Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold181
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: 2212501
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 130279 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1913062 original size:102 final size:101
Alignment explanation
Indices: 1912930--1913123 Score: 255
Period size: 102 Copynumber: 1.9 Consensus size: 101
1912920 ATCAATGATG
* * **
1912930 TTCGGTTCACATAGTAGCCTACACATAGTACTATACATGTGACCATTACCA-GCCGATACACGTA
1 TTCGGTACACATAGTAGCCTACACATAGTACTACACATGCAACC--TACCATGCCGATACACGTA
*
1912994 GTAGGCTGCACATAGTACTACACACGTGATCGAAACTA
64 GTAGCCTGCACATAGTACTACACACGTGATCGAAACTA
* * * * * *
1913032 TTCGGTACGCATAGTAGCCTACACATAGTACTACACATGCAACCTATCATTCTGGTACGCGTAGT
1 TTCGGTACACATAGTAGCCTACACATAGTACTACACATGCAACCTACCATGCCGATACACGTAGT
*
1913097 AGCCTGCACATAGTATTACACACGTGA
66 AGCCTGCACATAGTACTACACACGTGA
1913124 CCATCACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
100 4 0.05
101 36 0.46
102 39 0.49
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (101 bp):
TTCGGTACACATAGTAGCCTACACATAGTACTACACATGCAACCTACCATGCCGATACACGTAGT
AGCCTGCACATAGTACTACACACGTGATCGAAACTA
Found at i:1916634 original size:16 final size:16
Alignment explanation
Indices: 1916613--1916643 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1916603 AAAAATATCG
1916613 AAAAAATTGAAATTAA
1 AAAAAATTGAAATTAA
*
1916629 AAAAAATTGTAATTA
1 AAAAAATTGAAATTA
1916644 CAAATCCAGA
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:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAAAATTGAAATTAA
Found at i:1917091 original size:101 final size:101
Alignment explanation
Indices: 1916916--1917118 Score: 397
Period size: 101 Copynumber: 2.0 Consensus size: 101
1916906 AGTGAGTGTG
1916916 AGTGCAAACACGAGTGGTGTGTCATTTATATTTTCTTTGCGAGAGATATCCGTGAGCTTTGTGGT
1 AGTGCAAACACGAGTGGTGTGTCATTTATATTTTCTTTGCGAGAGATATCCGTGAGCTTTGTGGT
1916981 GAGGATCATTTACTATTAATTGTCTTTTGTTTACTA
66 GAGGATCATTTACTATTAATTGTCTTTTGTTTACTA
*
1917017 AGTGCAAACACGAGTGGTGTGTCATTTATATTTTCTTTGCGAGAGATATTCGTGAGCTTTGTGGT
1 AGTGCAAACACGAGTGGTGTGTCATTTATATTTTCTTTGCGAGAGATATCCGTGAGCTTTGTGGT
1917082 GAGGATCATTTACTATTAATTGTCTTTTGTTTACTA
66 GAGGATCATTTACTATTAATTGTCTTTTGTTTACTA
1917118 A
1 A
1917119 CATTTGCTGA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (101 bp):
AGTGCAAACACGAGTGGTGTGTCATTTATATTTTCTTTGCGAGAGATATCCGTGAGCTTTGTGGT
GAGGATCATTTACTATTAATTGTCTTTTGTTTACTA
Found at i:1917760 original size:21 final size:21
Alignment explanation
Indices: 1917673--1917760 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
1917663 AAAAACAAGG
*
1917673 GAGGAAAAAGAAAAACG-AGAA
1 GAGGAAAATGAAAAA-GAAGAA
* **
1917694 GAGAAAAATGAAAGTGAA-AA
1 GAGGAAAATGAAAAAGAAGAA
*
1917714 -A-GAAATTGAAAGAA-AAGAA
1 GAGGAAAATGAAA-AAGAAGAA
* *
1917733 AATGAAAATGAAAAAGAAGAA
1 GAGGAAAATGAAAAAGAAGAA
1917754 GAGGAAA
1 GAGGAAA
1917761 GCAAGAGAGA
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
18 10 0.20
19 3 0.06
20 6 0.12
21 31 0.62
ACGTcount: A:0.67, C:0.01, G:0.25, T:0.07
Consensus pattern (21 bp):
GAGGAAAATGAAAAAGAAGAA
Found at i:1919816 original size:49 final size:48
Alignment explanation
Indices: 1919759--1919854 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 48
1919749 TTTAATATGT
*
1919759 TTAGTTTAATTAATTCAGTTGTTTT-AATTTTCTTTAGCTGCTTAAATAC
1 TTAGTTTAATTAATTAAGTTGTTTTGAA-TTT-TTTAGCTGCTTAAATAC
*
1919808 TTAGTTTAATTAATTAAGTTGTTTTGAATTTTTTAGTTGCTTAAATA
1 TTAGTTTAATTAATTAAGTTGTTTTGAATTTTTTAGCTGCTTAAATA
1919855 ATTTCGGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 15 0.34
49 27 0.61
50 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.54
Consensus pattern (48 bp):
TTAGTTTAATTAATTAAGTTGTTTTGAATTTTTTAGCTGCTTAAATAC
Found at i:1922968 original size:27 final size:27
Alignment explanation
Indices: 1922924--1922986 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1922914 CACTGCTGTT
* * *
1922924 GAAAAGGAAGTTGTTGAAGAA-GAAGAA
1 GAAAAAGAAGTTGCTGAA-AATGAAAAA
*
1922951 GAAGAAGAAGTTGCTGAAAATGAAAAA
1 GAAAAAGAAGTTGCTGAAAATGAAAAA
1922978 GAAAAAGAA
1 GAAAAAGAA
1922987 AATGAAGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.57, C:0.02, G:0.29, T:0.13
Consensus pattern (27 bp):
GAAAAAGAAGTTGCTGAAAATGAAAAA
Found at i:1940046 original size:18 final size:19
Alignment explanation
Indices: 1940020--1940061 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1940010 TAACCTTCTT
*
1940020 CTAAATCAACTAGGGT-TC
1 CTAAGTCAACTAGGGTATC
* *
1940038 CTAAGTCAAGTTGGGTATC
1 CTAAGTCAACTAGGGTATC
1940057 CTAAG
1 CTAAG
1940062 ATCACTAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (19 bp):
CTAAGTCAACTAGGGTATC
Found at i:1941994 original size:12 final size:12
Alignment explanation
Indices: 1941977--1942002 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1941967 AGCCATACGC
1941977 CCGTGTGCTAGG
1 CCGTGTGCTAGG
1941989 CCGTGTGCTAGG
1 CCGTGTGCTAGG
1942001 CC
1 CC
1942003 ATGTAACTAC
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:0.08, C:0.31, G:0.38, T:0.23
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:1943091 original size:30 final size:30
Alignment explanation
Indices: 1943055--1943124 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
1943045 TTTGTCCCAA
* *
1943055 CCCTTTTCATAGCTCGATAGTCAAAGCTAT
1 CCCTTTTCATAGCTCAATAGCCAAAGCTAT
** *
1943085 CCCTTTTCGCAGCTCAATAGCCGAAGCTAT
1 CCCTTTTCATAGCTCAATAGCCAAAGCTAT
1943115 CCCTTTTCAT
1 CCCTTTTCAT
1943125 TATTTGATGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (30 bp):
CCCTTTTCATAGCTCAATAGCCAAAGCTAT
Found at i:1943170 original size:29 final size:29
Alignment explanation
Indices: 1943113--1943303 Score: 170
Period size: 30 Copynumber: 6.4 Consensus size: 29
1943103 AGCCGAAGCT
* *
1943113 ATCCCTTTTCATTATTTGATGGTTGTCACC
1 ATCCCTTTTCATT-GTTGATGGTCGTCACC
1943143 ATCCCTTTTCATTGTTGATGGTCGTCACC
1 ATCCCTTTTCATTGTTGATGGTCGTCACC
* * * * *
1943172 ATCCCTTTTCATATTTTGATAGCCG-AAGCT
1 ATCCCTTTTCAT-TGTTGATGGTCGTCA-CC
