Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2127
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: 40665
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:159 original size:27 final size:27
Alignment explanation
Indices: 108--159 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
98 GGACGAAGCT
*
108 AAAGGAAAAGTATATGTGCCCCAAGAA
1 AAAGGAAAAGTATATGTGCACCAAGAA
*
135 AAAGGAAAAGTATATGTGCATCAAG
1 AAAGGAAAAGTATATGTGCACCAAG
160 GAAGGAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.17
Consensus pattern (27 bp):
AAAGGAAAAGTATATGTGCACCAAGAA
Found at i:829 original size:27 final size:27
Alignment explanation
Indices: 790--849 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
780 ATATAAAGCT
**
790 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGG-TGGAGTATCCCCGAGGAAATAAC
*
818 GGGGTGGAGTATCCCCGATGAAATAAC
1 GGGGTGGAGTATCCCCGAGGAAATAAC
845 GGGGT
1 GGGGT
850 CTCGAGTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.20
Consensus pattern (27 bp):
GGGGTGGAGTATCCCCGAGGAAATAAC
Found at i:912 original size:108 final size:106
Alignment explanation
Indices: 651--914 Score: 298
Period size: 106 Copynumber: 2.5 Consensus size: 106
641 GAGTATCTCG
* * *
651 ATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGCGTTGGAGTATTCCCTCGAAAATAACGGGA
1 ATTGTGAAAAATTAGTATTTTAGAAATAAAATCGGCGTTGGAGTATCCCCTCGAAAATAACGGGA
* * * * *
716 CTTGAGTATCCCTGATGACATAACGGGTTGGAGTACCCCCG
66 CTGGAGTATCCCCGATGAAATAACGGGTTCGAGTACCCCCA
** * * * * * * *
757 ATAATGAACAATCAATATTTTAGATAT-AAAGCTGGGGTTGGAGTATCCCCTCGGAAATAACGGG
1 ATTGTGAAAAATTAGTATTTTAGAAATAAAATC-GGCGTTGGAGTATCCCCTCGAAAATAACGGG
*
821 -GTGGAGTATCCCCGATGAAATAACGGGGTCTCGAGTATCCCCCA
65 ACTGGAGTATCCCCGATGAAATAAC-GGGT-TCGAGTA-CCCCCA
* *
865 ATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGCGTTGGAGTATCCCC
1 ATTGTGAAAAATTAGTATTTTAGAAATAAAATCGGCGTTGGAGTATCCCC
915 GATTGCGGTA
Statistics
Matches: 125, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
105 24 0.19
106 51 0.41
107 6 0.05
108 40 0.32
109 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (106 bp):
ATTGTGAAAAATTAGTATTTTAGAAATAAAATCGGCGTTGGAGTATCCCCTCGAAAATAACGGGA
CTGGAGTATCCCCGATGAAATAACGGGTTCGAGTACCCCCA
Found at i:3375 original size:20 final size:20
Alignment explanation
Indices: 3352--3456 Score: 117
Period size: 20 Copynumber: 5.8 Consensus size: 20
3342 TACATTGTAA
3352 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
3372 AATGTATCGATAC--T-A-C
1 AATGTATCGATACAATGAGC
3388 AATGTAT-GATACAATGAGC
1 AATGTATCGATACAATGAGC
3407 AATGTATCGATACAAT----
1 AATGTATCGATACAATGAGC
*
3423 -A--TATCGATACAATGAGT
1 AATGTATCGATACAATGAGC
3440 AATGTATCGATACAATG
1 AATGTATCGATACAATG
3457 CAAAATGATC
Statistics
Matches: 73, Mismatches: 0, Indels: 24
0.75 0.00 0.25
Matches are distributed among these distances:
13 12 0.16
15 6 0.08
16 8 0.11
17 2 0.03
18 3 0.04
19 8 0.11
20 34 0.47
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:3401 original size:35 final size:36
Alignment explanation
Indices: 3352--3452 Score: 156
Period size: 35 Copynumber: 2.9 Consensus size: 36
3342 TACATTGTAA
3352 AATGTATCGATACAATGAGCAATGTATCGATACTAC
1 AATGTATCGATACAATGAGCAATGTATCGATACTAC
3388 AATGTAT-GATACAATGAGCAATGTATCG--A-TAC
1 AATGTATCGATACAATGAGCAATGTATCGATACTAC
* *
3420 AATATATCGATACAATGAGTAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
3453 AATGCAAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
32 9 0.15
33 21 0.36
35 22 0.37
36 7 0.12
