Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold40
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: 1915636
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 67970 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1797364 original size:26 final size:26
Alignment explanation
Indices: 1797328--1797384 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
1797318 TACCCTAATT
1797328 ATATATTTTTTTATTTTTAATCAAAC
1 ATATATTTTTTTATTTTTAATCAAAC
*
1797354 ATATA-TTTTTTATTTTTAATCAAAT
1 ATATATTTTTTTATTTTTAATCAAAC
1797379 ATATAT
1 ATATAT
1797385 ATTATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATATTTTTTTATTTTTAATCAAAC
Found at i:1798719 original size:27 final size:26
Alignment explanation
Indices: 1798678--1798751 Score: 103
Period size: 27 Copynumber: 2.8 Consensus size: 26
1798668 GCACACCTTA
*
1798678 GCTCTTTGTGAGCTTCCCGTTTAAAG
1 GCTCTTTGTGAGCTTCCCGATTAAAG
* *
1798704 GCTCTTTCATGAGCTTCCTGATTAAAG
1 GCTCTTT-GTGAGCTTCCCGATTAAAG
*
1798731 CCTCTTTGTGAGCTTCCCGAT
1 GCTCTTTGTGAGCTTCCCGAT
1798752 ATGGCTCTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 19 0.46
27 22 0.54
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (26 bp):
GCTCTTTGTGAGCTTCCCGATTAAAG
Found at i:1798761 original size:26 final size:26
Alignment explanation
Indices: 1798679--1798762 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
1798669 CACACCTTAG
*
1798679 CTCTTTGTGAGCTTCCCGTTTAAAGGCT
1 CTCTTTGTGAGCTTCCCG-AT-AAGGCT
** * *
1798707 CT-TTCATGAGCTTCCTGATTAAAGC-
1 CTCTTTGTGAGCTTCCCGA-TAAGGCT
*
1798732 CTCTTTGTGAGCTTCCCGATATGGCT
1 CTCTTTGTGAGCTTCCCGATAAGGCT
1798758 CTCTT
1 CTCTT
1798763 CAACTTCTCG
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
25 6 0.14
26 22 0.51
27 13 0.30
28 2 0.05
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.39
Consensus pattern (26 bp):
CTCTTTGTGAGCTTCCCGATAAGGCT
Found at i:1798927 original size:25 final size:25
Alignment explanation
Indices: 1798812--1798930 Score: 93
Period size: 25 Copynumber: 4.8 Consensus size: 25
1798802 TGGCTCTTTG
*
1798812 GAGCTACCCGTTAT-TGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCACAT
* **
1798836 AAGCTT--C-TTAATTATGGCTCTTAT
1 GAGCTTCCCGTT-A-TATGGCTCACAT
* * **
1798860 GAGCTTCCCGTTATATAGCCCGGAT
1 GAGCTTCCCGTTATATGGCTCACAT
* * *
1798885 AAGCTTCTCGTTACATGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCACAT
1798910 GAGCTTCCCGTTATATGGCTC
1 GAGCTTCCCGTTATATGGCTC
1798931 GAGAGAGTGC
Statistics
Matches: 70, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
21 2 0.03
22 2 0.03
23 1 0.01
24 17 0.24
25 44 0.63
26 2 0.03
27 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCACAT
Found at i:1803880 original size:39 final size:39
Alignment explanation
Indices: 1803826--1803938 Score: 217
Period size: 39 Copynumber: 2.9 Consensus size: 39
1803816 TGTTTTAGAC
1803826 ATGGGACCTAATGATAATTCAATTGATGTGCCCTTCCAA
1 ATGGGACCTAATGATAATTCAATTGATGTGCCCTTCCAA
*
1803865 ATGGGACCTAATGATAATTCAATTGATGTGCCCTTCCAC
1 ATGGGACCTAATGATAATTCAATTGATGTGCCCTTCCAA
1803904 ATGGGACCTAATGATAATTCAATTGATGTGCCCTT
1 ATGGGACCTAATGATAATTCAATTGATGTGCCCTT
1803939 AGTCTTAGGT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (39 bp):
ATGGGACCTAATGATAATTCAATTGATGTGCCCTTCCAA
Found at i:1808364 original size:16 final size:16
Alignment explanation
Indices: 1808343--1808374 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1808333 ATGATGAAAG
1808343 GCTGATTGATTTAGTT
1 GCTGATTGATTTAGTT
1808359 GCTGATTGATTTAGTT
1 GCTGATTGATTTAGTT