*** * * * *
1943202 ATCCCTTTTCACAATTCGATAGCCG-AAGCT
1 ATCCCTTTTCATTGTT-GATGGTCGTCA-CC
*
1943232 ATCCCTTTTCATTGTTCGATGGTTGTCACC
1 ATCCCTTTTCATTGTT-GATGGTCGTCACC
*
1943262 ATCCCTTTTCATTGTTGATGGTCGTCACT
1 ATCCCTTTTCATTGTTGATGGTCGTCACC
1943291 ATCCCTTTTCATT
1 ATCCCTTTTCATT
1943304 ATTTTGATAG
Statistics
Matches: 137, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
29 53 0.39
30 83 0.61
31 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (29 bp):
ATCCCTTTTCATTGTTGATGGTCGTCACC
Found at i:1943194 original size:89 final size:89
Alignment explanation
Indices: 1943101--1943317 Score: 260
Period size: 89 Copynumber: 2.4 Consensus size: 89
1943091 TCGCAGCTCA
* ** *
1943101 ATAGCCGAAGCTATCCCTTTTCATTATTTGATGGTTGTCA-CCATCCCTTTTCATTGTT-GATGG
1 ATAGCCGAAGCTATCCCTTTTCATTATTTGATAGCCG-AAGCCATCCCTTTTCATTGTTCGATGG
*
1943164 TCGTCACCATCCCTTTTCATATTTTG
65 TCGTCACCATCCCTTTTCAT-TGTTG
** * *
1943190 ATAGCCGAAGCTATCCCTTTTCACAATTCGATAGCCGAAGCTATCCCTTTTCATTGTTCGATGGT
1 ATAGCCGAAGCTATCCCTTTTCATTATTTGATAGCCGAAGCCATCCCTTTTCATTGTTCGATGGT
*
1943255 TGTCACCATCCCTTTTCATTGTTG
66 CGTCACCATCCCTTTTCATTGTTG
* * *
1943279 ATGGTCGTCA-CTATCCCTTTTCATTATTTTGATAGCCGA
1 ATAGCCG-AAGCTATCCCTTTTCATTA-TTTGATAGCCGA
1943318 TGATTGTGGA
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
88 1 0.01
89 71 0.66
90 36 0.33
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.40
Consensus pattern (89 bp):
ATAGCCGAAGCTATCCCTTTTCATTATTTGATAGCCGAAGCCATCCCTTTTCATTGTTCGATGGT
CGTCACCATCCCTTTTCATTGTTG
Found at i:1943266 original size:119 final size:119
Alignment explanation
Indices: 1943055--1943317 Score: 409
Period size: 119 Copynumber: 2.2 Consensus size: 119
1943045 TTTGTCCCAA
** * * * * *
1943055 CCCTTTTCATAGCTCGATAGTCAAAGCTATCCCTTTTCGCAGCTCAATAGCCGAAGCTATCCCTT
1 CCCTTTTCATATTTTGATAGCCGAAGCTATCCCTTTTCACAACTCAATAGCCGAAGCTATCCCTT
*
1943120 TTCATTATTTGATGGTTGTCACCATCCCTTTTCATTGTTGATGGTCGTCACCAT
66 TTCATTATTCGATGGTTGTCACCATCCCTTTTCATTGTTGATGGTCGTCACCAT
* *
1943174 CCCTTTTCATATTTTGATAGCCGAAGCTATCCCTTTTCACAATTCGATAGCCGAAGCTATCCCTT
1 CCCTTTTCATATTTTGATAGCCGAAGCTATCCCTTTTCACAACTCAATAGCCGAAGCTATCCCTT
* *
1943239 TTCATTGTTCGATGGTTGTCACCATCCCTTTTCATTGTTGATGGTCGTCACTAT
66 TTCATTATTCGATGGTTGTCACCATCCCTTTTCATTGTTGATGGTCGTCACCAT
1943293 CCCTTTTCATTATTTTGATAGCCGA
1 CCCTTTTCA-TATTTTGATAGCCGA
1943318 TGATTGTGGA
Statistics
Matches: 131, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 116 0.89
120 15 0.11
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.39
Consensus pattern (119 bp):
CCCTTTTCATATTTTGATAGCCGAAGCTATCCCTTTTCACAACTCAATAGCCGAAGCTATCCCTT
TTCATTATTCGATGGTTGTCACCATCCCTTTTCATTGTTGATGGTCGTCACCAT
Found at i:1946615 original size:26 final size:25
Alignment explanation
Indices: 1946561--1946619 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
1946551 GAACTAACGT
1946561 CAATTTAATTTGTCTAAACTAAGAC
1 CAATTTAATTTGTCTAAACTAAGAC
* *
1946586 CAATTTATTTTGTCTTAAGCTAAGAC
1 CAATTTAATTTGTC-TAAACTAAGAC
1946612 CAATTTAA
1 CAATTTAA
1946620 ATCACATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (25 bp):
CAATTTAATTTGTCTAAACTAAGAC
Found at i:1951521 original size:558 final size:557
Alignment explanation
Indices: 1950467--1951582 Score: 2223
Period size: 558 Copynumber: 2.0 Consensus size: 557
1950457 AAATTTGTTC
1950467 AAGCTCCCATCCATGCACTTGAAATAATGGTGGTGGCTGCTCATTAATGTATGCACCAAATTTAT
1 AAGCTCCCATCCATGCACTTGAAATAATGGTGGTGGCTGCTCATTAATGTATGCACCAAATTTAT
1950532 GCATGCTTAAAGGCTAAGCAAGCTCCAATAGTCACATTTAGCTCCTTGGATAGATGGTAGCATTA
66 GCATGCTTAAAGGCTAAGCAAGCTCCAATAGTCACATTTAGCTCCTTGGATAGATGGTAGCATTA
1950597 ATTGGTGCATAAGAATGATCAAAAGACTTCTTCTAAATGCTGCTCATACACTCCCTCAAATGGAC
131 ATTGGTGCATAAGAATGATCAAAAGACTTCTTCTAAATGCTGCTCATACACTCCCTCAAATGGAC
1950662 TGCACATTTATGGCATTTGTGAAGACCAAATGTTCACATTCCAGCCCTTGGACGTACATGTATGT
196 TGCACATTTATGGCATTTGTGAAGACCAAATGTTCACATTCCAGCCCTTGGACGTACATGTATGT
1950727 TCAGCAATAAAGAATCTTCATGAAAAGCTGCTTGGAAGAAAACAATTAGTAGCTCCCTTGGTGCA
261 TCAGCAATAAAGAATCTTCATGAAAAGCTGCTTGGAAGAAAACAATTAGTAGCTCCCTTGGTGCA
1950792 TGAACGTCCAAGTTCATGCTCTCCTTAATTGTTGTTCATTGAATGTGTTATTGAGCAGCCAATGT
326 TGAACGTCCAAGTTCATGCTCTCCTTAATTGTTGTTCATTGAATGTGTTATTGAGCAGCCAATGT
1950857 ATCCAGCAACATCCAGGTGCAAATCCCTTCCCCTAATGTCGTCCAATGAACCACTTGAATAGCAG
391 ATCCAGCAACATCCAGGTGCAAATCCCTTCCCCTAATGTCGTCCAATGAACCACTTGAATAGCAG
1950922 CCAATACATCCAACCTACAAGACAACATTAAAGGTTAGTTCTTAATGCCACATAAAACTAAATTT
456 CCAATACATCCAACCTACAAGACAACATTAAAGGTTAGTTCTTAATGCCACATAAAACTAAATTT
1950987 TAGACACACTTAATTTGTCTAGACGCTAGACACAATTA
521 TAGACACACTTAATTTGTCTAGACG-TAGACACAATTA
1951025 AAGCTCCCATCCATGCACTTGAAATAATGGTGGTGGCTGCTCATTAATGTATGCACCAAATTTAT
1 AAGCTCCCATCCATGCACTTGAAATAATGGTGGTGGCTGCTCATTAATGTATGCACCAAATTTAT
1951090 GCATGCTTAAAGGCTAAGCAAGCTCCAATAGTCACATTTAGCTCCTTGGATAGATGGTAGCATTA
66 GCATGCTTAAAGGCTAAGCAAGCTCCAATAGTCACATTTAGCTCCTTGGATAGATGGTAGCATTA
1951155 ATTGGTGCATAAGAATGATCAAAAGACTTCTTCTAAATGCTGCTCATACACTCCCTCAAATGGAC
131 ATTGGTGCATAAGAATGATCAAAAGACTTCTTCTAAATGCTGCTCATACACTCCCTCAAATGGAC
1951220 TGCACATTTATGGCATTTGTGAAGACCAAATGTTCACATTCCAGCCCTTGGACGTACATGTATGT
196 TGCACATTTATGGCATTTGTGAAGACCAAATGTTCACATTCCAGCCCTTGGACGTACATGTATGT
1951285 TCAGCAATAAAGAATCTTCATGAAAAGCTGCTTGGAAGAAAACAATTAGTAGCTCCCTTGGTGCA
261 TCAGCAATAAAGAATCTTCATGAAAAGCTGCTTGGAAGAAAACAATTAGTAGCTCCCTTGGTGCA
1951350 TGAACGTCCAAGTTCATGCTCTCCTTAATTGTTGTTCATTGAATGTGTTATTGAGCAGCCAATGT
326 TGAACGTCCAAGTTCATGCTCTCCTTAATTGTTGTTCATTGAATGTGTTATTGAGCAGCCAATGT
1951415 ATCCAGCAACATCCAGGTGCAAATCCCTTCCCCTAATGTCGTCCAATGAACCACTTGAATAGCAG
391 ATCCAGCAACATCCAGGTGCAAATCCCTTCCCCTAATGTCGTCCAATGAACCACTTGAATAGCAG
1951480 CCAATACATCCAACCTACAAGACAACATTAAAGGTTAGTTCTTAATGCCACATAAAACTAAATTT
456 CCAATACATCCAACCTACAAGACAACATTAAAGGTTAGTTCTTAATGCCACATAAAACTAAATTT
1951545 TAGACACACTTAATTTGTCTAGACGTAGACACAATTA
521 TAGACACACTTAATTTGTCTAGACGTAGACACAATTA
1951582 A
1 A
1951583 GGTGTTTGAA
Statistics
Matches: 558, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
