Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 150 of 150
Found at i:45621378 original size:24 final size:24
Alignment explanation
Indices: 45621351--45621399 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
45621341 TATGATAGAT
45621351 TCTGCTCTGCATATAATGTGTTAG
1 TCTGCTCTGCATATAATGTGTTAG
45621375 TCTGCTCTGCATATAATGTGTTAG
1 TCTGCTCTGCATATAATGTGTTAG
45621399 T
1 T
45621400 TCAGATCGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (24 bp):
TCTGCTCTGCATATAATGTGTTAG
Found at i:45635599 original size:15 final size:15
Alignment explanation
Indices: 45635579--45635620 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
45635569 TGGACTTCTC
45635579 TTTCTTTTTTTCTTT
1 TTTCTTTTTTTCTTT
45635594 TTTCTTTTTTT-TTT
1 TTTCTTTTTTTCTTT
* *
45635608 TTCCATTTTTTCT
1 TTTCTTTTTTTCT
45635621 AAATTACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTTTTCTTT
Found at i:45637292 original size:32 final size:32
Alignment explanation
Indices: 45637251--45637314 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
45637241 CTGTTAAAAT
45637251 TTGTTACTAACCTTCTCATTCATACCAACCGA
1 TTGTTACTAACCTTCTCATTCATACCAACCGA
45637283 TTGTTACTAACCTTCTCATTCATACCAACCGA
1 TTGTTACTAACCTTCTCATTCATACCAACCGA
45637315 AAACCCTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.34
Consensus pattern (32 bp):
TTGTTACTAACCTTCTCATTCATACCAACCGA
Found at i:45646421 original size:7 final size:6
Alignment explanation
Indices: 45646413--45646439 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45646403 TTTAAAATTA
45646413 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
45646440 TATTTATTAT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:45646427 original size:13 final size:13
Alignment explanation
Indices: 45646405--45646439 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
45646395 AAAAGTATTT
*
45646405 TAAAATTAAAAAA
1 TAAAAATAAAAAA
45646418 TAAAAAT-AAAAA
1 TAAAAATAAAAAA
45646430 TAAAAATAAA
1 TAAAAATAAA
45646440 TATTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:45647610 original size:2 final size:2
Alignment explanation
Indices: 45647603--45647639 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45647593 CTGAGGTATT
45647603 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
45647640 TTTGGGTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:45651070 original size:24 final size:24
Alignment explanation
Indices: 45651043--45651088 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
45651033 CTTCATATGT
45651043 ATATATATATGCATGTATTTCAAC
1 ATATATATATGCATGTATTTCAAC
*
45651067 ATATATATATGTATGTATTTCA
1 ATATATATATGCATGTATTTCA
45651089 TTATATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (24 bp):
ATATATATATGCATGTATTTCAAC
Found at i:45651094 original size:24 final size:24
Alignment explanation
Indices: 45651042--45651094 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
45651032 GCTTCATATG
45651042 TATATATATATGCATGTATTTCAA
1 TATATATATATGCATGTATTTCAA
* * *
45651066 CATATATATATGTATGTATTTCAT
1 TATATATATATGCATGTATTTCAA
45651090 TATAT
1 TATAT
45651095 CATTGAGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (24 bp):
TATATATATATGCATGTATTTCAA
Found at i:45658974 original size:27 final size:27
Alignment explanation
Indices: 45658943--45659002 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
45658933 AAAAAAAAGG
45658943 GTTCAAACCTCAATTTGAGGATACTTA
1 GTTCAAACCTCAATTTGAGGATACTTA
45658970 GTTCAAACCTCAATTTGAGGATACTTA
1 GTTCAAACCTCAATTTGAGGATACTTA
45658997 GTTCAA
