Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 17 of 210
Found at i:5967071 original size:23 final size:23
Alignment explanation
Indices: 5967045--5967096 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
5967035 TAGTTGAAAG
* *
5967045 CTGTAATATCCCGAAAATTACTA
1 CTGTAATACCCCAAAAATTACTA
5967068 CTGTAATACCCCAAAAATTACTA
1 CTGTAATACCCCAAAAATTACTA
*
5967091 CAGTAA
1 CTGTAA
5967097 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (23 bp):
CTGTAATACCCCAAAAATTACTA
Found at i:5973080 original size:23 final size:23
Alignment explanation
Indices: 5973054--5973097 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5973044 ATAAATTATT
5973054 TTTATTACTTTAAAT-ATAAAACA
1 TTTATTAC-TTAAATCATAAAACA
*
5973077 TTTATTTCTTAAATCATAAAA
1 TTTATTACTTAAATCATAAAA
5973098 TAGAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTATTACTTAAATCATAAAACA
Found at i:5982119 original size:16 final size:16
Alignment explanation
Indices: 5982098--5982129 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5982088 ATTTTGTTGC
*
5982098 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
5982114 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
5982130 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:5982415 original size:51 final size:50
Alignment explanation
Indices: 5982357--5982479 Score: 137
Period size: 48 Copynumber: 2.5 Consensus size: 50
5982347 TCGGTTCACA
* *
5982357 TAGTAGCCTACACATAGTACTACACGTGTGA-CCATCA-CTATCCAATCCACG
1 TAGTAGCCT-CACATAGTACTACACATGTGATCCA--AGCTATCCAATACACG
* **
5982408 TAGTAG-C-CACATAGTACTACACATGTGATCGAAGCTATCCGGTACACG
1 TAGTAGCCTCACATAGTACTACACATGTGATCCAAGCTATCCAATACACG
5982456 TAGTAGCCTGCACATAGTACTACA
1 TAGTAGCCT-CACATAGTACTACA
5982480 TACGTGACTA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
47 1 0.02
48 37 0.60
49 3 0.05
50 1 0.02
51 20 0.32
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTCACATAGTACTACACATGTGATCCAAGCTATCCAATACACG
Found at i:5984296 original size:30 final size:31
Alignment explanation
Indices: 5984257--5984316 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5984247 AGAGGTGGGA
*
5984257 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
5984288 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
5984317 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:5986757 original size:23 final size:23
Alignment explanation
Indices: 5986727--5986802 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
5986717 CCAATAGGAA
5986727 AAGTGATAGTAACACTATGGTGC
1 AAGTGATAGTAACACTATGGTGC
*** *
5986750 AAGTGATAG-AAGTGTTATAGTGC
1 AAGTGATAGTAA-CACTATGGTGC
**
5986773 AAAGTGATAGTGGCACTATGGTGC
1 -AAGTGATAGTAACACTATGGTGC
5986797 AAGTGA
1 AAGTGA
5986803 CAGAGGCACT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 2 0.05
23 22 0.55
24 16 0.40
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.26
Consensus pattern (23 bp):
AAGTGATAGTAACACTATGGTGC
Found at i:5986810 original size:23 final size:23
Alignment explanation
Indices: 5986769--5986894 Score: 110
Period size: 23 Copynumber: 5.4 Consensus size: 23
5986759 AAGTGTTATA
* *
5986769 GTGCAAAGTGATAGTGGCACTATG
1 GTGC-AAGTGATAGAGGCACTACG
*
5986793 GTGCAAGTGACAGAGGCACTACG
1 GTGCAAGTGATAGAGGCACTACG
* * * * *
5986816 ATGCAAGTGATTGTGACGCTACG
1 GTGCAAGTGATAGAGGCACTACG
* * *
5986839 ATGCAAGTGACAGAGGCACTACA
1 GTGCAAGTGATAGAGGCACTACG
* *
5986862 GTGCAAG-CAGTAGTGGCACTACG
1 GTGCAAGTGA-TAGAGGCACTACG
5986885 GTGCAAGTGA
1 GTGCAAGTGA
5986895 ATGGCACTTC
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
22 1 0.01
23 73 0.92
24 5 0.06
ACGTcount: A:0.30, C:0.18, G:0.33, T:0.19
Consensus pattern (23 bp):
GTGCAAGTGATAGAGGCACTACG
Found at i:5986884 original size:46 final size:46
Alignment explanation
Indices: 5986778--5986894 Score: 148
Period size: 46 Copynumber: 2.5 Consensus size: 46
5986768 AGTGCAAAGT
* *
5986778 GATAGTGGCACTATGGTGCAAGTGACAGAGGCACTACGATGCAAGT
1 GATAGTGGCACTACGGTGCAAGTGACAGAGGCACTACGATGCAAGA
* * * *
5986824 GATTGTGACGCTACGATGCAAGTGACAGAGGCACTAC-AGTGCAAGCA
1 GATAGTGGCACTACGGTGCAAGTGACAGAGGCACTACGA-TGCAAG-A
5986871 G-TAGTGGCACTACGGTGCAAGTGA
1 GATAGTGGCACTACGGTGCAAGTGA
5986895 ATGGCACTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 1 0.02
46 57 0.97
47 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (46 bp):
GATAGTGGCACTACGGTGCAAGTGACAGAGGCACTACGATGCAAGA
Found at i:5988132 original size:2 final size:2
Alignment explanation
Indices: 5988125--5988171 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5988115 TAAAATCATT
5988125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5988167 TA TA T
1 TA TA T
5988172 CATTTAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5989592 original size:16 final size:17
Alignment explanation
Indices: 5989571--5989602 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5989561 AAATATGCAA
5989571 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
5989587 TCACATAACTTCATAT
1 TCACATAACTTCATAT
5989603 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:5989914 original size:43 final size:42
Alignment explanation
Indices: 5989763--5989926 Score: 169
Period size: 43 Copynumber: 3.9 Consensus size: 42
5989753 GACTCGTACA
* * *
5989763 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-ATCG
5989806 ATGCC-ACTGTCCCAGACAG-GGTCTTACAC--AAATCA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAA-CACAAT-CG
* *
5989847 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAA-TCG
*
5989890 ATGCCAACGTCCCAGACGCT-GTCTTACACGAAAACAC
1 ATGCCAACGTCCCAGACG-TGGTCTTACACGTAAACAC
5989927 GTATCGAAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
40 2 0.02
41 29 0.28
42 6 0.06
43 62 0.61
44 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAATCG
Found at i:6000050 original size:25 final size:25
Alignment explanation
Indices: 6000029--6000206 Score: 94
Period size: 25 Copynumber: 7.1 Consensus size: 25
6000019 TATGAGCGTT
*
6000029 CTGATATTTGGCTCTCACGAGCTTC
1 CTGATACTTGGCTCTCACGAGCTTC
6000054 CTGATACTTGGCTCTCACGAGCTTC
1 CTGATACTTGGCTCTCACGAGCTTC
** * * * *
6000079 CCAACACTTGGATCTTATGAGCTT-
1 CTGATACTTGGCTCTCACGAGCTTC
* * **
6000103 ATCGATTA-ATGGCTCTCTTGAGCTTC
1 CT-GA-TACTTGGCTCTCACGAGCTTC
