Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4402.1
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: 62629
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2488 original size:26 final size:26
Alignment explanation
Indices: 2459--2518 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
2449 GCCCTTTGAA
* * *
2459 TCATTCGATATTTCGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAATG
*
2485 TCATTCTCAATATCTCGCACGCTAAATG
1 TCA-T-TCAATATCTCGCACACTAAATG
2513 TCATTC
1 TCATTC
2519 TCAATATTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAATG
Found at i:2502 original size:28 final size:28
Alignment explanation
Indices: 2466--2525 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
2456 GAATCATTCG
* *
2466 ATATTTCGCACACTAAGTGTCATTCTCA
1 ATATCTCGCACACTAAATGTCATTCTCA
*
2494 ATATCTCGCACGCTAAATGTCATTCTCA
1 ATATCTCGCACACTAAATGTCATTCTCA
2522 ATAT
1 ATAT
2526 TCCGTACACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (28 bp):
ATATCTCGCACACTAAATGTCATTCTCA
Found at i:14581 original size:30 final size:30
Alignment explanation
Indices: 14547--14607 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
14537 TCCTTAACTC
14547 AAAC-TTTGACAAAATTACAATTTTGCCCCT
1 AAACTTTTG-CAAAATTACAATTTTGCCCCT
* * *
14577 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
14607 A
1 A
14608 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:16662 original size:56 final size:55
Alignment explanation
Indices: 16602--16706 Score: 129
Period size: 56 Copynumber: 1.9 Consensus size: 55
16592 ACGGTTGCTT
* ** *
16602 GGCACGGGTGTGTCGCATGCCCGTGTTAATTTTGACAGGTTTGGCCACGGTTTCAA
1 GGCACGGGCGTGTCGCACACCCGTGTT-ATTTTGACAGGTTTGCCCACGGTTTCAA
* * **
16658 GGCACGGGCGTGTCTCACACCCGTGTTGTTTTGGTAGGTTTGCCCACGG
1 GGCACGGGCGTGTCGCACACCCGTGTTATTTTGACAGGTTTGCCCACGG
16707 CCATGTCGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
55 18 0.44
56 23 0.56
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.30
Consensus pattern (55 bp):
GGCACGGGCGTGTCGCACACCCGTGTTATTTTGACAGGTTTGCCCACGGTTTCAA
Found at i:18772 original size:21 final size:22
Alignment explanation
Indices: 18739--18779 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18729 TTCATTTATG
*
18739 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
18760 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
18780 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:19257 original size:28 final size:28
Alignment explanation
Indices: 19189--19267 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
19179 GAATCATTTG
*
19189 ATATTTCGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
19217 ATATCTT-GCACACTAAGTGCCATTCTCA
1 ATAT-TTCGCACACTAAGTGCCATTCTCA
* **
19245 ATATTTCGTACACCGAGTGCCAT
1 ATATTTCGCACACTAAGTGCCAT
19268 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 2 0.04
28 41 0.91
29 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:25206 original size:27 final size:27
Alignment explanation
Indices: 24915--25297 Score: 441
Period size: 27 Copynumber: 14.2 Consensus size: 27
24905 AAAGTACTCC
24915 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
24942 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
24969 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * *
24996 CGATTTTTAAAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
25023 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * *
25050 CGATTTTTAAAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
25077 CGATTTATAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
25104 C-AGTTTACAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
25131 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
25158 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
25185 CAATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * *
25212 CGATTTGTAAAATTACCGTTTTACCTT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
25239 TGATTTACAGAATTACTAG-GTTACCC-
1 CGATTTACAGAATTAC-CGTTTTACCCT
* * *
25265 CCAGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
25293 TGATT
1 CGATT
25298 GTGAAATTAC
Statistics
Matches: 306, Mismatches: 42, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.01
27 298 0.97
28 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:25332 original size:27 final size:27
Alignment explanation
Indices: 25302--25489 Score: 216
Period size: 27 Copynumber: 7.0 Consensus size: 27
25292 TTGATTGTGA
*
25302 AATTACTAAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTATAGGGTAG
*
