Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 90 of 352
Found at i:28541268 original size:34 final size:34
Alignment explanation
Indices: 28541225--28541294 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
28541215 AAAGAAAGAA
28541225 TAGGGTTCGAACCTTGGAAATAACATGGTTTGTG
1 TAGGGTTCGAACCTTGGAAATAACATGGTTTGTG
28541259 TAGGGTTCGAACCTTGGAAATAACATGGTTTGTG
1 TAGGGTTCGAACCTTGGAAATAACATGGTTTGTG
28541293 TA
1 TA
28541295 TGCAATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (34 bp):
TAGGGTTCGAACCTTGGAAATAACATGGTTTGTG
Found at i:28543093 original size:27 final size:27
Alignment explanation
Indices: 28543063--28543161 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
28543053 TTTAGTTTAC
28543063 TAAAATTACCGAAATATCCTTAG-TTTG
1 TAAAATTACCGAAATA-CCTTAGATTTG
* * * *
28543090 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCTTAGATTTG
* * *
28543117 TAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACCGAAATACCTTAGATTTG
28543144 TAAAATTACC-AAAGTACC
1 TAAAATTACCGAAA-TACC
28543162 CCCGATTTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 7 0.11
27 55 0.89
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (27 bp):
TAAAATTACCGAAATACCTTAGATTTG
Found at i:28543162 original size:54 final size:54
Alignment explanation
Indices: 28543063--28543169 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
28543053 TTTAGTTTAC
* * *
28543063 TAAAATTACCGAAATATCCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATATCCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTG
* * *
28543117 TAAAATTACTGAAATA-CCTTCGACTTGTAAAATTAC-CAAAGTACCCCCGATTT
1 TAAAATTACCGAAATATCCTTAG-CTTGTAAAAATACTCAAA-TACCCCCGATTT
28543170 ACAGAATTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 8 0.18
54 37 0.82
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (54 bp):
TAAAATTACCGAAATATCCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTG
Found at i:28543177 original size:27 final size:27
Alignment explanation
Indices: 28543147--28543207 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
28543137 CGACTTGTAA
28543147 AATTACCAAAGTACCCCCGATTTACAG
1 AATTACCAAAGTACCCCCGATTTACAG
***** *
28543174 AATTACTGTTTTACCCCCGATTTACAT
1 AATTACCAAAGTACCCCCGATTTACAG
28543201 AATTACC
1 AATTACC
28543208 GTTTTACCCC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAGTACCCCCGATTTACAG
Found at i:28543211 original size:27 final size:27
Alignment explanation
Indices: 28543158--28543369 Score: 259
Period size: 27 Copynumber: 7.9 Consensus size: 27
28543148 ATTACCAAAG
*
28543158 TACCCCCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
28543185 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28543212 TACCC-CTGATTTACATAATTA-TCGTTT
1 TACCCTC-GATTTACAGAATTACT-GTTT
* * *
28543239 TACCCTTGACTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28543266 TACCCTCGATTTATAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
*
28543293 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
28543320 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28543347 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
28543370 AAAATACCCT
Statistics
Matches: 164, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.01
27 160 0.98
28 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:28543377 original size:27 final size:27
Alignment explanation
Indices: 28543320--28543572 Score: 156
Period size: 27 Copynumber: 9.3 Consensus size: 27
28543310 ATTACTGTTT
****
28543320 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTTGATTTACAAAATTACTAAAA
*
28543347 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* ** *
28543374 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
** *
28543401 TACCCCTTG-TTTGTAAAATTACCAAAA
1 TA-CCCTTGATTTACAAAATTACTAAAA
* ** *
28543428 TACCCTTGGTTTGTAAAATTA-TCGAAA
1 TACCCTTGATTTACAAAATTACT-AAAA
** *** *
28543455 TACCCTCAATTCGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* *
28543482 TACCCCTGATTTACAAAGTTAC-AGAAA
1 TACCCTTGATTTACAAAATTACTA-AAA
28543509 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTAC--AAAATTACTA-AAA
* * *
28543538 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACTAAAA
*
28543565 TACGCTTG
1 TACCCTTG
28543573 GTTTGTAGAT
Statistics
Matches: 183, Mismatches: 32, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
26 7 0.04
27 144 0.79
28 13 0.07
29 19 0.10
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACTAAAA
Found at i:28543381 original size:54 final size:54
Alignment explanation
Indices: 28543091--28543379 Score: 199
Period size: 54 Copynumber: 5.4 Consensus size: 54
28543081 CTTAGTTTGT
* ** *** * * **
28543091 AAAAATACTGAAA-TACCCTCGATTTGTAAAATTACTGAAATACCTTCGACTTGT
1 AAAATTACT-AAATTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTAC
* * * * *
28543145 AAAATTACCAAAGTACCCCCGATTTACAGAATTACTGTTTTACCCCCGATTTAC
1 AAAATTACTAAATTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTAC
* **** * * *
28543199 ATAATTACCGTTTTACCC-CTGATTTACATAATTA-TCGTTTTACCCTTGACTTAC
1 AAAATTACTAAATTACCCTC-GATTTACAAAATTACT-GTTTTACCCTCGATTTAC
* ** * * *
28543253 AGAATTACTATTTTACCCTCGATTTATAGAATTA-TCGTTTTACCCTCGATTTAT
1 AAAATTACTAAATTACCCTCGATTTACAAAATTACT-GTTTTACCCTCGATTTAC
* *** *
28543307 AGAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTAC
1 AAAATTACTAAATTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTAC
*
28543361 AAAATTACTAAAATACCCT
1 AAAATTACTAAATTACCCT
28543380 TGGTTTGTAA
Statistics
Matches: 189, Mismatches: 41, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
53 5 0.03
54 182 0.96
55 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (54 bp):
AAAATTACTAAATTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTAC
Found at i:28543405 original size:54 final size:54
Alignment explanation
Indices: 28543347--28543599 Score: 197
Period size: 54 Copynumber: 4.6 Consensus size: 54
28543337 ATTACTGTTT
** *
28543347 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
* * *
28543401 TACCCCTTG-TTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTATCGAAA
1 TA-CCCTCGATTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
* * * * ** *
28543455 TACCCTCAATTCGTAAAATTACCAAAATACCCCTGATTTACAAAGTTA-CAGAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCA-AAA
* * * * ** **
28543509 TACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGA-TTTGT-AAAATTACCA-AAATACCCTTGGTTTGTAAAATTACCAAAA
* * * * * *
28543565 TACGCTTGGTTTGTAGATTTACCAAAACACCCTTG
1 TACCCTCGATTTGTAAAATTACCAAAATACCCTTG
28543600 TAGGATGAAA
Statistics
Matches: 157, Mismatches: 34, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
53 5 0.03
54 101 0.64
55 14 0.09
56 37 0.24
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (54 bp):
TACCCTCGATTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
Found at i:28543405 original size:81 final size:81
Alignment explanation
Indices: 28543104--28543503 Score: 241
Period size: 81 Copynumber: 4.9 Consensus size: 81
28543094 AATACTGAAA
* * * **
28543104 TACCCTCGATTTGTAAAATTACTGAAATA-CCTTCGACTTGTAAAATTACCAAAGTACCCCCGAT
1 TACCCTCGATTTATAAAATTACTGAAATACCCTT-GATTTGTAAAATTACCAAAATACCCTTGAT
* *
28543168 TTACAGAATTACTGTTT
65 TTACAAAATTACTATTT
* * * * *** * ** * * **** *
28543185 TACCCCCGATTTACATAATTACCGTTTTACCCCTGATTTACATAATTATCGTTTTACCCTTGACT
1 TACCCTCGATTTATAAAATTACTGAAATACCCTTGATTTGTAAAATTACCAAAATACCCTTGATT
*
28543250 TACAGAATTACTATTT
66 TACAAAATTACTATTT
* *** * * * *****
28543266 TACCCTCGATTTATAGAATTA-TCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGAT
1 TACCCTCGATTTATAAAATTACT-GAAATACCCTTGATTTGTAAAATTACCAAAATACCCTTGAT
*
28543330 TTACAAAATTACTGTTT
65 TTACAAAATTACTATTT
* * *
28543347 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTTG-T
1 TACCCTCGATTTATAAAATTACTGAAATACCCTTGATTTGTAAAATTACCAAAATA-CCCTTGAT
** * ***
28543411 TTGTAAAATTACCAAAA
65 TTACAAAATTACTATTT
* * * ** * *
28543428 TACCCTTGGTTTGTAAAATTA-TCGAAATACCCTCAATTCGTAAAATTACCAAAATACCCCTGAT
1 TACCCTCGATTTATAAAATTACT-GAAATACCCTTGATTTGTAAAATTACCAAAATACCCTTGAT
*
28543492 TTACAAAGTTAC
65 TTACAAAATTAC
28543504 AGAAATACCC
Statistics
Matches: 243, Mismatches: 70, Indels: 12
0.75 0.22 0.04
Matches are distributed among these distances:
80 6 0.02
81 227 0.93
82 10 0.04
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (81 bp):
TACCCTCGATTTATAAAATTACTGAAATACCCTTGATTTGTAAAATTACCAAAATACCCTTGATT
TACAAAATTACTATTT
Found at i:28543510 original size:81 final size:83
Alignment explanation
Indices: 28543386--28543541 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 83
28543376 CCCTTGGTTT
* * *
28543386 GTAAAATTACCAAAATACCCCTTGTTTGTAAAATTACCAAAATACCCTTG-GTTTGT-AAAATTA
1 GTAAAATTACCAAAATACCCCTTGATTGTAAAATTACCAAAATACCCTTGACTTTCTAAAAATTA
*
28543449 TCGAAATACCCTCAATTC
66 TAGAAATACCCTCAATTC
28543467 GTAAAATTACCAAAATACCCC-TGATT-TACAAAGTTA-CAGAAATACCCTTGACTTTCTAAAAA
1 GTAAAATTACCAAAATACCCCTTGATTGTA-AAA-TTACCA-AAATACCCTTGACTTTCTAAAAA
28543529 TTATAGAAATACC
63 TTATAGAAATACC
28543542 ATTGGTTTAC
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
79 2 0.03
80 9 0.14
81 35 0.53
82 4 0.06
83 16 0.24
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (83 bp):
GTAAAATTACCAAAATACCCCTTGATTGTAAAATTACCAAAATACCCTTGACTTTCTAAAAATTA
TAGAAATACCCTCAATTC
Found at i:28543693 original size:26 final size:26
Alignment explanation
Indices: 28543617--28543693 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
28543607 AAATGACTAA
* *
28543617 AATACCCCTATTAGGTAAAAAGACCGT
1 AATACCCCTGTT-GGTAAAATGACCGT
* *
28543644 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGT-TGGTAAAATGACCGT
28543671 AATACCCCTGTTGGTAAAATGAC
1 AATACCCCTGTTGGTAAAATGAC
28543694 GAATATGCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
26 11 0.27
27 29 0.71
28 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (26 bp):
AATACCCCTGTTGGTAAAATGACCGT
Found at i:28544525 original size:26 final size:26
Alignment explanation
Indices: 28544496--28544619 Score: 169
Period size: 26 Copynumber: 4.8 Consensus size: 26
28544486 GAGGAAGTGC
*
28544496 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCA
*
28544522 AAAAGGGCTTATGCCTCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCA
**
28544548 AAAAGGGCTTATGCCCCAGTTTATTA
1 AAAAGGGCTTATGCCCCAGTTTACCA
* * *
28544574 AAAAGGGCTTATGCTCCAGGTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCA
*
28544600 AAAAGGGCTT-TTCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28544620 ATTAAAGAGG
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
25 7 0.08
26 78 0.92
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCA
Found at i:28544823 original size:42 final size:42
Alignment explanation
Indices: 28544764--28544855 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
28544754 TAGTCTCCCC
* ** *
28544764 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTA
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
*
28544806 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
28544848 AAATGGGC
1 AAATGGGC