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (36 bp):
AATGTATCGATACAATGAGCAATGTATCGATACTAC
Found at i:3427 original size:13 final size:13
Alignment explanation
Indices: 3406--3435 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3396 ATACAATGAG
*
3406 CAATGTATCGATA
1 CAATATATCGATA
3419 CAATATATCGATA
1 CAATATATCGATA
3432 CAAT
1 CAAT
3436 GAGTAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (13 bp):
CAATATATCGATA
Found at i:3437 original size:33 final size:33
Alignment explanation
Indices: 3356--3455 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
3346 TTGTAAAATG
*
3356 TATCGATACAATGAGCAATGTATCGATACTACAATG
1 TATCGATACAATGAGCAATGTATCG--A-TACAATA
3392 TAT-GATACAATGAGCAATGTATCGATACAATA
1 TATCGATACAATGAGCAATGTATCGATACAATA
*
3424 TATCGATACAATGAGTAATGTATCGATACAAT
1 TATCGATACAATGAGCAATGTATCGATACAAT
3456 GCAAAATGAT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
32 9 0.15
33 28 0.46
35 21 0.34
36 3 0.05
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (33 bp):
TATCGATACAATGAGCAATGTATCGATACAATA
Found at i:3463 original size:20 final size:19
Alignment explanation
Indices: 3332--3472 Score: 115
Period size: 20 Copynumber: 7.7 Consensus size: 19
3322 AAAATGCCTG
* * *
3332 AATGTATTGATACATTGTAA
1 AATGTATCGATACAATG-AC
3352 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
3372 AATGTATCGATAC--T-AC
1 AATGTATCGATACAATGAC
3388 AATGTAT-GATACAATGAGC
1 AATGTATCGATACAATGA-C
3407 AATGTATCGATACAAT---
1 AATGTATCGATACAATGAC
*
3423 -A--TATCGATACAATGAGT
1 AATGTATCGATACAATGA-C
*
3440 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
3460 AATG-ATCGATACA
1 AATGTATCGATACA
3473 TCTGGTAAAC
Statistics
Matches: 103, Mismatches: 4, Indels: 29
0.76 0.03 0.21
Matches are distributed among these distances:
13 12 0.12
15 6 0.06
16 8 0.08
17 2 0.02
18 3 0.03
19 18 0.17
20 53 0.51
21 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:3505 original size:13 final size:13
Alignment explanation
Indices: 3487--3516 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3477 GTAAACCCAG
3487 AATGTATCGATAA
1 AATGTATCGATAA
*
3500 AATGTATCGATAC
1 AATGTATCGATAA
3513 AATG
1 AATG
3517 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAA
Found at i:3525 original size:20 final size:20
Alignment explanation
Indices: 3500--3554 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
3490 GTATCGATAA
*
3500 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATAAAC
*
3520 AATGTATCGATGCAATAAAC
1 AATGTATCGATACAATAAAC
3540 AATGTATCGATACAA
1 AATGTATCGATACAA
3555 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATAAAC
Found at i:7438 original size:20 final size:20
Alignment explanation
Indices: 7413--7452 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
7403 ATTGGGCTTA
*
7413 ATGTATCGATATAATTTATT
1 ATGTATCGATACAATTTATT
7433 ATGTATCGATACAATTTATT
1 ATGTATCGATACAATTTATT
7453 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (20 bp):
ATGTATCGATACAATTTATT
Found at i:8814 original size:27 final size:27
Alignment explanation
Indices: 8776--8830 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
8766 AGACGAAGCT
**
8776 AAAGGAAAAGTATATGTGCCCCAAGGA
1 AAAGGAAAAGTATATGTGCAACAAGGA
8803 AAAGGAAAAGTATATGTGCAACAAGGA
1 AAAGGAAAAGTATATGTGCAACAAGGA
8830 A
1 A
8831 GGAACAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.25, T:0.15
Consensus pattern (27 bp):
AAAGGAAAAGTATATGTGCAACAAGGA
Found at i:9501 original size:16 final size:16
Alignment explanation
