Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold979
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: 30099
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:739 original size:20 final size:20
Alignment explanation
Indices: 710--761 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
700 TATTGATACT
*
710 TATCAGTACATTCACAAATG
1 TATCAATACATTCACAAATG
* **
730 TATCTATACATTCACTCATG
1 TATCAATACATTCACAAATG
750 TATCAATACATT
1 TATCAATACATT
762 TGTGTCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (20 bp):
TATCAATACATTCACAAATG
Found at i:9748 original size:79 final size:77
Alignment explanation
Indices: 9637--9834 Score: 211
Period size: 79 Copynumber: 2.5 Consensus size: 77
9627 AACGGGGTTA
* * * * * * *
9637 GAGTGTCCCCTTGAAATGACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TT-AGAAA
1 GAGTATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTGAGAAA
9700 AAAACATCGGGATTG
65 AAAAC--CGGGATTG
* *
9715 GAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAA
1 GAGTATCCCCTCG-AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTGAGAA
* * *
9780 TAAAGCCGGGGTTG
64 AAAAACCGGGATTG
*
9794 GAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 GAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGAT
9835 GAAATAACGA
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
78 12 0.12
79 79 0.78
80 3 0.03
81 7 0.07
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (77 bp):
GAGTATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTGAGAAAA
AAACCGGGATTG
Found at i:9826 original size:28 final size:28
Alignment explanation
Indices: 9786--9857 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
9776 GGAATAAAGC
** *
9786 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
9814 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
9842 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
9858 TCGACTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:9842 original size:107 final size:110
Alignment explanation
Indices: 9707--9942 Score: 302
Period size: 108 Copynumber: 2.2 Consensus size: 110
9697 AAAAAAACAT
* * * *
9707 CGGGATTGGAGTATCCCC--TCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT
1 CGGGGTTGGAGTATCCCCGATCGAAAATAACGAGGTTGGAGTATCCCCAACTATGAAAAATCAAT
* * * *
9770 A-TTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAA
66 ATTTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
* * * ***
9814 CGGGGTTGGAGTATCCCCGAT-G-AAATAACGAGGTTGGAGTATCCTCGACTGTGAAAAATTGGT
1 CGGGGTTGGAGTATCCCCGATCGAAAATAACGAGGTTGGAGTATCCCCAACTATGAAAAATCAAT
*
9877 ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAA
66 ATTTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
9922 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
9943 TGTGAAGAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
107 50 0.45
108 60 0.54
109 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (110 bp):
CGGGGTTGGAGTATCCCCGATCGAAAATAACGAGGTTGGAGTATCCCCAACTATGAAAAATCAAT
ATTTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
Found at i:9993 original size:82 final size:80
Alignment explanation
Indices: 9814--9995 Score: 274
Period size: 80 Copynumber: 2.2 Consensus size: 80
9804 TCGGAAGTAA
* *
9814 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGACTGTGAAAAATTGGTAT
1 CGGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAAAAATTGGTAT
9879 TTTTGGAAATAAAAT
66 TTTTGGAAATAAAAT
* ** * * *
9894 CGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTG
1 CGGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAA-AAATTGGTA
9959 TTTTTCGGAAATAAAAT
65 TTTTT-GGAAATAAAAT
9976 CGGGGTTGGAGTATCCCCGA
1 CGGGGTTGGAGTATCCCCGA
9996 TTATAGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 48 0.54
81 13 0.15
82 28 0.31
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAAAAATTGGTAT
TTTTGGAAATAAAAT
Found at i:10022 original size:51 final size:50
Alignment explanation
Indices: 9922--10096 Score: 181
Period size: 52 Copynumber: 3.4 Consensus size: 50
9912 TCGGAAATAA
* * *
9922 CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTCGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGTG--TTT-GAAAATAAAAC
*
9976 CGGGGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGA-AAAATTAGTGT-TTGAAAATAAAAC
* * * **
10027 CAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTGA-AAATAAAAC
*
10079 CGGAGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
10097 TCGGAAATAA
Statistics
Matches: 103, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
51 34 0.33
52 35 0.34
53 10 0.10