* * * *
6000129 CCGTTA-TATGGCTATCACGAGATTC
1 CTGATACT-TGGCTCTCACGAGCTTC
* * *
6000154 CTGATA-TATGCCTCTCATGAGTTTC
1 CTGATACT-TGGCTCTCACGAGCTTC
* * * *
6000179 CCGATATTTGGCTCACATGAGCTTC
1 CTGATACTTGGCTCTCACGAGCTTC
6000204 CTG
1 CTG
6000207 TTTATGGCTC
Statistics
Matches: 114, Mismatches: 34, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
24 2 0.02
25 110 0.96
26 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (25 bp):
CTGATACTTGGCTCTCACGAGCTTC
Found at i:6000205 original size:50 final size:50
Alignment explanation
Indices: 6000014--6000279 Score: 150
Period size: 50 Copynumber: 5.3 Consensus size: 50
6000004 ACACACCACA
* * *
6000014 GCTCTTATGAGCGTT-CTGATATTTGGCTCTCACGAGCTTCCTGATACT-TG
1 GCTCTCATGAGC-TTCCCGATATTTGGCTCACACGAGCTTCCTGATA-TATG
* * * * * ** * *
6000064 GCTCTCACGAGCTTCCCAACACTTGGATCTTATGAGCTT-ATCGAT-TAATG
1 GCTCTCATGAGCTTCCCGATATTTGGCTCACACGAGCTTCCT-GATAT-ATG
* * * *
6000114 GCTCTCTTGAGCTTCCCGTTATATGGCT-ATCACGAGATTCCTGATATATG
1 GCTCTCATGAGCTTCCCGATATTTGGCTCA-CACGAGCTTCCTGATATATG
* * * *
6000164 CCTCTCATGAGTTTCCCGATATTTGGCTCACATGAGCTTCCTG-TTTATG
1 GCTCTCATGAGCTTCCCGATATTTGGCTCACACGAGCTTCCTGATATATG
* * * ** * * * **
6000213 GCTCGT-ATAAGCTTCCAGATAATTGGCTCGTAAGAGTTTCCTGTTATACA
1 GCTC-TCATGAGCTTCCCGATATTTGGCTCACACGAGCTTCCTGATATATG
*
6000263 GCTCACATGAGCTTCCC
1 GCTCTCATGAGCTTCCC
6000280 ATTACATGGG
Statistics
Matches: 159, Mismatches: 46, Indels: 22
0.70 0.20 0.10
Matches are distributed among these distances:
48 1 0.01
49 40 0.25
50 115 0.72
51 3 0.02
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (50 bp):
GCTCTCATGAGCTTCCCGATATTTGGCTCACACGAGCTTCCTGATATATG
Found at i:6005225 original size:14 final size:14
Alignment explanation
Indices: 6005206--6005233 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6005196 ACCGCTCAAA
6005206 ACCATTGCTACATT
1 ACCATTGCTACATT
6005220 ACCATTGCTACATT
1 ACCATTGCTACATT
6005234 TTACAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
ACCATTGCTACATT
Found at i:6006167 original size:30 final size:31
Alignment explanation
Indices: 6006131--6006195 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
6006121 GTCAATCAAT
*
6006131 TATTCAAAACTTTTCATTTAAGTTACT-AAC
1 TATTCAAAACTTTTCATTTAAGTCACTGAAC
*
6006161 TATTCAAAACTTTTTATTTAAGTCACTGAAC
1 TATTCAAAACTTTTCATTTAAGTCACTGAAC
6006192 TATT
1 TATT
6006196 AAGTTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (31 bp):
TATTCAAAACTTTTCATTTAAGTCACTGAAC
Found at i:6007255 original size:12 final size:12
Alignment explanation
Indices: 6007235--6007278 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
6007225 CATTATGCTA
*
6007235 TTAACTATTATT
1 TTAAATATTATT
6007247 TTAAATATTATT
1 TTAAATATTATT
**
6007259 TTAAATGAGAATT
1 TTAAAT-ATTATT
6007272 TTAAATA
1 TTAAATA
6007279 ATAGAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (12 bp):
TTAAATATTATT
Found at i:6018061 original size:24 final size:24
Alignment explanation
Indices: 6018033--6018084 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
6018023 TTAGTAAGTC
* *
6018033 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
6018057 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
6018081 AAAT
1 AAAT
6018085 CCTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:6024655 original size:22 final size:22
Alignment explanation
Indices: 6024627--6024675 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
6024617 TGACAGGTCA
* *
6024627 TGTCTCGAGACATATAGGCTTT
1 TGTCTCGAGACAAACAGGCTTT
*
6024649 TGTCTCGAGACAAACATGCTTT
1 TGTCTCGAGACAAACAGGCTTT
6024671 TGTCT
1 TGTCT
6024676 AAAGACATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (22 bp):
TGTCTCGAGACAAACAGGCTTT
Found at i:6030322 original size:51 final size:52
Alignment explanation
Indices: 6030242--6030460 Score: 223
Period size: 51 Copynumber: 4.3 Consensus size: 52
6030232 TTAACACGTA
* * *
6030242 TGTAGTACTAAGTGCAGTCTACTACGTGTATC-GATAGATAATGGTCACATG
1 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
* * * * ** *
6030293 TGTACTACTATGTGCAGGCTACTATGTGTACCGAAT-GACCTTGGTCACGTG
1 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
* * * * * * *
6030344 TGTAGTACTATGTGAAAGCTACTACGTGAATCGGAAAG-C-TTGATCACGTG
1 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
*
6030394 TGTAGTACTATGTGTAGGCTACTACGTGTATCGGAT-GACAATGGTCACATG
1 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
* *
6030445 GGTGGTACTATGTGCA
1 TGTAGTACTATGTGCA
6030461 AACCACCGAA
Statistics
Matches: 135, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.01
50 43 0.32
51 88 0.65
52 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (52 bp):
TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
Found at i:6030402 original size:50 final size:50
Alignment explanation
Indices: 6030332--6030428 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
6030322 ACCGAATGAC
*
6030332 CTTGGTCACGTGTGTAGTACTATGTGAAAGCTACTACGTGAATCGGAAAG
1 CTTGATCACGTGTGTAGTACTATGTGAAAGCTACTACGTGAATCGGAAAG
* * *
6030382 CTTGATCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGA
1 CTTGATCACGTGTGTAGTACTATGTGAAAGCTACTACGTGAATCGGA
6030429 TGACAATGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (50 bp):
CTTGATCACGTGTGTAGTACTATGTGAAAGCTACTACGTGAATCGGAAAG
Found at i:6034194 original size:43 final size:42
Alignment explanation
Indices: 6034146--6034241 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 42
6034136 TTCTATTCTA
*
6034146 GGTTTTTA-TCTCACTTTTACGACTCTCTTTTTCTGGGTTTATG
1 GGTTTTTAGTCTCACTTTGACG-CT-TCTTTTTCTGGGTTTATG
* ** * *
6034189 GGTTTTTAGTTGTTTCTTTGATGGTTCTTTTTCTGGGTTTATG
1 GGTTTTTAG-TCTCACTTTGACGCTTCTTTTTCTGGGTTTATG
6034232 GGTTTTTAGT
1 GGTTTTTAGT
6034242 TGTTTCTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.02
43 35 0.78
44 1 0.02
45 8 0.18
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.57
Consensus pattern (42 bp):
GGTTTTTAGTCTCACTTTGACGCTTCTTTTTCTGGGTTTATG
Found at i:6034242 original size:43 final size:43
Alignment explanation
Indices: 6034171--6034259 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
6034161 TTTACGACTC
6034171 TCTTTTTCTGGGTTTATGGGTTTTTAGTTGTTTCTTTGATGGT
1 TCTTTTTCTGGGTTTATGGGTTTTTAGTTGTTTCTTTGATGGT