28544856 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
Found at i:28544928 original size:31 final size:31
Alignment explanation
Indices: 28544893--28544953 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
28544883 GTTTCGACCC
* *
28544893 AGTGAAATGATTTATGAAAAGGCTTTGGCCT
1 AGTGAAATGATTTATGAAAAGACTTCGGCCT
*
28544924 AGTGATATGATTTATGAAAAGACTTCGGCC
1 AGTGAAATGATTTATGAAAAGACTTCGGCC
28544954 CAGTAATCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (31 bp):
AGTGAAATGATTTATGAAAAGACTTCGGCCT
Found at i:28550020 original size:9 final size:9
Alignment explanation
Indices: 28550006--28550061 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
28549996 TAACCTAAAA
28550006 TTATTAATT
1 TTATTAATT
28550015 TTATTAATT
1 TTATTAATT
*
28550024 TTAAT-ATT
1 TTATTAATT
28550032 TTATTTAATT
1 TTA-TTAATT
28550042 AATTATTAATT
1 --TTATTAATT
28550053 ATT-TTAATT
1 -TTATTAATT
28550062 ATTTATCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 6 0.15
9 20 0.49
10 6 0.15
11 6 0.15
12 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTATTAATT
Found at i:28555756 original size:15 final size:15
Alignment explanation
Indices: 28555738--28555769 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28555728 CAAACAAATC
28555738 ATCAATTCTCAAAAA
1 ATCAATTCTCAAAAA
*
28555753 ATCAATTCTCGAAAA
1 ATCAATTCTCAAAAA
28555768 AT
1 AT
28555770 GATACTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (15 bp):
ATCAATTCTCAAAAA
Found at i:28565142 original size:70 final size:71
Alignment explanation
Indices: 28565027--28565212 Score: 175
Period size: 70 Copynumber: 2.6 Consensus size: 71
28565017 TTCATTATAT
* * * * * * * * *
28565027 TATCTCATATGGCTGAATATATAAGTTCAAGT-TATCATCACATGTAACCTAATGTTCAAGTTTA
1 TATCTCATATGGCCGAATATACAAATTCAA-TATAACCTCACATGTAACCGAATATACAAGTTCA
28565091 ATA-AAA
65 ATATAAA
* *
28565097 TATCTCATATGGCCGAATATACAAATTCAATATAACCTCATATGTAATCGAATATACAAGTTCAA
1 TATCTCATATGGCCGAATATACAAATTCAATATAACCTCACATGTAACCGAATATACAAGTTCAA
*
28565162 TATAAC
66 TATAAA
* * *
28565168 T-TCACA-A-GCAGCCGAATATACAAACTCAATATGACCTCACATGTA
1 TATCTCATATG--GCCGAATATACAAATTCAATATAACCTCACATGTA
28565213 CATACTTATG
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
68 1 0.01
69 2 0.02
70 90 0.94
71 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (71 bp):
TATCTCATATGGCCGAATATACAAATTCAATATAACCTCACATGTAACCGAATATACAAGTTCAA
TATAAA
Found at i:28565152 original size:35 final size:35
Alignment explanation
Indices: 28565109--28565212 Score: 127
Period size: 35 Copynumber: 3.0 Consensus size: 35
28565099 TCTCATATGG
*
28565109 CCGAATATACAAATTCAATATAACCTCATATGTAA
1 CCGAATATACAAATTCAATATAACCTCACATGTAA
* * * * * *
28565144 TCGAATATACAAGTTCAATATAACTTCACAAGCAG
1 CCGAATATACAAATTCAATATAACCTCACATGTAA
* *
28565179 CCGAATATACAAACTCAATATGACCTCACATGTA
1 CCGAATATACAAATTCAATATAACCTCACATGTA
28565213 CATACTTATG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (35 bp):
CCGAATATACAAATTCAATATAACCTCACATGTAA
Found at i:28572870 original size:15 final size:15
Alignment explanation
Indices: 28572846--28572883 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
28572836 ACAGGCTCAG
28572846 AAAT-ATTATTGACA
1 AAATCATTATTGACA
28572860 AAATCATTATTGACA
1 AAATCATTATTGACA
28572875 AAATCATTA
1 AAATCATTA
28572884 ACTCAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (15 bp):
AAATCATTATTGACA
Found at i:28581393 original size:48 final size:48
Alignment explanation
Indices: 28581332--28581510 Score: 286
Period size: 48 Copynumber: 3.7 Consensus size: 48
28581322 CGCACCCTAG
* * *
28581332 GTGCTAATATCATGACCCGAAGCCAAATCAATGTAACTCGCGCCTAAA
1 GTGCCAATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTAAA
* *
28581380 GTTCCAATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCCAAA
1 GTGCCAATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTAAA
* * *
28581428 GTGCCAAAATCATGGCCCAAAGCCAAATCAATGTAACTCGCACCTGAA
1 GTGCCAATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTAAA
28581476 GTGCCAATATCATGGCCCGAAGCCAAATCAATGTA
1 GTGCCAATATCATGGCCCGAAGCCAAATCAATGTA
28581511 TTCCCTAATG
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 119 1.00
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (48 bp):
GTGCCAATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCTAAA
Found at i:28581643 original size:37 final size:37
Alignment explanation
Indices: 28581593--28581667 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
28581583 TGTCGAATGT
*
28581593 ATCCGCAAATTCGTAATTCACAATTTATCCAATATCA
1 ATCCGCAAATTCGTAATTCACAATTTATCAAATATCA
*
28581630 ATCCGCAAATTCGTAATTCACAATTTATGAAATATCA
1 ATCCGCAAATTCGTAATTCACAATTTATCAAATATCA
28581667 A
1 A
28581668 GGCATTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (37 bp):
ATCCGCAAATTCGTAATTCACAATTTATCAAATATCA
Found at i:28586875 original size:159 final size:159
Alignment explanation
Indices: 28586586--28586905 Score: 552
Period size: 159 Copynumber: 2.0 Consensus size: 159
28586576 ATATCCTCAA
*
28586586 AGGGCTTGGGATAAGTCTAGAATATTTAGGATATACTTCCAAGTTTTGGGAAGTCGATTACCTTG
1 AGGGCTTAGGATAAGTCTAGAATATTTAGGATATACTTCCAAGTTTTGGGAAGTCGATTACCTTG
*
28586651 ATTCCATGTAAACCAATCTCGAAGATATGTTGCACTAAGCAATTTGGATATCAAATATAGGCTTG
66 ATTCCATGCAAACCAATCTCGAAGATATGTTGCACTAAGCAATTTGGATATCAAATATAGGCTTG
**
28586716 TTGCTGCCCAAAGTATCTGCTAGAATCAT
131 TTGCCACCCAAAGTATCTGCTAGAATCAT
**
28586745 AGGGCTTAGGATAAGTCTAGAATATTTAGGATATACTTCCAAGTTTTGGGAAGTCGATTGTCTTG
1 AGGGCTTAGGATAAGTCTAGAATATTTAGGATATACTTCCAAGTTTTGGGAAGTCGATTACCTTG
*
28586810 ATTCCATGCAAACCAATCTCGAAGATATGTTGCACTAAGCAGTTTGGATATCAAATAT-GAGCTT
66 ATTCCATGCAAACCAATCTCGAAGATATGTTGCACTAAGCAATTTGGATATCAAATATAG-GCTT
*
28586874 GTTGCCACCCAATGTATCTGCTAGAATCAT
130 GTTGCCACCCAAAGTATCTGCTAGAATCAT
28586904 AG
1 AG
28586906 CCCAAAGATT
Statistics
Matches: 152, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
158 1 0.01
159 151 0.99
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (159 bp):
AGGGCTTAGGATAAGTCTAGAATATTTAGGATATACTTCCAAGTTTTGGGAAGTCGATTACCTTG
ATTCCATGCAAACCAATCTCGAAGATATGTTGCACTAAGCAATTTGGATATCAAATATAGGCTTG
TTGCCACCCAAAGTATCTGCTAGAATCAT
Found at i:28602516 original size:46 final size:48
Alignment explanation
Indices: 28602465--28602595 Score: 157
Period size: 46 Copynumber: 2.8 Consensus size: 48
28602455 ATGGTTGAGC
28602465 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACTAG
* * *
28602512 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTA-G
*
28602557 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28602596 GCGGGTTACA
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
42 2 0.03
43 5 0.07
45 3 0.04
46 29 0.41
47 28 0.40
48 2 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (48 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTAG
Found at i:28609205 original size:23 final size:23
Alignment explanation
Indices: 28609175--28609219 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
28609165 CTCAAAATAC
28609175 TAAGATTAGGGTCCGAGACTAAG
1 TAAGATTAGGGTCCGAGACTAAG
28609198 TAAGATTAGGGTCCGAGACTAA
1 TAAGATTAGGGTCCGAGACTAA
28609220 AGTTACGTTG
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:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (23 bp):
TAAGATTAGGGTCCGAGACTAAG
Found at i:28612864 original size:35 final size:35
Alignment explanation
Indices: 28612824--28612945 Score: 97
Period size: 35 Copynumber: 3.5 Consensus size: 35
28612814 CTGATTAGCA
28612824 TTGGGCACATATTACTTCAGACATTCCTATGAGTG
1 TTGGGCACATATTACTTCAGACATTCCTATGAGTG
* * * *
28612859 TTGGGCACACATTACTTTA-A-ATGTACTGATAAGTG
1 TTGGGCACATATTACTTCAGACAT-TCCT-ATGAGTG
* * ** * *
28612894 CTAGGTGCATATTATTTCAGACATTCCAATGAGTG
1 TTGGGCACATATTACTTCAGACATTCCTATGAGTG
*
28612929 TTGAGCAC-TCATTACTT
1 TTGGGCACAT-ATTACTT
28612946 TAGATGTACC
Statistics
Matches: 62, Mismatches: 20, Indels: 10
0.67 0.22 0.11
Matches are distributed among these distances:
33 2 0.03
34 5 0.08
35 50 0.81
36 3 0.05
37 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (35 bp):
TTGGGCACATATTACTTCAGACATTCCTATGAGTG
Found at i:28612973 original size:70 final size:70
Alignment explanation
Indices: 28612831--28612979 Score: 192
Period size: 70 Copynumber: 2.1 Consensus size: 70
28612821 GCATTGGGCA
* * * * **
28612831 CATATTACTTCAGACATTCCTATGAGTGTTGGGCACACATTACTTTAAATGTACTGATAAGTGCT
1 CATATTATTTCAGACATTCCAATGAGTGTTGAGCACACATTACTTTAAATGTACCGATAAGCACT
28612896 AGGTG
66 AGGTG
* * *
28612901 CATATTATTTCAGACATTCCAATGAGTGTTGAGCACTCATTACTTTAGATGTACCGTTAAGCACT
1 CATATTATTTCAGACATTCCAATGAGTGTTGAGCACACATTACTTTAAATGTACCGATAAGCACT
28612966 -GGATG
66 AGG-TG
*
28612971 CATTTTATT
1 CATATTATT
28612980 GAAGAGTTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
69 2 0.03
70 66 0.97
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (70 bp):
CATATTATTTCAGACATTCCAATGAGTGTTGAGCACACATTACTTTAAATGTACCGATAAGCACT
AGGTG
Found at i:28613795 original size:31 final size:31
Alignment explanation
Indices: 28613758--28613836 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
28613748 TTGACGGCCA
* *
28613758 AATAACTTAAATAAAAACTTTTAAATAGTTT
1 AATAACTTAAATAAAAAATTTTAAATAATTT
*
28613789 AGTAACTTAAATAAAAAATTTTAAATAATTT
1 AATAACTTAAATAAAAAATTTTAAATAATTT
* *
28613820 AATGACTAAAATAAAAA
1 AATAACTTAAATAAAAA
28613837 TTTATTCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (31 bp):
AATAACTTAAATAAAAAATTTTAAATAATTT
Found at i:28613838 original size:30 final size:30
Alignment explanation
Indices: 28613766--28613864 Score: 103
Period size: 31 Copynumber: 3.3 Consensus size: 30
28613756 CAAATAACTT
* * *
28613766 AAATAAAAACTTTTAAATAGTTTAGTAACTT
1 AAATAAAAA-TTTTAAATAATTTAGTGACTA
*
28613797 AAATAAAAAATTTTAAATAATTTAATGACTA
1 AAAT-AAAAATTTTAAATAATTTAGTGACTA
**
28613828 AAATAAAAATTTATTCATAATTTAGTGA--A
1 AAATAAAAATTT-TAAATAATTTAGTGACTA
28613857 AAATAAAA
1 AAATAAAA
28613865 TAATTTACTA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.15
30 8 0.14
31 37 0.63
32 5 0.08
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATAAAAATTTTAAATAATTTAGTGACTA
Found at i:28614994 original size:6 final size:6
Alignment explanation
Indices: 28614974--28615007 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
28614964 CTATGTGTTC
*
28614974 TTTATT TTATTTT TTTATT TTTATT TTTATT TTT
1 TTTATT TT-TATT TTTATT TTTATT TTTATT TTT
28615008 TTCACAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:28620453 original size:16 final size:16
Alignment explanation
Indices: 28620432--28620462 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28620422 TGTATTCTTT
28620432 ATTTTATTTTTATTTC
1 ATTTTATTTTTATTTC
28620448 ATTTTATTTTTATTT
1 ATTTTATTTTTATTT
28620463 TTTTCACATG
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:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTATTTTTATTTC
Found at i:28622257 original size:31 final size:31
Alignment explanation
Indices: 28622222--28622290 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
28622212 ATTGAAGTAC
* * *
28622222 TTTTGGAAAGATTTAG-CTCTTATTTGAGCAT