1808375 ATCTTCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
GCTGATTGATTTAGTT
Found at i:1808416 original size:16 final size:17
Alignment explanation
Indices: 1808395--1808428 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1808385 ATTGTTTAAA
1808395 AAGAAAAAAGAAA-AAG
1 AAGAAAAAAGAAATAAG
*
1808411 AAGAAAAGAGAAATAAG
1 AAGAAAAAAGAAATAAG
1808428 A
1 A
1808429 GAATTGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAGAAATAAG
Found at i:1815122 original size:24 final size:25
Alignment explanation
Indices: 1815097--1815189 Score: 86
Period size: 24 Copynumber: 3.8 Consensus size: 25
1815087 TGGTTATCCA
*
1815097 GAGCTTTCCGTTAATGGCTCTTCA-
1 GAGCTTCCCGTTAATGGCTCTTCAT
* * * *
1815121 GAGCTGCCCATTATTGGCTC-GCAT
1 GAGCTTCCCGTTAATGGCTCTTCAT
*
1815145 GAGCTTCCTGATT-ATGGCTCTT-AT
1 GAGCTTCCCG-TTAATGGCTCTTCAT
1815169 GAGCTTCCCGTTATATGGCTC
1 GAGCTTCCCGTTA-ATGGCTC
1815190 GGGAGAGTGC
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
23 4 0.08
24 40 0.75
25 9 0.17
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.35
Consensus pattern (25 bp):
GAGCTTCCCGTTAATGGCTCTTCAT
Found at i:1821086 original size:128 final size:128
Alignment explanation
Indices: 1820891--1821146 Score: 453
Period size: 128 Copynumber: 2.0 Consensus size: 128
1820881 AAGACAGGGG
* *
1820891 AATACAAAATGCATAATTTAATTATAAACACATATTAATGACTAATATCACAACTATCATATGCG
1 AATAAAAAATGCACAATTTAATTATAAACACATATTAATGACTAATATCACAACTATCATATGCG
1820956 AACCTTTTGAATTCATACATATCAGCACATTATTTCAA-ACTACATTCAATTTACACATGCTAT
66 AACCTTTTGAATTCATACATATCAGCACATTATTT-AATACTACATTCAATTTACACATGCTAT
1821019 AATAAAAAATGCACAATTTAATTATTAAA-ACATATTAATGACTAATATCACAACTATCATATGC
1 AATAAAAAATGCACAATTTAATTA-TAAACACATATTAATGACTAATATCACAACTATCATATGC
*
1821083 GAACCTTTTGAATTCATACATATTAGCACATTATTTAATACTACATTCAATTTACACATGCTAT
65 GAACCTTTTGAATTCATACATATCAGCACATTATTTAATACTACATTCAATTTACACATGCTAT
1821147 CATATTTCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
127 2 0.02
128 117 0.95
129 4 0.03
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (128 bp):
AATAAAAAATGCACAATTTAATTATAAACACATATTAATGACTAATATCACAACTATCATATGCG
AACCTTTTGAATTCATACATATCAGCACATTATTTAATACTACATTCAATTTACACATGCTAT
Found at i:1822583 original size:21 final size:18
Alignment explanation
Indices: 1822559--1822607 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 18
1822549 AATTATTATA
1822559 TAATACATATATACATTTACT
1 TAATA-ATATA-ACATTT-CT
*
1822580 TAATAAT-TAAGATTTCT
1 TAATAATATAACATTTCT
1822597 TAATAATATAA
1 TAATAATATAA
1822608 TATATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.35
18 8 0.31
19 2 0.08
20 2 0.08
21 5 0.19
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATAATATAACATTTCT
Found at i:1837123 original size:16 final size:16
Alignment explanation
Indices: 1837099--1837129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1837089 CTTGGACTCA
*
1837099 AATCGAATCCAAGTCG
1 AATCAAATCCAAGTCG
1837115 AATCAAATCCAAGTC
1 AATCAAATCCAAGTC
1837130 AAAGAACAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (16 bp):
AATCAAATCCAAGTCG
Found at i:1841417 original size:21 final size:21
Alignment explanation
Indices: 1841369--1841410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1841359 TTTTCCTAAG
* *
1841369 ATGTGAATTGGATTGAATTGA
1 ATGTAAATTGGATTAAATTGA
*
1841390 ATGTAAATTGTATTAAATTGA
1 ATGTAAATTGGATTAAATTGA
1841411 TGTTAAACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (21 bp):
ATGTAAATTGGATTAAATTGA
Found at i:1841860 original size:25 final size:25