6034214 TCTTTTTCTGGGTTTATGGGTTTTTAGTTGTTTCTTTGATGGT
1 TCTTTTTCTGGGTTTATGGGTTTTTAGTTGTTTCTTTGATGGT
6034257 TCT
1 TCT
6034260 AGTTGCATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.07, C:0.08, G:0.25, T:0.61
Consensus pattern (43 bp):
TCTTTTTCTGGGTTTATGGGTTTTTAGTTGTTTCTTTGATGGT
Found at i:6051487 original size:20 final size:20
Alignment explanation
Indices: 6051462--6051499 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6051452 TTTGGTTATC
6051462 ACATGTTCAAATATCTAAGT
1 ACATGTTCAAATATCTAAGT
**
6051482 ACATGTTTGAATATCTAA
1 ACATGTTCAAATATCTAA
6051500 TCCCATTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
ACATGTTCAAATATCTAAGT
Found at i:6054232 original size:51 final size:51
Alignment explanation
Indices: 6054155--6054366 Score: 285
Period size: 51 Copynumber: 4.3 Consensus size: 51
6054145 ACTTCTGATC
* * * *
6054155 AGTGACAAGTGATGAGTGGTAACTTTAGCTACACTTATCTAATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
*
6054206 AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
6054257 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
* * * *
6054308 AGTG---A-TG---AGTGGTAGCTTTAGTTACATTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
*
6054352 AATGACAAGTGATAA
1 AGTGACAAGTGATAA
6054367 ATGTGATCCG
Statistics
Matches: 143, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
44 36 0.25
47 3 0.02
48 3 0.02
51 101 0.71
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:6054256 original size:44 final size:44
Alignment explanation
Indices: 6054206--6054365 Score: 194
Period size: 44 Copynumber: 3.5 Consensus size: 44
6054196 ATCAGTGACA
6054206 AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAGTGAC
1 AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTG---A-T--C
*
6054256 AAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC
1 -AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATC
* * *
6054301 AGTGACAAGTGATGAGTGGTAGCTTTAGTTACATTTATCTGATC
1 AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATC
* * *
6054345 AGGGACAAATGACAAGTGATA
1 AGTGACAAGTGATAAGTGATA
6054366 AATGTGATCC
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
44 56 0.57
45 1 0.01
47 1 0.01
48 1 0.01
51 40 0.40
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATC
Found at i:6059356 original size:14 final size:14
Alignment explanation
Indices: 6059339--6059429 Score: 75
Period size: 14 Copynumber: 6.7 Consensus size: 14
6059329 CAATGTTCTA
* *
6059339 TTCCATATATCTGT
1 TTCCATATAACTAT
6059353 TTCCATATAACTGA-
1 TTCCATATAACT-AT
*
6059367 TT-CATATAACCAT
1 TTCCATATAACTAT
*
6059380 TT-CATATATCTAT
1 TTCCATATAACTAT
*
6059393 TTCCATATAACCAT
1 TTCCATATAACTAT
*
6059407 TT-CATATATCTACT
1 TTCCATATAACTA-T
6059421 TT-CATATAA
1 TTCCATATAA
6059430 TCGATTCATA
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
12 1 0.02
13 29 0.46
14 33 0.52
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (14 bp):
TTCCATATAACTAT
Found at i:6059382 original size:27 final size:27
Alignment explanation
Indices: 6059356--6059429 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
6059346 TATCTGTTTC
6059356 CATATAACTGA-TT-CATATAACCATTT
1 CATATAACT-ATTTCCATATAACCATTT
*
6059382 CATATATCTATTTCCATATAACCATTT
1 CATATAACTATTTCCATATAACCATTT
*
6059409 CATATATCTACTTT-CATATAA
1 CATATAACTA-TTTCCATATAA
6059430 TCGATTCATA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.02
26 10 0.23
27 30 0.68
28 3 0.07
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.42
Consensus pattern (27 bp):
CATATAACTATTTCCATATAACCATTT
Found at i:6059411 original size:40 final size:41
Alignment explanation
Indices: 6059342--6059428 Score: 115
Period size: 40 Copynumber: 2.1 Consensus size: 41
6059332 TGTTCTATTC
* *
6059342 CATATATCTGTTTCCATATAACTGATTCATATAACCA-TTT
1 CATATATCTATTTCCATATAACTCATTCATATAACCACTTT
* *
6059382 CATATATCTATTTCCATATAAC-CATTTCATATATCTACTTT
1 CATATATCTATTTCCATATAACTCA-TTCATATAACCACTTT
6059423 CATATA
1 CATATA
6059429 ATCGATTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
39 1 0.02
40 31 0.76
41 9 0.22
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (41 bp):
CATATATCTATTTCCATATAACTCATTCATATAACCACTTT
Found at i:6059412 original size:13 final size:13
Alignment explanation
Indices: 6059367--6059429 Score: 72
Period size: 13 Copynumber: 4.7 Consensus size: 13
6059357 ATATAACTGA
6059367 TTCATATAACCAT
1 TTCATATAACCAT
* *
6059380 TTCATATATCTAT
1 TTCATATAACCAT
6059393 TTCCATATAACCAT
1 TT-CATATAACCAT
* *
6059407 TTCATATATCTACT
1 TTCATATAACCA-T
6059421 TTCATATAA
1 TTCATATAA
6059430 TCGATTCATA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
13 21 0.51
14 20 0.49
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:6059439 original size:27 final size:26
Alignment explanation
Indices: 6059367--6059429 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 26
6059357 ATATAACTGA
6059367 TTCATATAACCATTTCATATATCTAT
1 TTCATATAACCATTTCATATATCTAT
6059393 TTCCATATAACCATTTCATATATCTACT
1 TT-CATATAACCATTTCATATATCTA-T
6059421 TTCATATAA
1 TTCATATAA
6059430 TCGATTCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 2 0.06
27 30 0.86
28 3 0.09
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (26 bp):
TTCATATAACCATTTCATATATCTAT
Found at i:6062951 original size:98 final size:98
Alignment explanation
Indices: 6062819--6063015 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
6062809 CTAAAAATAA
* *
6062819 TAAAGGAAATATTCCGAGTTTGGGATTTTGGAGGAATTGTGCCCTAACGTATTGGGGGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGGGTGATTTC
*
6062884 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATATTGGATAAGTGGATGTTCTTTTAAAG
* *
6062917 TAAATGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGGGTGATTTC
6062982 TTAAATATTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATATTGGATAAGTGGATGTTCTTTTAAAG
6063015 T
1 T
6063016 TTTATTGCAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.27, C:0.09, G:0.26, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGGGTGATTTC
TTAAATATTGGATAAGTGGATGTTCTTTTAAAG
Found at i:6066989 original size:14 final size:15
Alignment explanation
Indices: 6066972--6067000 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6066962 AAATATGTTG