1 TTTTGAAAAGATCTAGTC-CTTATTTGACCAT
*
28622253 TTTTGAAAAGGTCTAGTCCTTATTTGACCA-
1 TTTTGAAAAGATCTAGTCCTTATTTGACCAT
28622283 TTTTGAAA
1 TTTTGAAA
28622291 TGTTTGATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 8 0.24
31 24 0.73
32 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (31 bp):
TTTTGAAAAGATCTAGTCCTTATTTGACCAT
Found at i:28625751 original size:6 final size:6
Alignment explanation
Indices: 28625740--28625783 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
28625730 TGGTTTTTTC
* *
28625740 AAAATG AAAATG GAAATG GAAATG AAAATG AAAATG AGAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG A
28625784 TTAATTTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:28625764 original size:18 final size:19
Alignment explanation
Indices: 28625741--28625783 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
28625731 GGTTTTTTCA
*
28625741 AAATGAAAATGGAAATG-G
1 AAATGAAAATGAAAATGAG
28625759 AAATGAAAATGAAAATGAG
1 AAATGAAAATGAAAATGAG
28625778 AAATGA
1 AAATGA
28625784 TTAATTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.16
Consensus pattern (19 bp):
AAATGAAAATGAAAATGAG
Found at i:28633488 original size:17 final size:16
Alignment explanation
Indices: 28633446--28633492 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
28633436 TACTTAACAA
28633446 AAGAGTTCGCCAAACC
1 AAGAGTTCGCCAAACC
* *
28633462 ACAGATTTCGCCAAAGCT
1 A-AGAGTTCGCCAAA-CC
28633480 AAGAGTTCGCCAA
1 AAGAGTTCGCCAA
28633493 TTGGCGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 1 0.04
17 23 0.88
18 2 0.08
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (16 bp):
AAGAGTTCGCCAAACC
Found at i:28633548 original size:33 final size:33
Alignment explanation
Indices: 28633506--28633572 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28633496 GCGTAATAAT
28633506 CACAACTCTATACTTAACCATCACAAACATGTA
1 CACAACTCTATACTTAACCATCACAAACATGTA
28633539 CACAACTCTATACTTAACCATCACAAACATGTA
1 CACAACTCTATACTTAACCATCACAAACATGTA
28633572 C
1 C
28633573 TTACTCTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.31, G:0.03, T:0.24
Consensus pattern (33 bp):
CACAACTCTATACTTAACCATCACAAACATGTA
Found at i:28649696 original size:21 final size:21
Alignment explanation
Indices: 28649661--28649719 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
28649651 AATTAAGTTT
* **
28649661 ATTTAAAAT-AAAAATATTAA
1 ATTTAAATTAAAAAATAAAAA
28649681 ATTTAAATTAAAAAATAAAAA
1 ATTTAAATTAAAAAATAAAAA
28649702 ATTATAATATTAAAAAAT
1 ATT-TAA-ATTAAAAAAT
28649720 TATTGATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 12 0.36
22 3 0.09
23 10 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTTAAATTAAAAAATAAAAA
Found at i:28650030 original size:15 final size:15
Alignment explanation
Indices: 28650010--28650040 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28650000 TTTTTTTAGA
28650010 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
28650025 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
28650040 A
1 A
28650041 AAAAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:28650089 original size:24 final size:24
Alignment explanation
Indices: 28650011--28650089 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
28650001 TTTTTTAGAA
* *
28650011 TTTTAGAATTATATATTTTAGAATT
1 TTTTAAAAATATATATTTTA-AATT
*
28650036 TTATAAAAA-AT-TATTTTAAACCTT
1 TTTTAAAAATATATATTTTAAA--TT
*
28650060 TCTTAAAAATATATA-TTTACAATT
1 TTTTAAAAATATATATTTTA-AATT
28650084 TTTTAA
1 TTTTAA
28650090 TAATTTTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.16
24 18 0.42
25 12 0.28
26 4 0.09
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.51
Consensus pattern (24 bp):
TTTTAAAAATATATATTTTAAATT
Found at i:28652040 original size:42 final size:42
Alignment explanation
Indices: 28651930--28652051 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 42
28651920 TACCGTACCA
* * * *
28651930 ATGCCATATCCCAAATATGGTCTTATA-TATAGTCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGA-AGTCTCATATCG
* * * *
28651972 ATTCCAATAGCCTAGATATAGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
28652015 ATGCCATATCCCAGATATGGTCTTACACGTAA-TCTCA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCA
28652052 GTAACCCTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
42 30 0.46
43 34 0.52
44 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:28675176 original size:82 final size:82
Alignment explanation
Indices: 28675055--28675218 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
28675045 TTTAACATAG
*
28675055 GTAAGCTATTACACACGAACTTAATTTATTTGAGTTCATCATTTTTCCTTAACATATCATACTTT
1 GTAAGCCATTACACACGAACTTAATTTATTTGAGTTCATCATTTTTCCTTAACATATCATACTTT
28675120 CAATGAAACTTAATTAT
66 CAATGAAACTTAATTAT
28675137 GTAAGCCATTACACACGAACTTAATTTATTTGAGTTCATCATTTTTCCTTAACATATCATACTTT
1 GTAAGCCATTACACACGAACTTAATTTATTTGAGTTCATCATTTTTCCTTAACATATCATACTTT
28675202 CAATGAAACTTAATTAT
66 CAATGAAACTTAATTAT
28675219 ACATACTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (82 bp):
GTAAGCCATTACACACGAACTTAATTTATTTGAGTTCATCATTTTTCCTTAACATATCATACTTT
CAATGAAACTTAATTAT
Found at i:28676657 original size:24 final size:24
Alignment explanation
Indices: 28676629--28676676 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28676619 AACATTTACG
28676629 ATTTAGTTCCTTTTAATTAATTAA
1 ATTTAGTTCCTTTTAATTAATTAA
28676653 ATTTAGTTCCTTTTAATTAATTAA
1 ATTTAGTTCCTTTTAATTAATTAA
28676677 TTATCTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTAGTTCCTTTTAATTAATTAA
Found at i:28682346 original size:42 final size:41
Alignment explanation
Indices: 28682314--28682464 Score: 142
Period size: 42 Copynumber: 3.6 Consensus size: 41
28682304 GAGTTTAAGA
* *
28682314 GTAAGACCATATCTGGAATATGGCATCGTTATGAGATTTTGT
1 GTAAGACCATATCTGGAATATGGCATCGATATGAGA-TTAGT
* * * * * * *
28682356 GTAAAACTATGTCTGGGACATGGCATCGATATGAGAATCGT
1 GTAAGACCATATCTGGAATATGGCATCGATATGAGATTAGT
* * * *
28682397 GTAAGAACATAGCTGGACTATTGGCATCGATATGAGACTCA-T
1 GTAAGACCATATCTGGAATA-TGGCATCGATATGAGA-TTAGT
*
28682439 GTAAGACCATATCTGGGATATGGCAT
1 GTAAGACCATATCTGGAATATGGCAT
28682465 TGGTATGATT
Statistics
Matches: 84, Mismatches: 23, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
41 21 0.25
42 63 0.75
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (41 bp):
GTAAGACCATATCTGGAATATGGCATCGATATGAGATTAGT
Found at i:28686905 original size:276 final size:276
Alignment explanation
Indices: 28686412--28686968 Score: 1096
Period size: 276 Copynumber: 2.0 Consensus size: 276
28686402 CTTGATTGGT
*
28686412 TGTAATGACCCGATAGTCACGAGTATCAGAAAGTGTATTTTCAGGTCTCCATTTTCAGAAAATGG
1 TGTAATGACCCGATAGTCACGAGTATCAGAAAGTGTATTTTCAGGTCTCCATTTTCAGAAAACGG
28686477 ATTCGTAAATATTTAATAAAAATATTTACGAAGTTAGTTGTGTGGTTAATTAGATTTTGATTCGG
66 ATTCGTAAATATTTAATAAAAATATTTACGAAGTTAGTTGTGTGGTTAATTAGATTTTGATTCGG
28686542 TGAATTTGTTTAATTTATGAGTAATTAGGTGTAAGGACTAGATTGCATATAGGGAGAAAGTTAAA
131 TGAATTTGTTTAATTTATGAGTAATTAGGTGTAAGGACTAGATTGCATATAGGGAGAAAGTTAAA
28686607 TTATAGATTAGAGAAAAGTGAAGGGACTAAATAAGCAATTAAACCTTAAATTAACAAGTGTGTGG
196 TTATAGATTAGAGAAAAGTGAAGGGACTAAATAAGCAATTAAACCTTAAATTAACAAGTGTGTGG
28686672 TATTGGTAATGACATG
261 TATTGGTAATGACATG
28686688 TGTAATGACCCGATAGTCACGAGTATCAGAAAGTGTATTTTCAGGTCTCCATTTTCAGAAAACGG
1 TGTAATGACCCGATAGTCACGAGTATCAGAAAGTGTATTTTCAGGTCTCCATTTTCAGAAAACGG
*
28686753 ATTCGTAAATATTTAATAAAAATATTTATGAAGTTAGTTGTGTGGTTAATTAGATTTTGATTCGG
66 ATTCGTAAATATTTAATAAAAATATTTACGAAGTTAGTTGTGTGGTTAATTAGATTTTGATTCGG
28686818 TGAATTTGTTTAATTTATGAGTAATTAGGTGTAAGGACTAGATTGCATATAGGGAGAAAGTTAAA
131 TGAATTTGTTTAATTTATGAGTAATTAGGTGTAAGGACTAGATTGCATATAGGGAGAAAGTTAAA
28686883 TTATAGATTAGAGAAAAGTGAAGGGACTAAATAAGCAATTAAACCTTAAATTAACAAGTGTGTGG
196 TTATAGATTAGAGAAAAGTGAAGGGACTAAATAAGCAATTAAACCTTAAATTAACAAGTGTGTGG
28686948 TATTGGTAATGACATG
261 TATTGGTAATGACATG
28686964 TGTAA
1 TGTAA
28686969 CATTTAAATA
Statistics
Matches: 279, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
276 279 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (276 bp):
TGTAATGACCCGATAGTCACGAGTATCAGAAAGTGTATTTTCAGGTCTCCATTTTCAGAAAACGG
ATTCGTAAATATTTAATAAAAATATTTACGAAGTTAGTTGTGTGGTTAATTAGATTTTGATTCGG
TGAATTTGTTTAATTTATGAGTAATTAGGTGTAAGGACTAGATTGCATATAGGGAGAAAGTTAAA
TTATAGATTAGAGAAAAGTGAAGGGACTAAATAAGCAATTAAACCTTAAATTAACAAGTGTGTGG
TATTGGTAATGACATG
Found at i:28687453 original size:18 final size:19
Alignment explanation
Indices: 28687424--28687459 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28687414 GTACAATTTT
*
28687424 TGAAATTTAGAGATTTGAG
1 TGAAATTTAGAGAGTTGAG
28687443 TGAAA-TTAGAGAGTTGA
1 TGAAATTTAGAGAGTTGA
28687460 ATTTAGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGAGAGTTGAG
Found at i:28692580 original size:47 final size:47
Alignment explanation
Indices: 28692438--28692946 Score: 878
Period size: 47 Copynumber: 10.8 Consensus size: 47
28692428 ATTTAGGATT
28692438 CGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGC
28692487 CGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGC
28692536 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
28692583 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
28692630 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
* *
28692677 TGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
28692724 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
28692771 CGATGTGATGAATGTGAAAGTGTATATA--TGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
28692816 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
* * * *
28692863 CGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
* * * *
28692910 CAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
28692947 TCCCGAAGGG
Statistics
Matches: 444, Mismatches: 14, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
45 45 0.10
47 328 0.74
49 71 0.16
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
Found at i:28693120 original size:37 final size:37
Alignment explanation
Indices: 28693064--28693142 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28693054 CCGAGCTCTA
* * *
28693064 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
28693101 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
28693138 AAGAC
1 AAGAC
28693143 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:28694857 original size:43 final size:43
Alignment explanation
Indices: 28694796--28694880 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
28694786 TTCAAAGTAT
*
28694796 GTTAAATCACCCCATCTAACATTCAACCAATATGCCTAACATA
1 GTTAAATCACACCATCTAACATTCAACCAATATGCCTAACATA
*
28694839 GTTAAATCACACCATCTAACATTCAATCAATATGCCTAACAT
1 GTTAAATCACACCATCTAACATTCAACCAATATGCCTAACAT
28694881 GGGCACCTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.27
Consensus pattern (43 bp):
GTTAAATCACACCATCTAACATTCAACCAATATGCCTAACATA
Found at i:28695459 original size:37 final size:37
Alignment explanation
Indices: 28695414--28695522 Score: 141
Period size: 37 Copynumber: 3.0 Consensus size: 37
28695404 GATATTTCAA
28695414 CCGA-AACATGCCAGATGCTCATAAGAGCTAATCCAC
1 CCGATAACATGCCAGATGCTCATAAGAGCTAATCCAC