Indices: 9482--9540 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
9472 TATATATACT
9482 TTTTATAATATAAATA
1 TTTTATAATATAAATA
9498 TTTTAGTAAT-TAAATA
1 TTTTA-TAATATAAATA
*
9514 TATTA-AA-ATAAATTA
1 TTTTATAATATAAA-TA
*
9529 TTCTTGTAATAT
1 TT-TTATAATAT
9541 TATGTCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 17 0.50
17 6 0.18
18 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (16 bp):
TTTTATAATATAAATA
Found at i:14101 original size:29 final size:29
Alignment explanation
Indices: 14040--14103 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
14030 CATATGCCAT
*** *
14040 TTTAAATTAAGTCATCAATTAGATGTCAT
1 TTTAAATTAAGTCATCAATTAGATCAAAA
* *
14069 TTTAAATTAAGTGATCAATTATATCAAAA
1 TTTAAATTAAGTCATCAATTAGATCAAAA
14098 TTTAAA
1 TTTAAA
14104 CTAATTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTAAATTAAGTCATCAATTAGATCAAAA
Found at i:18866 original size:323 final size:323
Alignment explanation
Indices: 18278--18923 Score: 1274
Period size: 323 Copynumber: 2.0 Consensus size: 323
18268 CCAACCCAGC
18278 CAAATCAAACAAAGGGATGATGTATCTGTTTATGTTTATATAGTAATCTATATATTTCTAAGTTT
1 CAAATCAAACAAAGGGATGATGTATCTGTTTATGTTTATATAGTAATCTATATATTTCTAAGTTT
18343 GAGTTTTAGTCCTCTCTATCCTCTACTAAAAGATAAATTGTTTTAAGTTACGCTTTACATTTTAT
66 GAGTTTTAGTCCTCTCTATCCTCTACTAAAAGATAAATTGTTTTAAGTTACGCTTTACATTTTAT
18408 AAATTTCGACTCTTTTTATATTAAAACCCGTATTTGTTTTCACACATACATACATGCATGTTTAT
131 AAATTTCGACTCTTTTTATATTAAAACCCGTATTTGTTTTCACACATACATACATGCATGTTTAT
18473 GAAGTGCCTTTGTTCTCATATTTGCACAATGCACATATGGAATTATCCAATTATGTCGTTTGCTA
196 GAAGTGCCTTTGTTCTCATATTTGCACAATGCACATATGGAATTATCCAATTATGTCGTTTGCTA
18538 TAACACCTTTTAATGAACAGGAAAATTTTATGTTGAAGCTCAACCTAACTATATAAAAATATT
261 TAACACCTTTTAATGAACAGGAAAATTTTATGTTGAAGCTCAACCTAACTATATAAAAATATT
*
18601 CAAATCAAACAAAGGGATGATGTATCTGTTTATGTTTATATGGTAATCTATATATTTCTAAGTTT
1 CAAATCAAACAAAGGGATGATGTATCTGTTTATGTTTATATAGTAATCTATATATTTCTAAGTTT
*
18666 GAGTTTTAGTCCTTTCTATCCTCTACTAAAAGATAAATTGTTTTAAGTTACGCTTTACATTTTAT
66 GAGTTTTAGTCCTCTCTATCCTCTACTAAAAGATAAATTGTTTTAAGTTACGCTTTACATTTTAT
18731 AAATTTCGACTCTTTTTATATTAAAACCCGTATTTGTTTTCACACATACATACATGCATGTTTAT
131 AAATTTCGACTCTTTTTATATTAAAACCCGTATTTGTTTTCACACATACATACATGCATGTTTAT
18796 GAAGTGCCTTTGTTCTCATATTTGCACAATGCACATATGGAATTATCCAATTATGTCGTTTGCTA
196 GAAGTGCCTTTGTTCTCATATTTGCACAATGCACATATGGAATTATCCAATTATGTCGTTTGCTA
18861 TAACACCTTTTAATGAACAGGAAAATTTTATGTTGAAGCTCAACCTAACTATATAAAAATATT
261 TAACACCTTTTAATGAACAGGAAAATTTTATGTTGAAGCTCAACCTAACTATATAAAAATATT
18924 ATGTGGTTTA
Statistics
Matches: 321, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
323 321 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (323 bp):
CAAATCAAACAAAGGGATGATGTATCTGTTTATGTTTATATAGTAATCTATATATTTCTAAGTTT
GAGTTTTAGTCCTCTCTATCCTCTACTAAAAGATAAATTGTTTTAAGTTACGCTTTACATTTTAT
AAATTTCGACTCTTTTTATATTAAAACCCGTATTTGTTTTCACACATACATACATGCATGTTTAT
GAAGTGCCTTTGTTCTCATATTTGCACAATGCACATATGGAATTATCCAATTATGTCGTTTGCTA
TAACACCTTTTAATGAACAGGAAAATTTTATGTTGAAGCTCAACCTAACTATATAAAAATATT
Found at i:19060 original size:19 final size:19
Alignment explanation
Indices: 19018--19062 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
19008 TACTTTTTCT
19018 TTAAAAAAATAGATCACTC
1 TTAAAAAAATAGATCACTC
* *
19037 ATAAAAAAATTA-ATCTCTC
1 TTAAAAAAA-TAGATCACTC
19056 TTAAAAA
1 TTAAAAA
19063 TATATTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (19 bp):
TTAAAAAAATAGATCACTC
Found at i:24823 original size:2 final size:2
Alignment explanation
Indices: 24816--24845 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24806 CTCAACGTGA