25329 AATTTCTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTATAGGGTAG
* *
25356 AATTACTGAAATACCCTTATAGGATAG
1 AATTACTGAAATACCCCTATAGGGTAG
** *
25383 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTATAGGGTAG
* *
25410 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTATAGGGTAG
* * *
25437 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTATAGGGTAG
* * * *
25464 AATTACCGAGATACCCTTGTAGGGTA
1 AATTACTGAAATACCCCTATAGGGTA
25490 AAATAACCAT
Statistics
Matches: 140, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
27 140 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTATAGGGTAG
Found at i:25368 original size:54 final size:54
Alignment explanation
Indices: 25302--25489 Score: 252
Period size: 54 Copynumber: 3.5 Consensus size: 54
25292 TTGATTGTGA
* * * * *
25302 AATTACTAAAATACCCCTATAGGGTAGAATTTCTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* *
25356 AATTACTGAAATACCCTTATAGGATAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* *
25410 AATTA-TCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
25464 AATTACCGAGATACCCTTGTAGGGTA
1 AATTACTGAAATACCCTTATAGGGTA
25490 AAATAACCAT
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 118 0.99
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (54 bp):
AATTACTGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
Found at i:25408 original size:81 final size:81
Alignment explanation
Indices: 25302--25489 Score: 252
Period size: 81 Copynumber: 2.3 Consensus size: 81
25292 TTGATTGTGA
* * * *
25302 AATTACTAAAATACCCCTATAGGGTAGAATT-TCTGAAATACCCCTATAGGGTAGAATTACTGAA
1 AATTACCAAAATACCCCTGTAGGGTAGAATTATC-GAAATACCCCTATAGGGTAGAAATACCGAA
*
25366 ATACCCTTATAGGATAG
65 ATACCCCTATAGGATAG
* *
25383 AATTACCAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAGAAATACCGAAA
1 AATTACCAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTATAGGGTAGAAATACCGAAA
* *
25448 TACCCCTGTAGGGTAG
66 TACCCCTATAGGATAG
* * *
25464 AATTACCGAGATACCCTTGTAGGGTA
1 AATTACCAAAATACCCCTGTAGGGTA
25490 AAATAACCAT
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 92 0.98
82 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (81 bp):
AATTACCAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTATAGGGTAGAAATACCGAAA
TACCCCTATAGGATAG
Found at i:25734 original size:27 final size:26
Alignment explanation
Indices: 25696--25778 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
25686 CGGAGGAAGC
25696 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
25723 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * **
25749 GTATTTGGTGACTCTATCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
25776 GTT
1 GTT
25779 GACCGATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 10 0.20
27 40 0.80
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:26111 original size:27 final size:27
Alignment explanation
Indices: 26089--26162 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
26079 TAGGTGGGTT
*
26089 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
26116 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
** *
26143 TTTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
26163 CAGCCATGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.12
27 35 0.85
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:26289 original size:6 final size:6
Alignment explanation
Indices: 26280--26424 Score: 122
Period size: 6 Copynumber: 23.8 Consensus size: 6
26270 TTGCATTCAC
* *
26280 ATTCTG ATTCTG ATTCTG -TCACATA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
26329 ATTCTG -TTACTA ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATT-CTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
*
26378 -TTACTA ATAT-TG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 ATT-CTG AT-TCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
26425 CATTTTGGTT
Statistics
Matches: 113, Mismatches: 12, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
5 9 0.08
6 92 0.81
7 9 0.08
8 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:27054 original size:27 final size:27
Alignment explanation
Indices: 27016--27070 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
27006 TAATGGAAAC
27016 ATGGTTTTCGAAAAACACTTCAATGTG
1 ATGGTTTTCGAAAAACACTTCAATGTG
27043 ATGGTTTTCGAAAAACACTTCAATGTG
1 ATGGTTTTCGAAAAACACTTCAATGTG
27070 A
1 A
27071 CACGCCAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (27 bp):
ATGGTTTTCGAAAAACACTTCAATGTG
Found at i:34783 original size:6 final size:6
Alignment explanation
Indices: 34765--34903 Score: 58