557 13 0.02
558 545 0.98
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (557 bp):
AAGCTCCCATCCATGCACTTGAAATAATGGTGGTGGCTGCTCATTAATGTATGCACCAAATTTAT
GCATGCTTAAAGGCTAAGCAAGCTCCAATAGTCACATTTAGCTCCTTGGATAGATGGTAGCATTA
ATTGGTGCATAAGAATGATCAAAAGACTTCTTCTAAATGCTGCTCATACACTCCCTCAAATGGAC
TGCACATTTATGGCATTTGTGAAGACCAAATGTTCACATTCCAGCCCTTGGACGTACATGTATGT
TCAGCAATAAAGAATCTTCATGAAAAGCTGCTTGGAAGAAAACAATTAGTAGCTCCCTTGGTGCA
TGAACGTCCAAGTTCATGCTCTCCTTAATTGTTGTTCATTGAATGTGTTATTGAGCAGCCAATGT
ATCCAGCAACATCCAGGTGCAAATCCCTTCCCCTAATGTCGTCCAATGAACCACTTGAATAGCAG
CCAATACATCCAACCTACAAGACAACATTAAAGGTTAGTTCTTAATGCCACATAAAACTAAATTT
TAGACACACTTAATTTGTCTAGACGTAGACACAATTA
Found at i:1954130 original size:45 final size:45
Alignment explanation
Indices: 1954066--1954152 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
1954056 CGGATCCTAG
* * *
1954066 GTGGATTCAGTACATAGCAACCACCTTATTAATCAATGATGTCTA
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCTA
*
1954111 GTGGAATCAGCACATAGCAACCGCCTTACTAATCAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1954153 TCGGTGCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCTA
Found at i:1957433 original size:46 final size:45
Alignment explanation
Indices: 1957377--1957509 Score: 185
Period size: 46 Copynumber: 2.9 Consensus size: 45
1957367 AGGAAATGAT
*
1957377 TAAGACCATAGTTGAAAGACACTATGACACTATACAGGAAAATAAA
1 TAAGA-CATAGTTGAAAGACACTATGGCACTATACAGGAAAATAAA
**
1957423 TAAGATCATAGTTGAAAGACACTATGGCACTATAGTGGAAAATAAA
1 TAAGA-CATAGTTGAAAGACACTATGGCACTATACAGGAAAATAAA
* *
1957469 TAAGACTATAGTTGAAAGGCACTATGGCACCATACCAGGAA
1 TAAGAC-ATAGTTGAAAGACACTATGGCACTATA-CAGGAA
1957510 TGAGTATGAC
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.01
46 72 0.94
47 4 0.05
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (45 bp):
TAAGACATAGTTGAAAGACACTATGGCACTATACAGGAAAATAAA
Found at i:1957457 original size:24 final size:24
Alignment explanation
Indices: 1957430--1957498 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 24
1957420 AAATAAGATC
1957430 ATAGTTGAAAGACACTATGGCACT
1 ATAGTTGAAAGACACTATGGCACT
* * * *
1957454 ATAGTGGAAA-ATA-AATAAG-ACT
1 ATAGTTGAAAGACACTAT-GGCACT
*
1957476 ATAGTTGAAAGGCACTATGGCAC
1 ATAGTTGAAAGACACTATGGCAC
1957499 CATACCAGGA
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
22 14 0.44
23 5 0.16
24 13 0.41
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (24 bp):
ATAGTTGAAAGACACTATGGCACT
Found at i:1964363 original size:22 final size:22
Alignment explanation
Indices: 1964320--1964384 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1964310 CCTTTTTGAA
*
1964320 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAAAT
**
1964343 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* * *
1964365 CCCTTACCGTTTCATACCAA
1 CCATTACCATTTCGTACCAA
1964385 TTCCCAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:1965016 original size:13 final size:12
Alignment explanation
Indices: 1964998--1965042 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 12
1964988 ATAGATTTCA
1964998 TGAATTTTCTTTT
1 TGAATTTT-TTTT
1965011 TGAA-TTTTTTT
1 TGAATTTTTTTT
1965022 TGAA--TTTTTT
1 TGAATTTTTTTT
1965032 TGAATTTTTTT
1 TGAATTTTTTT
1965043 ACAATACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.33
11 8 0.27
12 8 0.27
13 4 0.13
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (12 bp):
TGAATTTTTTTT
Found at i:1965020 original size:10 final size:10
Alignment explanation
Indices: 1965007--1965042 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
1964997 ATGAATTTTC
1965007 TTTTTGAATTT
1 TTTTTGAA-TT
1965018 TTTTTGAATT
1 TTTTTGAATT
1965028 TTTTTGAATT
1 TTTTTGAATT
1965038 TTTTT
1 TTTTT
1965043 ACAATACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (10 bp):
TTTTTGAATT
Found at i:1965023 original size:11 final size:11
Alignment explanation
Indices: 1965007--1965042 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1964997 ATGAATTTTC
1965007 TTTTTGAATTT
1 TTTTTGAATTT
1965018 TTTTTGAA-TT
1 TTTTTGAATTT
1965028 TTTTTGAATTT
1 TTTTTGAATTT
1965039 TTTT
1 TTTT
1965043 ACAATACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (11 bp):
TTTTTGAATTT
Found at i:1969926 original size:20 final size:20
Alignment explanation
Indices: 1969903--1969942 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1969893 AATTAAAACT
1969903 AGACACAATTAATTAAGTTA
1 AGACACAATTAATTAAGTTA
* *
1969923 AGACATAATTAATTCAGTTA
1 AGACACAATTAATTAAGTTA
1969943 GGACTAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
AGACACAATTAATTAAGTTA
Found at i:1988176 original size:15 final size:16
Alignment explanation
Indices: 1988146--1988179 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1988136 TTTTTTTTAA
1988146 TAATTCACGATTTTTT
1 TAATTCACGATTTTTT
*
1988162 TAATTCAC-TTTTTTT
1 TAATTCACGATTTTTT
1988177 TAA
1 TAA
1988180 AAATTTCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.26, C:0.12, G:0.03, T:0.59
Consensus pattern (16 bp):
TAATTCACGATTTTTT
Found at i:1989516 original size:20 final size:20
Alignment explanation
Indices: 1989493--1989537 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1989483 AATTAAAACT
1989493 AGACACAATTAATTAAGTTA
1 AGACACAATTAATTAAGTTA
* *
1989513 AGACATAATTAATTCAGTTA
1 AGACACAATTAATTAAGTTA
*
1989533 GGACA
1 AGACA
1989538 AACACATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (20 bp):
AGACACAATTAATTAAGTTA
Found at i:1990169 original size:12 final size:12
Alignment explanation
Indices: 1990148--1990177 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1990138 TCAGGCAGTT
*
1990148 ACACGGCCTAGC
1 ACACGACCTAGC
1990160 ACACGACCTAGC
1 ACACGACCTAGC
1990172 ACACGA
1 ACACGA
1990178 GAGTATGTGG
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:0.33, C:0.40, G:0.20, T:0.07
Consensus pattern (12 bp):
ACACGACCTAGC
Found at i:1990382 original size:30 final size:30
Alignment explanation
Indices: 1990346--1990418 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
1990336 ACAAAGGAAA