24816 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
24846 GTGAGATGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25142 original size:14 final size:13
Alignment explanation
Indices: 25117--25149 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
25107 AAAATTTCTT
25117 AATTAA-TTTTTA
1 AATTAATTTTTTA
25129 AATATAATTTTTTA
1 AAT-TAATTTTTTA
25143 AATTAAT
1 AATTAAT
25150 ATGTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 7 0.37
14 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATTAATTTTTTA
Found at i:25308 original size:23 final size:23
Alignment explanation
Indices: 25235--25308 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
25225 AAATTTTATA
*
25235 AAAATAATATTAAAT-AAAATGAT
1 AAAATAATAATAAATAAAAAT-AT
* ** *
25258 -AAATAATTATTTATAAACAT-T
1 AAAATAATAATAAATAAAAATAT
25279 AATAATAATAATAAATAAAAATAT
1 AA-AATAATAATAAATAAAAATAT
25303 AAAATA
1 AAAATA
25309 TAAAATATCA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 23 0.61
24 3 0.08
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (23 bp):
AAAATAATAATAAATAAAAATAT
Found at i:25493 original size:18 final size:17
Alignment explanation
Indices: 25467--25501 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25457 TATGTATATT
*
25467 TATATATAAATAAATAAA
1 TATACATAAA-AAATAAA
25485 TATACATAAAAAATAAA
1 TATACATAAAAAATAAA
25502 AAATAATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TATACATAAAAAATAAA
Found at i:25520 original size:21 final size:25
Alignment explanation
Indices: 25472--25518 Score: 73
Period size: 22 Copynumber: 2.0 Consensus size: 25
25462 ATATTTATAT
25472 ATAAATAAATAAATATACATAAAAA
1 ATAAATAAATAAATATACATAAAAA
25497 ATAAA-AAAT-AATAT-CATAAAAA
1 ATAAATAAATAAATATACATAAAAA
25519 TATTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 4 0.18
25 5 0.23
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (25 bp):
ATAAATAAATAAATATACATAAAAA
Found at i:26106 original size:18 final size:18
Alignment explanation
Indices: 26083--26131 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
26073 AAAATTAAAT
*
26083 TAATTTTATATATTTTTA
1 TAATTTTATATATATTTA
26101 TAATTTT-TATAATATTTA
1 TAATTTTATAT-ATATTTA
*
26119 TATATTTAATATA
1 TA-ATTTTATATA
26132 CCCATTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 5 0.19
20 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATTTTATATATATTTA
Found at i:26343 original size:24 final size:25
Alignment explanation
Indices: 26292--26346 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
26282 TTTACATAAA
*
26292 ATAAAAA-TAATTATATTATTAAAT
1 ATAAAAATTAATTATATTATAAAAT
26316 -TAAAAATTAATTATA-TA-AAAATT
1 ATAAAAATTAATTATATTATAAAA-T
26339 ATAAAAAT
1 ATAAAAAT
26347 AATGAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.11
23 9 0.33
24 15 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAAAAATTAATTATATTATAAAAT
Found at i:26638 original size:13 final size:13
Alignment explanation
Indices: 26619--26657 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
26609 ACAGCATTCT
26619 CTGTATCGATACA
1 CTGTATCGATACA
*
26632 TTGTATCGATACA
1 CTGTATCGATACA
*
26645 CTATATCGATACA
1 CTGTATCGATACA
26658 AAGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:26824 original size:20 final size:20
Alignment explanation
Indices: 26789--26829 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
26779 CAAATTTCTT
26789 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
26811 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