Period size: 6 Copynumber: 22.3 Consensus size: 6
34755 AAGAAACATT
* * *
34765 ATCAGA A-CTAGA ATCAGA ATCAG- GTGACAGA ATCAGA ATTAGA ATCAGT
1 ATCAGA ATC-AGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA
* * *
34814 ATCAGGTA A-CAGA ATCAAA ATCAGA ATTAGT ATCAGGTA A-CAGA ATCA-A
1 ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
*
34863 TATCAGA ATCA-A TATCAGGTA AT-AGA ATCAAAA ATCAGA AT
1 -ATCAGA ATCAGA -ATCA-G-A ATCAGA ATC-AGA ATCAGA AT
34904 GTGAATGCAA
Statistics
Matches: 100, Mismatches: 14, Indels: 38
0.66 0.09 0.25
Matches are distributed among these distances:
5 11 0.11
6 66 0.66
7 17 0.17
8 5 0.05
9 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.22
Consensus pattern (6 bp):
ATCAGA
Found at i:34801 original size:31 final size:31
Alignment explanation
Indices: 34765--34903 Score: 156
Period size: 31 Copynumber: 4.5 Consensus size: 31
34755 AAGAAACATT
* * *
34765 ATCAGAACTAGAATCAGAATCAGGTGACAGA
1 ATCAGAAATAGAATCAGTATCAGGTAACAGA
*
34796 ATCAGAATTAGAATCAGTATCAGGTAACAGA
1 ATCAGAAATAGAATCAGTATCAGGTAACAGA
*
34827 ATCA-AAATCAGAATTAGTATCAGGTAACAGA
1 ATCAGAAAT-AGAATCAGTATCAGGTAACAGA
* * *
34858 ATCA-ATATCAGAATCAATATCAGGTAATAGA
1 ATCAGAAAT-AGAATCAGTATCAGGTAACAGA
*
34889 ATCAAAAATCAGAAT
1 ATCAGAAAT-AGAAT
34904 GTGAATGCAA
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
30 3 0.03
31 84 0.88
32 9 0.09
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.22
Consensus pattern (31 bp):
ATCAGAAATAGAATCAGTATCAGGTAACAGA
Found at i:34866 original size:19 final size:19
Alignment explanation
Indices: 34805--34868 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 19
34795 AATCAGAATT
*
34805 AGAATCAGTATCAGGTAAC
1 AGAATCAATATCAGGTAAC
34824 AGAATCAA-A--A--T--C
1 AGAATCAATATCAGGTAAC
* *
34836 AGAATTAGTATCAGGTAAC
1 AGAATCAATATCAGGTAAC
34855 AGAATCAATATCAG
1 AGAATCAATATCAG
34869 AATCAATATC
Statistics
Matches: 33, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
12 7 0.21
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 20 0.61
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (19 bp):
AGAATCAATATCAGGTAAC
Found at i:34871 original size:62 final size:63
Alignment explanation
Indices: 34774--34903 Score: 183
Period size: 62 Copynumber: 2.1 Consensus size: 63
34764 TATCAGAACT
* * *
34774 AGAATCAGAATCAGGTGACAGAATCAGAATTAGAATCAGTATCAGGTAACAGAATC-AAAATC
1 AGAATCAGAATCAGGTAACAGAATCAGAATCAGAATCAATATCAGGTAACAGAATCAAAAATC
* * *
34836 AGAATTAGTATCAGGTAACAGAATCA-ATATCAGAATCAATATCAGGTAATAGAATCAAAAATC
1 AGAATCAGAATCAGGTAACAGAATCAGA-ATCAGAATCAATATCAGGTAACAGAATCAAAAATC
34899 AGAAT
1 AGAAT
34904 GTGAATGCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
61 1 0.02
62 48 0.80
63 11 0.18
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (63 bp):
AGAATCAGAATCAGGTAACAGAATCAGAATCAGAATCAATATCAGGTAACAGAATCAAAAATC
Found at i:35075 original size:27 final size:27
Alignment explanation
Indices: 35033--35141 Score: 121
Period size: 27 Copynumber: 4.0 Consensus size: 27
35023 CATTGCTGCT
* * *
35033 CAGATATCAAATATTGTGACAGAGTCAC
1 CAGATA-CAGATATTGTGGCAGAGCCAC
35061 CAGATACAGATATTGTGGCAGAGCCAC
1 CAGATACAGATATTGTGGCAGAGCCAC
*
35088 CAGA-ACAGATATTTGTGGCATAGCCAC
1 CAGATACAGATA-TTGTGGCAGAGCCAC
* * * *
35115 CAGAAATAGATAATGTGGCAAAGCCAC
1 CAGATACAGATATTGTGGCAGAGCCAC
35142 TTAACATAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 7 0.10
27 53 0.74
28 12 0.17
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (27 bp):
CAGATACAGATATTGTGGCAGAGCCAC
Found at i:35328 original size:22 final size:22
Alignment explanation
Indices: 35300--35364 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
35290 GCAAATACGT
*
35300 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
35322 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
35344 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
35365 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:36134 original size:27 final size:26
Alignment explanation
Indices: 35810--36147 Score: 327
Period size: 27 Copynumber: 12.6 Consensus size: 26
35800 TACCCCATAA
*
35810 GGGTATCTCGGTAATTCTACCTTACAG
1 GGGTATTTCGGTAATTCTACC-TACAG
* **
35837 GAGTATTTTAGTAATTCTACCTACA-
1 GGGTATTTCGGTAATTCTACCTACAG
*
35862 GGGTATTTCGGTAATTCTACCCTATAG
1 GGGTATTTCGGTAATTCTA-CCTACAG
* * *
35889 GGGTATTGCGATAATTCTACCCTATAG
1 GGGTATTTCGGTAATTCTA-CCTACAG
* *
35916 GGGTATTTCGATAATTCTACCTTATAG
1 GGGTATTTCGGTAATTCTACC-TACAG
*
35943 GGGTATTTCGGTAATTCTACCCTAAAG
1 GGGTATTTCGGTAATTCTA-CCTACAG
* *
35970 GGGTATTGCGATAATTCTATCCTACAG