1990346 AAGAAAATCAAGATCCACTTTCTTGTTTTC
1 AAGAAAATCAAGATCCACTTTCTTGTTTTC
1990376 AAGAAAATCAAGATCCACTTTCTTGTTTTC
1 AAGAAAATCAAGATCCACTTTCTTGTTTTC
1990406 AAGAAAATCAAGA
1 AAGAAAATCAAGA
1990419 AATCGAGTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (30 bp):
AAGAAAATCAAGATCCACTTTCTTGTTTTC
Found at i:1992161 original size:23 final size:23
Alignment explanation
Indices: 1992135--1992178 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1992125 TGTTACAGTG
* *
1992135 TAATATCCCGAAAATTACTACTA
1 TAATACCCCAAAAATTACTACTA
1992158 TAATACCCCAAAAATTACTAC
1 TAATACCCCAAAAATTACTAC
1992179 AGTAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (23 bp):
TAATACCCCAAAAATTACTACTA
Found at i:2002338 original size:9 final size:9
Alignment explanation
Indices: 2002324--2002381 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
2002314 TTTGGTTAAA
2002324 AATTAACCG
1 AATTAACCG
*
2002333 AATTAACCA
1 AATTAACCG
2002342 AATTAACCG
1 AATTAACCG
2002351 AATTAACCG
1 AATTAACCG
*
2002360 AATTACCCG
1 AATTAACCG
*
2002369 AATTACCCG
1 AATTAACCG
2002378 AATT
1 AATT
2002382 GAATCACTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:2002411 original size:17 final size:17
Alignment explanation
Indices: 2002389--2002449 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
2002379 ATTGAATCAC
2002389 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
2002406 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
2002426 TACATAGTTAAAAACAT
1 TACATAATTAAAAACAT
2002443 TACATAA
1 TACATAA
2002450 GTCTGGAAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
17 19 0.61
20 12 0.39
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:2002426 original size:37 final size:37
Alignment explanation
Indices: 2002380--2002453 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
2002370 ATTACCCGAA
2002380 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
2002417 TTGAATCACTACATAGTTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
2002454 GGAAATTAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:2002623 original size:38 final size:39
Alignment explanation
Indices: 2002579--2002656 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
2002569 GACTTGGAGT
*
2002579 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
2002617 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
2002656 T
1 T
2002657 TAGGTTGGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:2002668 original size:17 final size:17
Alignment explanation
Indices: 2002641--2002687 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
2002631 AGTTTTATTG
2002641 GGTTGGGTAATTGGGTTA
1 GGTT-GGTAATTGGGTTA
*
2002659 GGTTGGTAATTGGGTTG
1 GGTTGGTAATTGGGTTA
2002676 GGTTGGATAATT
1 GGTTGG-TAATT
2002688 TTATTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (17 bp):
GGTTGGTAATTGGGTTA
Found at i:2008707 original size:23 final size:23
Alignment explanation
Indices: 2008672--2008737 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
2008662 CGGTTTTGGG
* * *
2008672 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACAAAATGGTAATGCGA
* *
2008695 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACAAAATGGTAATGCGA
* *
2008718 TTTGGTACGAAATGTTAATG
1 TTTGGTACAAAATGGTAATG
2008738 GTTCAAAAAG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (23 bp):
TTTGGTACAAAATGGTAATGCGA
Found at i:2020985 original size:16 final size:13
Alignment explanation
Indices: 2020953--2020977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2020943 AATCCAGAAC
2020953 TTCACACAATAAA
1 TTCACACAATAAA
2020966 TTCACACAATAA
1 TTCACACAATAA
2020978 TACATTCAAA
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
TTCACACAATAAA
Found at i:2026984 original size:28 final size:28
Alignment explanation
Indices: 2026942--2027141 Score: 280
Period size: 28 Copynumber: 7.2 Consensus size: 28
2026932 CTATTCAGTA
2026942 ACAGT-ACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* *
2026969 ACAGCAACAATATGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* *
2026997 ACA-CAACAATGTGGGCCTTAGACCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* *
2027024 ACAGTAACAATATGGGCCTTAGCCCAAA
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
2027052 ACAGTAACAATGTGGGCCTTAACCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* *
2027080 ATAGTAACAATGTGGGCCTTAACCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
2027108 ATAGTAACAATGTGGGCCTTAGCCCTAA-
1 ACAGTAACAATGTGGGCCTTAGCCC-AAT
2027136 ACAGTA
1 ACAGTA
2027142 TCAGTACCGT
Statistics
Matches: 156, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
27 29 0.19
28 125 0.80
29 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:2027279 original size:26 final size:26
Alignment explanation
Indices: 2027250--2027326 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
2027240 ACACACCAAT
*
2027250 ATCGCAGCAAAGCTGCCAGTAATAGA
1 ATCGCAGCAAAGCTGCCAGTAACAGA
*
2027276 ATCGCAGCAAAGCTGCCAGTAACAGT
1 ATCGCAGCAAAGCTGCCAGTAACAGA
* *
2027302 ATTGCAACAAAGCTGCCAGTAACAG
1 ATCGCAGCAAAGCTGCCAGTAACAG
2027327 TATACTTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGTAACAGA
Found at i:2027506 original size:27 final size:26
Alignment explanation
Indices: 2027476--2028289 Score: 287
Period size: 27 Copynumber: 30.3 Consensus size: 26
2027466 GGGTATAATA
* *
2027476 GTCATTTTACAATATGGGGCTATTTTG
1 GTCATTTTACCATATGGGG-TATTTCG
* *
2027503 GTCATTTTACCTTATCGGGGTAATTCG
1 GTCATTTTACCATAT-GGGGTATTTCG
*
2027530 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCATAT-GGGGTATTTCG
* * * *
2027557 ATCATTTCACCCT-TCGGGGTATTTTG
1 GTCATTTTACCATAT-GGGGTATTTCG
* * *
2027583 ATCATTTCACC-TTTCGGGGTATTTCG
1 GTCATTTTACCATAT-GGGGTATTTCG
* * * *
2027609 GTTATTTTACCCTATGAGGGTAATTCA
1 GTCATTTTACCATATG-GGGTATTTCG
* *
2027636 GTCATCTTACCCTATGGGGATATTTCG
1 GTCATTTTACCATATGGGG-TATTTCG
* * * *
2027663 GTTA-TTT-CTCTTTTCGGGAGTATTTCA
1 GTCATTTTAC-CATAT-GGG-GTATTTCG
* * * * *
2027690 ATTATTTCACCCTTTGGGGGTATTTCG