6066972 GTGAAATA-ATAGAA
1 GTGAAATACATAGAA
6066986 GTGAAATACATAGAA
1 GTGAAATACATAGAA
6067001 ATTTGATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (15 bp):
GTGAAATACATAGAA
Found at i:6073738 original size:17 final size:16
Alignment explanation
Indices: 6073713--6073762 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
6073703 CGAAAAATTT
6073713 TTAAAACACGAGGATC
1 TTAAAACACGAGGATC
**
6073729 TTAGAAACACGAAAATTC
1 TTA-AAACACGAGGA-TC
6073747 TTAAAAGCACGAGGAT
1 TTAAAA-CACGAGGAT
6073763 TTTTTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.11
17 13 0.48
18 11 0.41
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (16 bp):
TTAAAACACGAGGATC
Found at i:6073787 original size:17 final size:17
Alignment explanation
Indices: 6073691--6073849 Score: 102
Period size: 18 Copynumber: 8.8 Consensus size: 17
6073681 AATAATTATT
6073691 TTTTTGAGAACACGAAAAA
1 TTTTTGA-AACACG-AAAA
* **
6073710 TTTTTAAAACACGAGGA
1 TTTTTGAAACACGAAAA
* *
6073727 TCTTAGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * **
6073744 TTCTTAAAAGCACGAGGATTT
1 TTTTTGAAA-CACGA--A-AA
6073765 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* *
6073782 TTTTTGAAAATACGGAAA
1 TTTTTG-AAACACGAAAA
* * *
6073800 TTTTTAAAACACAGGAAT
1 TTTTTGAAACAC-GAAAA
*
6073818 TTTTTGGAAACATGAAAA
1 TTTTT-GAAACACGAAAA
6073836 TTTTTGAAACACGA
1 TTTTTGAAACACGA
6073850 TTAGTTTTTT
Statistics
Matches: 105, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
17 38 0.36
18 43 0.41
19 11 0.10
20 6 0.06
21 7 0.07
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:6073822 original size:36 final size:35
Alignment explanation
Indices: 6073691--6073849 Score: 115
Period size: 36 Copynumber: 4.4 Consensus size: 35
6073681 AATAATTATT
**
6073691 TTTTTGAGAACACGAAAAATTTTT-AAAACACGAGGA
1 TTTTTGA-AACACG-AAAATTTTTGAAAACACGAAAA
* * * **
6073727 TCTTAGAAACACGAAAATTCTT-AAAAGCACGAGGATTT
1 TTTTTGAAACACGAAAATTTTTGAAAA-CACGA--A-AA
* *
6073765 TTTTTGAAACACGAAAATTTTTGAAAATACGGAAA
1 TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
* * * * *
6073800 TTTTTAAAACACAGGAATTTTTTGGAAACATGAAAA
1 TTTTTGAAACAC-GAAAATTTTTGAAAACACGAAAA
6073836 TTTTTGAAACACGA
1 TTTTTGAAACACGA
6073850 TTAGTTTTTT
Statistics
Matches: 95, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
34 12 0.13
35 23 0.24
36 34 0.36
38 22 0.23
39 4 0.04
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (35 bp):
TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
Found at i:6073858 original size:54 final size:56
Alignment explanation
Indices: 6073733--6073848 Score: 157
Period size: 54 Copynumber: 2.1 Consensus size: 56
6073723 AGGATCTTAG
* * * *
6073733 AAACACGAAAATTCTTAAAAGCACGAGGATTTTTTTTGAAACACGAAAATTTTTGA
1 AAACACGGAAATTTTTAAAAGCACGAGGAATTTTTTGGAAACACGAAAATTTTTGA
* *
6073789 AAATACGGAAATTTTTAAAA-CAC-AGGAATTTTTTGGAAACATGAAAATTTTTG-
1 AAACACGGAAATTTTTAAAAGCACGAGGAATTTTTTGGAAACACGAAAATTTTTGA
6073842 AAACACG
1 AAACACG
6073849 ATTAGTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 6 0.11
54 27 0.51
55 3 0.06
56 17 0.32
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (56 bp):
AAACACGGAAATTTTTAAAAGCACGAGGAATTTTTTGGAAACACGAAAATTTTTGA
Found at i:6074344 original size:20 final size:19
Alignment explanation
Indices: 6074319--6074370 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
6074309 AATTTTGAGC
6074319 CTTTTCCTTTTTTTCTCTTT
1 CTTTT-CTTTTTTTCTCTTT
*
6074339 CTTTTCTCTTTTTTCTTTTT
1 CTTTTCT-TTTTTTCTCTTT
6074359 CTTTTCTTTTTT
1 CTTTTCTTTTTT
6074371 CTTTTTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
CTTTTCTTTTTTTCTCTTT
Found at i:6074345 original size:11 final size:11
Alignment explanation
Indices: 6074319--6074375 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
6074309 AATTTTGAGC
6074319 CTTTTC-CTTT
1 CTTTTCTCTTT
6074329 -TTTTCTCTTT
1 CTTTTCTCTTT
6074339 CTTTTCTC-TT
1 CTTTTCTCTTT
*
6074349 -TTTTCTTTTT
1 CTTTTCTCTTT
*
6074359 CTTTTCTTTTTT
1 CTTTTC-TCTTT
6074371 CTTTT
1 CTTTT
6074376 TTTCTTCAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
9 11 0.27
10 8 0.20
11 12 0.29
12 10 0.24
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
CTTTTCTCTTT
Found at i:6074381 original size:20 final size:20
Alignment explanation
Indices: 6074327--6074376 Score: 77
Period size: 18 Copynumber: 2.6 Consensus size: 20
6074317 GCCTTTTCCT
*
6074327 TTTTTTCTCTTTCTTTTCTC
1 TTTTTTCTTTTTCTTTTCTC
6074347 TTTTTTCTTTTTC-TTT-TC
1 TTTTTTCTTTTTCTTTTCTC
6074365 TTTTTTCTTTTT
1 TTTTTTCTTTTT
6074377 TTCTTCAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 14 0.48
19 3 0.10
20 12 0.41
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTCTTTTCTC
Found at i:6074381 original size:26 final size:26
Alignment explanation
Indices: 6074328--6074377 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
6074318 CCTTTTCCTT
6074328 TTTTTCTCTTTCTTTTCTCTTTTTTC
1 TTTTTCTCTTTCTTTTCTCTTTTTTC
*
6074354 TTTTTCT-TTTCTTTTTTCTTTTTT
1 TTTTTCTCTTTCTTTTCTCTTTTTT
6074378 TCTTCAGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTTTCTCTTTCTTTTCTCTTTTTTC
Found at i:6074600 original size:18 final size:18
Alignment explanation
Indices: 6074574--6074608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6074564 CCTAATCTGC
*
6074574 TGGGCCTGCTGGGTGTTG
1 TGGGCCTGCTGGCTGTTG
*
6074592 TGGGTCTGCTGGCTGTT
1 TGGGCCTGCTGGCTGTT
6074609 CCGGGTCGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.46, T:0.37
Consensus pattern (18 bp):
TGGGCCTGCTGGCTGTTG
Found at i:6074861 original size:15 final size:16
Alignment explanation
Indices: 6074837--6074880 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
6074827 TCTCCTCCCC
*
6074837 TTTTCCTTTTCTT-CT
1 TTTTCTTTTTCTTCCT
6074852 TTTTCTTTTTCTTCCT
1 TTTTCTTTTTCTTCCT
* *
6074868 TTGTCTTTCTCTT
1 TTTTCTTTTTCTT
6074881 TTATTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTCTTTTTCTTCCT
Found at i:6075344 original size:58 final size:59
Alignment explanation
Indices: 6075268--6075402 Score: 188
Period size: 58 Copynumber: 2.3 Consensus size: 59
6075258 GTAAAATTAT
*
6075268 AATTTT-GAGAAAGTTTAGGGGTT-AATATGTAATTTTGAGAAAGTTTAGAGGTCAAAATGT
1 AATTTTAGA-AAAGTTTAGGGGTTGAA-ATGTAATTTTGAGAAAGTTTAG-GGTCAAAATGA
* *