1 GTTCAA
45659003 GCTCTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (27 bp):
GTTCAAACCTCAATTTGAGGATACTTA
Found at i:45659941 original size:18 final size:19
Alignment explanation
Indices: 45659918--45659953 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
45659908 TTATTGAAGA
45659918 ATTAGTTTGTAG-TTTTTC
1 ATTAGTTTGTAGATTTTTC
*
45659936 ATTAGTTTTTAGATTTTT
1 ATTAGTTTGTAGATTTTT
45659954 TCCCTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.19, C:0.03, G:0.14, T:0.64
Consensus pattern (19 bp):
ATTAGTTTGTAGATTTTTC
Found at i:45662390 original size:45 final size:45
Alignment explanation
Indices: 45662340--45662437 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 45
45662330 AATAAAAATT
*
45662340 TGTTTTTTGATCAAAGAGCAAATTTGCCCTTTAACCATGTCAATC
1 TGTTTTTTGAGCAAAGAGCAAATTTGCCCTTTAACCATGTCAATC
* * *
45662385 TGTTTTTTGAGCAAAGAGCAAATTTGCTCTTTAACTATGTCAATT
1 TGTTTTTTGAGCAAAGAGCAAATTTGCCCTTTAACCATGTCAATC
45662430 TGTTTTTT
1 TGTTTTTT
45662438 AATCTAACGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (45 bp):
TGTTTTTTGAGCAAAGAGCAAATTTGCCCTTTAACCATGTCAATC
Found at i:45666767 original size:66 final size:66
Alignment explanation
Indices: 45666661--45666793 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
45666651 ACTAAATGAC
45666661 CCAATAGGAAATCATGATAAAATTCAACATGTAACACGAAAAAACAAGAGGGATGAGAGAATGTA
1 CCAATAGGAAATCATGATAAAATTCAACATGTAACACGAAAAAACAAGAGGGATGAGAGAATGTA
45666726 A
66 A
45666727 CCAATAGGAAATCATGATAAAATTCAACATGTAACACGAAAAAACAAGAGGGATGAGAGAATGTA
1 CCAATAGGAAATCATGATAAAATTCAACATGTAACACGAAAAAACAAGAGGGATGAGAGAATGTA
45666792 A
66 A
45666793 C
1 C
45666794 ATAAGCTTGC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.51, C:0.13, G:0.20, T:0.17
Consensus pattern (66 bp):
CCAATAGGAAATCATGATAAAATTCAACATGTAACACGAAAAAACAAGAGGGATGAGAGAATGTA
A
Found at i:45667606 original size:15 final size:13
Alignment explanation
Indices: 45667572--45667596 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45667562 AGAGGGTTTT
45667572 TTTTTTCAATTTC
1 TTTTTTCAATTTC
45667585 TTTTTTCAATTT
1 TTTTTTCAATTT
45667597 TGGTTTTTTC
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:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTCAATTTC
Found at i:45673375 original size:31 final size:30
Alignment explanation
Indices: 45673333--45673428 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 30
45673323 ACTAAAATAG
*
45673333 TCACTTTTGTTTGACTCATGTTACATTTTAA
1 TCACTTATGTTTGACT-ATGTTACATTTTAA
* * *
45673364 TCACTTATGTTTGA-AATGTTACGTTTTAG
1 TCACTTATGTTTGACTATGTTACATTTTAA
* *
45673393 TCACTTATGTTATCACGT-TGTAACATTTTAA
1 TCACTTATGTT-TGAC-TATGTTACATTTTAA
45673424 TCACT
1 TCACT
45673429 GAGCCGTTAG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
29 23 0.43
30 2 0.04
31 28 0.53
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (30 bp):
TCACTTATGTTTGACTATGTTACATTTTAA
Found at i:45673396 original size:29 final size:30
Alignment explanation
Indices: 45673330--45673403 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
45673320 ACTACTAAAA
* *
45673330 TAGTCACTTTTGTTTGACTCATGTTACATTT
1 TAGTCACTTATGTTTGAC-AATGTTACATTT
* *
45673361 TAATCACTTATGTTTGA-AATGTTACGTTT
1 TAGTCACTTATGTTTGACAATGTTACATTT
45673390 TAGTCACTTATGTT
1 TAGTCACTTATGTT
45673404 ATCACGTTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 23 0.61
31 15 0.39
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (30 bp):
TAGTCACTTATGTTTGACAATGTTACATTT
Found at i:45676166 original size:147 final size:147
