Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 186 of 186
Found at i:61657328 original size:16 final size:16
Alignment explanation
Indices: 61657307--61657337 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
61657297 CCAATTTGTG
61657307 AAAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
61657323 AAAAATAAAATAAAA
1 AAAAATAAAATAAAA
61657338 AACATACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:61665464 original size:39 final size:40
Alignment explanation
Indices: 61665443--61666406 Score: 931
Period size: 39 Copynumber: 24.6 Consensus size: 40
61665433 GCTCCTCGTT
*
61665443 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCA
* *
61665483 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665522 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665561 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665600 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665639 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665678 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665717 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665756 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665795 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665834 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665873 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665912 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665951 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61665990 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61666029 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61666068 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61666107 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61666146 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61666185 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61666224 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61666263 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
* *
61666302 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATA-TAGTAACTCGCA
** * * *
61666341 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TCGCA
*
61666382 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
61666407 CAACATTCAA
Statistics
Matches: 909, Mismatches: 9, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
38 2 0.00
39 851 0.94
40 44 0.05
41 12 0.01
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCA
Found at i:61665568 original size:78 final size:78
Alignment explanation
Indices: 61665443--61666406 Score: 1790
Period size: 78 Copynumber: 12.3 Consensus size: 78
61665433 GCTCCTCGTT
* * *
61665443 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGA
61665508 ATTAGTATCTCGCA
65 ATTAGTATCTCGCA
61665522 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665587 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61665600 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665665 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61665678 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665743 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61665756 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665821 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61665834 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665899 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61665912 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665977 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61665990 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61666055 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61666068 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61666133 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61666146 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61666211 TTAGTATCTCGCA
66 TTAGTATCTCGCA
61666224 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61666289 TTAGTATCTCGCA
66 TTAGTATCTCGCA
* *
61666302 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG-
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG-GCTTAGCCCGGA
* *
61666366 ATATGGTCA-CTTAGCA
65 AT-TAGT-ATC-TCGCA
61666382 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
61666407 CAACATTCAA
Statistics
Matches: 873, Mismatches: 7, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
78 817 0.94
79 36 0.04
80 20 0.02
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTATCTCGCA
Found at i:61665617 original size:117 final size:117
Alignment explanation
Indices: 61665443--61666406 Score: 1790
Period size: 117 Copynumber: 8.2 Consensus size: 117
61665433 GCTCCTCGTT
* * *
61665443 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGA
61665508 ATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
65 ATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61665561 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665626 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
66 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61665678 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665743 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