54 24 0.23
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTGAAAATAAAAC
Found at i:10101 original size:185 final size:185
Alignment explanation
Indices: 9846--10238 Score: 621
Period size: 185 Copynumber: 2.1 Consensus size: 185
9836 AAATAACGAG
* * * * *
9846 GTTGGAGTATCCTCGACTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GTTGGAGTATCCACGATTGTGGAAAAATTAGTATTTTAGG-AATAAAACCGGAGTTGGAGTATCC
9910 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTCGGAAATAAAA
65 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTCGGAAATAAAA
* *
9975 TCGGGGTTGGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAACCAGGA
130 TCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAACC-GGA
* *
10032 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTTGGAGTATCC
1 GTTGGAGTATCCACGATTGTGGAAAAATTAGTATTTTAG-GAATAAAACCGGAGTTGGAGTATCC
*
10095 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAA
65 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTCGGAAATAAAA
* *
10160 TCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
130 TCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAACCGGA
*
10216 GTTGGAATATCCACGATTGTGGA
1 GTTGGAGTATCCACGATTGTGGA
10239 GAATTGATAA
Statistics
Matches: 191, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
184 3 0.02
185 172 0.90
186 15 0.08
187 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (185 bp):
GTTGGAGTATCCACGATTGTGGAAAAATTAGTATTTTAGGAATAAAACCGGAGTTGGAGTATCCC
CTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTCGGAAATAAAAT
CGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAACCGGA
Found at i:10137 original size:133 final size:130
Alignment explanation
Indices: 9976--10227 Score: 312
Period size: 133 Copynumber: 1.9 Consensus size: 130
9966 GAAATAAAAT
*
9976 CGGGGTTGGAGTATCCCCGATTATAGAAAATTAGTG-TCTTGAAAATAAAACCAGGA-TTGGAGT
1 CGGGGTTGGAGTATCCCCGATTATAG-AAATTAGTGTTCTTGAAAATAAAACC-GGAGTTAGAGT
* * ** *
10039 ATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGGAGTTGGAGTATCCCCTCGGAA
64 ATCCCCGATTATAG-AAAATTAGTGTTTTGA-AAATAAAACCGGAGTTGGAATATCCCCTCGGAA
10103 ATAA
127 ATAA
* * * * *
10107 CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAG
1 CGGGGTTGGAGTATCCCCGATTAT--AGAAATTAGTG-TTCTTGAAAATAAAACCGGAGTTAGAG
*
10172 TATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCC
63 TATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCC
10228 ACGATTGTGG
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
131 23 0.22
132 8 0.08
133 40 0.39
134 32 0.31
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (130 bp):
CGGGGTTGGAGTATCCCCGATTATAGAAATTAGTGTTCTTGAAAATAAAACCGGAGTTAGAGTAT
CCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCTCGGAAATAA
Found at i:10207 original size:51 final size:53
Alignment explanation
Indices: 10115--10233 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
10105 AACGGGGTTG
* * *
10115 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
10169 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
10220 GAATATCCACGATT
1 GAGTATCCCCGATT
10234 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:12626 original size:13 final size:13
Alignment explanation
Indices: 12608--12633 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12598 ACAAAGATCC
12608 ATGTATCGATACA
1 ATGTATCGATACA
12621 ATGTATCGATACA
1 ATGTATCGATACA
12634 CAGAAAAATG
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:12629 original size:33 final size:33
Alignment explanation
Indices: 12587--12653 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12577 AAAATTTCCA
***
12587 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
12620 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
12653 A
1 A
12654 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:12697 original size:19 final size:18
Alignment explanation
Indices: 12673--12740 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
12663 CAGTAGCTAA
12673 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
12692 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
12707 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
12724 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
12741 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:12713 original size:13 final size:13
Alignment explanation
Indices: 12695--12719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12685 ACAATACTTA
12695 TGTATCGATACAT
1 TGTATCGATACAT
12708 TGTATCGATACA
1 TGTATCGATACA
12720 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12717 original size:32 final size:32