Alignment explanation
Indices: 45675912--45676182 Score: 425
Period size: 147 Copynumber: 1.8 Consensus size: 147
45675902 AGGATGTTCT
* *
45675912 TGCATTTAAAAAGGCACGTGAACAGGCACAGCAAGGGAACGATAAGAAGCAGGCAGAGGCAGGTA
1 TGCATTTAAAAAGGCACGTAAACAGGCACAGCAAGGGAACGATAAGAAGCAGGCAGAGGCAGATA
* * * *
45675977 CAATGACGGAAGAGAAAAAGAAGCAGGATCAGGAATTAGAGGAGCAAGAACGACAAGAAGTGTTC
66 CAATGACGAAAGAGAAAAAGAAGCAGAATCAGAAATTAGAGGAGCAAGAACGAAAAGAAGTGTTC
45676042 TTCACCAAGAATGCTCG
131 TTCACCAAGAATGCTCG
* * * * *
45676059 TGCATTTACAAAGGCATGTAAACAGGCACAGCAATGGAAGGCTAAGAAGCAGGCAGAGGCAGATA
1 TGCATTTAAAAAGGCACGTAAACAGGCACAGCAAGGGAACGATAAGAAGCAGGCAGAGGCAGATA
**
45676124 CCCTGACGAAAGAGAAAAAGAAGCAGAATCAGAAATTAGAGGAGCAAGAACGAAAAGAA
66 CAATGACGAAAGAGAAAAAGAAGCAGAATCAGAAATTAGAGGAGCAAGAACGAAAAGAA
45676183 ATGGAGAAGA
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
147 111 1.00
ACGTcount: A:0.44, C:0.16, G:0.29, T:0.11
Consensus pattern (147 bp):
TGCATTTAAAAAGGCACGTAAACAGGCACAGCAAGGGAACGATAAGAAGCAGGCAGAGGCAGATA
CAATGACGAAAGAGAAAAAGAAGCAGAATCAGAAATTAGAGGAGCAAGAACGAAAAGAAGTGTTC
TTCACCAAGAATGCTCG
Found at i:45677819 original size:2 final size:2
Alignment explanation
Indices: 45677812--45677977 Score: 164
Period size: 2 Copynumber: 95.0 Consensus size: 2
45677802 TCAATTTAAT
45677812 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
45677852 -G AG -G AG -G AG -G AG -G AG AG AG AG AG AG -G AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
45677887 AG -G AG -G AG -G AG -G AG -G AG -G AG -G AG -G AG -G AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
45677919 AG AG -G AG -G AG -G AG AG AG AG AG -G AG -G AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
45677956 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
45677978 NNNNNNNNNN
Statistics
Matches: 140, Mismatches: 0, Indels: 48
0.74 0.00 0.26
Matches are distributed among these distances:
1 24 0.17
2 116 0.83
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45677849 original size:3 final size:3
Alignment explanation
Indices: 45677841--45677945 Score: 135
Period size: 3 Copynumber: 34.0 Consensus size: 3
45677831 GAGAGAGAGA
45677841 GAG GAG GA- GAG GAG GAG GAG GAG GA- GAG AGAG AGAG GAG GA- GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG -GAG -GAG GAG GAG GAG
45677885 AGAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG AGAG GAG GAG GAG
1 -GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG -GAG GAG GAG GAG
45677932 AGAG AGAG GAG GAG
1 -GAG -GAG GAG GAG
45677946 AGAGAGAGAG
Statistics
Matches: 95, Mismatches: 0, Indels: 14
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.06
3 69 0.73
4 20 0.21
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:45678093 original size:8 final size:8
Alignment explanation
Indices: 45678080--45678116 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
45678070 NNNNNNNNGA
45678080 GAGAGAGG
1 GAGAGAGG
45678088 GAGAGAGG
1 GAGAGAGG
45678096 GAGAGAGG
1 GAGAGAGG
45678104 GAGAGAGG
1 GAGAGAGG
45678112 GAGAG
1 GAGAG
45678117 GGAGAGGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:45678099 original size:6 final size:6
Alignment explanation
Indices: 45678082--45678128 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
45678072 NNNNNNGAGA
*
45678082 GAGAGG GAGAGAG G-GAGA GAG-GG AGAGAGG GAGAGG GAGAGG GAGAG
1 GAGAGG GAGAG-G GAGAGG GAGAGG -GAGAGG GAGAGG GAGAGG GAGAG
45678129 CTGAGCTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 2 0.06
6 29 0.83