* * *
28695450 CTGATAACATGTCAGATGCTCATAAGAGCCAATCCAC
1 CCGATAACATGCCAGATGCTCATAAGAGCTAATCCAC
* * *
28695487 CCGATAACACGCCA-ATTGCTCCTAAGAGCTAGTCCA
1 CCGATAACATGCCAGA-TGCTCATAAGAGCTAATCCA
28695523 ACTAAAAACA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
36 4 0.06
37 58 0.94
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (37 bp):
CCGATAACATGCCAGATGCTCATAAGAGCTAATCCAC
Found at i:28697406 original size:29 final size:29
Alignment explanation
Indices: 28697374--28697430 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
28697364 CTGGTTTGTC
* *
28697374 AAGTCAGTTAGTTAGTTAG-TAGTTAGTTG
1 AAGTCAATTAGTT-GTTAGCTAGGTAGTTG
*
28697403 AAGTCAATTGGTTGTTAGCTAGGTAGTT
1 AAGTCAATTAGTTGTTAGCTAGGTAGTT
28697431 TTTACTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.40
Consensus pattern (29 bp):
AAGTCAATTAGTTGTTAGCTAGGTAGTTG
Found at i:28701794 original size:31 final size:30
Alignment explanation
Indices: 28701737--28701795 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
28701727 ATTAGATAAA
* *
28701737 ATCTAATTACAAAATAATAACATAAAATTG
1 ATCTAATTAAAAAATAAGAACATAAAATTG
28701767 ATCTAATTAAAAAAATAAGAA-AGTAAAAT
1 ATCTAATT-AAAAAATAAGAACA-TAAAAT
28701796 CTATATAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (30 bp):
ATCTAATTAAAAAATAAGAACATAAAATTG
Found at i:28707402 original size:15 final size:14
Alignment explanation
Indices: 28707372--28707410 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
28707362 TTTAATCTAT
28707372 TATTTCTATTACTA
1 TATTTCTATTACTA
*
28707386 TATTTCTATATATTA
1 TATTTCTAT-TACTA
28707401 TATTTCTATT
1 TATTTCTATT
28707411 TGTATTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTCTATTACTA
Found at i:28707461 original size:3 final size:3
Alignment explanation
Indices: 28707416--28707563 Score: 77
Period size: 3 Copynumber: 49.0 Consensus size: 3
28707406 CTATTTGTAT
* * * *
28707416 TTA TGTA TTA ATA TCA TTA TT- TTCA TTA TTT TTA -TA CTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * * * *
28707461 TTT TCTA TTA TTA TTA CTA TTT TTA TTG CTA TTA TCTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
** * ** * * *
28707508 TCC CTA TTA TTA TTA ACA -TA TCA TTA TTC TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
28707555 TCA TTA TTA
1 TTA TTA TTA
28707564 ACGTAATATT
Statistics
Matches: 104, Mismatches: 34, Indels: 14
0.68 0.22 0.09
Matches are distributed among these distances:
2 5 0.05
3 89 0.86
4 10 0.10
ACGTcount: A:0.29, C:0.09, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:28707696 original size:3 final size:3
Alignment explanation
Indices: 28707688--28707752 Score: 114
Period size: 3 Copynumber: 21.7 Consensus size: 3
28707678 TATATTACTC
28707688 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28707736 TTA TT- TTA CTTA TTA TT
1 TTA TTA TTA -TTA TTA TT
28707753 TACCTATTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28719970 original size:14 final size:15
Alignment explanation
Indices: 28719951--28719986 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
28719941 ACTTTTTATT
28719951 TTTTATTTA-TTTTA
1 TTTTATTTATTTTTA
28719965 TTTTA-TTATTTTTA
1 TTTTATTTATTTTTA
28719979 TTTT-TTTA
1 TTTTATTTA
28719987 GTAGATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 17 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTATTTATTTTTA
Found at i:28723732 original size:46 final size:46
Alignment explanation
Indices: 28723645--28723732 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
28723635 TGAAGAAGCA
* *
28723645 ACAAATCCTATACCCTTGAGTTGCAGTGGGATAGATTGAAGATGGT
1 ACAAATCCTATACCCCTGAGTTGCAGTGGGATAGATAGAAGATGGT
28723691 ACAAATCCTATACCCCTGAGTTGCAGTGGGAT-GCATAGAAGA
1 ACAAATCCTATACCCCTGAGTTGCAGTGGGATAG-ATAGAAGA
28723733 AACCACAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (46 bp):
ACAAATCCTATACCCCTGAGTTGCAGTGGGATAGATAGAAGATGGT
Found at i:28723741 original size:46 final size:46
Alignment explanation
Indices: 28723636--28723742 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 46
28723626 TTAATTGATT
* *
28723636 GAAGAAGCAACAAATCCTATACCCTTGAGTTGCAGTGGGATAGATT
1 GAAGAAGCAACAAATCCTATACCCCTGAGTTGCAGTGGGATAGATA
* **
28723682 GAAGATGGTACAAATCCTATACCCCTGAGTTGCAGTGGGAT-GCATA
1 GAAGAAGCAACAAATCCTATACCCCTGAGTTGCAGTGGGATAG-ATA
* *
28723728 GAAGAAACCACAAAT
1 GAAGAAGCAACAAAT
28723743 TTTATCTCCC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 1 0.02
46 50 0.98
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (46 bp):
GAAGAAGCAACAAATCCTATACCCCTGAGTTGCAGTGGGATAGATA
Found at i:28724166 original size:45 final size:43
Alignment explanation
Indices: 28724099--28724202 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 43
28724089 CATACCCTTG
28724099 AAGTTGTAGTGGAGCAAATTGAAGCCACTAAA-CCTTATCTCCCTA
1 AAGTTGTAGTGGAGCAAATTGAAG---CTAAAGCCTTATCTCCCTA
* ** * *
28724144 AAGTTGCAGTGGAGCACGTTGAAGTTAAAGTCTTATCTCCCTA
1 AAGTTGTAGTGGAGCAAATTGAAGCTAAAGCCTTATCTCCCTA
28724187 AAGTTGTAGTGGAGCA
1 AAGTTGTAGTGGAGCA
28724203 GACTGAAGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 4 0.08
43 27 0.52
45 21 0.40
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (43 bp):
AAGTTGTAGTGGAGCAAATTGAAGCTAAAGCCTTATCTCCCTA
Found at i:28724210 original size:43 final size:44
Alignment explanation
Indices: 28724132--28724244 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 44
28724122 GCCACTAAAC
* * *
28724132 CTTATCTCCCTAAAGTTGCAGTGGAGCACGTTGAAGTTA-AAGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCACGCTGAAGATACAAAT
*
28724175 CTTATCTCCCTAAAGTTGTAGTGGAGCA-GACTGAAGATAGCAAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCACG-CTGAAGATA-CAAAT
* *
28724220 CTTATTTCCCTGAAGTTGCAGTGGA
1 CTTATCTCCCTAAAGTTGCAGTGGA
28724245 ATATATTGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
42 1 0.02
43 34 0.57
45 25 0.42
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCACGCTGAAGATACAAAT
Found at i:28724236 original size:45 final size:45
Alignment explanation
Indices: 28724097--28724572 Score: 257
Period size: 45 Copynumber: 10.6 Consensus size: 45
28724087 TCCATACCCT
* * ** *
28724097 TGAAGTTGTAGTGGAGCAAATTGAAGCCA-CTAAACCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGC-AAATCTTATCTCCC
* * *
28724142 TAAAGTTGCAGTGGAGCACG-TTGAAGTTA--AAGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCA-GATTGAAGATAGCAAATCTTATCTCCC
* * * *
28724185 TAAAGTTGTAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCC
** * * * *
28724230 TGAAGTTGCAGTGGAATATATTGAAGCTATAAATAAACAGATCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTGAAG------AT-AGCAAATCTTATCTCCC
* * * * *
28724282 TAAAGTTGTAGTAGAGCAGA-T---CATAGCAAACCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCC
* * * *
28724323 TGAAGTTGCAGTGGAGCAAACTGAAGATAGCGAATCTTATTTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCC
* * * * * **
28724368 TGAATTTGAAGTGGAACAGATTGAAGCTATAAATAAACAGATCTTATCTCTT
1 TGAAGTTGCAGTGGAGCAGATTGAAG------AT-AGCAAATCTTATCTCCC
* * *
28724420 TGAAGTTGCAGTAGAGCAGA-T---CATAGCAAACCTTAT-TCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCC
* * * * *
28724460 TGAAGTTGCAATGAAGCA-AGTTAAAGTTA--AAGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGA-TTGAAGATAGCAAATCTTATCTCCC
* *
28724503 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATTTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCC
* **
28724548 TG-AGTTACAGTGGAATAGATTGAAG
1 TGAAGTTGCAGTGGAGCAGATTGAAG
28724573 TTATAAATAA
Statistics
Matches: 321, Mismatches: 79, Indels: 63
0.69 0.17 0.14
Matches are distributed among these distances:
39 1 0.00
40 17 0.05
41 39 0.12
42 13 0.04
43 63 0.20
44 23 0.07
45 105 0.33
51 6 0.02
52 54 0.17
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (45 bp):
TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCC
Found at i:28724254 original size:88 final size:92
Alignment explanation
Indices: 28724099--28724351 Score: 236
Period size: 88 Copynumber: 2.8 Consensus size: 92
28724089 CATACCCTTG
* ** * * *
28724099 AAGTTGTAGTGGAGCAAATTGAAGCCA-CTAAACCTTATCTCCCTAAAGTTGCAGTGGAGCACGT
1 AAGTTGTAGTGGAGCAGA-TGAAGATAGC-AAACCTTATCTCCCTGAAGTTGCAGTGGAACACAT
28724163 TGAAG-T-T-AA-AG-TCTTATCTCCCTA
64 TGAAGATATAAACAGATCTTATCTCCCTA
* * * *
28724187 AAGTTGTAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAATATATT
1 AAGTTGTAGTGGAGCAGA-TGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAACACATT
*
28724252 GAAGCTATAAATAAACAGATCTTATCTCTCTA
65 GAAG--AT--ATAAACAGATCTTATCTCCCTA
* * * * *
28724284 AAGTTGTAGTAGAGCAGAT---CATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTG
1 AAGTTGTAGTGGAGCAGATGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAACACATTG
28724346 AAGATA
66 AAGATA
28724352 GCGAATCTTA
Statistics
Matches: 135, Mismatches: 20, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
88 56 0.41
89 2 0.01
91 3 0.02
93 39 0.29
94 1 0.01
95 2 0.01
96 3 0.02
97 29 0.21
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (92 bp):
AAGTTGTAGTGGAGCAGATGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAACACATTG
AAGATATAAACAGATCTTATCTCCCTA
Found at i:28724346 original size:138 final size:138
Alignment explanation
Indices: 28724175--28724528 Score: 507
Period size: 138 Copynumber: 2.6 Consensus size: 138
28724165 AAGTTAAAGT
* * *
28724175 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
* * *
28724240 GTGGAATATATTGAAGCTATAAATAAACAGATCTTATCTCTCTAAAGTTGTAGTAGAGCAGATCA
66 GTGGAACAGATTGAAGCTATAAATAAACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCA
28724305 TAGCAAAC
131 TAGCAAAC
* * *
28724313 CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCGAATCTTATTTCCCTGAATTTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
* *
28724378 GTGGAACAGATTGAAGCTATAAATAAACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCA
66 GTGGAACAGATTGAAGCTATAAATAAACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCA
28724443 TAGCAAAC
131 TAGCAAAC
* * ** * * * *
28724451 CTTAT-TCCCTGAAGTTGCAATGAAGCAAGTTAAAGTTA--AAGTCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
*
28724513 GTGGAGCAGATTGAAG
66 GTGGAACAGATTGAAG
28724529 ATAGCGAATC
Statistics
Matches: 193, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
135 34 0.18
137 27 0.14
138 132 0.68
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (138 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
GTGGAACAGATTGAAGCTATAAATAAACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCA
TAGCAAAC
Found at i:28724348 original size:93 final size:95
Alignment explanation
Indices: 28724174--28724348 Score: 237
Period size: 93 Copynumber: 1.8 Consensus size: 95
28724164 GAAGTTAAAG
* * * *
28724174 TCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGC
1 TCTTATCTCCCTAAAGTTGTAGTAGAGCAGACT--ACATAGCAAACCTTATCTCCCTGAAGTTGC
* * *
28724239 AGTGGAATATATTGAAGCTATAAATAAACAGA
64 AGTGGAACAAACTGAAGCTATAAATAAACAGA
*
28724271 TCTTATCTCTCTAAAGTTGTAGTAGAGCAGA-T-CATAGCAAACCTTATCTCCCTGAAGTTGCAG
1 TCTTATCTCCCTAAAGTTGTAGTAGAGCAGACTACATAGCAAACCTTATCTCCCTGAAGTTGCAG