6075328 AA-TTTA-AAAAGTTTAGGGGTTGAAGTGTAATTTTGAGAAATTTTAGGGTCAAAATGA
1 AATTTTAGAAAAGTTTAGGGGTTGAAATGTAATTTTGAGAAAGTTTAGGGTCAAAATGA
6075385 AATTTTAGAAAAGTTTAG
1 AATTTTAGAAAAGTTTAG
6075403 AGGTCAAAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
57 12 0.18
58 38 0.56
59 16 0.24
60 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (59 bp):
AATTTTAGAAAAGTTTAGGGGTTGAAATGTAATTTTGAGAAAGTTTAGGGTCAAAATGA
Found at i:6075413 original size:30 final size:30
Alignment explanation
Indices: 6075267--6075413 Score: 167
Period size: 30 Copynumber: 5.0 Consensus size: 30
6075257 GGTAAAATTA
* * *
6075267 TAATTTTGAGAAAGTTTAGGGGTTAATATG
1 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
6075297 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
* * ** *
6075327 TAA-TTT-AAAAAGTTTAGGGGTTGAAGTG
1 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
*
6075355 TAATTTTGAGAAATTTTAG-GGTCAAAATG
1 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
*
6075384 AAATTTT-AGAAAAGTTTAGAGGTCAAAATG
1 TAATTTTGAG-AAAGTTTAGAGGTCAAAATG
6075414 CAAAAAATTA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
28 22 0.22
29 27 0.28
30 49 0.50
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
TAATTTTGAGAAAGTTTAGAGGTCAAAATG
Found at i:6076001 original size:20 final size:19
Alignment explanation
Indices: 6075931--6076118 Score: 86
Period size: 18 Copynumber: 9.7 Consensus size: 19
6075921 AAGAATATTA
* *
6075931 AAAATTAGAAAAAAT-TAT
1 AAAATTATAAAAATTATAT
* * *
6075949 CAAACTATTAAAA-TAT-T
1 AAAATTATAAAAATTATAT
6075966 AAAATATATATGAAAATTGATAT
1 AAAAT-TATA--AAAATT-ATAT
6075989 AAAATTATAAAAA-TATA-
1 AAAATTATAAAAATTATAT
* * *
6076006 AAAGTCTA-ATAAATTATAA
1 AAAAT-TATAAAAATTATAT
*
6076025 AAAATTATAAAAATATATTT
1 AAAATTATAAAAAT-TATAT
*
6076045 AAAATTTTATAAAAACGTATGA-
1 AAAA--TTATAAAAA-TTAT-AT
* *
6076067 AAATTCTATAAAAATTATAA
1 AAAAT-TATAAAAATTATAT
* *
6076087 AAAAGTAT-TAAATTATAT
1 AAAATTATAAAAATTATAT
*
6076105 AAACTTATAAAAAT
1 AAAATTATAAAAAT
6076119 AAAAAAAATC
Statistics
Matches: 127, Mismatches: 24, Indels: 37
0.68 0.13 0.20
Matches are distributed among these distances:
17 13 0.10
18 38 0.30
19 18 0.14
20 22 0.17
21 9 0.07
22 21 0.17
23 6 0.05
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (19 bp):
AAAATTATAAAAATTATAT
Found at i:6076031 original size:10 final size:10
Alignment explanation
Indices: 6075978--6076135 Score: 64
Period size: 10 Copynumber: 16.3 Consensus size: 10
6075968 AATATATATG
*
6075978 AAAATTGATAT
1 AAAATT-ATAA
6075989 AAAATTAT-A
1 AAAATTATAA
6075998 AAAA-TAT--
1 AAAATTATAA
* *
6076005 AAAAGTCTAA
1 AAAATTATAA
*
6076015 TAAATTATAA
1 AAAATTATAA
6076025 AAAATTATAA
1 AAAATTATAA
*
6076035 AAATATATTTAA
1 AAA-AT-TATAA
**
6076047 AATTTTATAA
1 AAAATTATAA
** *
6076057 AAACGTAT-G
1 AAAATTATAA
*
6076066 AAAATTCTATA
1 AAAATTATA-A
6076077 AAAATTATAA
1 AAAATTATAA
*
6076087 AAAAGTAT--
1 AAAATTATAA
* *
6076095 TAAATTATAT
1 AAAATTATAA
*
6076105 AAACTTAT-A
1 AAAATTATAA
*
6076114 AAAA-TAAAA
1 AAAATTATAA
*
6076123 AAAATCATAA
1 AAAATTATAA
6076133 AAA
1 AAA
6076136 CTTTAATTGA
Statistics
Matches: 107, Mismatches: 29, Indels: 23
0.67 0.18 0.14
Matches are distributed among these distances:
7 4 0.04
8 13 0.12
9 17 0.16
10 50 0.47
11 17 0.16
12 6 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAATTATAA
Found at i:6076047 original size:22 final size:23
Alignment explanation
Indices: 6076013--6076059 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
6076003 ATAAAAGTCT
6076013 AATAAATTATAAAAAATTATAAA
1 AATAAATTATAAAAAATTATAAA
* **
6076036 AATATATT-TAAAATTTTATAAA
1 AATAAATTATAAAAAATTATAAA
6076058 AA
1 AA
6076060 CGTATGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAAATTATAAAAAATTATAAA
Found at i:6076070 original size:32 final size:31
Alignment explanation
Indices: 6075985--6076117 Score: 97
Period size: 28 Copynumber: 4.6 Consensus size: 31
6075975 ATGAAAATTG
* *
6075985 ATAT-AAAATTAT-AAAAA-TATAAAAGTCT
1 ATATAAAAATTATAAAAAAGTATAAAAATAT
*
6076013 A-AT--AAATTATAAAAAATTATAAAAATAT
1 ATATAAAAATTATAAAAAAGTATAAAAATAT
* * * *
6076041 ATTTAAAATTTTATAAAAACGTATGAAAAT-T
1 ATATAAAA-ATTATAAAAAAGTATAAAAATAT
* *
6076072 CTATAAAAATTATAAAAAAGTAT-TAAAT-T
1 ATATAAAAATTATAAAAAAGTATAAAAATAT
*
6076101 ATAT-AAACTTATAAAAA
1 ATATAAAAATTATAAAAA
6076118 TAAAAAAAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
26 7 0.08
27 7 0.08
28 23 0.27
29 9 0.11
30 13 0.15
31 9 0.11
32 17 0.20
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (31 bp):
ATATAAAAATTATAAAAAAGTATAAAAATAT
Found at i:6081937 original size:26 final size:27
Alignment explanation
Indices: 6081908--6081964 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
6081898 TTTATGCTTT
*
6081908 TTTTATAAAATCTTA-TAATTTGTAAA
1 TTTTATAAAATCTTATTAATTTGCAAA
* * *
6081934 TTTTATTAAATTTTATTATTTTGCAAA
1 TTTTATAAAATCTTATTAATTTGCAAA
6081961 TTTT
1 TTTT
6081965 CTATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTTATAAAATCTTATTAATTTGCAAA
Found at i:6082762 original size:22 final size:22
Alignment explanation
Indices: 6082737--6082868 Score: 149
Period size: 22 Copynumber: 6.0 Consensus size: 22
6082727 AAATTCAATA
*
6082737 TCAATTTCTTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
6082759 TCAA-TTCCTTTCAAAATTTCTC
1 TCAATTTCC-TTCAAAAATTCTC
* * *
6082781 TCAATTCCCTTCAAAATTTCTA
1 TCAATTTCCTTCAAAAATTCTC
*
6082803 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
* * *
6082825 TCAAATTCCTTCCAAAATCCTC
1 TCAATTTCCTTCAAAAATTCTC
* *
6082847 TCAAATTCCTTCAAAAAATCTC
1 TCAATTTCCTTCAAAAATTCTC
6082869 CAAATCCATA
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
21 3 0.03
22 89 0.94
23 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:6082848 original size:66 final size:66
Alignment explanation
Indices: 6082735--6082862 Score: 188
Period size: 66 Copynumber: 1.9 Consensus size: 66
6082725 ACAAATTCAA
* * *
6082735 TATCAATTTCTTTCAAAAATTCTCTCAATTCCTTTCAAAATTTCTCTC-AATTCCCTTCAAAATT
1 TATCAATTTCCTTCAAAAATTCTCTCAATTCCTTCCAAAATTCCTCTCAAATT-CCTTCAAAATT
6082799 TC
65 TC
*
6082801 TATCAATTTCCTTCCAAAATTCTCTCAAATTCCTTCCAAAA-TCCTCTCAAATTCCTTCAAAA
1 TATCAATTTCCTTCAAAAATTCTCTC-AATTCCTTCCAAAATTCCTCTCAAATTCCTTCAAAA