1 GTCATTTTACCATAT-GGGGTATTTCG
* *
2027717 ATCATTTTACTCATCGAT--GGTATTTTG
1 GTCATTTTAC-CAT--ATGGGGTATTTCG
* * *
2027744 GTCATTTTACCCTTTGAGGGAATTTCG
1 GTCATTTTACCATATG-GGGTATTTCG
* * * *
2027771 ATCATTTTACTC-TGTAGAGGTATTTCA
1 GTCATTTTAC-CATAT-GGGGTATTTCG
* *
2027798 GTCATTTTACCCTGTAGGGGTATTTCG
1 GTCATTTTACCATAT-GGGGTATTTCG
* *
2027825 GTCATTTTACCCT-TCGAGGGTATTTCA
1 GTCATTTTACCATAT-G-GGGTATTTCG
* *
2027852 GTCATTTTACCCT-TCAGGGGTATTTCA
1 GTCATTTTACCATAT--GGGGTATTTCG
* * * *
2027879 ATCATTTTACCTTTTAAGGGTATTTCG
1 GTCATTTTACCATAT-GGGGTATTTCG
* * **
2027906 GTCATTTTACCCAT-CGAGGATATTTTA
1 GTCATTTTA-CCATATG-GGGTATTTCG
* ** * * *
2027933 GTCATTTTACCCT-TCAAGGCATCTCA
1 GTCATTTTACCATAT-GGGGTATTTCG
* * *
2027959 GTTATTTTACCCT-TCGAGGGTATTTTG
1 GTCATTTTACCATAT-G-GGGTATTTCG
* *
2027986 ATCATTTTACCCT-TCGAGGGTATTTCG
1 GTCATTTTACCATAT-G-GGGTATTTCG
* * *
2028013 ATCATTTTACCTTTTGAGGGTATTTCG
1 GTCATTTTACCATATG-GGGTATTTCG
* * * **
2028040 ATCATTTTACCCTTTAAAGGTATTTCG
1 GTCATTTTACCATAT-GGGGTATTTCG
* *
2028067 GTCATTTTACCA-ATCGAGGATATTTTG
1 GTCATTTTACCATAT-G-GGGTATTTCG
* *
2028094 GTCATTTTACCCT-TCGAGGGCATTTCG
1 GTCATTTTACCATAT-G-GGGTATTTCG
* * * **
2028121 ATCATTTTACCCTACGAGATTATTTCG
1 GTCATTTTACCATATG-GGGTATTTCG
* * *
2028148 ATCATTTTACCCT-TCGAGGGTATTTTG
1 GTCATTTTACCATAT-G-GGGTATTTCG
* *
2028175 GTCATTTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCATATG-GGGTATTTCG
* * *
2028202 ATCATTTTACCCT-TCGAGGGTATTTTG
1 GTCATTTTACCATAT-G-GGGTATTTCG
* * *
2028229 GTCATTTTACCCTGTAGGGGTATTTTG
1 GTCATTTTACCATAT-GGGGTATTTCG
*
2028256 GTCATTTTACC-TATCAAGGGTATTTCG
1 GTCATTTTACCATAT--GGGGTATTTCG
2028283 GTCATTT
1 GTCATTT
2028290 GCCCACAAAT
Statistics
Matches: 635, Mismatches: 116, Indels: 72
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.00
25 2 0.00
26 82 0.13
27 521 0.82
28 27 0.04
29 1 0.00
30 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCATATGGGGTATTTCG
Found at i:2027661 original size:54 final size:53
Alignment explanation
Indices: 2027476--2028289 Score: 657
Period size: 54 Copynumber: 15.1 Consensus size: 53
2027466 GGGTATAATA
** * * * *
2027476 GTCATTTTACAATATGGGGCTATTTTGGTCATTTTACCTTATCG-GGGTAATTCG
1 GTCATTTTACCCTATGGGG-TATTTCGATCATTTTACCCT-TCGAGGGTATTTCG
* *
2027530 GTCATTTTACCCTATGGGGGTATTTCGATCATTTCACCCTTCG-GGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* * * * * * *
2027583 ATCATTTCA-CCTTTCGGGGTATTTCGGTTATTTTACCCTAT-GAGGGTAATTCA
1 GTCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCT-TCGAGGGTATTTCG
* * * ** *
2027636 GTCATCTTACCCTATGGGGATATTTCGGTTATTTCT-CTTTTCG-GGAGTATTTCA
1 GTCATTTTACCCTATGGGG-TATTTCGATCATTT-TACCCTTCGAGG-GTATTTCG
* * * * * * * *
2027690 ATTATTTCACCCTTTGGGGGTATTTCGATCATTTTACTCATCGATGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* * * * *
2027744 GTCATTTTACCCTTTGAGGGAATTTCGATCATTTTACTCTGTAGA-GGTATTTCA
1 GTCATTTTACCCTATG-GGGTATTTCGATCATTTTACCCT-TCGAGGGTATTTCG
* * *
2027798 GTCATTTTACCCTGTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCA
1 GTCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* * **
2027852 GTCATTTTACCCT-TCAGGGGTATTTCAATCATTTTACCTTTTAAGGGTATTTCG
1 GTCATTTTACCCTAT--GGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* * * * * *
2027906 GTCATTTTACCC-ATCGAGGATATTT-TAGTCATTTTACCCTTC-AAGGCATCTCA
1 GTCATTTTACCCTAT-G-GGGTATTTCGA-TCATTTTACCCTTCGAGGGTATTTCG
* *
2027959 GTTATTTTACCCT-TCGAGGGTATTTTGATCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTAT-G-GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* * * ** *
2028013 ATCATTTTACCTTTTGAGGGTATTTCGATCATTTTACCCTTTAAAGGTATTTCG
1 GTCATTTTACCCTATG-GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* * * * *
2028067 GTCATTTTA-CCAATCGAGGATATTTTGGTCATTTTACCCTTCGAGGGCATTTCG
1 GTCATTTTACCCTAT-G-GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* * ** *
2028121 ATCATTTTACCCTACGAGATTATTTCGATCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* *
2028175 GTCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
* * * *
2028229 GTCATTTTACCCTGTAGGGGTATTTTGGTCATTTTA-CCTATCAAGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCT-TCGAGGGTATTTCG
2028283 GTCATTT
1 GTCATTT
2028290 GCCCACAAAT
Statistics
Matches: 624, Mismatches: 109, Indels: 54
0.79 0.14 0.07
Matches are distributed among these distances:
52 26 0.04
53 95 0.15
54 484 0.78
55 19 0.03
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCG
Found at i:2027820 original size:81 final size:81
Alignment explanation
Indices: 2027496--2028289 Score: 573
Period size: 81 Copynumber: 9.8 Consensus size: 81
2027486 AATATGGGGC
* * * *
2027496 TATTTTGGTCATTTTACCTTATCG-GGGTAA-TTCGGTCATTTTACCC-TATGGGGGTATTTCGA
1 TATTTCGGTCATTTTACCCT-TCGAGGG-AATTTCGATCATTTTACCCTTA-GAGGGTATTTCGA
* *
2027558 TCATTTCACCCTTCG-GGG
63 TCATTTTACCCTTAGAGGG
* * * * * * * *
2027576 TATTTTGATCATTTCACCTTTCG-GGGTATTTCGGTTATTTTACCC-TATGAGGGTAATTC-AGT
1 TATTTCGGTCATTTTACCCTTCGAGGGAATTTCGATCATTTTACCCTTA-GAGGGTATTTCGA-T
*
2027638 CATCTTACCC-TATG-GGG
64 CATTTTACCCTTA-GAGGG
* ** * * * * * *
2027655 ATATTTCGGTTATTTCT-CTTTTCG-GGAGTATTTCAATTATTTCACCCTTTGGGGGTATTTCGA
1 -TATTTCGGTCATTT-TACCCTTCGAGG-GAATTTCGATCATTTTACCCTTAGAGGGTATTTCGA
* * * *
2027718 TCATTTTACTCATCGATGG
63 TCATTTTACCCTTAGAGGG
* * *
2027737 TATTTTGGTCATTTTACCCTTTGAGGGAATTTCGATCATTTTACTCTGTAGA-GGTATTTC-AGT
1 TATTTCGGTCATTTTACCCTTCGAGGGAATTTCGATCATTTTACCCT-TAGAGGGTATTTCGA-T
2027800 CATTTTACCCTGTAG-GGG
64 CATTTTACCCT-TAGAGGG
* *
2027818 TATTTCGGTCATTTTACCCTTCGAGGGTATTTC-AGTCATTTTACCCTTCAG-GGGTATTTCAAT
1 TATTTCGGTCATTTTACCCTTCGAGGGAATTTCGA-TCATTTTACCCTT-AGAGGGTATTTCGAT
*
2027881 CATTTTACCTTTTA-AGGG
64 CATTTTACC-CTTAGAGGG
* * * *
2027899 TATTTCGGTCATTTTACCCATCGA-GGATATTT-TAGTCATTTTACCCTTCA-A-GGCATCTC-A
1 TATTTCGGTCATTTTACCCTTCGAGGGA-ATTTCGA-TCATTTTACCCTT-AGAGGGTATTTCGA
* *
2027959 GTTATTTTACCCTTCGAGGG
63 -TCATTTTACCCTTAGAGGG
* * * * *
2027979 TATTTTGATCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCTTTTGAGGGTATTTCGATCA
1 TATTTCGGTCATTTTACCCTTCGAGGGAATTTCGATCATTTTACCCTTAGAGGGTATTTCGATCA
*
2028044 TTTTACCCTTTA-AAGG
66 TTTTACCC-TTAGAGGG
** * * * *
2028060 TATTTCGGTCATTTTACCAATCGA-GGATATTTTGGTCATTTTACCCTTCGAGGGCATTTCGATC
1 TATTTCGGTCATTTTACCCTTCGAGGGA-ATTTCGATCATTTTACCCTTAGAGGGTATTTCGATC
**
2028124 ATTTTACCC-TACGAGAT
65 ATTTTACCCTTA-GAGGG
* * * * *
2028141 TATTTCGATCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTTGAGGGTATTTCGATCA
1 TATTTCGGTCATTTTACCCTTCGAGGGAATTTCGATCATTTTACCCTTAGAGGGTATTTCGATCA
*
2028206 TTTTACCCTTCGAGGG
66 TTTTACCCTTAGAGGG
* * * * * *
2028222 TATTTTGGTCATTTTACCCTGTAG-GGGTATTTTGGTCATTTTA-CCTATCA-AGGGTATTTCGG
1 TATTTCGGTCATTTTACCCT-TCGAGGGAATTTCGATCATTTTACCCT-T-AGAGGGTATTTCGA
2028284 TCATTT
63 TCATTT
2028290 GCCCACAAAT
Statistics
Matches: 583, Mismatches: 91, Indels: 79
0.77 0.12 0.10
Matches are distributed among these distances:
78 3 0.01
79 51 0.09
80 105 0.18
81 403 0.69
82 21 0.04
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (81 bp):
TATTTCGGTCATTTTACCCTTCGAGGGAATTTCGATCATTTTACCCTTAGAGGGTATTTCGATCA
TTTTACCCTTAGAGGG
Found at i:2029697 original size:19 final size:19
Alignment explanation
Indices: 2029667--2029712 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2029657 CTTCAAATGC
*
2029667 TCACATGGTCTAAGCTATG
1 TCACACGGTCTAAGCTATG
*
2029686 TCAGACGGTCTAAGCTATG
1 TCACACGGTCTAAGCTATG
2029705 TCACACGG
1 TCACACGG
2029713 CTATGTGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (19 bp):
TCACACGGTCTAAGCTATG
Found at i:2052383 original size:51 final size:52
Alignment explanation
Indices: 2052325--2052429 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
2052315 TATTAGCCTC
2052325 TTTTCTCTCTGTC-TTTGTACTTACCCTTTCTCCCTTACCCCCTCACAAAAT
1 TTTTCTCTCTGTCTTTTGTACTTACCCTTTCTCCCTTACCCCCTCACAAAAT
2052376 TTTTCTCTCTGTCTTTTGTACTTACCCTTTCTCCCTTACCCCCTCACAAAAT
1 TTTTCTCTCTGTCTTTTGTACTTACCCTTTCTCCCTTACCCCCTCACAAAAT
2052428 TT
1 TT
2052430 CATCATTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 13 0.25
52 40 0.75
ACGTcount: A:0.15, C:0.36, G:0.04, T:0.45
Consensus pattern (52 bp):
TTTTCTCTCTGTCTTTTGTACTTACCCTTTCTCCCTTACCCCCTCACAAAAT
Found at i:2060754 original size:20 final size:20
Alignment explanation
Indices: 2060711--2060755 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2060701 TAAGATTGAG
*
2060711 CTGAATTGAGCTCAAATGAG
1 CTGAATTGAGCTCAAATGAC
* * *
2060731 CTGACTTGAGCTCGAGTGAC
1 CTGAATTGAGCTCAAATGAC
2060751 CTGAA
1 CTGAA
2060756 CTAAGTTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
CTGAATTGAGCTCAAATGAC
Found at i:2062602 original size:27 final size:26
Alignment explanation
Indices: 2062558--2062608 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
2062548 TTTCACTTCC
2062558 TTTTTCAATCTCAATTTCTTTTTTCT
1 TTTTTCAATCTCAATTTCTTTTTTCT
* *
2062584 TTTTCTCACTCTCATTTTCTTTTTT
1 TTTT-TCAATCTCAATTTCTTTTTT
2062609 GATTTCTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTTCAATCTCAATTTCTTTTTTCT
Found at i:2070394 original size:20 final size:20
Alignment explanation
Indices: 2070348--2070399 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
2070338 ATTGGGTTAA
*
2070348 GATTAAGCTGAATTGAGCTC
1 GATTGAGCTGAATTGAGCTC
* * *
2070368 AAATGAGCTGACTTGAGCTC
1 GATTGAGCTGAATTGAGCTC
*
2070388 GATTGAGTTGAA
1 GATTGAGCTGAA
2070400 CTATGTTAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (20 bp):
GATTGAGCTGAATTGAGCTC
Found at i:2073182 original size:23 final size:23
Alignment explanation
Indices: 2073152--2073196 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2073142 GGTTGGATTA
2073152 CATCTTATCTATATGAAAACATT
1 CATCTTATCTATATGAAAACATT
2073175 CATCTTATCTATATGAAAACAT
1 CATCTTATCTATATGAAAACAT
2073197 AGTTCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (23 bp):
CATCTTATCTATATGAAAACATT
Found at i:2085569 original size:17 final size:15
Alignment explanation
Indices: 2085549--2085582 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
2085539 GATTAATTAT
2085549 TTAAAAATTTATAAAAA
1 TTAAAAA-TTA-AAAAA
2085566 TTAAAAATTAAAAAA
1 TTAAAAATTAAAAAA
2085581 TT
1 TT
2085583 CAATTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAAATTAAAAAA
Found at i:2087722 original size:28 final size:28
Alignment explanation
Indices: 2087665--2087724 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2087655 GGACAACACA
* * *
2087665 AAGACATGATTTTAATGTGTAATATACT
1 AAGACATGATTTAAATATGTAACATACT
* *
2087693 AAGACATGATTTAAATATGTAGCATGCT
1 AAGACATGATTTAAATATGTAACATACT
2087721 AAGA
1 AAGA
2087725 AAAAATAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (28 bp):
AAGACATGATTTAAATATGTAACATACT
Found at i:2089548 original size:33 final size:33
Alignment explanation
Indices: 2089505--2089603 Score: 121
Period size: 33 Copynumber: 3.0 Consensus size: 33
2089495 TTCTTGGTCA
2089505 CTCTCTTCACTCGTTTCTTTTGCAAG-CTCTTTTT
1 CTCT-TTCACTCGTTTCTTTTGC-AGTCTCTTTTT
* *
2089539 CTCTTTCACTTGTTTCTTTTTCAGTCTCTTTTT
1 CTCTTTCACTCGTTTCTTTTGCAGTCTCTTTTT
* *
2089572 C-CTTTTCACTCATTTCTTTTTCAGTCTCTTTT
1 CTC-TTTCACTCGTTTCTTTTGCAGTCTCTTTT
2089604 GTTTTTATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
32 3 0.05
33 52 0.88
34 4 0.07
ACGTcount: A:0.08, C:0.27, G:0.06, T:0.59
Consensus pattern (33 bp):
CTCTTTCACTCGTTTCTTTTGCAGTCTCTTTTT
Found at i:2089577 original size:18 final size:18
Alignment explanation
Indices: 2089518--2089603 Score: 69
Period size: 15 Copynumber: 5.1 Consensus size: 18
2089508 TCTTCACTCG
*
2089518 TTTCTTTTGCAAG-CTCTT
1 TTTCTTTTTC-AGTCTCTT
* *
2089536 TTTCTCTTTCA--CT-TG
1 TTTCTTTTTCAGTCTCTT
2089551 TTTCTTTTTCAGTCTCTT
1 TTTCTTTTTCAGTCTCTT
* *
2089569 TTTCCTTTTCA--CTC-A
1 TTTCTTTTTCAGTCTCTT
2089584 TTTCTTTTTCAGTCTCTT
1 TTTCTTTTTCAGTCTCTT
2089602 TT
1 TT
2089604 GTTTTTATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
15 21 0.40
16 5 0.09
17 6 0.11
18 21 0.40
ACGTcount: A:0.08, C:0.24, G:0.06, T:0.62
Consensus pattern (18 bp):
TTTCTTTTTCAGTCTCTT
Found at i:2089649 original size:24 final size:23
Alignment explanation
