Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold165.1
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: 1724686
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 30232 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:1587906 original size:11 final size:11
Alignment explanation
Indices: 1587863--1587905 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
1587853 GAATTAACCG
1587863 AATTACCCGAA
1 AATTACCCGAA
1587874 AATTACCCG--
1 AATTACCCGAA
1587883 AATTACCCGAA
1 AATTACCCGAA
1587894 AATTACCC-AA
1 AATTACCCGAA
1587904 AA
1 AA
1587906 AGTTCGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.30
10 4 0.13
11 17 0.57
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (11 bp):
AATTACCCGAA
Found at i:1588909 original size:38 final size:38
Alignment explanation
Indices: 1588858--1588932 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
1588848 GATGACTCCA
* * *
1588858 CAATCCCATATTTTCCTCCTCAAGTCACTCTAACACTT
1 CAATCCCATATTTTCCTCCTAAAATCACTCCAACACTT
*
1588896 CAATCTCATATTTTCCTCCTAAAATCACTCCAACACT
1 CAATCCCATATTTTCCTCCTAAAATCACTCCAACACT
1588933 CCCCCACCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.29, C:0.36, G:0.01, T:0.33
Consensus pattern (38 bp):
CAATCCCATATTTTCCTCCTAAAATCACTCCAACACTT
Found at i:1592637 original size:37 final size:39
Alignment explanation
Indices: 1592596--1592682 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
1592586 TCGATGAGGT
* *
1592596 ACTGGGTACCAACT-TT-CTTCG-GCTTTGCTGATGAGAC
1 ACTGGGTACCAACTATTGCTTCGAACTAT-CTGATGAGAC
** *
1592633 ACTGGGTGTCAACTATTGCTTCGAACTATCTGATGAGGC
1 ACTGGGTACCAACTATTGCTTCGAACTATCTGATGAGAC
1592672 ACTGGGTACCA
1 ACTGGGTACCA
1592683 TACTGGAGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
37 12 0.30
38 2 0.05
39 23 0.57
40 3 0.08
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (39 bp):
ACTGGGTACCAACTATTGCTTCGAACTATCTGATGAGAC
Found at i:1596736 original size:18 final size:17
Alignment explanation
Indices: 1596713--1596746 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1596703 CGGTTCGTAC
1596713 TATCAATAGTAGTTTCAG
1 TATCAA-AGTAGTTTCAG
*
1596731 TATCAAATTAGTTTCA
1 TATCAAAGTAGTTTCA
1596747 ATTTAAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
TATCAAAGTAGTTTCAG
Found at i:1608280 original size:15 final size:15
Alignment explanation
Indices: 1608260--1608308 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1608250 TTTAGTTTAG
1608260 TTTATATTTTAGTCA
1 TTTATATTTTAGTCA
* **
1608275 TTTATATTTAAAACA
1 TTTATATTTTAGTCA
*
1608290 -TTATATTTTAGTTA
1 TTTATATTTTAGTCA
1608304 TTTAT
1 TTTAT
1608309 GATATTTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (15 bp):
TTTATATTTTAGTCA
Found at i:1610947 original size:13 final size:13
Alignment explanation
Indices: 1610929--1610955 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1610919 TATGAATTTG
1610929 GCCCATTGTAATT
1 GCCCATTGTAATT
1610942 GCCCATTGTAATT
1 GCCCATTGTAATT
1610955 G
1 G
1610956 GACTTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (13 bp):
GCCCATTGTAATT
Found at i:1613663 original size:152 final size:151
Alignment explanation
Indices: 1613489--1613784 Score: 434
Period size: 152 Copynumber: 2.0 Consensus size: 151
1613479 TTCGTTTTTT
* * *
1613489 TAAGGTTTTTTTTAAATTTATTTAAAAAACACAGTAAATTAATACAGTTCAAACATGATGTACTA
1 TAAGGATTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACAGTTCAAACATAATGTACTA
* * * *
1613554 AAATAATGTAAAATAATAAAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGA
66 AAATAATGTAAAATAAAAAAATTACAAAAATAATATA-TTTT-TTAAAAGTAATAAAATCCG-GA
1613618 AAAAATACGAACAAAGGGCCGAAA
128 AAAAATACGAACAAAGGGCCGAAA
* * *
1613642 TAAGGATTTTTTT-AATTTATTTAAAAAATACACTAAATTAATACATTTCAAATATAATGTACTA
1 TAAGGATTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACAGTTCAAACATAATGTACTA
** *
1613706 AAATAATGTAAAATAAAAAAATTTTAAAAATAGTATATTTTTTAAAAGTAATAAAATCCGGAAAA