1 GGGTATTTCGGTAATTCTA-CCTACAG
* *
35997 GGGTATTCCTGTAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTA-CCTACAG
* *
36024 AGGTATTCCGGTAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTA-CCTACAG
* **
36051 GGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTCTACCTAC-AG
* * **
36078 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTCTACCTAC-AG
* *
36105 GGGTATTTTGGTAATTCTATCCTACGG
1 GGGTATTTCGGTAATTCTA-CCTACAG
*
36132 GGGTATTTCAGTAATT
1 GGGTATTTCGGTAATT
36148 TCACAATCGA
Statistics
Matches: 270, Mismatches: 35, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.06
26 14 0.05
27 235 0.87
28 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (26 bp):
GGGTATTTCGGTAATTCTACCTACAG
Found at i:36189 original size:27 final size:27
Alignment explanation
Indices: 36152--36289 Score: 179
Period size: 27 Copynumber: 5.1 Consensus size: 27
36142 GTAATTTCAC
*
36152 AATCGAGGGTAAAATGGTAATTTTATA
1 AATCGAGGGTAAAATGGTAATTCTATA
36179 AA-CTGAGGGTAAAATGGTAATTCTATA
1 AATC-GAGGGTAAAATGGTAATTCTATA
* *
36206 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTATA
* * * *
36233 AATCAAGGGTGAAACGATAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTATA
* *
36260 AATCGAGGGTAAAATGGTCATTCTACA
1 AATCGAGGGTAAAATGGTAATTCTATA
36287 AAT
1 AAT
36290 TGAAGGCATT
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.01
27 92 0.98
28 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTATA
Found at i:36335 original size:27 final size:26
Alignment explanation
Indices: 36292--36383 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 26
36282 CTACAAATTG
* * *
36292 AAGGCATTTCAGTAATTTTGTAAACC
1 AAGGTATTTCAATAATTTTGTAAATC
36318 AATGGTATTTCAATAATTTT-TAGAAAGTC
1 AA-GGTATTTCAATAATTTTGT--AAA-TC
*
36347 AAGGATATTTCTATAATTTTGTAAATC
1 AAGG-TATTTCAATAATTTTGTAAATC
36374 AAGGGTATTT
1 AA-GGTATTT
36384 TGGTAGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
26 3 0.05
27 24 0.44
28 10 0.18
29 17 0.31
30 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (26 bp):
AAGGTATTTCAATAATTTTGTAAATC
Found at i:36588 original size:27 final size:27
Alignment explanation
Indices: 36376--36581 Score: 270
Period size: 27 Copynumber: 7.6 Consensus size: 27
36366 TGTAAATCAA
* *
36376 GGGTATTTTGGTAGTTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * *
36402 AGGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
* *
36430 TGGTATTTTGATAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
36457 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
*
36484 GGGCATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * *
36511 GGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTACAAACTAG
* * *
36538 TGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAG
36565 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
36582 GGTAAACAAA
Statistics
Matches: 154, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
27 153 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:43518 original size:48 final size:48
Alignment explanation
Indices: 43413--43545 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 48
43403 CTCAATCGAT
* * * *
43413 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATTCCCG
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGCAACTTATCCCCA
* *
43461 GAGTACCTATACCATGGCCCAAAGCCAAATCAAGGCAA-TT-TGCCTCCA
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGCAACTTAT-CC-CCA
* * * *
43509 AAGTGCCTATAACATGGCTCGAAGCCAAACCAAGGCA
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGCA
43546 TAACTCGCAG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
46 1 0.01
47 3 0.04
48 67 0.94
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGCAACTTATCCCCA
Found at i:47299 original size:79 final size:81
Alignment explanation
Indices: 47190--47372 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
47180 TACTCGTTCA
* *
47190 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
47253 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
47270 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
47333 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
47349 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
47373 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:47372 original size:40 final size:40
Alignment explanation
Indices: 47169--47372 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
47159 CGGAATTTAA
** *
47169 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
47209 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