7 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:45686058 original size:21 final size:21
Alignment explanation
Indices: 45686025--45686071 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
45686015 ACCTTCGTTG
* * *
45686025 TTTTCCTTTTCTTTCTTTCGC
1 TTTTTCTTGTCTTTCTTGCGC
*
45686046 TTTTTCTTGTCTTTCTTGCTC
1 TTTTTCTTGTCTTTCTTGCGC
45686067 TTTTT
1 TTTTT
45686072 TAGTTGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.70
Consensus pattern (21 bp):
TTTTTCTTGTCTTTCTTGCGC
Found at i:45687262 original size:16 final size:17
Alignment explanation
Indices: 45687241--45687277 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
45687231 GTTAAAATAA
*
45687241 TTTAGGGTTTTA-TTTT
1 TTTAGGGTTTAAGTTTT
45687257 TTTAGGGTTTAAGTTTT
1 TTTAGGGTTTAAGTTTT
45687274 TTTA
1 TTTA
45687278 AAAAATTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (17 bp):
TTTAGGGTTTAAGTTTT
Found at i:45687309 original size:25 final size:24
Alignment explanation
Indices: 45687258--45687310 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 24
45687248 TTTTATTTTT
45687258 TTAGGGTTTAAGTTTTTTTAAAAAA
1 TTAGGGTTTAAG-TTTTTTAAAAAA
45687283 TTAGGGTTTAAAG-TTTTTAAAATAA
1 TTAGGGTTT-AAGTTTTTTAAAA-AA
45687308 TTA
1 TTA
45687311 ATTAAACTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 9 0.35
25 14 0.54
26 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (24 bp):
TTAGGGTTTAAGTTTTTTAAAAAA
Found at i:45687365 original size:34 final size:34
Alignment explanation
Indices: 45687298--45687386 Score: 128
Period size: 34 Copynumber: 2.6 Consensus size: 34
45687288 GTTTAAAGTT
* *
45687298 TTTAAAAT-AATTAATTAAACTAGGTTTTAGGGG
1 TTTAAAATAAATAAATTAAATTAGGTTTTAGGGG
45687331 TTTAAAATAAATAAATTAAATTAGGGTTTT-GGGG
1 TTTAAAATAAATAAATTAAATTA-GGTTTTAGGGG
*
45687365 TTTAAAATAAATAAATGAAATT
1 TTTAAAATAAATAAATTAAATT
45687387 GGGATTTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
33 8 0.16
34 37 0.73
35 6 0.12
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (34 bp):
TTTAAAATAAATAAATTAAATTAGGTTTTAGGGG
Found at i:45687720 original size:126 final size:126
Alignment explanation
Indices: 45687495--45687886 Score: 453
Period size: 125 Copynumber: 3.1 Consensus size: 126
45687485 TGATTTTGTT
* * * * *
45687495 TTTTTCTACAGTAATTTCAGAAAAATTAATTTTGAGAAGACGGA-TCTGAAAAGATAATGTC-AA
1 TTTTTCTACAGTAGTTCCTGAAAAA-TAATTTTGAGAAGAC-GATTCTGAAAAAATAGTGTCAAA
* * * *
45687558 AAACGCTTCAAGCAGGGTGTATTGTCAGCAAAATTACTAAAAAAAGCTCCAACATG-G-ATGC-T
64 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCC--CATGTGAACGCTT
45687620 C
126 C
* * *
45687621 TTTTTCTACAGCAGTTCCTGAAAAATAATTTTGAGATGACGATTATGAAAAAATAGTGTCAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAA
* * * * *
45687686 ACGCTTCAAGAATGATGCACTATCATCAAAATTACTGAAAAAAGCTCCCATGTGAACGCTTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCATGTGAACGCTTC
* *
45687748 TTTTTCTAAAGTAGTTCCT-AAAAA-AATTTTGAGACGACGATTCTGAAAAAATAGTGTCAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAA
* * *
45687811 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCCCACGT-AGACGC-TA
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCATGTGA-ACGCTTC
45687871 TTTTT-TACAGTAGTTC
1 TTTTTCTACAGTAGTTC
45687887 TTGCTTGGCC
Statistics
Matches: 230, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
122 10 0.04
123 7 0.03
124 24 0.10
125 98 0.43
126 73 0.32
127 18 0.08
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCATGTGAACGCTTC
Found at i:45691867 original size:46 final size:46
Alignment explanation