*
28724334 TGGAGCAAACTGAAG
66 TGGAACAAACTGAAG
28724349 ATAGCGAATC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
93 39 0.57
96 1 0.01
97 29 0.42
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (95 bp):
TCTTATCTCCCTAAAGTTGTAGTAGAGCAGACTACATAGCAAACCTTATCTCCCTGAAGTTGCAG
TGGAACAAACTGAAGCTATAAATAAACAGA
Found at i:28724636 original size:45 final size:45
Alignment explanation
Indices: 28724585--28724787 Score: 146
Period size: 45 Copynumber: 4.5 Consensus size: 45
28724575 ATAAATAATC
* * *
28724585 TGAAGATAGCAGGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGAT
1 TGAAGATAGCAGATCTTATCTCCCTGAACTTGCAGTGGAGCAGAT
*
28724630 TGAAGATAGCAGATCTTATCTCCCTGAACTTGCAGTGGATCAGAT
1 TGAAGATAGCAGATCTTATCTCCCTGAACTTGCAGTGGAGCAGAT
* ** * * * **
28724675 CGAAGCCA-CA-ATCCTTATCTCTCTGAAGTTGCAGTAGAATAGGA-
1 TGAAGATAGCAGAT-CTTATCTCCCTGAACTTGCAGTGGAGCA-GAT
* * * * * * * *
28724719 TAAAAATACACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGT
1 TGAAGATA-GCAGATCTTATCTCCCTGAACTTGCAGTGGAGCAGAT
28724765 TGAA-ATTAGCA-ATTCTTATCTCC
1 TGAAGA-TAGCAGA-TCTTATCTCC
28724788 TTTAAGTTCC
Statistics
Matches: 123, Mismatches: 27, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
43 2 0.02
44 29 0.24
45 61 0.50
46 30 0.24
47 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (45 bp):
TGAAGATAGCAGATCTTATCTCCCTGAACTTGCAGTGGAGCAGAT
Found at i:28725225 original size:23 final size:23
Alignment explanation
Indices: 28725199--28725249 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
28725189 ACCCAAAATG
28725199 CCCAAACAAATTAAGTTACACGA
1 CCCAAACAAATTAAGTTACACGA
*
28725222 CCCAAACAAATTAAGTTACACGG
1 CCCAAACAAATTAAGTTACACGA
28725245 CCCAA
1 CCCAA
28725250 CATGCCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.45, C:0.29, G:0.10, T:0.16
Consensus pattern (23 bp):
CCCAAACAAATTAAGTTACACGA
Found at i:28726460 original size:15 final size:14
Alignment explanation
Indices: 28726427--28726465 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
28726417 TTTAATCTAT
28726427 TATTTCTATTACAA
1 TATTTCTATTACAA
**
28726441 TATTTCTATGTATTA
1 TATTTCTAT-TACAA
28726456 TATTTCTATT
1 TATTTCTATT
28726466 TGTATTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (14 bp):
TATTTCTATTACAA
Found at i:28726517 original size:3 final size:3
Alignment explanation
Indices: 28726471--28726606 Score: 77
Period size: 3 Copynumber: 46.0 Consensus size: 3
28726461 CTATTTGTAT
* * *
28726471 TTA TGTA TTA ATA TCA TTA TT- TTCA TTA TT- TT- TTA -TA CTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * * *
28726514 TTA TTA CTA TTA TTA TTG CTA TTA TCTA TTA TTA TTA TCT- CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA
** * * * *
28726560 TTA TTA ACA -TA TCA TTA TTC TTA TTA TTA TTT TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28726607 ACCACTACAG
Statistics
Matches: 100, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
2 10 0.10
3 81 0.81
4 9 0.09
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:28726678 original size:39 final size:39
Alignment explanation
Indices: 28726629--28726734 Score: 131
Period size: 39 Copynumber: 2.7 Consensus size: 39
28726619 AAACAGGTTT
* * * *
28726629 TTAGCGGCGCTTTTCAAAAAATGTCGTTATAGGTTCAAA
1 TTAGCGGCGCTTTTCAAAAAACGCCGCTATAGGTACAAA
* *
28726668 TTAGCAGCGCTTTTCAAAAAACGCCGCTATAGGTACACA
1 TTAGCGGCGCTTTTCAAAAAACGCCGCTATAGGTACAAA
* *
28726707 CTAGCGGCGCTTTTTAAAAAAACGCCGC
1 TTAGCGGCGC-TTTTCAAAAAACGCCGC
28726735 AAAACTTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
39 41 0.72
40 16 0.28
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (39 bp):
TTAGCGGCGCTTTTCAAAAAACGCCGCTATAGGTACAAA
Found at i:28727177 original size:40 final size:39
Alignment explanation
Indices: 28727108--28727200 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 39
28727098 TTTAGTGGCT
* *
28727108 TTAGCAGCGCTTTTTAAAAACGCCGCTATAGGTCGAGTA
1 TTAGCGGCGCTTTTTAAAAACGCAGCTATAGGTCGAGTA
28727147 TTAGCGGCGCTTTTTGAAAAACGCAGCTATAGGTCGAGTA
1 TTAGCGGCGCTTTTT-AAAAACGCAGCTATAGGTCGAGTA
*
28727187 TAAGCGGCG-TTTTT
1 TTAGCGGCGCTTTTT
28727201 CATTTCATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 19 0.38
40 31 0.62
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (39 bp):
TTAGCGGCGCTTTTTAAAAACGCAGCTATAGGTCGAGTA
Found at i:28727460 original size:15 final size:14
Alignment explanation
Indices: 28727440--28727477 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
28727430 AATATTTTAA
28727440 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
28727454 GGGTTTAAGGATTAT
1 -GGTTTATGGATTAT
28727469 GGTTTATGG
1 GGTTTATGG
28727478 TTTAAGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:28727461 original size:22 final size:21
Alignment explanation
Indices: 28727435--28727483 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
28727425 TGTTAAATAT
*
28727435 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
*
28727457 TTTAAGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
28727478 TTTAAG
1 TTTAAG
28727484 AGTTAGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:28727493 original size:21 final size:21
Alignment explanation
Indices: 28727450--28727532 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
28727440 GGTTTATGGA
*
28727450 TTATGGGTTTAAG-GATTATGGT
1 TTAT-GGTTTAAGAG-TTAGGGT
28727472 TTATGGTTTAAGAGTTAGGGT
1 TTATGGTTTAAGAGTTAGGGT
** * * *
28727493 TTAAAGCTTAGGAGTTAGGGG
1 TTATGGTTTAAGAGTTAGGGT
* * *
28727514 TTAGGGGTTAAGTGTTAGG
1 TTATGGTTTAAGAGTTAGG
28727533 TTTTTAAGGT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 44 0.90
22 5 0.10
ACGTcount: A:0.24, C:0.01, G:0.36, T:0.39
Consensus pattern (21 bp):
TTATGGTTTAAGAGTTAGGGT
Found at i:28727888 original size:7 final size:7
Alignment explanation
Indices: 28727876--28727914 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
28727866 ATATATTTTG
28727876 GGTTTAT
1 GGTTTAT
28727883 GGTTTA-
1 GGTTTAT
*
28727889 GATTTAT
1 GGTTTAT
28727896 GGTTTAT
1 GGTTTAT
*
28727903 GATTTAT
1 GGTTTAT
28727910 GGTTT
1 GGTTT
28727915 GGGGTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (7 bp):
GGTTTAT
Found at i:28727896 original size:13 final size:14
Alignment explanation
Indices: 28727878--28727914 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
28727868 ATATTTTGGG
28727878 TTTATGGTTTA-GA
1 TTTATGGTTTATGA
28727891 TTTATGGTTTATGA
1 TTTATGGTTTATGA
28727905 TTTATGGTTT
1 TTTATGGTTT
28727915 GGGGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (14 bp):
TTTATGGTTTATGA
Found at i:28727923 original size:14 final size:13
Alignment explanation
Indices: 28727872--28727916 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
28727862 ATATATATAT
*
28727872 TTTGGGTTTATGG
1 TTTGGATTTATGG
*
28727885 TTTAGATTTATGG
1 TTTGGATTTATGG
*
28727898 TTTATGATTTATGG
1 TTT-GGATTTATGG
28727912 TTTGG
1 TTTGG
28727917 GGTTTATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.56
Consensus pattern (13 bp):
TTTGGATTTATGG
Found at i:28728548 original size:9 final size:8
Alignment explanation
Indices: 28728530--28728608 Score: 58
Period size: 7 Copynumber: 9.9 Consensus size: 8
28728520 TTTATATGTT
28728530 AATTTAAA
1 AATTTAAA
28728538 AATTATAAA
1 AATT-TAAA
28728547 AATCTTCAAAA
1 AAT-TT--AAA
28728558 AATTT-AA
1 AATTTAAA
*
28728565 AATCT-AA
1 AATTTAAA
28728572 AA-TTAAA
1 AATTTAAA
28728579 AA-TTAAA
1 AATTTAAA
* *
28728586 AAATAAAA
1 AATTTAAA
*
28728594 AACTTAAA
1 AATTTAAA
28728602 AATTTAA
1 AATTTAA
28728609 TATTTAATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
6 1 0.02
7 21 0.36
8 20 0.34
9 8 0.14
10 3 0.05
11 6 0.10
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (8 bp):
AATTTAAA
Found at i:28728587 original size:14 final size:14
Alignment explanation
Indices: 28728555--28728605 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
28728545 AAAATCTTCA
*
28728555 AAAAATTTAAAATCT
1 AAAAATTAAAAAT-T
28728570 -AAAATTAAAAATT
1 AAAAATTAAAAATT
*
28728583 AAAAAATAAAAAACTT
1 -AAAAATTAAAAA-TT
28728599 AAAAATT
1 AAAAATT
28728606 TAATATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.37
15 16 0.53
16 2 0.07
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAATTAAAAATT
Found at i:28728588 original size:15 final size:16
Alignment explanation
Indices: 28728570--28728608 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28728560 TTTAAAATCT
28728570 AAAATTAAAAA-TTAA
1 AAAATTAAAAACTTAA
*
28728585 AAAATAAAAAACTTAA
1 AAAATTAAAAACTTAA
*
28728601 AAATTTAA
1 AAAATTAA
28728609 TATTTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATTAAAAACTTAA
Found at i:28728592 original size:20 final size:21
Alignment explanation
Indices: 28728555--28728608 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
28728545 AAAATCTTCA
**
28728555 AAAAATTTAAAATCTAAAATT
1 AAAAATTTAAAAAATAAAATT
28728576 AAAAA-TTAAAAAATAAAAAACTT
1 AAAAATTTAAAAAAT--AAAA-TT
28728599 AAAAATTTAA
1 AAAAATTTAA
28728609 TATTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.26
21 5 0.19
22 4 0.15
23 7 0.26
24 4 0.15
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAATTTAAAAAATAAAATT
Found at i:28733482 original size:129 final size:129
Alignment explanation
Indices: 28733251--28733524 Score: 347
Period size: 129 Copynumber: 2.1 Consensus size: 129
28733241 ATAATTTTAA
* * *
28733251 ATGTTCTTTAGCGGCATTTTTTGAGAAAAGCGCAGCTAAAGGTTTATATTATAGTGGCGTTTGTG
1 ATGTTCTTTAGCGGCAGTTTGTGAGAAAAGCGCAGCTAAAGGTTTATATTATAGCGGCGTTTGTG
* * *
28733316 GCAAAAGCGCCGCTAAAGGTCATGTTCTTTAACGGCGTTTGTCAGAAAAGTGCCACTTAAGGCC
66 GCAAAAGCACCGCTAAAGGTCATGTTCTTTAACGGCGTTTGTCAGAAAAGCGCCACTAAAGGCC
* *
28733380 ATGTTCTTTAGCGGC-GTTTGTGAGAAAAGCGCCGCTAAAGGTCATGT-TCTT-TAGCGGCGTTT
1 ATGTTCTTTAGCGGCAGTTTGTGAGAAAAGCGCAGCTAAAGGT--T-TATATTATAGCGGCGTTT
* ** * * * *
28733442 TTGGGGAAAGCACCGCTAAAGGTCATGTTCTTTAATGGCGTTTTTGAGAAAAGCGCCGCTAAAGG
63 GTGGCAAAAGCACCGCTAAAGGTCATGTTCTTTAACGGCGTTTGTCAGAAAAGCGCCACTAAAGG
*
28733507 TC
128 CC
*
28733509 ATGTTCTATAGCGGCA
1 ATGTTCTTTAGCGGCA
28733525 TTTTTTTTCA
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
128 24 0.19
129 95 0.77
130 4 0.03
131 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (129 bp):
ATGTTCTTTAGCGGCAGTTTGTGAGAAAAGCGCAGCTAAAGGTTTATATTATAGCGGCGTTTGTG
GCAAAAGCACCGCTAAAGGTCATGTTCTTTAACGGCGTTTGTCAGAAAAGCGCCACTAAAGGCC
Found at i:28733529 original size:43 final size:43
Alignment explanation
Indices: 28733251--28733529 Score: 314
Period size: 43 Copynumber: 6.5 Consensus size: 43
28733241 ATAATTTTAA
* *
28733251 ATGTTCTTTAGCGGCATTTTTTGAGAAAAGCGCAGCTAAAGGT-
1 ATGTTCTTTAGCGGC-GTTTTTGAGAAAAGCGCCGCTAAAGGTC
* * *
28733294 -T-TATATTATAGTGGCGTTTGTG-GCAAAAGCGCCGCTAAAGGTC
1 ATGT-TCTT-TAGCGGCGTTTTTGAG-AAAAGCGCCGCTAAAGGTC
* * * * * * *
28733337 ATGTTCTTTAACGGCGTTTGTCAGAAAAGTGCCACTTAAGGCC
1 ATGTTCTTTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTC
*
28733380 ATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTC
* * *
28733423 ATGTTCTTTAGCGGCGTTTTTGGGGAAAGCACCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTC
**
28733466 ATGTTCTTTAATGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTC
* *
28733509 ATGTTCTATAGCGGCATTTTT
1 ATGTTCTTTAGCGGCGTTTTT
28733530 TTTCATAAAC
Statistics
Matches: 197, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.01
42 26 0.13
43 163 0.83
44 5 0.03
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
ATGTTCTTTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTC
Found at i:28733691 original size:21 final size:24
Alignment explanation
Indices: 28733649--28733693 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
28733639 ATTACATTTG
28733649 TTATTATTTTATTATGTATCATTA
1 TTATTATTTTATTATGTATCATTA
28733673 TTATT-TTTTATTAT-T-TCATTA
1 TTATTATTTTATTATGTATCATTA
28733694 CCCTCTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 9 0.43
24 5 0.24
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATTATTTTATTATGTATCATTA
Found at i:28740853 original size:4 final size:4
Alignment explanation
Indices: 28740853--28740907 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
28740843 CTATATATAT
* * * *
28740853 ATAG ATAG ATAA ATAG ATAG ATAG ATAG ATAT ATAG ATAT ATAG ATAT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
28740901 ATAG ATA
1 ATAG ATA
28740908 TATTAAAGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (4 bp):
ATAG
Found at i:28740908 original size:8 final size:8
Alignment explanation
Indices: 28740844--28740910 Score: 89
Period size: 8 Copynumber: 8.4 Consensus size: 8
28740834 AAACTTACCC
*
28740844 TATATATA
1 TATAGATA
28740852 TATAGATA
1 TATAGATA
* *
28740860 GATAAATA
1 TATAGATA
*
28740868 GATAGATA
1 TATAGATA
*
28740876 GATAGATA
1 TATAGATA
28740884 TATAGATA
1 TATAGATA
28740892 TATAGATA
1 TATAGATA
28740900 TATAGATA
1 TATAGATA
28740908 TAT
1 TAT
28740911 TAAAGATAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 54 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (8 bp):
TATAGATA
Found at i:28746831 original size:177 final size:177
Alignment explanation
Indices: 28746528--28747110 Score: 731
Period size: 177 Copynumber: 3.3 Consensus size: 177
28746518 CTTTAGGCAA
* * ** * *
28746528 ATAAGGCTGGTGACTTAAATCTGCTCCATTGCCAATACATGGAGATAAGATTCT-CCATCCTCAA
1 ATAAGGCTAGTGACTAAAATCTGCTCCATTGCCGGTACATGGAGATAAGATT-TGCCATCTTCGA
* * * * *
28746592 TCTACTCCGCAACTACTTTAGGGAAAT-AGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCA
65 TCTACTCCACTACTAC-TTAGGGAGATAAGATCTTAAATCTTCAGTCTGCTTCCTTGCTACCTCA
* * *
28746656 AAAAGATAAGACTAAAATCGCCAACCTGCTCTCTTGCTACCTCAGAGAG
129 GAAAGATAAGACTACAATCACCAACCTGCTCTCTTGCTACCTCAGAGAG
* *
28746705 ATAAGGCTAGTGGCTAAAATCTGCTCCATTGCTGGTACATGGAGATAAGATTTGCCATCTTCGAT
1 ATAAGGCTAGTGACTAAAATCTGCTCCATTGCCGGTACATGGAGATAAGATTTGCCATCTTCGAT
* * * * *
28746770 CTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATCTTCAGTTTGCTTCCTTGCTACCTCAGG
66 CTACTCCACTACTACTTAGGGAGATAAGATCTTAAATCTTCAGTCTGCTTCCTTGCTACCTCAGA
* * ** * *
28746835 AAGGTAAGACTACAATCACCAACCTACAATCTTTCTACCTCAGAGCG
131 AAGATAAGACTACAATCACCAACCTGCTCTCTTGCTACCTCAGAGAG
* * * *
28746882 ATAAGGCCAGTGACTAAAATCTGCTCCATTGTCGGTACATTGAGATAAGATTCGCCATCTTCGAT
1 ATAAGGCTAGTGACTAAAATCTGCTCCATTGCCGGTACATGGAGATAAGATTTGCCATCTTCGAT
* * * *
28746947 CTACTCCACTACTACTTAGGGAGATAAGATCTTAAATCTTCAATCTACTTTCTTGTTACCTCAGA
66 CTACTCCACTACTACTTAGGGAGATAAGATCTTAAATCTTCAGTCTGCTTCCTTGCTACCTCAGA
**
28747012 AAGATAAGACT-CAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAG
131 AAGATAAGACTACAATCACCAACCTGCTCTCTTGCTACCTCAGAGAG
* * ** * *
28747058 ATAAGGCCTTGAGGTTTAAACCTGCTCCATTGCCGGTACATGGAGATAAGATT
1 ATAAGG-CTAGTGACTAAAATCTGCTCCATTGCCGGTACATGGAGATAAGATT
28747111 CACCTCTCCC
Statistics
Matches: 345, Mismatches: 58, Indels: 6
0.84 0.14 0.01
Matches are distributed among these distances:
176 44 0.13
177 301 0.87
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (177 bp):
ATAAGGCTAGTGACTAAAATCTGCTCCATTGCCGGTACATGGAGATAAGATTTGCCATCTTCGAT
CTACTCCACTACTACTTAGGGAGATAAGATCTTAAATCTTCAGTCTGCTTCCTTGCTACCTCAGA
AAGATAAGACTACAATCACCAACCTGCTCTCTTGCTACCTCAGAGAG
Found at i:28747031 original size:43 final size:43
Alignment explanation
Indices: 28746981--28747062 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
28746971 TAAGATCTTA
* * *
28746981 AATCTTCAATCTACTTTCTTGTTACCTCAGAAAGATAAGACTC
1 AATCTTCAACCTACTCTCTTGCTACCTCAGAAAGATAAGACTC
* *
28747024 AATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAG
1 AATCTTCAACCTACTCTCTTGCTACCTCAGAAAGATAAG
28747063 GCCTTGAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (43 bp):
AATCTTCAACCTACTCTCTTGCTACCTCAGAAAGATAAGACTC
Found at i:28747208 original size:44 final size:44
Alignment explanation
Indices: 28747124--28747210 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
28747114 CTCTCCCAAT
** **
28747124 CTTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGA
1 CTTCAATCTTCAACCTGCTTCCTTGCTACCACAGGAAGATAAGA
28747168 CTTCAATCTTCAACCTGC-TCTCTTGCTACCACA-GAGAGATAAG
1 CTTCAATCTTCAACCTGCTTC-CTTGCTACCACAGGA-AGATAAG
28747211 GTCAGTGGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (44 bp):
CTTCAATCTTCAACCTGCTTCCTTGCTACCACAGGAAGATAAGA
Found at i:28747245 original size:147 final size:147
Alignment explanation
Indices: 28746975--28747258 Score: 408
Period size: 147 Copynumber: 1.9 Consensus size: 147
28746965 GGGAGATAAG
* *
28746975 ATCTTAAATCTTCAATCTACTTTCTTGTTACCTCAGAAAGATAAGACTCAATCTTCAACCTGCTC
1 ATCTTAAATCTTCAATCTACTTCCTTGCTACCTCAGAAAGATAAGACTCAATCTTCAACCTGCTC
* * * * * *
28747040 TCTTGCTACCTCAGAGAGATAAGGCCTTGAGGTTTAAACCTGCTCCATTGCCGGTACATGGAGAT
66 TCTTGCTACCACAGAGAGATAAGGCCTAGAGGCTAAAACCTACTCCATTGCCGATACATGGAGAT
28747105 AAGATTCACCTCTCCCA
131 AAGATTCACCTCTCCCA
* * * * *
28747122 ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTTCAATCTTCAACCTGCT
1 ATCTTAAATCTTCAATCTACTTCCTTGCTACCTCAGAAAGATAAGAC-TCAATCTTCAACCTGCT
* * *
28747187 CTCTTGCTACCACAGAGAGATAAGGTC-AGTGGCTAAAATCTACTCCATTGCCGATACATGGAGA
65 CTCTTGCTACCACAGAGAGATAAGGCCTAGAGGCTAAAACCTACTCCATTGCCGATACATGGAGA
28747251 TAAGATTC
130 TAAGATTC
28747259 GCCATCTTCG
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
147 78 0.65
148 42 0.35
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (147 bp):
ATCTTAAATCTTCAATCTACTTCCTTGCTACCTCAGAAAGATAAGACTCAATCTTCAACCTGCTC
TCTTGCTACCACAGAGAGATAAGGCCTAGAGGCTAAAACCTACTCCATTGCCGATACATGGAGAT
AAGATTCACCTCTCCCA
Found at i:28747361 original size:44 final size:45
Alignment explanation
Indices: 28747288--28747387 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
28747278 GCTACTGCTT
* * * *
28747288 AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCACTGTAGCCTC
1 AGGGAGATAAGATCTTCAATATTCAGTCTGCTCCACTGCAACCTC
** * * *
28747333 AGGGAGATAAGA-CTTGTATATTGAGTCTGCTCCATTGCAACTTC
1 AGGGAGATAAGATCTTCAATATTCAGTCTGCTCCACTGCAACCTC
28747377 AGGGAGATAAG
1 AGGGAGATAAG
28747388 GCTGGTGACT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 34 0.74
45 12 0.26
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (45 bp):
AGGGAGATAAGATCTTCAATATTCAGTCTGCTCCACTGCAACCTC
Found at i:28747409 original size:324 final size:324
Alignment explanation
Indices: 28746798--28747432 Score: 819
Period size: 324 Copynumber: 2.0 Consensus size: 324
28746788 GGGAGATAAG
* * *
28746798 ATCTTTAATCTTCAGTTTGCTTCCTTGCTACCTCAGGAAGGTAAGACTACAATCACCAACCTACA
1 ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCACCAACCTACA
* * * * * * *
28746863 ATCTTTCTACCTCAGAGCGATAAGGCCAGTGACTAAAATCTGCTCCATTGTCGGTACATTGAGAT
66 ATCTTGCTACCACAGAGAGATAAGGCCAGTGACTAAAATCTACTCCATTGCCGATACATGGAGAT
28746928 AAGATTCGCCATCTTCGATCTACTCCACTACTACTTAGGGAGATAAGATCTTAAATCTTCAATCT
131 AAGATTCGCCATCTTCGATCTACTCCACTACTACTTAGGGAGATAAGATCTTAAATCTTCAATCT
* * *
28746993 ACTTTCTTGTTACCTCAGAAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAG
196 ACTTTCCTGTTACCTCAGAAAGATAAGACTCAATATTCAACCTGCTCTCTTGCAACCTCAGAGAG
* ** *
28747058 ATAAGGCCTTGAGGTTTAAACCTGCTCCATTGCCGGTACATGGAGATAAGATTCACCTCTCCCA
261 ATAAGGCCTGGAGACTTAAACCTGCTCCATTGCCGGTACATAGAGATAAGATTCACCTCTCCCA
* * ** * *
28747122 ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTTCAATCTTCAACCTGCT
1 ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCACCAACCTACA
* * *
28747187 CTCTTGCTACCACAGAGAGATAAGGTCAGTGGCTAAAATCTACTCCATTGCCGATACATGGAGAT
66 ATCTTGCTACCACAGAGAGATAAGGCCAGTGACTAAAATCTACTCCATTGCCGATACATGGAGAT
* * * * *
28747252 AAGATTCGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCT
131 AAGATTCGCCATCTTCGATCTACTCCACTACTACTTAGGGAGATAAGATCTTAAATCTTCAATCT
* ** ** * ** *
28747317 GC-TTCACTG-TAGCCTCAGGGAGATAAGACTTGTATATTGAGTCTGCTC-CATTGCAACTTCAG
196 ACTTTC-CTGTTA-CCTCAGAAAGATAAGAC-TCAATATTCAACCTGCTCTC-TTGCAACCTCAG
* * *
28747379 GGAGATAAGG-CTGGTGACTTAAATCTGCTCCATTGCCGGTACATAGAGATAAGA
257 AGAGATAAGGCCTGGAGACTTAAACCTGCTCCATTGCCGGTACATAGAGATAAGA
28747433 CTCGTCATCT
Statistics
Matches: 264, Mismatches: 43, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
323 5 0.02
324 228 0.86
325 31 0.12
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (324 bp):
ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCACCAACCTACA
ATCTTGCTACCACAGAGAGATAAGGCCAGTGACTAAAATCTACTCCATTGCCGATACATGGAGAT
AAGATTCGCCATCTTCGATCTACTCCACTACTACTTAGGGAGATAAGATCTTAAATCTTCAATCT
ACTTTCCTGTTACCTCAGAAAGATAAGACTCAATATTCAACCTGCTCTCTTGCAACCTCAGAGAG
ATAAGGCCTGGAGACTTAAACCTGCTCCATTGCCGGTACATAGAGATAAGATTCACCTCTCCCA
Found at i:28747430 original size:177 final size:177
Alignment explanation
Indices: 28747122--28747443 Score: 400
Period size: 177 Copynumber: 1.8 Consensus size: 177
28747112 ACCTCTCCCA
* *
28747122 ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTTCAATCTTCAACCTGCT
1 ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATATTCAACCTGCT
* * *
28747187 CTCTTGCTACCACAGAGAGATAAGGTCAGTGGCTAAAATCTACTCCATTGCCGATACATGGAGAT
66 CTCTTGCAACCACAGAGAGATAAGGTCAGTGACTAAAATCTACTCCATTGCCGATACATAGAGAT
*
28747252 AAGATTCGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAG
131 AAGACTCGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAG
* ** * **
28747299 ATCTTCAATCTTCAGTCTGCTTCAC-TG-TAGCCTCAGGGAGATAAGACTTGTATATTGAGTCTG
1 ATCTTCAATCTTCAGTCTGCTTC-CTTGCTA-CCTCAGGAAGATAAGACTTCAATATTCAACCTG
** * * * * *
28747362 CTC-CATTGCAACTTCAGGGAGATAAGG-CTGGTGACTTAAATCTGCTCCATTGCCGGTACATAG
64 CTCTC-TTGCAACCACAGAGAGATAAGGTC-AGTGACTAAAATCTACTCCATTGCCGATACATAG
*
28747425 AGATAAGACTCGTCATCTT
127 AGATAAGACTCGCCATCTT
28747444 TGGTCTATTC
Statistics
Matches: 121, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
176 4 0.03
177 116 0.96
178 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (177 bp):
ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATATTCAACCTGCT
CTCTTGCAACCACAGAGAGATAAGGTCAGTGACTAAAATCTACTCCATTGCCGATACATAGAGAT
AAGACTCGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAG
Found at i:28747463 original size:177 final size:177
Alignment explanation
Indices: 28747122--28747520 Score: 394
Period size: 177 Copynumber: 2.3 Consensus size: 177
28747112 ACCTCTCCCA
* * *
28747122 ATCTTCAATCTTCAGTCTGCTTC-CTTGCTA-CCTTAGGAAGATAAGACTTCAATCTTCAACCTG