66 AAATAATGTAAAATAAAAAAATTACAAAAATAATATATTTTTTAAAAGTAATAAAATCCGGAAAA
1613771 AATACGAACAAAGG
131 AATACGAACAAAGG
1613785 ACTTAAACAC
Statistics
Matches: 129, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
150 19 0.15
151 17 0.13
152 70 0.54
153 23 0.18
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (151 bp):
TAAGGATTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACAGTTCAAACATAATGTACTA
AAATAATGTAAAATAAAAAAATTACAAAAATAATATATTTTTTAAAAGTAATAAAATCCGGAAAA
AATACGAACAAAGGGCCGAAA
Found at i:1614570 original size:16 final size:18
Alignment explanation
Indices: 1614531--1614572 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1614521 AAAATTCATA
1614531 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
1614548 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
1614565 A-ATTTATA
1 ATATTTATA
1614573 ATACATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:1617680 original size:11 final size:11
Alignment explanation
Indices: 1617664--1617746 Score: 75
Period size: 11 Copynumber: 7.9 Consensus size: 11
1617654 AAATAGGGAT
1617664 TTGAGAGGAAA
1 TTGAGAGGAAA
*
1617675 TTGAGAGCAAA
1 TTGAGAGGAAA
**
1617686 TTGAGATTAAA
1 TTGAGAGGAAA
*
1617697 -T-AG-GG-AT
1 TTGAGAGGAAA
**
1617704 TTGAGATAAAA
1 TTGAGAGGAAA
1617715 TTGAGAGGAAA
1 TTGAGAGGAAA
*
1617726 TTGAGAGCAAA
1 TTGAGAGGAAA
1617737 TTGAGAGGAA
1 TTGAGAGGAA
1617747 TGATTTATTT
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 4 0.07
10 1 0.02
11 48 0.87
ACGTcount: A:0.45, C:0.02, G:0.30, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:1617707 original size:40 final size:40
Alignment explanation
Indices: 1617652--1617731 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
1617642 TAAAGCTCTT
*
1617652 TTAAATAGGGATTTGAGAGGAAATTGAGAGCAAATTGAGA
1 TTAAATAGGGATTTGAGAGAAAATTGAGAGCAAATTGAGA
* *
1617692 TTAAATAGGGATTTGAGATAAAATTGAGAGGAAATTGAGA
1 TTAAATAGGGATTTGAGAGAAAATTGAGAGCAAATTGAGA
1617732 GCAAATTGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.44, C:0.01, G:0.29, T:0.26
Consensus pattern (40 bp):
TTAAATAGGGATTTGAGAGAAAATTGAGAGCAAATTGAGA
Found at i:1620058 original size:52 final size:48
Alignment explanation
Indices: 1620039--1620241 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
1620029 TGACAAGTGG
* *
1620039 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
1620085 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
1620137 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
1620183 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
1620229 AAAGTGATAAGTG
1 AAAGTGATAAGTG
1620242 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:1620093 original size:98 final size:98
Alignment explanation
Indices: 1619973--1620241 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
1619963 TTTGAGTACT
*
1619973 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
1620038 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
1620071 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
1620136 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
1620169 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
1620234 GATAAGTG
65 GAAAAGTG
1620242 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:1620249 original size:37 final size:37
Alignment explanation
Indices: 1620205--1620350 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
1620195 GATAGCTTTA
*
1620205 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1620242 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
1620279 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
1620316 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1620351 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:1623880 original size:21 final size:21
Alignment explanation
Indices: 1623854--1623894 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1623844 ATCTGCTCAA
* *