Indices: 45691801--45692099 Score: 455
Period size: 46 Copynumber: 6.6 Consensus size: 46
45691791 TTTGAGTACT
*
45691801 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCTTTATCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* **
45691846 TCTGATCAA-TATACAAAGTGATAAGTGGTAATTTTAGCTACACTTA
1 TCTGATCAAGT-GACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
45691892 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
45691938 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
45691984 TCTGATCAAGTGACAAAGTGATAAGTGGTACCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
45692030 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACGCTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
45692075 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
45692100 ATCATACATA
Statistics
Matches: 234, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
43 12 0.05
44 5 0.02
45 26 0.11
46 191 0.82
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:45694588 original size:51 final size:51
Alignment explanation
Indices: 45694512--45694631 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
45694502 ACTTCTGATC
* * *
45694512 AGTGACAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAATGATAGCTTTAGCTACACTTATCTAATCAATGACA
* * *
45694563 AGTGACAAGTGATAAGTGATAGCTTTAGCTACGCTTATCTAATCAATGATA
1 AGTGACAAGTGATAAATGATAGCTTTAGCTACACTTATCTAATCAATGACA
**
45694614 AGCAACAAGTGATAAATG
1 AGTGACAAGTGATAAATG
45694632 TGATCCGTGT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAATGATAGCTTTAGCTACACTTATCTAATCAATGACA
Found at i:45698324 original size:13 final size:14
Alignment explanation
Indices: 45698295--45698327 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
45698285 TAATACCAAA
45698295 TAAATTTAGAAATT
1 TAAATTTAGAAATT
*
45698309 TAAATTTA-ATATT
1 TAAATTTAGAAATT
45698322 TAAATT
1 TAAATT
45698328 ATTAAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TAAATTTAGAAATT
Found at i:45705091 original size:12 final size:12
Alignment explanation
Indices: 45705074--45705100 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
45705064 AGTTTTCTAC
45705074 AGAACTAGCAAG
1 AGAACTAGCAAG
45705086 AGAACTAGCAAG
1 AGAACTAGCAAG
45705098 AGA
1 AGA
45705101 GGTGGCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.26, T:0.07
Consensus pattern (12 bp):
AGAACTAGCAAG
Found at i:45715159 original size:15 final size:15
Alignment explanation
Indices: 45715139--45715169 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
45715129 AGTTGTAGTT
45715139 ACATGATTTATTTTG
1 ACATGATTTATTTTG
45715154 ACATGATTTATTTTG
1 ACATGATTTATTTTG
45715169 A
1 A
45715170 TCTAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (15 bp):
ACATGATTTATTTTG
Found at i:45722001 original size:33 final size:33
Alignment explanation
Indices: 45721961--45722024 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
45721951 TGGATGATAG
45721961 TAATAATAGTAACCCCCTAACCCCTAAAACCAA
1 TAATAATAGTAACCCCCTAACCCCTAAAACCAA
* * *
45721994 TAATAATAGTAAGCCCCTAAGCCGTAAAACC
1 TAATAATAGTAACCCCCTAACCCCTAAAACC
45722025 CTCACTCCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.44, C:0.30, G:0.08, T:0.19
Consensus pattern (33 bp):
TAATAATAGTAACCCCCTAACCCCTAAAACCAA
Found at i:45722201 original size:3 final size:3
Alignment explanation
Indices: 45722195--45722245 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
45722185 AAAAAAAAAA
*
45722195 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
45722243 AAG
1 AAG