26830 TTCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:29210 original size:13 final size:13
Alignment explanation
Indices: 29192--29217 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29182 TACACACAGT
29192 ATGTATCGATACA
1 ATGTATCGATACA
29205 ATGTATCGATACA
1 ATGTATCGATACA
29218 CCATAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:29234 original size:33 final size:32
Alignment explanation
Indices: 29174--29237 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
29164 TAGCCAAATT
**
29174 TGTATCGATACACACAGTATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
29206 TGTATCGATACACCATAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
29238 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:33715 original size:27 final size:27
Alignment explanation
Indices: 33680--33757 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 27
33670 CAACAACAAG
*
33680 CCACAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * * * *
33707 CCATCATTTTTGATAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
33734 CCACCATTTTTTACAAACACAAAA
1 CCACCATTTTTGACAAACA-AAAA
33758 AGTGATTTTT
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 36 0.92
28 3 0.08
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:34223 original size:18 final size:18
Alignment explanation
Indices: 34173--34224 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
34163 AGACAAATAA
34173 ATGTTTA-A-TAATAA-C
1 ATGTTTACATTAATAACC
*
34188 ATGTTTTATCATTTATAACC
1 ATG-TTTA-CATTAATAACC
34208 ATGTTTACATTAATAAC
1 ATGTTTACATTAATAAC
34225 TTAGTTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.10
16 4 0.13
18 10 0.33
19 9 0.30
20 4 0.13
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGTTTACATTAATAACC
Found at i:34369 original size:2 final size:2
Alignment explanation
Indices: 34307--34357 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
34297 GAGAAGAAAT
34307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34349 TA TA TA TA T
1 TA TA TA TA T
34358 TATTTTTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34478 original size:24 final size:24
Alignment explanation
Indices: 34433--34478 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
34423 ATATATAATT
* *
34433 ATATATTAAAATATAATTTTTTTG
1 ATATATAAAAATATAATATTTTTG
34457 ATATATAAAAAT-TAAATATTTT
1 ATATATAAAAATAT-AATATTTT
34479 CCAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATATAAAAATATAATATTTTTG
Found at i:35429 original size:351 final size:345
Alignment explanation
Indices: 34643--35394 Score: 812
Period size: 351 Copynumber: 2.1 Consensus size: 345
34633 CAATCAGTAT
* * * *
34643 GCTATTCTTCCTTTTTCTTTTCAAAATAATTATAAAATCATTTTTTATATAAAGATATTTCTATT
1 GCTATTCTTTCTTTTTCTCTTCAAAATAATTGTAAAATCA-TTTTTATAT--A-ATATTACTA-T
* * * * *
34708 TCCTTATCAATAATTATTTATTGTAATAACAGTGTAATAAATATGTTTAGTTAATTCATTCATTT
61 TCGTAATTAAT-ATTATTTATTGTAATAACAATATAATAAATATGTTTAGTTAATTCATTCATTT
34773 GGTAATTATATTTTAATATATAAAAATTAAATATTTAAAATTACATATTCTCCAAAAATAAAAAA
125 GGTAATTATATTTTAATATATAAAAATTAAATATTTAAAATTACATATTCTCCAAAAATAAAAAA
* *
34838 ATTTACTAAATTAATTTTAAAAATGAAATAAAAAATTATAAAATACAACTTTTTTAAAATTAGGT
190 ATTTACTAAATTAATTTTAAAAATGAAATAAAAAACTATAAAATACAACTTTTTTAAAATCAGGT
* * ** * *
34903 GAGAAAATTCATTAAAAAAACTTAAGTTGATATTTTTTACCAATTGAATTTTACCGTTTTAGTTG
255 GAGAAAATTCATTAAAAAAACTCAAGTTAATATTTTTTA-CAATCAAATTTCACAGTTTTAGTTG
* *
34968 TGGGAGTCTAAATCGGCTAACTGCTCC
319 TGAGAGTCAAAATCGGCTAACTGCTCC
* *