66 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61665795 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665860 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
66 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61665912 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61665977 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
66 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61666029 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61666094 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
66 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61666146 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
61666211 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
66 TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61666263 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
* * * *
61666328 TTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG-ATATGGTCA-CTTAGCA
66 TTAGTATCTCGCACAAATGCCTTCGG-GCTTAGCCCGGAAT-TAGT-ATC-TCGCA
61666382 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
61666407 CAACATTCAA
Statistics
Matches: 834, Mismatches: 7, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
117 778 0.93
118 36 0.04
119 20 0.02
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (117 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:61671968 original size:158 final size:158
Alignment explanation
Indices: 61671680--61671995 Score: 632
Period size: 158 Copynumber: 2.0 Consensus size: 158
61671670 TATCGACATT
61671680 TCGTTCTATCTCGACGTTCATTCCCAACACTGGCGACCGAAGTGCCTCGTGTACCCACAGGGGGT
1 TCGTTCTATCTCGACGTTCATTCCCAACACTGGCGACCGAAGTGCCTCGTGTACCCACAGGGGGT
61671745 CGATCACGATCTCGTCTAAAAAGGCCCGAAGTGCCTCTAAACTGGCCCGCATCATCTCGAAATTT
66 CGATCACGATCTCGTCTAAAAAGGCCCGAAGTGCCTCTAAACTGGCCCGCATCATCTCGAAATTT
61671810 CTTCGATGCCTGTTGAAGAGACTTTCCC
131 CTTCGATGCCTGTTGAAGAGACTTTCCC
61671838 TCGTTCTATCTCGACGTTCATTCCCAACACTGGCGACCGAAGTGCCTCGTGTACCCACAGGGGGT
1 TCGTTCTATCTCGACGTTCATTCCCAACACTGGCGACCGAAGTGCCTCGTGTACCCACAGGGGGT
61671903 CGATCACGATCTCGTCTAAAAAGGCCCGAAGTGCCTCTAAACTGGCCCGCATCATCTCGAAATTT
66 CGATCACGATCTCGTCTAAAAAGGCCCGAAGTGCCTCTAAACTGGCCCGCATCATCTCGAAATTT
61671968 CTTCGATGCCTGTTGAAGAGACTTTCCC
131 CTTCGATGCCTGTTGAAGAGACTTTCCC
61671996 GAAGATCTTT
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 158 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (158 bp):
TCGTTCTATCTCGACGTTCATTCCCAACACTGGCGACCGAAGTGCCTCGTGTACCCACAGGGGGT
CGATCACGATCTCGTCTAAAAAGGCCCGAAGTGCCTCTAAACTGGCCCGCATCATCTCGAAATTT
CTTCGATGCCTGTTGAAGAGACTTTCCC
Found at i:61672489 original size:48 final size:48
Alignment explanation
Indices: 61672431--61672526 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
61672421 TTTAGGCATT
61672431 CATCGAGTGTACAAGATAGCTCATCGAGTACCCGGATAGTGTTGTCCA
1 CATCGAGTGTACAAGATAGCTCATCGAGTACCCGGATAGTGTTGTCCA
*
61672479 CATCGGGTGTACAAGATAGCTCATCGAGTACCCGGATAGTGTTGTCCA
1 CATCGAGTGTACAAGATAGCTCATCGAGTACCCGGATAGTGTTGTCCA
61672527 ACCAAAATTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (48 bp):
CATCGAGTGTACAAGATAGCTCATCGAGTACCCGGATAGTGTTGTCCA
Found at i:61674399 original size:40 final size:40
Alignment explanation
Indices: 61674355--61674538 Score: 207
Period size: 39 Copynumber: 4.7 Consensus size: 40
61674345 GCTCCTCATT
* *
61674355 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
61674395 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
61674434 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * ** *
61674473 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGCCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
61674514 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
61674539 CAACATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
38 2 0.02
39 71 0.57
40 40 0.32
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:61682977 original size:46 final size:46
Alignment explanation
Indices: 61682924--61683014 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
61682914 TATATATACA
* *
61682924 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
* *
61682970 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATAT
61683015 ATATACACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
Found at i:61683086 original size:47 final size:47
Alignment explanation
Indices: 61683033--61683324 Score: 496
Period size: 47 Copynumber: 6.2 Consensus size: 47
61683023 TTCCATGTTC
* *
61683033 ATCACATTGGCCATTCTGCCTTATCACATATATGCATGTTCACATTT
1 ATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTT
61683080 ATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTT
1 ATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTT
61683127 ATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTT
1 ATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTT
61683174 ATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTT
1 ATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTT
*
61683221 ATCACATTGGCCATTCGGCCTTATCACACATATGTGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTAT--CACATATGTGCATGTTCACATTT
* * *
61683270 ATCACATTGGCCACTT-GGCCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCA-TTCGGCCTTATCACATATGTGCATGTTCACATTT