1623854 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1623875 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1623895 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1630127 original size:4 final size:4
Alignment explanation
Indices: 1630118--1630150 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1630108 AACTTGAGCC
1630118 TTTA TTTA TTTA TTT- TTTA TTTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA T
1630151 GTACAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.11
4 20 0.74
5 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:1633312 original size:45 final size:45
Alignment explanation
Indices: 1633248--1633340 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
1633238 ACAGATACTC
* *
1633248 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
* * *
1633293 GGTGGAATCAGCACATAGCAACCACGTTACTAATTAATGATGTTT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
1633338 GGT
1 GGT
1633341 TCACATAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
Found at i:1633440 original size:51 final size:50
Alignment explanation
Indices: 1633342--1633533 Score: 163
Period size: 51 Copynumber: 3.8 Consensus size: 50
1633332 ATGTTTGGTT
*
1633342 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCAATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCAATA
** * * *
1633393 CATGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATA-CCATCCAATA
* * * * * * * * **
1633444 CGCATAGTGGTCTGCACATAGTACTACATATGCGACC-TATCATTTCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCCAATA
* *
1633494 CACGTAGTAGCCTGCACCATAGTACTAGACACGTGACCAT
1 CACATAGTAGCCTGCA-CATAGTACTACACACGTGACCAT
1633534 CATTTTCACT
Statistics
Matches: 108, Mismatches: 27, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
49 1 0.01
50 20 0.19
51 84 0.78
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCAATA
Found at i:1643120 original size:12 final size:12
Alignment explanation
Indices: 1643105--1643134 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1643095 AATAATTAAA
1643105 TAAATTAGAAAT
1 TAAATTAGAAAT
*
1643117 TAAATTGGAAAT
1 TAAATTAGAAAT
1643129 TAAATT
1 TAAATT
1643135 CGGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:1662509 original size:29 final size:29
Alignment explanation
Indices: 1662470--1662525 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1662460 CCCATATTCG
1662470 CCCAATCTAAAACAAACCCAACCTAGCAT
1 CCCAATCTAAAACAAACCCAACCTAGCAT
* *
1662499 CCCAATTTAAAACAAAGCCAACCTAGC
1 CCCAATCTAAAACAAACCCAACCTAGC
1662526 TAATTGGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.36, G:0.05, T:0.14
Consensus pattern (29 bp):
CCCAATCTAAAACAAACCCAACCTAGCAT
Found at i:1665458 original size:3 final size:3
Alignment explanation
Indices: 1665443--1665477 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1665433 TTGCTGCGGT
*
1665443 TGA TGA GGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1665478 CTGTTTCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:1673095 original size:43 final size:42
Alignment explanation
Indices: 1673034--1673236 Score: 200
Period size: 43 Copynumber: 4.7 Consensus size: 42
1673024 AAAGCTTGTA
*
1673034 CGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAACTAT
1 CGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAA-TAT
*
1673077 CGATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATC-ATAT
1 CGATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCAATAT
* *
1673118 ACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA-AT
1 -CGATGCCAACGTCCCAGACGTGGTCTTACACGT-AA--TCAATAT
* *
1673163 CGATGCCAACGTCCCAAACGTGGTCTTACACGAAATCTCAA-AT
1 CGATGCCAACGTCCCAGACGTGGTCTTACACGTAA--TCAATAT
* * * *
1673206 TGATGCCAACATCCCAAATGTGGTCTTACAC
1 CGATGCCAACGTCCCAGACGTGGTCTTACAC
1673237 AAAATCACAA
Statistics
Matches: 139, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
41 3 0.02
42 30 0.22
43 71 0.51