Indices: 2089596--2089651 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
2089586 TCTTTTTCAG
* *
2089596 TCTCTTTTGTTTTTATTTCTTTT
1 TCTCTTTTGTTTTTATTTCATTC
2089619 TCTTCTTGTT-TTTTTCATTTCATTC
1 TC-TCTT-TTGTTTTT-ATTTCATTC
2089644 TCTCTTTT
1 TCTCTTTT
2089652 CTCAATCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 4 0.14
24 13 0.46
25 11 0.39
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.73
Consensus pattern (23 bp):
TCTCTTTTGTTTTTATTTCATTC
Found at i:2093176 original size:23 final size:23
Alignment explanation
Indices: 2093143--2093208 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
2093133 TCGGTTTAGG
* *
2093143 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
2093166 TTTGGTTCGAAATGGTATTACGA
1 TTTGGTACGAAATGGTAATGCGA
2093189 TTTGGTACGAAATGGTAATG
1 TTTGGTACGAAATGGTAATG
2093209 GTTCAAAAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:2095420 original size:50 final size:50
Alignment explanation
Indices: 2095353--2095487 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
2095343 GGGAATGAGA
* * * **
2095353 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACTGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * *
2095403 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * * *
2095453 TCCCATGTAAGACCATATCTGGAATATGGCATTGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG
2095488 TAGTACAGGA
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
Found at i:2095755 original size:20 final size:20
Alignment explanation
Indices: 2095730--2095778 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2095720 TGAGTTATTT
2095730 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
2095750 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
2095770 AAG-AAGCAA
1 AAGTAAGCAA
2095779 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:2097026 original size:28 final size:28
Alignment explanation
Indices: 2096969--2097030 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
2096959 GACAAAAAAA
* * *
2096969 AAGACATGATTTTAATGTGTAATATACT
1 AAGACATGATTTAAATATGTAACATACT
* *
2096997 AAGACATGATTTAAATATGTAGCATGCT
1 AAGACATGATTTAAATATGTAACATACT
2097025 AAGACA
1 AAGACA
2097031 AAATAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (28 bp):
AAGACATGATTTAAATATGTAACATACT
Found at i:2103067 original size:27 final size:28
Alignment explanation
Indices: 2103019--2103086 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
2103009 TCTAGTGGTG
* * * *
2103019 AAGAAAACGAGAGTGGAGGAAAA-GAGA
1 AAGAAAAAGAAAGTGAAAGAAAACGAGA
*
2103046 AAGAAAAAGAAAGTGAAAGAAAATCGAGT
1 AAGAAAAAGAAAGTGAAAGAAAA-CGAGA
*
2103075 GAGAAAAAGAAA
1 AAGAAAAAGAAA
2103087 AGAGTTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 19 0.58
29 14 0.42
ACGTcount: A:0.62, C:0.03, G:0.29, T:0.06
Consensus pattern (28 bp):
AAGAAAAAGAAAGTGAAAGAAAACGAGA
Found at i:2109617 original size:18 final size:17
Alignment explanation
Indices: 2109596--2109630 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2109586 CCTCAATCTC
*
2109596 TTTTTCAATTTTCTTTTT
1 TTTTTCAA-ATTCTTTTT
2109614 TTTTTCAAATTCTTTTT
1 TTTTTCAAATTCTTTTT
2109631 CACTCTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCAAATTCTTTTT
Found at i:2109628 original size:48 final size:47
Alignment explanation
Indices: 2109576--2109679 Score: 115
Period size: 46 Copynumber: 2.2 Consensus size: 47
2109566 TTGCTTACTC
*
2109576 TCTTTTTTTAC-CTCAATCTCTTTTTCAATTTTCTTTTT-TTTTTCAAAT
1 TCTTTTTTTACTCTCAATCTC--TTTCAA-TCTCTTTTTCTTTTTCAAAT
* * *
2109624 TC-TTTTTCACTCTCAATCTCTTTCGATCTCTTTTTCTTTTTCACAT
1 TCTTTTTTTACTCTCAATCTCTTTCAATCTCTTTTTCTTTTTCAAAT
*
2109670 GCTTTTTTTA
1 TCTTTTTTTA
2109680 TTTTATTACA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
45 8 0.17
46 15 0.32
47 13 0.28
48 11 0.23
ACGTcount: A:0.14, C:0.22, G:0.02, T:0.62
Consensus pattern (47 bp):
TCTTTTTTTACTCTCAATCTCTTTCAATCTCTTTTTCTTTTTCAAAT
Found at i:2109800 original size:16 final size:16
Alignment explanation
Indices: 2109779--2109811 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2109769 TCATCTCTTC
2109779 GATACTGATTCTTCAT
1 GATACTGATTCTTCAT
2109795 GATACTGATTCTTCAT
1 GATACTGATTCTTCAT
2109811 G
1 G
2109812 GATGAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (16 bp):
GATACTGATTCTTCAT
Found at i:2111042 original size:30 final size:30
Alignment explanation
Indices: 2110984--2111042 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2110974 TTGAAAAGGT
* *
2110984 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
2111014 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
2111043 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:2117716 original size:27 final size:27
Alignment explanation
Indices: 2117686--2117744 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
2117676 TTTCTCACAT
*
2117686 TTTTTTTCAATCTCA-ATCTCGTTTTTC
1 TTTTTCTCAATCTCACATCT-GTTTTTC
* *
2117713 TTTTTCTCACTCTCACTATCTTTTTTTC
1 TTTTTCTCAATCTCAC-ATCTGTTTTTC
2117741 TTTT
1 TTTT
2117745 CTCGAGTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.48
28 10 0.37
29 4 0.15
ACGTcount: A:0.12, C:0.24, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTTCTCAATCTCACATCTGTTTTTC
Found at i:2119140 original size:46 final size:46
Alignment explanation
Indices: 2119087--2119177 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
2119077 AAGAAAAGAC
*
2119087 CTCGACCCACTATCAA-GAATGATAGGAACCTGGGTATATGATGAAA
1 CTCGACCCACTATCAATG-ATGATAAGAACCTGGGTATATGATGAAA
*
2119133 CTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGAA
1 CTCGACCCACTATCAATGATGATAAGAACCTGGGTATATGATGAA
2119178 CGCCACACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 41 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (46 bp):
CTCGACCCACTATCAATGATGATAAGAACCTGGGTATATGATGAAA
Found at i:2153326 original size:20 final size:20
Alignment explanation
Indices: 2153301--2153342 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2153291 GAGGCCATCT
2153301 TTTGGTTAAAGAATGGTTTC