61683317 ATCACATT
1 ATCACATT
61683325 TGCCTTGGCT
Statistics
Matches: 237, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
47 192 0.81
49 43 0.18
50 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (47 bp):
ATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTT
Found at i:61692281 original size:19 final size:19
Alignment explanation
Indices: 61692254--61692290 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61692244 GTCGATTTTA
61692254 TCCCCACATGGTGTGTAGT
1 TCCCCACATGGTGTGTAGT
*
61692273 TCCCTACATGGTGTGTAG
1 TCCCCACATGGTGTGTAG
61692291 GCCCAGACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.32
Consensus pattern (19 bp):
TCCCCACATGGTGTGTAGT
Found at i:61704396 original size:20 final size:20
Alignment explanation
Indices: 61704336--61704554 Score: 87
Period size: 20 Copynumber: 10.9 Consensus size: 20
61704326 AAGGAGGAAG
* *
61704336 TATTGGTAGTTTATCTGCAT
1 TATTGGTAGCTTGTCTGCAT
* * * **
61704356 TACTAGTGGCTTGTCCACAT
1 TATTGGTAGCTTGTCTGCAT
61704376 TATTGGTAGCTTGTCTGCAT
1 TATTGGTAGCTTGTCTGCAT
* ** * * *
61704396 TACTGGCGGTTTATTTGCAT
1 TATTGGTAGCTTGTCTGCAT
* * * **
61704416 CACTGGTGGCTTGTCCACAT
1 TATTGGTAGCTTGTCTGCAT
* ** * * *
61704436 TACTGCCAGCTTGTTTACAG
1 TATTGGTAGCTTGTCTGCAT
* * * * *
61704456 TACTGGTGGTTTATCTACAT
1 TATTGGTAGCTTGTCTGCAT
* * *
61704476 CATTGGTGGCTTGTCTACAT
1 TATTGGTAGCTTGTCTGCAT
* *
61704496 TATTGGCAACTTGTCTGCAT
1 TATTGGTAGCTTGTCTGCAT
* * *
61704516 TATTAGTAGTTTATCTGCAT
1 TATTGGTAGCTTGTCTGCAT
* *
61704536 TATTGGTACCTGGTCTGCA
1 TATTGGTAGCTTGTCTGCA
61704555 CTACTTTTTG
Statistics
Matches: 141, Mismatches: 58, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 141 1.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
TATTGGTAGCTTGTCTGCAT
Found at i:61704542 original size:60 final size:60
Alignment explanation
Indices: 61704339--61704535 Score: 232
Period size: 60 Copynumber: 3.3 Consensus size: 60
61704329 GAGGAAGTAT
* * *
61704339 TGGTAGTTTATCTGCATTACTAGTGGCTTGTCCACATTATTGGTAGCTTGTCTGCATTAC
1 TGGTAGTTTATCTGCATCACTGGTGGCTTGTCCACATTATTGGCAGCTTGTCTGCATTAC
** * * * * * *
61704399 TGGCGGTTTATTTGCATCACTGGTGGCTTGTCCACATTACTGCCAGCTTGTTTACAGTAC
1 TGGTAGTTTATCTGCATCACTGGTGGCTTGTCCACATTATTGGCAGCTTGTCTGCATTAC
* * * * * *
61704459 TGGTGGTTTATCTACATCATTGGTGGCTTGTCTACATTATTGGCAACTTGTCTGCATTAT
1 TGGTAGTTTATCTGCATCACTGGTGGCTTGTCCACATTATTGGCAGCTTGTCTGCATTAC
*
61704519 TAGTAGTTTATCTGCAT
1 TGGTAGTTTATCTGCAT
61704536 TATTGGTACC
Statistics
Matches: 111, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 111 1.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (60 bp):
TGGTAGTTTATCTGCATCACTGGTGGCTTGTCCACATTATTGGCAGCTTGTCTGCATTAC
Found at i:61708933 original size:55 final size:55
Alignment explanation
Indices: 61708867--61708977 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
61708857 TCGCGACACA
61708867 AGTCCTGGTGTGTTGCGACATCAACTCTAGGAAAAATATTAAATACAAAGTAGGG
1 AGTCCTGGTGTGTTGCGACATCAACTCTAGGAAAAATATTAAATACAAAGTAGGG
*
61708922 AGTCCTGGTGTGTTGTGACATCAACTCTAGGAAAAATATTAAATACAAAGTAGGG
1 AGTCCTGGTGTGTTGCGACATCAACTCTAGGAAAAATATTAAATACAAAGTAGGG
61708977 A
1 A
61708978 CGTTTTGGTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (55 bp):
AGTCCTGGTGTGTTGCGACATCAACTCTAGGAAAAATATTAAATACAAAGTAGGG
Found at i:61715849 original size:48 final size:46
Alignment explanation
Indices: 61715780--61715899 Score: 150
Period size: 48 Copynumber: 2.6 Consensus size: 46
61715770 TGTCTTCGAC
* * *
61715780 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGACTCATTCCTGTCTCCAAAGCCATATA-A-ATAAT
* *
61715828 ATGGGCTTACATGACTCATTCCTGTCTCCAAAGCCATATAACTAAT
1 ATGGACTTACATGACTCATTCCTGTCTCCAAAGCCATATAAATAAT
* * *
61715874 ATCGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGACTCATTCCTGTC
61715900 CTGTCCTGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 26 0.41
47 1 0.02
48 36 0.57
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (46 bp):
ATGGACTTACATGACTCATTCCTGTCTCCAAAGCCATATAAATAAT
Found at i:61721834 original size:46 final size:47
Alignment explanation
Indices: 61721725--61721843 Score: 141
Period size: 48 Copynumber: 2.5 Consensus size: 47
61721715 TGCCATGTCT
* ** * * *
61721725 TTGACATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATA
1 TTGATATGGACTTACATGGCTCATTCCTGCCTCCAAAGCCATATATA
* * *
61721772 TATAATATGGTCTTACATGGCTCATTCTTGCCTCCAAAGCCATATA-A
1 T-TGATATGGACTTACATGGCTCATTCCTGCCTCCAAAGCCATATATA
61721819 TTGATATGGACTTACATGGCTCATT
1 TTGATATGGACTTACATGGCTCATT
61721844 TCTGTCTTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
46 22 0.37
47 3 0.05
48 35 0.58
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (47 bp):
TTGATATGGACTTACATGGCTCATTCCTGCCTCCAAAGCCATATATA
Found at i:61725499 original size:24 final size:23
Alignment explanation
Indices: 61725463--61725508 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
61725453 CATGTTCCCC
61725463 TGCTTTAATTCAAGAAACTCTTTG
1 TGCTTTAATTCAAGAAA-TCTTTG
*
61725487 TGCTTCTAA-TCAATAAATCTTT
1 TGCTT-TAATTCAAGAAATCTTT
61725509 CACTGATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (23 bp):
TGCTTTAATTCAAGAAATCTTTG
Done.