6082863 AATCTCCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
66 39 0.70
67 17 0.30
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (66 bp):
TATCAATTTCCTTCAAAAATTCTCTCAATTCCTTCCAAAATTCCTCTCAAATTCCTTCAAAATTT
C
Found at i:6082860 original size:10 final size:10
Alignment explanation
Indices: 6082761--6082861 Score: 53
Period size: 11 Copynumber: 9.2 Consensus size: 10
6082751 AAATTCTCTC
6082761 AATTCCTTTCAA
1 AATTCC-TTC-A
*
6082773 AATTTCTCTC-
1 AATTCCT-TCA
6082783 AATTCCCTTCAA
1 AATT-CCTTC-A
*
6082795 AATTTCTATCA
1 AATTCCT-TCA
*
6082806 ATTTCCTTCCAA
1 AATTCCTT-C-A
6082818 AATT-CTCTCA
1 AATTCCT-TCA
6082828 AATTCCTTCCA
1 AATTCCTT-CA
*
6082839 AAATCCTCTCA
1 AATTCCT-TCA
6082850 AATTCCTTCA
1 AATTCCTTCA
6082860 AA
1 AA
6082862 AAATCTCCAA
Statistics
Matches: 70, Mismatches: 8, Indels: 24
0.69 0.08 0.24
Matches are distributed among these distances:
10 18 0.26
11 33 0.47
12 19 0.27
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTCCTTCA
Found at i:6085263 original size:17 final size:18
Alignment explanation
Indices: 6085241--6085275 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6085231 TAAAATCCCT
6085241 AACCCT-ACTTAATTAAA
1 AACCCTAACTTAATTAAA
*
6085258 AACCCTAATTTAATTAAA
1 AACCCTAACTTAATTAAA
6085276 TTAAAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (18 bp):
AACCCTAACTTAATTAAA
Found at i:6085263 original size:23 final size:24
Alignment explanation
Indices: 6085229--6085446 Score: 167
Period size: 28 Copynumber: 8.6 Consensus size: 24
6085219 ACATTATTTG
* *
6085229 ATTAAAATCCCTAACCCTACTT-A
1 ATTAAAAACCCTAACCCTAATTAA
**
6085252 ATTAAAAACCCTAA-TTTAATTAA
1 ATTAAAAACCCTAACCCTAATTAA
6085275 ATTAAAAACCCTAA-CCTAATTTTATTAA
1 ATTAAAAACCCTAACCCT-A----ATTAA
*
6085303 ATTAAAAACCCTAACCTAACCTACTTAA
1 ATTAAAAACCCTAA-C---CCTAATTAA
*
6085331 ATTAAAAACCCTAACCTTATTTAATTAA
1 ATTAAAAACCCTAACC----CTAATTAA
*
6085359 ATTAAAAACCCTAACCCTACTT-A
1 ATTAAAAACCCTAACCCTAATTAA
*
6085382 ATTAAAAACCCTAACCTAATTTAATTAA
1 ATTAAAAACCCTAACC----CTAATTAA
*
6085410 ATTAAAAACCCTAACCCT-ATTTA
1 ATTAAAAACCCTAACCCTAATTAA
6085433 ATTAAAAACCCTAA
1 ATTAAAAACCCTAA
6085447 TTAAATTGTA
Statistics
Matches: 160, Mismatches: 15, Indels: 40
0.74 0.07 0.19
Matches are distributed among these distances:
22 4 0.03
23 64 0.40
24 7 0.04
27 5 0.03
28 76 0.47
32 1 0.01
33 3 0.02
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (24 bp):
ATTAAAAACCCTAACCCTAATTAA
Found at i:6085292 original size:28 final size:28
Alignment explanation
Indices: 6085261--6085438 Score: 242
Period size: 28 Copynumber: 6.5 Consensus size: 28
6085251 AATTAAAAAC
6085261 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
6085289 CCTAATTTTATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
** *
6085317 CCTAACCTACTTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
6085345 CCTTATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* *
6085373 CC----CTACTT-AATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
6085396 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
6085424 CCCT-ATTTAATTAAA
1 -CCTAATTTAATTAAA
6085439 AACCCTAATT
Statistics
Matches: 131, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.13
24 4 0.03
27 4 0.03
28 103 0.79
29 3 0.02
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (28 bp):
CCTAATTTAATTAAATTAAAAACCCTAA
Found at i:6085314 original size:51 final size:52
Alignment explanation
Indices: 6085251--6085446 Score: 272
Period size: 51 Copynumber: 3.8 Consensus size: 52
6085241 AACCCTACTT
** *
6085251 AATTAAAAACCCTAA-TTTAATTAAATTAAAAACCCTAACCTAATTTTATTA
1 AATTAAAAACCCTAACCCTAATTAAATTAAAAACCCTAACCTAATTTAATTA
* *
6085302 AATTAAAAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCTTATTTAATTA
1 AATTAAAAACCCTAA-C---CCTAATTAAATTAAAAACCCTAACCTAATTTAATTA
*
6085358 AATTAAAAACCCTAACCCTACTT-AATTAAAAACCCTAACCTAATTTAATTA
1 AATTAAAAACCCTAACCCTAATTAAATTAAAAACCCTAACCTAATTTAATTA
*
6085409 AATTAAAAACCCTAACCCT-ATTTAATTAAAAACCCTAA
1 AATTAAAAACCCTAACCCTAATTAAATTAAAAACCCTAA
6085447 TTAAATTGTA
Statistics
Matches: 132, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
50 2 0.02
51 76 0.58
52 7 0.05
55 1 0.01
56 46 0.35
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (52 bp):
AATTAAAAACCCTAACCCTAATTAAATTAAAAACCCTAACCTAATTTAATTA
Found at i:6088221 original size:22 final size:21
Alignment explanation
Indices: 6088143--6088221 Score: 54
Period size: 22 Copynumber: 3.7 Consensus size: 21
6088133 TAAAAATAAT
*
6088143 AAAATTTTAATTTAATACTT-TA
1 AAAATTATAATTT-ATA-TTATA
** * *
6088165 AAAATTATAA-AGATATAATC
1 AAAATTATAATTTATATTATA
*
6088185 AAAATTATATTTTTATTATTATA
1 AAAATTATA-ATTTA-TATTATA
6088208 AAAATTATAATTTA
1 AAAATTATAATTTA
6088222 ATTTCATCCC
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.02
20 13 0.31
22 14 0.33
23 14 0.33
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (21 bp):
AAAATTATAATTTATATTATA
Found at i:6089485 original size:16 final size:16
Alignment explanation
Indices: 6089442--6089535 Score: 66
Period size: 18 Copynumber: 5.6 Consensus size: 16
6089432 AATAACTTTA
*
6089442 TATATTTTTAAATATTT
1 TATATTTTT-TATATTT
*
6089459 TTTCATATTTTTATATTT
1 TAT-AT-TTTTTATATTT
*
6089477 TATATTTTTCATAATTT
1 TATATTTTTTAT-ATTT
*
6089494 ATATAATTTTTA-ATTT
1 -TATATTTTTTATATTT
*
6089510 CATA-TTTTTATTATTT
1 TATATTTTTTA-TATTT
*
6089526 TGTATTTTTT
1 TATATTTTTT
6089536 CTAGGATGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
14 6 0.10
15 3 0.05
16 16 0.26
17 13 0.21
18 19 0.31
19 4 0.07
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATATTT
Found at i:6091283 original size:21 final size:21
Alignment explanation
Indices: 6091257--6091297 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6091247 AATAATGAAA
*
6091257 ATAAAAAAATTAAATTAATAC
1 ATAAAAAAATTAAACTAATAC
**
6091278 ATAAAACTATTAAACTAATA
1 ATAAAAAAATTAAACTAATA
6091298 TACAAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAAAAAATTAAACTAATAC
Found at i:6097842 original size:21 final size:21
Alignment explanation
Indices: 6097784--6097835 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
6097774 GGGAGTAATG
6097784 TCGCGACATTAGCCTTTAGGA
1 TCGCGACATTAGCCTTTAGGA
6097805 TCGCGACATTAGCCTTTAGGA