Alignment explanation
Indices: 1841824--1841951 Score: 64
Period size: 25 Copynumber: 5.2 Consensus size: 25
1841814 ACACACCACA
1841824 GCTCTTATAAGCGTCCCGATATATG
1 GCTCTTATAAGCGTCCCGATATATG
* * *
1841849 GCTCTCTA-AAGCTTCCTGTTATATG
1 GCTCT-TATAAGCGTCCCGATATATG
* ** * **
1841874 GTTCTTACGAGCTTCTTGATA-ATTG
1 GCTCTTATAAGCGTCCCGATATA-TG
* * *
1841899 GCTCTTATGAGCTTCCCGATAAATG
1 GCTCTTATAAGCGTCCCGATATATG
* *** *
1841924 ACTCTCCGAAGCTTCCCGATAT-TG
1 GCTCTTATAAGCGTCCCGATATATG
1841948 GCTC
1 GCTC
1841952 GCTTGAACTT
Statistics
Matches: 81, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
24 8 0.10
25 70 0.86
26 3 0.04
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (25 bp):
GCTCTTATAAGCGTCCCGATATATG
Found at i:1841862 original size:87 final size:87
Alignment explanation
Indices: 1841700--1841869 Score: 216
Period size: 87 Copynumber: 2.0 Consensus size: 87
1841690 AGGTTCCCAA
* * * * * * *
1841700 TTGGCTGTGATCCTGCATGTGTTGTGGTCACACCATAGCTCTTACGAGTGTCCTAATATTTGGCT
1 TTGGCTGTGATCCTACATGTGTTGTGGACACACCACAGCTCTTACAAGCGTCCCAATATATGGCT
*
1841765 CTCACGAGCTTCCCGTTAATAT
66 CTCACAAGCTTCCCGTTAATAT
* * *
1841787 TTGGTTGTGATCCTACATGTGTTGTGGACACACCACAGCTCTTATAAGCGTCCCGATATATGGCT
1 TTGGCTGTGATCCTACATGTGTTGTGGACACACCACAGCTCTTACAAGCGTCCCAATATATGGCT
*
1841852 CTCTA-AAGCTTCCTGTTA
66 CTC-ACAAGCTTCCCGTTA
1841870 TATGGTTCTT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
87 69 0.99
88 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (87 bp):
TTGGCTGTGATCCTACATGTGTTGTGGACACACCACAGCTCTTACAAGCGTCCCAATATATGGCT
CTCACAAGCTTCCCGTTAATAT
Found at i:1842025 original size:25 final size:25
Alignment explanation
Indices: 1842003--1842051 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1841993 TATAGCTCGA
1842003 ATGACCTTCCTGTTACTTGGCTCAC
1 ATGACCTTCCTGTTACTTGGCTCAC
*
1842028 ATGAGCTTCCTGTTACTTGGCTCA
1 ATGACCTTCCTGTTACTTGGCTCA
1842052 AGAGAGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (25 bp):
ATGACCTTCCTGTTACTTGGCTCAC
Found at i:1854164 original size:21 final size:21
Alignment explanation
Indices: 1854140--1854192 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1854130 CATTGTTTCT
*
1854140 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
1854161 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
1854182 AATCTCACCGC
1 AATCTCACCGC
1854193 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:1857733 original size:20 final size:19
Alignment explanation
Indices: 1857705--1857744 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1857695 TAATTAAAGT
1857705 TAATCAAAT-CTAATTTAAC
1 TAATCAAATGCTAA-TTAAC
1857724 TAATCTAAATGCTAATTAAC
1 TAATC-AAATGCTAATTAAC
1857744 T
1 T
1857745 TTTAATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATCAAATGCTAATTAAC
Found at i:1861181 original size:2 final size:2
Alignment explanation
Indices: 1861174--1861200 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1861164 TGTTTTCTTT
1861174 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1861201 TAAAATCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1862924 original size:2 final size:2
Alignment explanation
Indices: 1862917--1862945 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1862907 GCTTTAATAC
1862917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1862946 CTTTCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1868183 original size:17 final size:18
Alignment explanation
Indices: 1868183--1868233 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