1 ATCTTCAATCTTCAGTCTGCTTCAC-TG-TAGCCTCAGGGAGATAAGACTTCAATATTCAACCTG
* * *
28747185 CTCTCTTGCTACCACAGAGAGATAAGGTCAGTGGCTAAAATCTACTCCATTGCCGATACATGGAG
64 CTCTCTTGCAACCACAGAGAGATAAGGTCAGTGACTAAAATCTACTCCATTGCCGATACATAGAG
* * * * * *
28747250 ATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAG
129 ATAAGACTCGCCATCTTCGATCTACTCCACTACTGCTTAAGAAAATAAG
** * **
28747299 ATCTTCAATCTTCAGTCTGCTTCACTGTAGCCTCAGGGAGATAAGACTTGTATATTGAGTCTGCT
1 ATCTTCAATCTTCAGTCTGCTTCACTGTAGCCTCAGGGAGATAAGACTTCAATATTCAACCTGCT
** * * * * *
28747364 C-CATTGCAACTTCAGGGAGATAAGG-CTGGTGACTTAAATCTGCTCCATTGCCGGTACATAGAG
66 CTC-TTGCAACCACAGAGAGATAAGGTC-AGTGACTAAAATCTACTCCATTGCCGATACATAGAG
* * * * *
28747427 ATAAGACTCGTCATCTTTGGTCTATTCCATTACTGCTTAAGAAAATAAG
129 ATAAGACTCGCCATCTTCGATCTACTCCACTACTGCTTAAGAAAATAAG
* * ** * * *
28747476 ACCTGCAATCTTCAACCTGC-TCTATTGCAGCTTCAGGGAGATAAG
1 ATCTTCAATCTTCAGTCTGCTTC-ACTGTAGCCTCAGGGAGATAAG
28747521 GTTTATAATC
Statistics
Matches: 181, Mismatches: 36, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
176 6 0.03
177 174 0.96
178 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (177 bp):
ATCTTCAATCTTCAGTCTGCTTCACTGTAGCCTCAGGGAGATAAGACTTCAATATTCAACCTGCT
CTCTTGCAACCACAGAGAGATAAGGTCAGTGACTAAAATCTACTCCATTGCCGATACATAGAGAT
AAGACTCGCCATCTTCGATCTACTCCACTACTGCTTAAGAAAATAAG
Found at i:28747811 original size:64 final size:64
Alignment explanation
Indices: 28747634--28747824 Score: 276
Period size: 63 Copynumber: 3.0 Consensus size: 64
28747624 TCATGTATCT
* * *
28747634 ATGCTTATGCCAAATAATTAGGATGCCATGATCGAAATGAATCAAATGCTCCTAACTAGATGAG
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
* ** *
28747698 ATGCTTATATC-AACGATTAGGATGCTATGATCGAAATGAACCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
* * * *
28747761 ATGCTTGTGTCAAATAATTAGGATGCTATAATCAAAATGGATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
28747825 TTATGAATGA
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
63 56 0.50
64 55 0.50
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (64 bp):
ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
Found at i:28748945 original size:20 final size:20
Alignment explanation
Indices: 28748920--28748962 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28748910 CTTTTTTCAA
28748920 TTTCTTTGATTGATTCTTTC
1 TTTCTTTGATTGATTCTTTC
** *
28748940 TTTCTTTTTTTGATTTTTTC
1 TTTCTTTGATTGATTCTTTC
28748960 TTT
1 TTT
28748963 TTATTTCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.74
Consensus pattern (20 bp):
TTTCTTTGATTGATTCTTTC
Found at i:28748977 original size:14 final size:13
Alignment explanation
Indices: 28748940--28748993 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 13
28748930 TGATTCTTTC
28748940 TTTCTTTTTTTGAT
1 TTTCTTTTTTT-AT
28748954 TTT-TTCTTTTTAT
1 TTTCTT-TTTTTAT
28748967 TTCTCTTTTTTTAT
1 TT-TCTTTTTTTAT
*
28748981 TTTGATTTTTTTA
1 TTT-CTTTTTTTA
28748994 AGGTCTCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 7 0.20
14 26 0.74
15 2 0.06
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTTTAT
Found at i:28748989 original size:26 final size:26
Alignment explanation
Indices: 28748929--28748990 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
28748919 ATTTCTTTGA
*
28748929 TTGATTCTTTCTTTCTTTTTTTGATTT
1 TTGATT-TTTATTTCTTTTTTTGATTT
** *
28748956 TTTCTTTTTATTTCTCTTTTTTTA-TT
1 TTGATTTTTATTTCT-TTTTTTGATTT
28748982 TTGATTTTT
1 TTGATTTTT
28748991 TTAAGGTCTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.08, C:0.10, G:0.05, T:0.77
Consensus pattern (26 bp):
TTGATTTTTATTTCTTTTTTTGATTT
Found at i:28754040 original size:29 final size:30
Alignment explanation
Indices: 28753981--28754038 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28753971 TCCGAGCCTT
*
28753981 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
28754011 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
28754039 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:28754268 original size:13 final size:13
Alignment explanation
Indices: 28754250--28754281 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28754240 TTTCCAGCAA
28754250 TTATGAATTTATT
1 TTATGAATTTATT
28754263 TTATGAATTTATT
1 TTATGAATTTATT
*
28754276 TGATGA
1 TTATGA
28754282 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:28754489 original size:50 final size:50
Alignment explanation
Indices: 28754376--28754617 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
28754366 ATTTGGGTAA
* * *
28754376 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
28754432 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
28754482 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
28754532 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
28754582 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
28754618 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:28754565 original size:100 final size:103
Alignment explanation
Indices: 28754376--28754625 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
28754366 ATTTGGGTAA
28754376 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
28754441 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
28754482 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
28754544 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
28754582 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
28754626 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:28761633 original size:29 final size:30
Alignment explanation
Indices: 28761574--28761631 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28761564 TCCGAGCCTT
*
28761574 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
28761604 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
28761632 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:28761861 original size:13 final size:13
Alignment explanation
Indices: 28761843--28761874 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28761833 TTTCCAGCAA
28761843 TTATGAATTTATT
1 TTATGAATTTATT
28761856 TTATGAATTTATT
1 TTATGAATTTATT
*
28761869 TGATGA
1 TTATGA
28761875 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:28762082 original size:50 final size:50
Alignment explanation
Indices: 28761969--28762210 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
28761959 ATTTGGGTAA
* * *
28761969 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
28762025 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
28762075 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
28762125 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
28762175 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
28762211 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:28762158 original size:100 final size:103
Alignment explanation
Indices: 28761969--28762218 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
28761959 ATTTGGGTAA
28761969 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
28762034 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
28762075 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
28762137 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
28762175 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
28762219 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:28771769 original size:48 final size:47
Alignment explanation
Indices: 28771715--28771888 Score: 181
Period size: 48 Copynumber: 3.6 Consensus size: 47
28771705 GTGAATTTCA
* * *
28771715 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATGTCGAGGCC
1 GATGCCATGTCCCAAACATGGTCTTATACTAGCTC-CATGTCGAGGCC
* * * *
28771763 GATGCCATGTCCCAGACATGGTCTTATACTAGCT-CTTGTCTCATTGCC
1 GATGCCATGTCCCAAACATGGTCTTATACTAGCTCCATGTC-GA-GGCC
* * *
28771811 GATGCCATGTTCCAAACATGGTCTTATACTAGCTCTTATGAT-GTGGCC
1 GATGCCATGTCCCAAACATGGTCTTATACTAGCTC-CATG-TCGAGGCC
* *
28771859 AATGCCATGTCCCAGACATGGTCTTATACT
1 GATGCCATGTCCCAAACATGGTCTTATACT
28771889 GGCACACATA
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
46 5 0.05
47 1 0.01
48 95 0.91
50 2 0.02
51 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (47 bp):
GATGCCATGTCCCAAACATGGTCTTATACTAGCTCCATGTCGAGGCC
Found at i:28771879 original size:96 final size:96
Alignment explanation
Indices: 28771715--28771888 Score: 278
Period size: 96 Copynumber: 1.8 Consensus size: 96
28771705 GTGAATTTCA
* *
28771715 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATGTCGAGGCCGATGCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCGCATGTCGAGGCCAATGCCATGTCCCAGAC
28771780 ATGGTCTTATACTAGCTCTTGTCTCATTGCC
66 ATGGTCTTATACTAGCTCTTGTCTCATTGCC
* ** *
28771811 GATGCCATGTTCCAAACATGGTCTTATACTAGCTCTTATGAT-GTGGCCAATGCCATGTCCCAGA
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCGCATG-TCGAGGCCAATGCCATGTCCCAGA
28771875 CATGGTCTTATACT
65 CATGGTCTTATACT
28771889 GGCACACATA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
96 70 0.99
97 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (96 bp):
GATGCCATGTTCCAAACATGGTCTTACACTAGCTCGCATGTCGAGGCCAATGCCATGTCCCAGAC
ATGGTCTTATACTAGCTCTTGTCTCATTGCC
Found at i:28777064 original size:35 final size:35
Alignment explanation
Indices: 28777024--28777094 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
28777014 TTTTCATGGG
28777024 TTAACACACCCAACAAAATTAGTCAAGTAACCAAC
1 TTAACACACCCAACAAAATTAGTCAAGTAACCAAC
28777059 TTAACACACCCAACAAAATTAGTCAAGTAACCAAC
1 TTAACACACCCAACAAAATTAGTCAAGTAACCAAC
28777094 T
1 T
28777095 ATCTCTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.48, C:0.28, G:0.06, T:0.18
Consensus pattern (35 bp):
TTAACACACCCAACAAAATTAGTCAAGTAACCAAC
Found at i:28779861 original size:34 final size:35
Alignment explanation
Indices: 28779823--28779899 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
28779813 GCACCCAGCG
* **
28779823 CTAGTCGGATAACCGAC-AATAATTGTGCCTTGCA
1 CTAGTCGGATAACCGACAAATAATTGTACCTAACA
** * *
28779857 CTAGTCAAATAATCGACAAATAATTTTACCTAACA
1 CTAGTCGGATAACCGACAAATAATTGTACCTAACA
28779892 CTAGTCGG
1 CTAGTCGG
28779900 GTAATTGAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
34 14 0.42
35 19 0.58
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (35 bp):
CTAGTCGGATAACCGACAAATAATTGTACCTAACA
Found at i:28782286 original size:40 final size:40
Alignment explanation
Indices: 28782231--28782454 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
28782221 TATTCGGATG
28782231 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
28782271 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
28782314 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * *
28782354 ACATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
28782394 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
28782434 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
28782455 ATACTTGGGT
Statistics
Matches: 163, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
39 13 0.08
40 112 0.69
41 1 0.01
43 37 0.23
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:28782374 original size:83 final size:80
Alignment explanation