1 TTTGGTTAAAGAATGGTTTC
2153321 TTTGGTTAAAGAATGGTTTC
1 TTTGGTTAAAGAATGGTTTC
2153341 TT
1 TT
2153343 CTCATCCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.48
Consensus pattern (20 bp):
TTTGGTTAAAGAATGGTTTC
Found at i:2161003 original size:22 final size:22
Alignment explanation
Indices: 2160949--2161012 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
2160939 TATTTGGGAA
* *
2160949 TTGGTACGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
2160971 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
* *
2160993 TTGGTATGAAATGGAAATGG
1 TTGGTACGAAATGGTAATGG
2161013 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:2162257 original size:10 final size:10
Alignment explanation
Indices: 2162242--2162283 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
2162232 TTTGCAAGTT
2162242 TTGAGCTAAA
1 TTGAGCTAAA
* *
2162252 TTGAGCTGAT
1 TTGAGCTAAA
*
2162262 TTGAGCT-CA
1 TTGAGCTAAA
2162271 TTGAGCTAAA
1 TTGAGCTAAA
2162281 TTG
1 TTG
2162284 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:2163822 original size:20 final size:20
Alignment explanation
Indices: 2163797--2163843 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2163787 AGCTCGTTTC
*
2163797 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
2163817 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
2163837 CAGCTCA
1 CAGCTCA
2163844 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:2172846 original size:21 final size:22
Alignment explanation
Indices: 2172820--2172878 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
2172810 TCAATTTCAA
2172820 CTCACT-TTTTCTTTTTGTTTT
1 CTCACTCTTTTCTTTTTGTTTT
*
2172841 CTCACTCTTTT-TTTCT-TTTT
1 CTCACTCTTTTCTTTTTGTTTT
2172861 C-CA-TCTTTTCTTTTTGTT
1 CTCACTCTTTTCTTTTTGTT
2172879 CCTTTGCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 6 0.18
19 6 0.18
20 7 0.21
21 10 0.30
22 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.69
Consensus pattern (22 bp):
CTCACTCTTTTCTTTTTGTTTT
Found at i:2172874 original size:20 final size:20
Alignment explanation
Indices: 2172820--2172878 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
2172810 TCAATTTCAA
2172820 CTCACTTTTTCTTTTTGTTTT
1 CTCAC-TTTTCTTTTTGTTTT
2172841 CTCACTCTTT-TTTTCT-TTTT
1 CTCACT-TTTCTTTT-TGTTTT
2172861 C-CATCTTTTCTTTTTGTT
1 CTCA-CTTTTCTTTTTGTT
2172879 CCTTTGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
19 6 0.18
20 18 0.55
21 9 0.27
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.69
Consensus pattern (20 bp):
CTCACTTTTCTTTTTGTTTT
Found at i:2172880 original size:18 final size:19
Alignment explanation
Indices: 2172822--2172880 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
2172812 AATTTCAACT
2172822 CACT-TTTTCTTTTTGTTTTC
1 CACTCTTTTCTTTTTG--TTC
*
2172842 TCACTCTTTT-TTTCTTTTTC
1 -CACTCTTTTCTTT-TTGTTC
2172862 CA-TCTTTTCTTTTTGTTC
1 CACTCTTTTCTTTTTGTTC
2172880 C
1 C
2172881 TTTGCCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 12 0.36
19 5 0.15
20 3 0.09
21 7 0.21
22 6 0.18
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (19 bp):
CACTCTTTTCTTTTTGTTC
Found at i:2175153 original size:10 final size:10
Alignment explanation
Indices: 2175138--2175179 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
2175128 TTTGCAAGTT
2175138 TTGAGCTAAA
1 TTGAGCTAAA
* *
2175148 TTGAGCTGAT
1 TTGAGCTAAA
*
2175158 TTGAGCT-CA
1 TTGAGCTAAA
2175167 TTGAGCTAAA
1 TTGAGCTAAA
2175177 TTG
1 TTG
2175180 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:2200234 original size:12 final size:12
Alignment explanation
Indices: 2200217--2200241 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2200207 AAAATATGAT
2200217 TTCAATGTGTAA
1 TTCAATGTGTAA
2200229 TTCAATGTGTAA
1 TTCAATGTGTAA
2200241 T
1 T
2200242 GTGTATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:2202521 original size:17 final size:17
Alignment explanation
Indices: 2202473--2202528 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2202463 GGAAATTACG
2202473 AAAAAAATT-GAGAATAA
1 AAAAAAATTCGA-AATAA
* *
2202490 AAAAAAGAGTACGAAGTAA
1 AAAAAA-A-TTCGAAATAA
2202509 AAAAAAATTCGAAA-AA
1 AAAAAAATTCGAAATAA
2202525 AAAA
1 AAAA
2202529 GTGAAGTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 6 0.19
17 11 0.34
18 2 0.06
19 11 0.34
20 2 0.06
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAAAAATTCGAAATAA
Found at i:2203412 original size:18 final size:18
Alignment explanation
Indices: 2203375--2203413 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2203365 AACAAAAAAG
* *
2203375 AAGAAAAAGAAATTGCAA
1 AAGAAAAAGAAATCGAAA
2203393 AAGAAAAAGAAATCGAAA
1 AAGAAAAAGAAATCGAAA
2203411 AAG
1 AAG
2203414 TGAGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.05, G:0.18, T:0.08
Consensus pattern (18 bp):
AAGAAAAAGAAATCGAAA
Found at i:2203464 original size:18 final size:18
Alignment explanation
Indices: 2203443--2203477 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2203433 AGAAAAGAAA
2203443 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
2203461 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
2203478 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:2203486 original size:16 final size:18
Alignment explanation
Indices: 2203465--2203503 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2203455 ATTGAGATTG
2203465 AGAAAAA-A-ATTGAAAA
1 AGAAAAAGATATTGAAAA
*
2203481 AGAAAAAGATGTTGAAAA
1 AGAAAAAGATATTGAAAA
2203499 AGAAA
1 AGAAA
2203504 CGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (18 bp):
AGAAAAAGATATTGAAAA
Found at i:2205661 original size:20 final size:20
Alignment explanation
Indices: 2205638--2205691 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2205628 TAATTTGTCT
*
2205638 TGTCTTAATTAAATTAAATG
1 TGTCTTAATTAAATTAAATA
* ** *
2205658 TGTCTTGATTTTATTAAGTA
1 TGTCTTAATTAAATTAAATA
2205678 TGTCTTAAATTAAA
1 TGTCTT-AATTAAA
2205692 ACATGAATTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (20 bp):
TGTCTTAATTAAATTAAATA
Done.