1868173 TAAAATTAAA
*
1868183 AAAATTTAAAAGTATTTT
1 AAAATTTAAAAATATTTT
1868201 AAAATTTAAAAA-ATTTT
1 AAAATTTAAAAATATTTT
*
1868218 AAAA-ATAAAAATATTT
1 AAAATTTAAAAATATTT
1868234 ATTATATTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 6 0.20
17 13 0.43
18 11 0.37
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTTAAAAATATTTT
Found at i:1868183 original size:28 final size:28
Alignment explanation
Indices: 1868158--1868224 Score: 109
Period size: 27 Copynumber: 2.4 Consensus size: 28
1868148 TTAAAAAATT
1868158 ATTTTAAAAATATTTTAAAA-TTAAAAA
1 ATTTTAAAAATATTTTAAAATTTAAAAA
* *
1868185 AATTTAAAAGTATTTTAAAATTTAAAAA
1 ATTTTAAAAATATTTTAAAATTTAAAAA
1868213 ATTTTAAAAATA
1 ATTTTAAAAATA
1868225 AAAATATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
ATTTTAAAAATATTTTAAAATTTAAAAA
Found at i:1868204 original size:18 final size:17
Alignment explanation
Indices: 1868183--1868221 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1868173 TAAAATTAAA
*
1868183 AAAATTTAAAAGTATTTT
1 AAAATTTAAAA-AATTTT
1868201 AAAATTTAAAAAATTTT
1 AAAATTTAAAAAATTTT
1868218 AAAA
1 AAAA
1868222 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAATTTAAAAAATTTT
Found at i:1870601 original size:17 final size:18
Alignment explanation
Indices: 1870601--1870651 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
1870591 TAAAATTAAA
*
1870601 AAAATTTAAAAGTATTTT
1 AAAATTTAAAAATATTTT
1870619 AAAATTTAAAAA-ATTTT
1 AAAATTTAAAAATATTTT
*
1870636 AAAA-ATAAAAATATTT
1 AAAATTTAAAAATATTT
1870652 ATTATATTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 6 0.20
17 13 0.43
18 11 0.37
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTTAAAAATATTTT
Found at i:1870601 original size:28 final size:28
Alignment explanation
Indices: 1870576--1870642 Score: 109
Period size: 27 Copynumber: 2.4 Consensus size: 28
1870566 TTAAAAAATT
1870576 ATTTTAAAAATATTTTAAAA-TTAAAAA
1 ATTTTAAAAATATTTTAAAATTTAAAAA
* *
1870603 AATTTAAAAGTATTTTAAAATTTAAAAA
1 ATTTTAAAAATATTTTAAAATTTAAAAA
1870631 ATTTTAAAAATA
1 ATTTTAAAAATA
1870643 AAAATATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
ATTTTAAAAATATTTTAAAATTTAAAAA
Found at i:1870622 original size:18 final size:17
Alignment explanation
Indices: 1870601--1870639 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1870591 TAAAATTAAA
*
1870601 AAAATTTAAAAGTATTTT
1 AAAATTTAAAA-AATTTT
1870619 AAAATTTAAAAAATTTT
1 AAAATTTAAAAAATTTT
1870636 AAAA
1 AAAA
1870640 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAATTTAAAAAATTTT
Found at i:1874277 original size:20 final size:20
Alignment explanation
Indices: 1874261--1874311 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1874251 ATTGCACTTT
1874261 GGTGCCTCTATTTGCACTAC
1 GGTGCCTCTATTTGCACTAC
*
1874281 AGTGCCTCT-TTGTGCACTAC
1 GGTGCCTCTATT-TGCACTAC
1874301 GGTGCCTCTAT
1 GGTGCCTCTAT
1874312 ATAGCGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.14, C:0.29, G:0.22, T:0.35
Consensus pattern (20 bp):
GGTGCCTCTATTTGCACTAC
Found at i:1882921 original size:22 final size:22
Alignment explanation
Indices: 1882895--1882962 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 22
1882885 AGTGCTATAC
1882895 AGAGAGCATAGATGTGCTAATT
1 AGAGAGCATAGATGTGCTAATT
* *
1882917 GGAGAGCACTA-ACGTGCTAATAATT
1 AGAGAGCA-TAGATGTGC---TAATT
*
1882942 AGAGAGCATTGATGTGCTAAT
1 AGAGAGCATAGATGTGCTAAT
1882963 AATCAGAGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
22 16 0.44
23 2 0.06
24 1 0.03
25 17 0.47