Indices: 28782235--28782454 Score: 293
Period size: 83 Copynumber: 2.7 Consensus size: 80
28782225 CGGATGATAT
* **
28782235 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
28782300 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
* *
28782318 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTACATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
28782383 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
28782398 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
28782455 ATACTTGGGT
Statistics
Matches: 125, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
79 16 0.13
80 44 0.35
81 2 0.02
83 63 0.50
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:28788518 original size:46 final size:46
Alignment explanation
Indices: 28788443--28789103 Score: 539
Period size: 46 Copynumber: 14.4 Consensus size: 46
28788433 TTGTTTTGTT
* ** * *
28788443 AATTGAAATGTTAAAGTGCTACAAATTGAAGTGTTTTAATGCTGTA
1 AATTGAAGTGTTAAAGTGCTGTAAATTGAAGTGTTTAAATGCTGCA
* * * * *
28788489 AATTAAAGTGTTAAAGTACTGCAAATTGAAGTGTTTGAATGCTGTA
1 AATTGAAGTGTTAAAGTGCTGTAAATTGAAGTGTTTAAATGCTGCA
** * *
28788535 AATTGAAGTGTTTAAA-TATTGTTAATTGAAATG-TTAAAGTGCTGCA
1 AATTGAAGTG-TTAAAGTGCTGTAAATTGAAGTGTTTAAA-TGCTGCA
*
28788581 AATTGAAGTGTTTTAA-TGCTGTAAATTGAAGTG-TTAAAGTGCTGCA
1 AATTGAAGTG-TTAAAGTGCTGTAAATTGAAGTGTTTAAA-TGCTGCA
* * * **
28788627 AATTGAAGTGTTTGAA-TGCTATAAATTGAAGTGTTTAAATGTTGTT
1 AATTGAAGTG-TTAAAGTGCTGTAAATTGAAGTGTTTAAATGCTGCA
* * * * * *
28788673 AATTGAAATGTTAAAGTGCTGCAAATTGAA-TAGTTTTAGTCCTGTA
1 AATTGAAGTGTTAAAGTGCTGTAAATTGAAGT-GTTTAAATGCTGCA
* * * **
28788719 AATTGAAGAGTTAAAGTGCTGCAAATTGAAGTGTTTGAATGCTATA
1 AATTGAAGTGTTAAAGTGCTGTAAATTGAAGTGTTTAAATGCTGCA
*
28788765 AATTGAAGTGTTTAAA-TACTGTAAATTGAAGTG-TTAAAGTGCTGCA
1 AATTGAAGTG-TTAAAGTGCTGTAAATTGAAGTGTTTAAA-TGCTGCA
* * *
28788811 ATTTGAAGTGTTTGAA-TGCTGTAAATTGAAGTGTTTAAATGCTGTA
1 AATTGAAGTG-TTAAAGTGCTGTAAATTGAAGTGTTTAAATGCTGCA
* * * *
28788857 AATTGAAGTGCTTAAA-TGTTGCAAATTGAAGTGTTTTAAGTACTGCA
1 AATTGAAGTG-TTAAAGTGCTGTAAATTGAAGTG-TTTAAATGCTGCA
* * * * * *
28788904 AATTGAAGTGTT-TAGTTGCTGGACATTG-AGATGTTT-TATCACTG-T
1 AATTGAAGTGTTAAAG-TGCTGTAAATTGAAG-TGTTTAAAT-GCTGCA
* * *
28788949 AATTGAGGTGTATAAA-TGCTGTTAATTG-AGATG-TTAAAGTGGTGCA
1 AATTGAAGTGT-TAAAGTGCTGTAAATTGAAG-TGTTTAAA-TGCTGCA
* * *
28788995 AATTGAAGTGTTAAAGTGGTGCAAATTGAAGTGTTTGAATGCTGCA
1 AATTGAAGTGTTAAAGTGCTGTAAATTGAAGTGTTTAAATGCTGCA
* * *
28789041 AATTGAAGTGTTTAAA-TGTTGTAAATTGAAGTGCTTAAATGTTGCA
1 AATTGAAGTG-TTAAAGTGCTGTAAATTGAAGTGTTTAAATGCTGCA
*
28789087 AATTGAAGTGTTTAAGT
1 AATTGAAGTGTTAAAGT
28789104 ACTTATTTTG
Statistics
Matches: 508, Mismatches: 83, Indels: 48
0.79 0.13 0.08
Matches are distributed among these distances:
44 2 0.00
45 50 0.10
46 392 0.77
47 64 0.13
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (46 bp):
AATTGAAGTGTTAAAGTGCTGTAAATTGAAGTGTTTAAATGCTGCA
Found at i:28788575 original size:115 final size:115
Alignment explanation
Indices: 28788438--28789099 Score: 736
Period size: 115 Copynumber: 5.8 Consensus size: 115
28788428 AAATGTTGTT
* *
28788438 TTGTTAATTGAAATGTTAAAGTGCTACAAATTGAAGTGTTTTAATGCTGTAAATTAAAGTGTTAA
1 TTGTTAATTGAAATGTTAAAGTGCTGCAAATTGAAGTGTTTTAATGCTGTAAATTGAAGTGTTAA
* *
28788503 AGTACTGCAAATTGAAGTGTTTGAATGCTGTAAATTGAAGTGTTTAAATA
66 AGTGCTGCAAATTGAAGTGTTTGAATGCTATAAATTGAAGTGTTTAAATA
28788553 TTGTTAATTGAAATGTTAAAGTGCTGCAAATTGAAGTGTTTTAATGCTGTAAATTGAAGTGTTAA
1 TTGTTAATTGAAATGTTAAAGTGCTGCAAATTGAAGTGTTTTAATGCTGTAAATTGAAGTGTTAA
*
28788618 AGTGCTGCAAATTGAAGTGTTTGAATGCTATAAATTGAAGTGTTTAAATG
66 AGTGCTGCAAATTGAAGTGTTTGAATGCTATAAATTGAAGTGTTTAAATA
* * *
28788668 TTGTTAATTGAAATGTTAAAGTGCTGCAAATTGAA-TAGTTTTAGTCCTGTAAATTGAAGAGTTA
1 TTGTTAATTGAAATGTTAAAGTGCTGCAAATTGAAGT-GTTTTAATGCTGTAAATTGAAGTGTTA
28788732 AAGTGCTGCAAATTGAAGTGTTTGAATGCTATAAATTGAAGTGTTTAAATA
65 AAGTGCTGCAAATTGAAGTGTTTGAATGCTATAAATTGAAGTGTTTAAATA
* * * * *
28788783 CTGTAAATTGAAGTGTTAAAGTGCTGCAATTTGAAGTGTTTGAATGCTGTAAATTGAAGTGTTTA
1 TTGTTAATTGAAATGTTAAAGTGCTGCAAATTGAAGTGTTTTAATGCTGTAAATTGAAGTG-TTA
* * * * ** *
28788848 AA-TGCTGTAAATTGAAGTGCTTAAATGTTGCAAATTGAAGTGTTTTAAGTA
65 AAGTGCTGCAAATTGAAGTGTTTGAATGCTATAAATTGAAGTG-TTTAAATA
* ** * * * * * *
28788899 CTGCAAATTGAAGTGTT-TAGTTGCTGGACATTG-AGATGTTTT-ATCACTGT-AATTGAGGTGT
1 TTGTTAATTGAAATGTTAAAG-TGCTGCAAATTGAAG-TGTTTTAAT-GCTGTAAATTGAAGTGT
** * * ** *
28788960 ATAAA-TGCTGTTAATTG-AGATG-TTAAAGTGGTGCAAATTGAAGTG-TTAAAGTG
63 -TAAAGTGCTGCAAATTGAAG-TGTTTGAA-TGCTATAAATTGAAGTGTTTAAA-TA
* ** * * * *
28789013 GTGCAAATTGAAGTGTTTGAA-TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGCTT
1 TTGTTAATTGAAATG-TTAAAGTGCTGCAAATTGAAGTGTTTTAATGCTGTAAATTGAAGTG-TT
*
28789077 AAA-TGTTGCAAATTGAAGTGTTT
64 AAAGTGCTGCAAATTGAAGTGTTT
28789100 AAGTACTTAT
Statistics
Matches: 481, Mismatches: 47, Indels: 37
0.85 0.08 0.07
Matches are distributed among these distances:
113 4 0.01
114 42 0.09
115 382 0.79
116 53 0.11
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.38
Consensus pattern (115 bp):
TTGTTAATTGAAATGTTAAAGTGCTGCAAATTGAAGTGTTTTAATGCTGTAAATTGAAGTGTTAA
AGTGCTGCAAATTGAAGTGTTTGAATGCTATAAATTGAAGTGTTTAAATA
Found at i:28788998 original size:23 final size:23
Alignment explanation
Indices: 28788972--28789103 Score: 146
Period size: 23 Copynumber: 5.7 Consensus size: 23
28788962 AAATGCTGTT
28788972 AATTG-AGATGTTAAAGTGGTGCA
1 AATTGAAG-TGTTAAAGTGGTGCA
28788995 AATTGAAGTGTTAAAGTGGTGCA
1 AATTGAAGTGTTAAAGTGGTGCA
* *
28789018 AATTGAAGTGTTTGAA-TGCTGCA
1 AATTGAAGTG-TTAAAGTGGTGCA
* *
28789041 AATTGAAGTGTTTAAA-TGTTGTA
1 AATTGAAGTG-TTAAAGTGGTGCA
*
28789064 AATTGAAGTGCTTAAA-TGTTGCA
1 AATTGAAGTG-TTAAAGTGGTGCA
*
28789087 AATTGAAGTGTTTAAGT
1 AATTGAAGTGTTAAAGT
28789104 ACTTATTTTG
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
22 4 0.04
23 88 0.90
24 6 0.06
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (23 bp):
AATTGAAGTGTTAAAGTGGTGCA
Found at i:28791135 original size:32 final size:32
Alignment explanation
Indices: 28791094--28791154 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
28791084 CATGACATAG
*
28791094 TTTCATTTACATTAGTGGAATTTATAGCCTGA
1 TTTCATTTACAGTAGTGGAATTTATAGCCTGA
28791126 TTTCATTTACAGTAGTGGAATTTATAGCC
1 TTTCATTTACAGTAGTGGAATTTATAGCC
28791155 CGATAAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (32 bp):
TTTCATTTACAGTAGTGGAATTTATAGCCTGA
Found at i:28794607 original size:12 final size:13
Alignment explanation
Indices: 28794590--28794624 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
28794580 TGACATAACG
28794590 GTAGATGTAGA-A
1 GTAGATGTAGACA
28794602 GTAGATGTA-ACA
1 GTAGATGTAGACA
28794614 GTAGATGTAGA
1 GTAGATGTAGA
28794625 GGTGGTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 19 0.90
13 1 0.05
ACGTcount: A:0.40, C:0.03, G:0.31, T:0.26
Consensus pattern (13 bp):
GTAGATGTAGACA
Found at i:28812457 original size:50 final size:47
Alignment explanation
Indices: 28812351--28812563 Score: 156
Period size: 47 Copynumber: 4.5 Consensus size: 47
28812341 AGACATGGTT
* * ** **
28812351 CAGACATGGTCTTACATTGACTCTCACATTAAGTTGATGCCATGTCC
1 CAGACATGGTCTTACACTGACTCTCACGTTCTGCCGATGCCATGTCC
* * * *
28812398 GAAATATGGTTTTACACTGACTCTCACGTATCCGTGCCGATGCCATGTCC
1 CAGACATGGTCTTACACTGACTCTCACGT-T-C-TGCCGATGCCATGTCC
* * *
28812448 CAGACATGGTCTTATACTAACACATCA--TT-TAGCCGATG-CATG-CC
1 CAGACATGGTCTTACACTGACTC-TCACGTTCT-GCCGATGCCATGTCC
28812492 CAGACAT-GTCTTACACT-AGCTCT--CGTCTCAATGCCGATGCCATGTCC
1 CAGACATGGTCTTACACTGA-CTCTCACGT-TC--TGCCGATGCCATGTCC
*
28812539 CAGACATGGTCTTACACTGGCTCTC
1 CAGACATGGTCTTACACTGACTCTC
28812564 GTAATGTGGC
Statistics
Matches: 129, Mismatches: 20, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
42 3 0.02
43 12 0.09
44 9 0.07
45 12 0.09
46 12 0.09
47 32 0.25
48 16 0.12
49 1 0.01
50 29 0.22
51 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (47 bp):
CAGACATGGTCTTACACTGACTCTCACGTTCTGCCGATGCCATGTCC
Found at i:28812556 original size:48 final size:46
Alignment explanation
Indices: 28812432--28812603 Score: 169
Period size: 47 Copynumber: 3.8 Consensus size: 46
28812422 CACGTATCCG
* * * * *
28812432 TGCCGATGCCATGTCCCAGACATGGTCTTATACTAACACATCATTTA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCGTTAA
28812479 -GCCGATG-CATG-CCCAGACAT-GTCTTACACTAGCTCTCGTCTCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGT-T-AA
*
28812523 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCG-TAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTTAA
* *
28812568 TGTGGCCAATG-CATGTCCCAAACAT-GTCTTACACTA
1 --T-GCCGATGCCATGTCCCAGACATGGTCTTACACTA
28812604 TCTCACAAAT
Statistics
Matches: 107, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 3 0.03
43 13 0.12
44 10 0.09
45 13 0.12
46 22 0.21
47 23 0.21
48 23 0.21
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (46 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTTAA
Found at i:28819075 original size:28 final size:28
Alignment explanation
Indices: 28819033--28819093 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
28819023 TCTATGGCTG
28819033 GTGTCTCTCACACGGCCATGACACGCCC
1 GTGTCTCTCACACGGCCATGACACGCCC
*
28819061 GTGTCTCTCATACGGCCATGACACGCCC
1 GTGTCTCTCACACGGCCATGACACGCCC
28819089 GTGTC
1 GTGTC
28819094 CTAGCCAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.16, C:0.39, G:0.23, T:0.21
Consensus pattern (28 bp):
GTGTCTCTCACACGGCCATGACACGCCC
Found at i:28820145 original size:47 final size:47
Alignment explanation
Indices: 28820072--28820224 Score: 218
Period size: 47 Copynumber: 3.3 Consensus size: 47
28820062 GGTATAATAC
*
28820072 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACGCTAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACGTTAAGT
* * *
28820119 CGACGCCATGTCCTAGACAGGGTCTTACACT-GACTCTCACGTTAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCACGTTAAGT
* * *
28820166 CGATGCCATGTCCCAGACATGGTCTTATACTAACTCTCATGTTAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACGTTAAGT
*
28820213 CGATACCATGTC
1 CGATGCCATGTC
28820225 TCACGTTAAG
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
46 1 0.01
47 92 0.99
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACGTTAAGT
Found at i:28820218 original size:23 final size:23
Alignment explanation
Indices: 28820192--28820239 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
28820182 ACATGGTCTT
* *
28820192 ATACTAACTCTCATGTTAAGTCG
1 ATACCAACTCTCACGTTAAGTCG
**
28820215 ATACCATGTCTCACGTTAAGTCG
1 ATACCAACTCTCACGTTAAGTCG
28820238 AT
1 AT
28820240 GCCATGTCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (23 bp):
ATACCAACTCTCACGTTAAGTCG
Found at i:28820244 original size:23 final size:23
Alignment explanation
Indices: 28820200--28820247 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
28820190 TTATACTAAC
*
28820200 TCTCATGTTAAGTCGATACCATG
1 TCTCACGTTAAGTCGATACCATG
*
28820223 TCTCACGTTAAGTCGATGCCATG
1 TCTCACGTTAAGTCGATACCATG
28820246 TC
1 TC
28820248 CCAAACATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (23 bp):
TCTCACGTTAAGTCGATACCATG
Done.