44 30 0.22
45 4 0.03
46 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (42 bp):
CGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAATAT
Found at i:1673192 original size:86 final size:84
Alignment explanation
Indices: 1673032--1673199 Score: 225
Period size: 86 Copynumber: 2.0 Consensus size: 84
1673022 GAAAAGCTTG
* * *
1673032 TACGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAACTATCGATGCCACTGTCCCAGACA
1 TACGATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAC-ATCGATGCCACTGTCCCAAACA
1673097 GGGTCTTACACGAAATCATA
65 GGGTCTTACACGAAATCATA
*
1673117 TACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAA
1 TACGATGCCAACGTCCCAGACATGGTCTTACACGT-AA--TCAACATCGATGCC-ACTGTCCCAA
1673180 AC-GTGGTCTTACACGAAATC
62 ACAG-GGTCTTACACGAAATC
1673200 TCAAATTGAT
Statistics
Matches: 74, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
85 33 0.45
86 35 0.47
87 2 0.03
88 4 0.05
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (84 bp):
TACGATGCCAACGTCCCAGACATGGTCTTACACGTAATCAACATCGATGCCACTGTCCCAAACAG
GGTCTTACACGAAATCATA
Found at i:1682846 original size:29 final size:28
Alignment explanation
Indices: 1682809--1682863 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
1682799 AAAATGAGAT
1682809 AAAAGAAAATA-GAAAAAATAACTATTTAC
1 AAAAGAAAA-AGGAAAAAA-AACTATTTAC
* *
1682838 AAAATAAAAAGGAAAAAAAATTATTT
1 AAAAGAAAAAGGAAAAAAAACTATTT
1682864 TCATTTATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (28 bp):
AAAAGAAAAAGGAAAAAAAACTATTTAC
Found at i:1685408 original size:63 final size:63
Alignment explanation
Indices: 1685333--1685471 Score: 172
Period size: 63 Copynumber: 2.2 Consensus size: 63
1685323 CAGGACCGAT
* ** * * * *
1685333 TGGTGGTGGGCCCAGGCTGAATGTTGAGTGTCATGCGTATAGGCCACAAAC-CATTGGGCCAAA
1 TGGTGGTGGGCCCAGGCCGAATGTTGAAAGCCATGAGTATAAGCCACAAACTC-TTGGCCCAAA
* *
1685396 TGGTGGTTGGCCCAGGCCGAATGTTGAAAGCCATGAGTATAAGCCACAAACTCTTGGCCCGAA
1 TGGTGGTGGGCCCAGGCCGAATGTTGAAAGCCATGAGTATAAGCCACAAACTCTTGGCCCAAA
*
1685459 TGGTGGAGGGCCC
1 TGGTGGTGGGCCC
1685472 CATGGTAGAG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 63 0.98
64 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (63 bp):
TGGTGGTGGGCCCAGGCCGAATGTTGAAAGCCATGAGTATAAGCCACAAACTCTTGGCCCAAA
Found at i:1686344 original size:15 final size:15
Alignment explanation
Indices: 1686324--1686352 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1686314 TTTCAAGTTA
1686324 AATAAAGTTGCTATG
1 AATAAAGTTGCTATG
1686339 AATAAAGTTGCTAT
1 AATAAAGTTGCTAT
1686353 AAGTGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (15 bp):
AATAAAGTTGCTATG
Found at i:1695427 original size:9 final size:9
Alignment explanation
Indices: 1695413--1695450 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
1695403 CACCAATCTG
1695413 TTATTCGAA
1 TTATTCGAA
*
1695422 TTATTCAAA
1 TTATTCGAA
*
1695431 TTATTCGAG
1 TTATTCGAA
1695440 TTATTCGAA
1 TTATTCGAA
1695449 TT
1 TT
1695451 GTAATATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:1695512 original size:18 final size:18
Alignment explanation
Indices: 1695489--1695524 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1695479 ATTCGAGTTG
*
1695489 ACTCGAATAATTCAAATA
1 ACTCGAATAATTAAAATA
1695507 ACTCGAATAATTAAAATA
1 ACTCGAATAATTAAAATA
1695525 CATGCTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.28
Consensus pattern (18 bp):
ACTCGAATAATTAAAATA
Found at i:1700307 original size:21 final size:21
Alignment explanation
Indices: 1700281--1700321 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1700271 AGACGAGCAA
* *
1700281 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1700302 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1700322 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1705513 original size:16 final size:16
Alignment explanation
Indices: 1705492--1705531 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1705482 TGTTTGGTTC
