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (103 bp):
CGGGGTTGGAGTATCCCCGATTAAAGAAAAATTGATGTTTTAAAAATAAAACCGGGGTTAGAGTA
TCCCCGATTAAGGAAAGTTAGTGTTCTAGAAATAAAAC
Found at i:14143 original size:51 final size:51
Alignment explanation
Indices: 14053--14151 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 51
14043 CTCGATTGGA
*
14053 AAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCAATTAAAGG
1 AAATTGGTG-TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCAATTAAAGG
* *
14105 AAATTGGTG-TTTGGAAAATAAAACCGGGGTTGGAGTATCCCCGATTA
1 AAATTGGTGTTTTGG-AAATAAAACCGGAGTTGGAGTATCCCCAATTA
14152 TGAGCAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 5 0.12
51 29 0.67
52 9 0.21
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.29
Consensus pattern (51 bp):
AAATTGGTGTTTTGGAAATAAAACCGGAGTTGGAGTATCCCCAATTAAAGG
Found at i:15174 original size:43 final size:43
Alignment explanation
Indices: 15092--15180 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 43
15082 TGCTGCTCTC
* * * * *
15092 GCTGGAGCTGCAGTCGCTGCTGCAGTTGTTGCTATTGTTGCGT
1 GCTGGAGCTACAGTCACTGCTGCAGTTGCTGCTACTGTTGCAT
* * *
15135 GCTGGAGCTACAGTCATTGCTGGAGTTGCTGCTGCTGTTGCAT
1 GCTGGAGCTACAGTCACTGCTGCAGTTGCTGCTACTGTTGCAT
15178 GCT
1 GCT
15181 AGAACTATTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.11, C:0.21, G:0.34, T:0.34
Consensus pattern (43 bp):
GCTGGAGCTACAGTCACTGCTGCAGTTGCTGCTACTGTTGCAT
Found at i:15564 original size:50 final size:50
Alignment explanation
Indices: 15509--15711 Score: 370
Period size: 50 Copynumber: 4.1 Consensus size: 50
15499 TCCATTCTCT
**
15509 TGCATGCCTCTACATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
1 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
15559 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
1 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
15609 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
1 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
* *
15659 TGCATGCCTCTGTATGTTTTGTCTCCAATTGTAATTTTTATGCTTTCCTA
1 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
15709 TGC
1 TGC
15712 TGCATTTTCT
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 149 1.00
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (50 bp):
TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
Found at i:15731 original size:26 final size:26
Alignment explanation
Indices: 15701--15788 Score: 158
Period size: 26 Copynumber: 3.4 Consensus size: 26
15691 AATTTTTATG
*
15701 CTTTCCTATGCTGCATTTTCTATTTC
1 CTTTCCCATGCTGCATTTTCTATTTC
15727 CTTTCCCATGCTGCATTTTCTATTTC
1 CTTTCCCATGCTGCATTTTCTATTTC
*
15753 CTTTCCCATGCTGTATTTTCTATTTC
1 CTTTCCCATGCTGCATTTTCTATTTC
15779 CTTTCCCATG
1 CTTTCCCATG
15789 ATGTTCGTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.11, C:0.30, G:0.08, T:0.51
Consensus pattern (26 bp):
CTTTCCCATGCTGCATTTTCTATTTC
Found at i:15929 original size:6 final size:6
Alignment explanation
Indices: 15895--15921 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15885 ATTATAATTT
15895 TTTGAA TTTGAA TTTGAA TTTGAA TTT
1 TTTGAA TTTGAA TTTGAA TTTGAA TTT
15922 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTGAA
Found at i:16703 original size:62 final size:60
Alignment explanation
Indices: 16543--17031 Score: 477
Period size: 56 Copynumber: 8.4 Consensus size: 60
16533 ATAAAGTGTA
* * * *
16543 TCCTGCTCTTTAAGGACTAAAAAGTGCCACCAACTCGTG-GGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
16597 TCCTGCTCTTTGAGAACTGAAAGGTGCCACCAACTAGTGTGGGCTTTGAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* *
16658 TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGAAA-GCG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAAGGCG
* * *
16720 TCCTGCTCTTTGAAGACT-AAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* * * *
16780 TCTTGCTCTTTGAGGATTAGAAAAATGCCACCAACTTGTGTAGGCTTT-----AAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * * * *
16836 ACCTGCTCTTTGAGGACTAAAAAATTGCCACCAACTTATGTAGGCTTT----G-AAAGACG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
16892 TCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* *
16953 TCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGG-TTT----TAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
17009 TCCTGCTCTTTGAGGACT-AAAAG
1 TCCTGCTCTTTGAGGACTGAAAAG
17032 GGTGAAAGGA
Statistics
Matches: 369, Mismatches: 45, Indels: 42
0.81 0.10 0.09
Matches are distributed among these distances:
54 38 0.10
55 30 0.08
56 98 0.27
59 6 0.02
60 47 0.13
61 50 0.14
62 97 0.26
63 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:16976 original size:173 final size:175
Alignment explanation
Indices: 16543--17030 Score: 602
Period size: 173 Copynumber: 2.8 Consensus size: 175
16533 ATAAAGTGTA
* * *
16543 TCCTGCTCTTTAAGGACTAAAAAGTGCCACCAACTCGTG-GGGCTTT-----G-AAAGGTGTCCT
1 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCT
* ** * *
16601 GCTCTTTGAGAACT-GAAAGGTGCCACCAACTAGTGTGGGCTTTGAAAAGAAAAGGTGTCCTGCT
65 GCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTT------AAAAGGCGTCCTGCT
** * *
16665 CTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGAAAGCG
124 CTTTGAGGACTAAAAAAGTGCCACCAACTTATGTAGGCTTTGAAA-G-G-AAGCG
* * * *
16720 TCCTGCTCTTTGAAGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGCGTCTTG
1 TCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTG
* * *
16785 CTCTTTGAGGATTAGAAAAATGCCACCAACTTGTGTAGGCTTTAAAAGGCGACCTGCTCTTTGAG
66 CTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAG
*
16850 GACTAAAAAATTGCCACCAACTTATGTAGGCTTTGAAA-G-A-CG
131 GACTAAAAAAGTGCCACCAACTTATGTAGGCTTTGAAAGGAAGCG
*
16892 TCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCT
1 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCT
*
16957 GCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGTTTTAAAAGGCGTCCTGCTCTTTGA
65 GCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGA
17022 GGACTAAAA
130 GGACTAAAA
17031 GGGTGAAAGG
Statistics
Matches: 273, Mismatches: 29, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
172 19 0.07
173 113 0.41
175 1 0.00
176 17 0.06
177 23 0.08
178 53 0.19
182 1 0.00
183 21 0.08
184 25 0.09
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (175 bp):
TCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTG
CTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAG
GACTAAAAAAGTGCCACCAACTTATGTAGGCTTTGAAAGGAAGCG
Done.