Alignment explanation
Indices: 12676--12738 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12666 TAGCTAATTA
*
12676 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
12708 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
12739 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:13469 original size:55 final size:55
Alignment explanation
Indices: 13374--14283 Score: 1174
Period size: 55 Copynumber: 16.3 Consensus size: 55
13364 ATAAACTGTA
* * * * *
13374 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGA-TGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
13429 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGATG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * * * **
13484 TCCTGATCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTT---AAG---AGGTG
* * *
13545 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
13600 TCCTGCTCTTTGAGGATTGGAACATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * * **
13655 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTT---AAG---AGGTG
* * * *
13716 TCCTGCTCTTTGAGGACTGAAAAATGCCATCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
13771 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
13826 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
13881 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
13936 TCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
13991 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
14046 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
14101 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
14156 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACTAACTTGGGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
14211 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
14266 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
14284 AAAAAGCGGA
Statistics
Matches: 761, Mismatches: 71, Indels: 46
0.87 0.08 0.05
Matches are distributed among these distances:
54 11 0.01
55 633 0.83
56 21 0.03
57 2 0.00
58 7 0.01
61 87 0.11
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:13850 original size:26 final size:26
Alignment explanation
Indices: 13821--13906 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
13811 GGGCTTTAAG
13821 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
13847 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
*
13875 GAGGTGTCCTGCTCTTTGAGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
13902 AGGTG
1 AGGTG
13907 CCACCAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 8 0.18
28 9 0.20
29 8 0.18
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:15290 original size:13 final size:12
Alignment explanation
Indices: 15266--15325 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
15256 CTTTTCTCTC
*
15266 TTTTTCTTTGTT
1 TTTTTTTTTGTT
15278 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
*
15291 TTTTTTCCTCT-TT
1 TTTTTT--TTTGTT
*
15304 TTTTTTTTTGCT
1 TTTTTTTTTGTT
15316 TTTTTTTTTG
1 TTTTTTTTTG
15326 AAGAGAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 2 0.05
12 17 0.43
13 19 0.47
14 2 0.05
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:15322 original size:16 final size:16
Alignment explanation
Indices: 15265--15324 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
15255 TCTTTTCTCT
* *
15265 CTTTTTCTTTGTTTTG
1 CTTTTTTTTTTTTTTG
* *
15281 TTTTTTTGTTTTTTTTC
1 CTTTTTT-TTTTTTTTG
*
15298 CTCTTTTTTTTTTTTG
1 CTTTTTTTTTTTTTTG
15314 CTTTTTTTTTT
1 CTTTTTTTTTT
15325 GAAGAGAAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (16 bp):
CTTTTTTTTTTTTTTG
Found at i:15322 original size:35 final size:37
Alignment explanation
Indices: 15252--15321 Score: 103
Period size: 34 Copynumber: 2.0 Consensus size: 37
15242 TAAGTAGGTT
15252 TTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTTTTTTG
1 TTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTTTTTTG
15289 TTTT-TTTTC-CTCTTTTT-TTT-TTTTGCTTTTTTT
1 TTTTCTTTTCTCTCTTTTTCTTTGTTTTG-TTTTTTT
15322 TTTGAAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 5 0.16
34 10 0.31
35 8 0.25
36 5 0.16
37 4 0.12
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (37 bp):
TTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTTTTTTG
Found at i:25734 original size:1 final size:1
Alignment explanation
Indices: 25728--25778 Score: 102
Period size: 1 Copynumber: 51.0 Consensus size: 1
25718 ATTGTCAAGT
25728 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
25779 TGTTATGAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Done.