1705492 GTTGTAATGGAATAAA
1 GTTGTAATGGAATAAA
*
1705508 GTTGTAATGGAATAGA
1 GTTGTAATGGAATAAA
*
1705524 GCTGTAAT
1 GTTGTAAT
1705532 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.33
Consensus pattern (16 bp):
GTTGTAATGGAATAAA
Found at i:1708631 original size:19 final size:19
Alignment explanation
Indices: 1708607--1708645 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1708597 AATGTATGAA
1708607 AATATCAGGTAAGCAGCAT
1 AATATCAGGTAAGCAGCAT
1708626 AATATCAGGTAAGCAGCAT
1 AATATCAGGTAAGCAGCAT
1708645 A
1 A
1708646 CTGTTTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (19 bp):
AATATCAGGTAAGCAGCAT
Found at i:1712125 original size:13 final size:13
Alignment explanation
Indices: 1712107--1712133 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1712097 CATGTAAAAT
1712107 ACAGTGAATTCAG
1 ACAGTGAATTCAG
1712120 ACAGTGAATTCAG
1 ACAGTGAATTCAG
1712133 A
1 A
1712134 TGTTGGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (13 bp):
ACAGTGAATTCAG
Found at i:1714780 original size:22 final size:24
Alignment explanation
Indices: 1714755--1714810 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
1714745 AGAAATAAAC
* *
1714755 ATATAAAAAAT-TCAAAAA-ATAT
1 ATATAAAAAATCTAAAAAACATAA
*
1714777 ATATATAAAATCTAAAAAACATAA
1 ATATAAAAAATCTAAAAAACATAA
1714801 ATTATAAAAA
1 A-TATAAAAA
1714811 CACGACAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 10 0.37
23 6 0.22
24 4 0.15
25 7 0.26
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (24 bp):
ATATAAAAAATCTAAAAAACATAA
Found at i:1714930 original size:15 final size:15
Alignment explanation
Indices: 1714907--1714936 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1714897 AACAATTTTT
*
1714907 TATAGAATTCTAAAA
1 TATAAAATTCTAAAA
1714922 TATAAAATTCTAAAA
1 TATAAAATTCTAAAA
1714937 AGGTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
TATAAAATTCTAAAA
Found at i:1715981 original size:140 final size:141
Alignment explanation
Indices: 1715710--1715990 Score: 471
Period size: 141 Copynumber: 2.0 Consensus size: 141
1715700 AAAGGATTCA
*
1715710 ACTAAAGACAGCTCAGTTGGACAGCCTCATCATGTTAACAGAGTTAATTAAGGTAAAATGTTTTT
1 ACTAAAGACAACTCAGTTGGACAGCCTCATCATGTTAACAGAGTTAATTAAGGTAAAATGTTTTT
* *
1715775 CTTTTTCTTACCGAAATTTCACTCTATTTTATGCATCAGCTGGAGAATATTGAAATCTCTG-TTT
66 CTTTTTCTTACCGAAATTTCACTCTATTTTATGCATCAACTAGAGAATATTGAAATCTCTGATTT
1715839 TTTATGAGTTT
131 TTTATGAGTTT
1715850 ACTAAAGACAACTCAGTTGGACAGCCTCATCATGTTAACAGAGTTAATTCAA-GTAAAATGTTTT
1 ACTAAAGACAACTCAGTTGGACAGCCTCATCATGTTAACAGAGTTAATT-AAGGTAAAATGTTTT
*
1715914 TCTTTTTTTTTATCC-AAATTTCACTCTATTTTATGCATCAACTAGAGAATATTGAAATCTCT-A
65 TC-TTTTTCTTA-CCGAAATTTCACTCTATTTTATGCATCAACTAGAGAATATTGAAATCTCTGA
1715977 TTTTTTATGAGTTT
128 TTTTTTATGAGTTT
1715991 GTTTTCAAGT
Statistics
Matches: 133, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
140 62 0.47
141 69 0.52
142 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (141 bp):
ACTAAAGACAACTCAGTTGGACAGCCTCATCATGTTAACAGAGTTAATTAAGGTAAAATGTTTTT
CTTTTTCTTACCGAAATTTCACTCTATTTTATGCATCAACTAGAGAATATTGAAATCTCTGATTT
TTTATGAGTTT
Found at i:1717185 original size:17 final size:17
Alignment explanation
Indices: 1717147--1717184 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1717137 TATATAGTGC
*
1717147 AAAAATATAAAACATAT
1 AAAAATATAAAAAATAT
1717164 AAAAATATAAAAAA-AT
1 AAAAATATAAAAAATAT
1717180 AAAAA
1 AAAAA
1717185 AAAANNNNNN
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAATATAAAAAATAT
Found at i:1717186 original size:8 final size:8
Alignment explanation
Indices: 1717147--1717184 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
1717137 TATATAGTGC
1717147 AAAAATAT
1 AAAAATAT
1717155 AAAACATAT
1 AAAA-ATAT
1717164 AAAAATAT
1 AAAAATAT
*
1717172 AAAAAAAT
1 AAAAATAT
1717180 AAAAA
1 AAAAA
1717185 AAAANNNNNN
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAATAT
Done.