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (22 bp):
AGAGAGCATAGATGTGCTAATT
Found at i:1882946 original size:25 final size:25
Alignment explanation
Indices: 1882912--1882972 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
1882902 ATAGATGTGC
*
1882912 TAATTGGAGAGCACTAACGTGCTAA
1 TAATTAGAGAGCACTAACGTGCTAA
* * *
1882937 TAATTAGAGAGCATTGATGTGCTAA
1 TAATTAGAGAGCACTAACGTGCTAA
*
1882962 TAATCAGAGAG
1 TAATTAGAGAG
1882973 AGCGCTAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (25 bp):
TAATTAGAGAGCACTAACGTGCTAA
Found at i:1889985 original size:43 final size:43
Alignment explanation
Indices: 1889833--1890005 Score: 138
Period size: 43 Copynumber: 4.0 Consensus size: 43
1889823 ACCTAGGATT
* * * * * *
1889833 TCGATATGTGATTTCGTGTAAGACCACGTTTGGGAC-GTTGGCA
1 TCGATATTTGATTACATGTAAGACCATGTCTAGGACAG-TGGCA
* * * *
1889876 TCGAT-TTGAGATTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATT-TGA-TTACATGTAAGACCATGTCTAGGACAGTGGCA
* * * *
1889920 TCG-TATATGATTTCATGTAAGACCCTGTCTAGGATAGTGGCA
1 TCGATATTTGATTACATGTAAGACCATGTCTAGGACAGTGGCA
* *
1889962 TCGATATTTGATTACATGTAAGACCACGTCTGGGAC-GTTGGCA
1 TCGATATTTGATTACATGTAAGACCATGTCTAGGACAG-TGGCA
1890005 T
1 T
1890006 TGTACAAGAT
Statistics
Matches: 104, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
42 31 0.30
43 42 0.40
44 31 0.30
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TCGATATTTGATTACATGTAAGACCATGTCTAGGACAGTGGCA
Found at i:1890686 original size:46 final size:46
Alignment explanation
Indices: 1890615--1890982 Score: 531
Period size: 46 Copynumber: 8.0 Consensus size: 46
1890605 TGTGATAACA
* * * **
1890615 AAATGTTGTCTATTTTTTAGTATATTATGTTGTCTAAATGTTGTTT
1 AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
* *
1890661 AAATGCTGTCCATTTTTGAACATATTATGTTGTCCGAATGTTGTTT
1 AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
* *
1890707 AAATGTTGTCCATTTTTTAGCATATTATGATGTCCGAATGTTGTTT
1 AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
* * ** *
1890753 AAATGCTGTCCATTTTTAAGGATATTATACTGTCTGAATGTTGTTT
1 AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
1890799 AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
1 AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
*
1890845 AAATGTTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
1 AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
*
1890891 AAATGTTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
1 AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
* * * *
1890937 AAATGCTATCCATTTTTGTA-CAAATCAATGATGTCCGAATGTTGTT
1 AAATGCTGTCCATTTTT-TAGCATAT-TATGTTGTCCGAATGTTGTT
1890983 ACTGTTGTTC
Statistics
Matches: 292, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
46 272 0.93
47 20 0.07
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (46 bp):
AAATGCTGTCCATTTTTTAGCATATTATGTTGTCCGAATGTTGTTT
Found at i:1892240 original size:20 final size:18
Alignment explanation
Indices: 1892193--1892241 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1892183 CAAGATAAAC
1892193 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
1892210 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
1892230 ATTAAATTAATA
1 ATTAAATTAATA
1892242 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:1897270 original size:50 final size:50
Alignment explanation
Indices: 1897216--1897379 Score: 132
Period size: 50 Copynumber: 3.1 Consensus size: 50
1897206 TAGTAACTTT
*
1897216 TTTTTTTTTTTACAATTTAACCTTGTTGTTTTGAAAACAAATCTCATACA