34995 GCTATTCTTTCTTTTTCTCTTCAAAATAATTGTAAAATCATTTTTATATAAAGATTTTTCTATTT
1 GCTATTCTTTCTTTTTCTCTTCAAAATAATTGTAAAATCATTTTTATAT--A-ATATTACTA-TT
* ** * * *
35060 CTTTCTTAATAATTATTTATTGTAATATCAATATAATAAATATGTTTAGTTAATTGATTCATTTT
62 CGTAATTAAT-ATTATTTATTGTAATAACAATATAATAAATATGTTTAGTTAATTCATTCATTTG
* * *
35125 GTTATTATATTTTAATATATAGAAATTAAATATTTCAAATTACATATTCTCCAAAAATTAAAAAA
126 GTAATTATATTTTAATATATAAAAATTAAATATTTAAAATTACATATTCTCCAAAAA-T--AAAA
* ** * *
35190 AAATTATTACTAAATTAATTTTAAATAATGAAATATAAAACTATAAAATTTAACTTTTTTTTAAG
188 AAA-T-TTACTAAATTAATTTTAAA-AATGAAATAAAAAACTATAAAATACAAC-TTTTTTAAAA
* *
35255 TCAGGTTAGAAAATTCATTAAAAAATTAAAACTCAAGTTAAT-TTTTTTA-AATCAAATTTCATT
249 TCAGGTGAGAAAATTCATT---AAA--AAAACTCAAGTTAATATTTTTTACAATCAAATTTCA-C
* * *
35318 ATTTTTAGTTGT-AGATGTCAAAATC-GATCAA-TGACTCAG
308 AGTTTTAGTTGTGAGA-GTCAAAATCGGCT-AACTG-CTC-C
* * * *
35357 GTTGTTTTTTCTTTTTCTCTTCAAAATAATTTTAAAAT
1 GCTATTCTTTCTTTTTCTCTTCAAAATAATTGTAAAAT
35395 GTTTTTAACT
Statistics
Matches: 344, Mismatches: 39, Indels: 24
0.85 0.10 0.06
Matches are distributed among these distances:
351 135 0.39
352 38 0.11
354 7 0.02
355 1 0.00
356 19 0.06
357 24 0.07
358 25 0.07
360 15 0.04
361 26 0.08
362 41 0.12
363 13 0.04
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (345 bp):
GCTATTCTTTCTTTTTCTCTTCAAAATAATTGTAAAATCATTTTTATATAATATTACTATTCGTA
ATTAATATTATTTATTGTAATAACAATATAATAAATATGTTTAGTTAATTCATTCATTTGGTAAT
TATATTTTAATATATAAAAATTAAATATTTAAAATTACATATTCTCCAAAAATAAAAAAATTTAC
TAAATTAATTTTAAAAATGAAATAAAAAACTATAAAATACAACTTTTTTAAAATCAGGTGAGAAA
ATTCATTAAAAAAACTCAAGTTAATATTTTTTACAATCAAATTTCACAGTTTTAGTTGTGAGAGT
CAAAATCGGCTAACTGCTCC
Found at i:35463 original size:21 final size:21
Alignment explanation
Indices: 35448--35488 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35438 TATTTATTAT
35448 TAAAATAATTACATTTTTAATA
1 TAAAA-AATTACATTTTTAATA
* *
35470 TAAAAAATTAAATATTTAA
1 TAAAAAATTACATTTTTAA
35489 AGTTGCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAAATTACATTTTTAATA
Found at i:36569 original size:21 final size:20
Alignment explanation
Indices: 36536--36601 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
36526 AACTAATAAA
*
36536 ATAAAAT-TATAATTTTTTTT
1 ATAAAATATATAA-TTTTATT
*
36556 ATAAAATATATAATTATATT
1 ATAAAATATATAATTTTATT
*
36576 ATAAAA-ATATAAATTTTATA
1 ATAAAATATAT-AATTTTATT
36596 ATAAAA
1 ATAAAA
36602 AATCTCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.10
20 31 0.77
21 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAATATATAATTTTATT
Found at i:38173 original size:24 final size:24
Alignment explanation
Indices: 38127--38174 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38117 ATATAGCTTG
* * * *
38127 TTTCTTTTTAATGTTTATTTATAT
1 TTTCTTCTTAATATATATATATAT
38151 TTTCTTCTTAATATATATATATAT
1 TTTCTTCTTAATATATATATATAT
38175 ATAATTATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTCTTCTTAATATATATATATAT
Found at i:38866 original size:59 final size:59
Alignment explanation
Indices: 38799--38917 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
38789 GTGGATAGTT
* *
38799 TTTTAGGGATAAGAAAGAAATTACTTGAATAATAATTGAATAGTTTTTTTAGCATTGGG
1 TTTTAGGGATAAGAAAGAAATTACTTGAATAATAATTGAATAATTTTTTTAGCACTGGG
38858 TTTTAGGGATAAGAAAGAAATTACTTGAATAATAATTGAATAATTTTTTTAGCACTGGG
1 TTTTAGGGATAAGAAAGAAATTACTTGAATAATAATTGAATAATTTTTTTAGCACTGGG
38917 T
1 T
38918 AATGTTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (59 bp):
TTTTAGGGATAAGAAAGAAATTACTTGAATAATAATTGAATAATTTTTTTAGCACTGGG
Done.