45722246 CTTCAATTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:45728223 original size:15 final size:14
Alignment explanation
Indices: 45728196--45728223 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45728186 AATTAGTGTT
45728196 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
45728210 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
45728224 TGGGGGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
GAAAACTAAAAAAA
Found at i:45732355 original size:2 final size:2
Alignment explanation
Indices: 45732348--45732390 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
45732338 CATATAATTA
45732348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45732390 A
1 A
45732391 CCAATTAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45733742 original size:77 final size:76
Alignment explanation
Indices: 45733635--45733845 Score: 332
Period size: 77 Copynumber: 2.7 Consensus size: 76
45733625 AAGAACTATT
* *
45733635 TATCGTGGCCCGAAACCAATTTATCTGATATGCATGGCCCGAAGCCAAATCGGTATAAATCGCAC
1 TATCATGG-CCGAAGCCAATTTATCTGATATGCATGGCCCGAAGCCAAATCGGTATAAATCGCAC
45733700 CCGAAGTGCTAA
65 CCGAAGTGCTAA
* * * *
45733712 TATCATGGTCCGAAGCCAATTTATCCGATATGCATGTCCCAAAGCCAAATCGATATAAATCGCAC
1 TATCATGG-CCGAAGCCAATTTATCTGATATGCATGGCCCGAAGCCAAATCGGTATAAATCGCAC
45733777 CCGAAGTGCTAA
65 CCGAAGTGCTAA
*
45733789 TATCATGGCCTGAAGCCAATTTATCTGATATGCATGGCCCGAAGCCAAATTGGTATA
1 TATCATGGCC-GAAGCCAATTTATCTGATATGCATGGCCCGAAGCCAAATCGGTATA
45733846 TCAAATTATA
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
76 2 0.02
77 119 0.98
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (76 bp):
TATCATGGCCGAAGCCAATTTATCTGATATGCATGGCCCGAAGCCAAATCGGTATAAATCGCACC
CGAAGTGCTAA
Found at i:45743349 original size:15 final size:15
Alignment explanation
Indices: 45743326--45743359 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
45743316 TTTTAGTATA
*
45743326 ATTTTTTATAAAAAT
1 ATTTATTATAAAAAT
*
45743341 ATTTATTATAAAATT
1 ATTTATTATAAAAAT
45743356 ATTT
1 ATTT
45743360 TTTACCGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTATTATAAAAAT
Found at i:45746420 original size:132 final size:132
Alignment explanation
Indices: 45746183--45746443 Score: 477
Period size: 132 Copynumber: 2.0 Consensus size: 132
45746173 TCTTTGTGTA
* *
45746183 ATGTACAACGTGAATGTGAAGTGCGTTTGTTTAATGAAGAAAAAGAAACGAGCAGCGGAATTAGC
1 ATGTACAACGTGAATGTGAAGTGCGTTTGTTTAATCAAGAAAAAGAAAAGAGCAGCGGAATTAGC
* *
45746248 ACCATCATCATCATGCAGTGCAAACTTGTCCATCTCTGCTTTGTTCTGCTCCTCTTCATTTCAAT
66 ACCATCATCATCATGCAATGCAAACTTGTCCATCTCTGCTTTGTTCTGCTCCTCTTCAATTCAAT
45746313 TT
131 TT
45746315 ATGTACAACGTGAATGTGAAGTGCGTTTGTTTAATCAAGAAAAAGAAAAGAGCAGCGGAATTAGC
1 ATGTACAACGTGAATGTGAAGTGCGTTTGTTTAATCAAGAAAAAGAAAAGAGCAGCGGAATTAGC
*
45746380 ACCATCATCATCATGCAATGCAAACTTGTCCATCTCTGCTTTGTTCTGCTCTTCTTCAATTCAA
66 ACCATCATCATCATGCAATGCAAACTTGTCCATCTCTGCTTTGTTCTGCTCCTCTTCAATTCAA
45746444 CTAAATTCGG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (132 bp):
ATGTACAACGTGAATGTGAAGTGCGTTTGTTTAATCAAGAAAAAGAAAAGAGCAGCGGAATTAGC
ACCATCATCATCATGCAATGCAAACTTGTCCATCTCTGCTTTGTTCTGCTCCTCTTCAATTCAAT
TT
Found at i:45760411 original size:19 final size:19
Alignment explanation
Indices: 45760387--45760426 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
45760377 ACTTTACAGG
45760387 TAACATATTAGAAACAAGT
1 TAACATATTAGAAACAAGT
45760406 TAACATATTAGAAACAAGT
1 TAACATATTAGAAACAAGT
45760425 TA
1 TA
45760427 TCCTATCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (19 bp):
TAACATATTAGAAACAAGT
Done.