1 TTTTTTTTTTTACAATTTAACCTTGTTGTTTTGAAAACAAATCTCATATA
* * * * * * * * *
1897266 TTTTTATATTTAGAATTTAGCTTTGTTGTTTTTAATAATTTAGTAA-CTTTATTTA
1 TTTTTTTTTTTACAATTTAACCTTGTTGTTTTGAA-AA--CA--AATC-TCATATA
* **
1897321 TTTATTTTTTTGTATAATTTAACCTTCCTGTTTTGAAAACAAATCTCATATA
1 TTT-TTTTTTT-TACAATTTAACCTTGTTGTTTTGAAAACAAATCTCATATA
1897373 TTTTTTT
1 TTTTTTT
1897380 GTTGGGATAC
Statistics
Matches: 84, Mismatches: 21, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
50 29 0.35
51 6 0.07
52 10 0.12
53 2 0.02
54 2 0.02
55 9 0.11
56 7 0.08
57 19 0.23
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (50 bp):
TTTTTTTTTTTACAATTTAACCTTGTTGTTTTGAAAACAAATCTCATATA
Found at i:1897366 original size:107 final size:100
Alignment explanation
Indices: 1897170--1897377 Score: 317
Period size: 100 Copynumber: 2.0 Consensus size: 100
1897160 TCTCCGTATA
1897170 TATATTTAGAATTTAGCTTTGTTGTTTTTAATAATTTAGTAACTTTTTTTTTTTTTTACAATTTA
1 TATATTTAGAATTTAGCTTTGTTGTTTTTAATAATTTAGTAACTTTTTTTTTTTTTTACAATTTA
**
1897235 ACCTTGTTGTTTTGAAAACAAATCTCATACATTTT
66 ACCTTCCTGTTTTGAAAACAAATCTCATACATTTT
1897270 TATATTTAGAATTTAGCTTTGTTGTTTTTAATAATTTAGTAACTTTATTTATTTATTTTTTTGTA
1 TATATTTAGAATTTAGCTTTGTTGTTTTTAATAATTTAGTAAC----TTT-TTT-TTTTTTT-TA
* *
1897335 TAATTTAACCTTCCTGTTTTGAAAACAAATCTCATATATTTT
59 CAATTTAACCTTCCTGTTTTGAAAACAAATCTCATACATTTT
1897377 T
1 T
1897378 TTGTTGGGAT
Statistics
Matches: 97, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
100 43 0.44
104 3 0.03
105 3 0.03
106 7 0.07
107 41 0.42
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.55
Consensus pattern (100 bp):
TATATTTAGAATTTAGCTTTGTTGTTTTTAATAATTTAGTAACTTTTTTTTTTTTTTACAATTTA
ACCTTCCTGTTTTGAAAACAAATCTCATACATTTT
Found at i:1900866 original size:12 final size:12
Alignment explanation
Indices: 1900849--1900874 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1900839 TATAAACTTA
1900849 TTTTTTATTAAT
1 TTTTTTATTAAT
1900861 TTTTTTATTAAT
1 TTTTTTATTAAT
1900873 TT
1 TT
1900875 AAAAGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTATTAAT
Found at i:1900892 original size:30 final size:30
Alignment explanation
Indices: 1900856--1900917 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
1900846 TTATTTTTTA
*
1900856 TTAATTTTTTTATTAATTTAAAAGCATTTG
1 TTAATTTTCTTATTAATTTAAAAGCATTTG
* * *
1900886 TTAATTTTCTTATTATTTTAGAGGCATTTG
1 TTAATTTTCTTATTAATTTAAAAGCATTTG
1900916 TT
1 TT
1900918 TGTTAAGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.58
Consensus pattern (30 bp):
TTAATTTTCTTATTAATTTAAAAGCATTTG
Found at i:1900977 original size:16 final size:16
Alignment explanation
Indices: 1900956--1901004 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
1900946 TTTGGTTCGC
1900956 TCTATTGGATTAGAGG
1 TCTATTGGATTAGAGG
1900972 TCTATTGGATTAGAGG
1 TCTATTGGATTAGAGG
* *
1900988 TGTATCGGATTAGAGG
1 TCTATTGGATTAGAGG
1901004 T
1 T
1901005 GTAATAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.24, C:0.06, G:0.33, T:0.37
Consensus pattern (16 bp):
TCTATTGGATTAGAGG
Found at i:1901051 original size:66 final size:66
Alignment explanation
Indices: 1900975--1901107 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
1900965 TTAGAGGTCT
1900975 ATTGGATTAGAGGTGTATCGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATCTAATG
1 ATTGGATTAGAGGTGTATCGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATCTAATG
1901040 G
66 G
1901041 ATTGGATTAGAGGTGTATCGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATCTAATG
1 ATTGGATTAGAGGTGTATCGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATCTAATG
1901106 G
66 G
1901107 A
1 A
1901108 ATAGAGGCGT
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:0.31, C:0.08, G:0.29, T:0.33
Consensus pattern (66 bp):
ATTGGATTAGAGGTGTATCGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATCTAATG
G
Found at i:1905262 original size:33 final size:33
Alignment explanation
Indices: 1905223--1905298 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
1905213 ATTATAAAAC
* *
1905223 ATGTATAATTGACCTAAAATTATTTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1905256 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1905289 ATGTATAATT
1 ATGTATAATT
1905299 CAAGTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:1910429 original size:5 final size:5
Alignment explanation
Indices: 1910389--1910414 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1910379 GCAAATTGGC
1910389 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
1910415 TCGGATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:1910849 original size:11 final size:11
Alignment explanation
Indices: 1910835--1910865 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1910825 CATATATATT
1910835 TAAAAATTATA
1 TAAAAATTATA
*
1910846 TAAAAATAATA
1 TAAAAATTATA
1910857 TAAAAATTA
1 TAAAAATTA
1910866 CGGGACAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:1911873 original size:30 final size:30
Alignment explanation
Indices: 1911839--1911903 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
1911829 CAATTTAACA
1911839 AACAAATGCCTATAAAATAATAACAAAATT
1 AACAAATGCCTATAAAATAATAACAAAATT
* *
1911869 AACAAATGCTTTTAAAATAATAACAAAATT
1 AACAAATGCCTATAAAATAATAACAAAATT
1911899 AACAA
1 AACAA
1911904 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTATAAAATAATAACAAAATT
Found at i:1913478 original size:25 final size:26
Alignment explanation
Indices: 1913416--1913478 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
1913406 GACAAATATA
1913416 TTTTTTTCAAC-TCTCTTAACTCACTGT
1 TTTTTTTC-ACTTCTCTTAACTCAC-GT
*
1913443 TTTCTTT--CTTCTCTTAACTCA-GT
1 TTTTTTTCACTTCTCTTAACTCACGT
1913466 TTTTTTTCACTTC
1 TTTTTTTCACTTC
1913479 CAAGCACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
23 8 0.26
24 1 0.03
25 16 0.52
27 6 0.19
ACGTcount: A:0.14, C:0.25, G:0.03, T:0.57
Consensus pattern (26 bp):
TTTTTTTCACTTCTCTTAACTCACGT
Found at i:1914153 original size:22 final size:22
Alignment explanation
Indices: 1914123--1914165 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1914113 ACACCAAAAC
*
1914123 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
*
1914145 AGGCCTTTAGTGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
1914166 AGCGCCGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:1914238 original size:76 final size:76
Alignment explanation
Indices: 1914109--1914253 Score: 209
Period size: 76 Copynumber: 1.9 Consensus size: 76
1914099 ATGATTAAAA
* * * *
1914109 CACTACACCAAAACAGGCTTTTAGCGGCGCTTTTTTAGGCCTTTAGTGGCGCTTTTTAGCGCCGC
1 CACTACACCAAAACAGGCTTTTAGCGGCGCTTTTTTAGGCCTTTAGCGACGCTTTTTAACGCCAC
1914174 TAAAAGTATTT
66 TAAAAGTATTT
* * * * *
1914185 CACTACACCAGAATAGGTTTTTAGCGGCGTTTTTTTATGCCTTTAGCGACGCTTTTTAACGCCAC
1 CACTACACCAAAACAGGCTTTTAGCGGCGCTTTTTTAGGCCTTTAGCGACGCTTTTTAACGCCAC
1914250 TAAA
66 TAAA
1914254 TGCATTTGCG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 60 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (76 bp):
CACTACACCAAAACAGGCTTTTAGCGGCGCTTTTTTAGGCCTTTAGCGACGCTTTTTAACGCCAC
TAAAAGTATTT
Done.