47249 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
47288 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
47328 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
47368 CCGGA
1 CCGGA
47373 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:51023 original size:44 final size:44
Alignment explanation
Indices: 50955--51078 Score: 160
Period size: 44 Copynumber: 2.8 Consensus size: 44
50945 ATTACATGTA
*
50955 TCGCATCCATAATGAACTCTGACCAACTCAACGAGCTCGGATGC
1 TCGCATCCATAATGAACTCAGACCAACTCAACGAGCTCGGATGC
* *
50999 TCGCATCCATAATGAACTCAGACCAACTCAATGAGCTTGGATGC
1 TCGCATCCATAATGAACTCAGACCAACTCAACGAGCTCGGATGC
* * * *
51043 -CTCATACATATTATGAACCCAGACCAGCTCAACGAG
1 TCGCATCCATA--ATGAACTCAGACCAACTCAACGAG
51079 TTTTGGATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 8 0.11
44 41 0.59
45 21 0.30
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (44 bp):
TCGCATCCATAATGAACTCAGACCAACTCAACGAGCTCGGATGC
Found at i:55975 original size:33 final size:35
Alignment explanation
Indices: 55934--56015 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 35
55924 TTTTAAAAAA
***
55934 TAAATTAGGGTTTAGATTTTTTAAAA-AAA-TAAT
1 TAAATTAGGGTTTAGAGGGTTTAAAATAAATTAAT
*
55967 TAAATTAGGTTTTA-AGGGTTTAAAATAAATTAAT
1 TAAATTAGGGTTTAGAGGGTTTAAAATAAATTAAT
56001 TAAATTAGGGTTTAG
1 TAAATTAGGGTTTAG
56016 TTTGTTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 8 0.20
33 16 0.39
34 17 0.41
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (35 bp):
TAAATTAGGGTTTAGAGGGTTTAAAATAAATTAAT
Found at i:56377 original size:127 final size:125
Alignment explanation
Indices: 56117--56512 Score: 478
Period size: 127 Copynumber: 3.2 Consensus size: 125
56107 GATTTTGTTT
* * * *
56117 TTTTTCTACAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGATTATGAAAAGATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAATTAATTTTGAGAAGACG-TTATGAAAAAATAGTGTCAAAA
* * * * * * *
56182 ACGCTTCAAGGAAGATGCACTATCAGTAAAATTACTGAAAGAAGCTCCCACGTGGACGT-TC
65 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCTACGTGGAC-TCTC
* * *
56243 TTCTTCTACAGTAGTTCCTGAAAAATTAATTTTGAGAAGACAGTTCTAAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAATTAATTTTGAGAAGAC-GTTATGAAAAAATAGTGTC-AAA
*
56308 AACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCTACGTGGACTCTC
64 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCTACGTGGACTCTC
* * * *
56370 TTTTTCTACAATAGTTCCTGAAAAAATAA-TTTGAGAAGTCGGTTATGAAAAAATAGTGTCAACA
1 TTTTTCTACAGTAGTTCCTGAAAAATTAATTTTGAGAAGAC-GTTATGAAAAAATAGTGTCAAAA
* * * * *
56434 ATGCTTCAAGTAGGATGCACTGTCAGCAAAATTACTG-AAAAAAGTTCTCACGCGGA-TGCTC
65 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCT-ACGTGGACT-CTC
56495 -TTTTCTACAGTAGTTCCT
1 TTTTTCTACAGTAGTTCCT
56513 ATTTGGCCTT
Statistics
Matches: 235, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
124 27 0.11
125 46 0.20
126 80 0.34
127 82 0.35
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCCTGAAAAATTAATTTTGAGAAGACGTTATGAAAAAATAGTGTCAAAAA
CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCTACGTGGACTCTC
Found at i:62537 original size:40 final size:40
Alignment explanation
Indices: 62477--62629 Score: 182
Period size: 40 Copynumber: 3.8 Consensus size: 40
62467 TATTCGAATG
* * *
62477 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGACTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
62517 ATATCTGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGACTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
62557 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGACTAAGACCCGAAGGCATTTGTGCTAGTGACT
** * *
62597 ATATCCGGGTTAAGTCCCGAAGGCATTTATGCT
1 ATATCCGGACTAAGACCCGAAGGCATTTGTGCT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.97
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGACTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:62617 original size:80 final size:80
Alignment explanation
Indices: 62477--62624 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 80
62467 TATTCGAATG
* * * *
62477 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACTATATCTGGACTAAGATCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGATCCGAAGGCA
62542 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
**
62557 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGTTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGAT-CCGAAGGC
62621 ATTT
65 ATTT
62625 ATGCT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.02
80 60 0.98
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGATCCGAAGGCA
TTTGTGCGAGTTGCT
Done.