1 TCGCGACATTAGCCTTTAGGA
6097826 TCGCGACATT
1 TCGCGACATT
6097836 GAGCTTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (21 bp):
TCGCGACATTAGCCTTTAGGA
Found at i:6099589 original size:50 final size:50
Alignment explanation
Indices: 6099475--6099716 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
6099465 ATTTGGGTAA
* * * *
6099475 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
6099531 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
6099581 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * * *
6099631 AGAGGTCCCCTATAATACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
**
6099681 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
6099717 TTTGGCATGT
Statistics
Matches: 165, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 92 0.56
51 28 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:6099671 original size:100 final size:103
Alignment explanation
Indices: 6099475--6099724 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
6099465 ATTTGGGTAA
6099475 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* *
6099540 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
* * * *
6099581 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
* *
6099643 TAATACCATGTCTGGGACATGGCATGGGCACCGACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
* *
6099681 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
6099725 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
Found at i:6104114 original size:13 final size:11
Alignment explanation
Indices: 6104105--6104207 Score: 50
Period size: 11 Copynumber: 10.2 Consensus size: 11
6104095 TAAAAAAATT
6104105 TATTTTAAAAA
1 TATTTTAAAAA
6104116 TATTTT--AAA
1 TATTTTAAAAA
6104125 -A--TTAAAAA
1 TATTTTAAAAA
* *
6104133 -AATTAAAAAA
1 TATTTTAAAAA
6104143 GTATTTTAAAAA
1 -TATTTTAAAAA
*
6104155 AATTTT--AAA
1 TATTTTAAAAA
6104164 -A--TTAAAAA
1 TATTTTAAAAA
6104172 -ATTTTAAAAAA
1 TATTTT-AAAAA
* *
6104183 GCATTTTAAAAG
1 -TATTTTAAAAA
6104195 TATTTTAAAAA
1 TATTTTAAAAA
6104206 TA
1 TA
6104208 AAAAATAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
6 4 0.06
8 10 0.14
9 6 0.08
10 8 0.11
11 27 0.38
12 12 0.17
13 5 0.07
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:6104131 original size:17 final size:17
Alignment explanation
Indices: 6104109--6104180 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 17
6104099 AAAATTTATT
*
6104109 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTTAAAA
**
6104126 TTAAAAAAATTAAAAAAGTA
1 TTAAAAAAATT-TTAAA--A
6104146 TTTTAAAAAAATTTTAAAA
1 --TTAAAAAAATTTTAAAA
6104165 TT-AAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
6104181 AAGCATTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
16 14 0.31
17 12 0.27
18 3 0.07
19 1 0.02
20 1 0.02
21 3 0.07
22 11 0.24
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:6104141 original size:40 final size:39
Alignment explanation
Indices: 6104066--6104212 Score: 168
Period size: 40 Copynumber: 3.6 Consensus size: 39
6104056 ATAAATATCA
* *
6104066 AAAAATTATTTTAAAAATTAAAACAAAAATAAAAAAATTTATTTT
1 AAAAA-TATTTT-AAAATT--AA-AAAAATTAAAAAA-GTATTTT
6104111 AAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTT
* * *
6104150 AAAAAAATTTTAAAATTAAAAAATTTTAAAAAAGCATTTT
1 AAAAATATTTTAAAATTAAAAAA-ATTAAAAAAGTATTTT
* *
6104190 AAAAGTATTTTAAAAATAAAAAA
1 AAAAATATTTTAAAATTAAAAAA
6104213 TAAAAATATT
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
39 28 0.30
40 46 0.49
41 2 0.02
43 6 0.06
44 6 0.06
45 5 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (39 bp):
AAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTT
Found at i:6104171 original size:29 final size:29
Alignment explanation
Indices: 6104131--6104193 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 29
6104121 TAAAATTAAA
6104131 AAAATTAAAAAAGTATTTTAAAAAA-ATTTT
1 AAAATTAAAAAA--ATTTTAAAAAACATTTT
6104161 AAAATT-AAAAAATTTTAAAAAAGCATTTT
1 AAAATTAAAAAAATTTTAAAAAA-CATTTT
6104190 AAAA
1 AAAA
6104194 GTATTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 11 0.35
29 14 0.45
30 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTAAAAAAATTTTAAAAAACATTTT
Found at i:6106389 original size:13 final size:13
Alignment explanation
Indices: 6106371--6106396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6106361 AGGATGAATC
6106371 AAATGAAAATAAA
1 AAATGAAAATAAA
6106384 AAATGAAAATAAA
1 AAATGAAAATAAA
6106397 TGAATAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAATGAAAATAAA
Found at i:6106513 original size:4 final size:4
Alignment explanation
Indices: 6106500--6106542 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
6106490 TGATTTTTTG
6106500 AATT -ATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
6106543 GAAGTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
AATT
Found at i:6111729 original size:23 final size:24
Alignment explanation
Indices: 6111687--6111736 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
6111677 AACATTGATG
* *
6111687 TGAGTTAATCTTTTGCTTGTTTAAT
1 TGAGTTAA-CTTTTGATTGTTAAAT
6111712 TGAGTTAA-TTTTGATTGTTAAAT
1 TGAGTTAACTTTTGATTGTTAAAT
6111735 TG
1 TG
6111737 TCTTCCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
25 8 0.35
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.54
Consensus pattern (24 bp):
TGAGTTAACTTTTGATTGTTAAAT
Found at i:6118096 original size:27 final size:29
Alignment explanation
Indices: 6118057--6118111 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
6118047 TTTACGAGGT
*
6118057 TTTTTTTTTAGAA-TTT-TGATTTTTTAA
1 TTTTTTTTAAGAACTTTATGATTTTTTAA
6118084 TTTTTTTTAAGAACTTTTATGATTTTTT
1 TTTTTTTTAAGAAC-TTTATGATTTTTT
6118112 TTACAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
29 3 0.12
30 9 0.38
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (29 bp):
TTTTTTTTAAGAACTTTATGATTTTTTAA
Found at i:6118101 original size:21 final size:21
Alignment explanation
Indices: 6118076--6118122 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
6118066 AGAATTTTGA
* *
6118076 TTTTTTAATTTTTTTTAAGAAC
1 TTTTATAATTTTTTTT-ACAAC
*
6118098 TTTTATGATTTTTTTTACAAC
1 TTTTATAATTTTTTTTACAAC
6118119 TTTT
1 TTTT
6118123 GTATAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTATAATTTTTTTTACAAC
Found at i:6118411 original size:21 final size:22
Alignment explanation
Indices: 6118374--6118425 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
6118364 TAACTTTAAA
**
6118374 AAAATTAAAATTGAAAATGATAT
1 AAAATT-AAATTGAAAAAAATAT
6118397 AAAATTAAA-TGAAAAAAATAT
1 AAAATTAAATTGAAAAAAATAT
6118418 ATAAATTA
1 A-AAATTA
6118426 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 9 0.35
23 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
AAAATTAAATTGAAAAAAATAT
Found at i:6118412 original size:22 final size:21
Alignment explanation
Indices: 6118374--6118425 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
6118364 TAACTTTAAA
*
6118374 AAAATTAAAATTGAAAATGATAT
1 AAAATT-AAATTGAAAA-AATAT
6118397 AAAATTAAA-TGAAAAAAATAT
1 AAAATTAAATTG-AAAAAATAT
6118418 ATAAATTA
1 A-AAATTA
6118426 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.27
22 13 0.50
23 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (21 bp):
AAAATTAAATTGAAAAAATAT
Found at i:6119497 original size:2 final size:2
Alignment explanation
Indices: 6119490--6119532 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6119480 AAACTCTCCA
6119490 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6119532 T
1 T
6119533 ATATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:6128061 original size:29 final size:31
Alignment explanation
Indices: 6128020--6128086 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
6128010 TTATTCAAAT
*
6128020 AATAT-TAAAAAAATA-ATTAATTACGAAAA
1 AATATATAAAAAAACATATTAATTACGAAAA
*
6128049 AATATATAAAAAAACATATTAATTATGAAAA
1 AATATATAAAAAAACATATTAATTACGAAAA
*
6128080 TATATAT
1 AATATAT
6128087 TTATTATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 5 0.15
30 9 0.27
31 19 0.58
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (31 bp):
AATATATAAAAAAACATATTAATTACGAAAA
Found at i:6128861 original size:27 final size:29
Alignment explanation
Indices: 6128816--6128873 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
6128806 AAAATGTTTA
*
6128816 TTTTCGTAATTAATCTATTTTTTTA-TAT
1 TTTTCGTAATTAATCTATTTTTGTATTAT
*
6128844 TTTTTGTAATTAAT-TATTTTTGTATTAT
1 TTTTCGTAATTAATCTATTTTTGTATTAT
6128872 TT
1 TT
6128874 AGATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTTCGTAATTAATCTATTTTTGTATTAT
Found at i:6135109 original size:13 final size:13
Alignment explanation
Indices: 6135093--6135119 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6135083 AAACTTAAAA
6135093 TTCTCTATAAATG
1 TTCTCTATAAATG
6135106 TTCTCTATAAATG
1 TTCTCTATAAATG
6135119 T
1 T
6135120 ATTATGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TTCTCTATAAATG
Found at i:6139160 original size:17 final size:15
Alignment explanation
Indices: 6139134--6139180 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
6139124 ACCCGCCAAA
*
6139134 TTATTATTTAATAAT
1 TTATTTTTTAATAAT
6139149 TAATATTTTTTAAT-AT
1 T--TATTTTTTAATAAT
6139165 TTATTCTTTTAATAAT
1 TTATT-TTTTAATAAT
6139181 AATTTGGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 5 0.19
17 10 0.37
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTTTTAATAAT
Found at i:6140545 original size:16 final size:15
Alignment explanation
Indices: 6140529--6140558 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
6140519 AACAAAAAGA
6140529 AATAGAAAGAAACAG
1 AATAGAAAGAAACAG
6140544 AATAGAAACGAAACA
1 AATAGAAA-GAAACA
6140559 AGGAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.10, G:0.17, T:0.07
Consensus pattern (15 bp):
AATAGAAAGAAACAG
Found at i:6140549 original size:15 final size:16
Alignment explanation
Indices: 6140516--6140558 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
6140506 AATAAATAAA
*
6140516 AGAAAC-AAAAAGAAAT
1 AGAAACGAAACAG-AAT
6140532 AGAAA-GAAACAGAAT
1 AGAAACGAAACAGAAT
6140547 AGAAACGAAACA
1 AGAAACGAAACA
6140559 AGGAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.70, C:0.09, G:0.16, T:0.05
Consensus pattern (16 bp):
AGAAACGAAACAGAAT
Found at i:6140576 original size:26 final size:25
Alignment explanation
Indices: 6140533--6140599 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 25
6140523 AAAAGAAATA
*
6140533 GAAAGAAACAGAATAGAAACGAAACAAGG
1 GAAAGAAA-A-AA-AGAAAAGAAA-AAGG
6140562 AGAAA-AAAAAAAGAAAAGAAAAAGG
1 -GAAAGAAAAAAAGAAAAGAAAAAGG
*
6140587 GAAAGAAAGAAAG
1 GAAAGAAAAAAAG
6140600 GAGAAATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 4 0.12
25 11 0.32
26 9 0.26
27 2 0.06
28 1 0.03
29 3 0.09
30 4 0.12
ACGTcount: A:0.70, C:0.04, G:0.24, T:0.01
Consensus pattern (25 bp):
GAAAGAAAAAAAGAAAAGAAAAAGG
Found at i:6146964 original size:43 final size:43
Alignment explanation
Indices: 6146868--6146967 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
6146858 ATGCCGGTAT
* ** *
6146868 AGAACATGACCTTTAGCGGTGCTTTTTCCACAAACACCGCTAT
1 AGAACATGACTTTTAGCGACGCTTTTTCCACAAACACCGCTAA
* *
6146911 AGAACTTGACTTTTAGCGACGCTTTTAT-CATAAACACCGCTAA
1 AGAACATGACTTTTAGCGACGCTTTT-TCCACAAACACCGCTAA
*
6146954 ATAACATGACTTTT
1 AGAACATGACTTTT
6146968 GACTTTTAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 47 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (43 bp):
AGAACATGACTTTTAGCGACGCTTTTTCCACAAACACCGCTAA
Found at i:6149322 original size:18 final size:19
Alignment explanation
Indices: 6149287--6149324 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6149277 ACCAATTTTC
6149287 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
6149306 AAAAATTCCAAAT-TTTAT
1 AAAAATTCAAAATATTTAT
6149324 A
1 A
6149325 TTATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:6149728 original size:25 final size:24
Alignment explanation
Indices: 6149681--6149730 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
6149671 CTCACCCATA
*
6149681 ATTTAAATTAAATAATAATTTTTT
1 ATTTAAATTAAATAATAAATTTTT
* * *
6149705 ATTTAAATTTAATTATAAAATTTT
1 ATTTAAATTAAATAATAAATTTTT
6149729 AT
1 AT
6149731 GTCATTAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTAAATTAAATAATAAATTTTT
Found at i:6149870 original size:14 final size:14
Alignment explanation
Indices: 6149841--6149869 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6149831 AATTTCCTTA
6149841 TTCTCTTTCTTTTT
1 TTCTCTTTCTTTTT
6149855 TTCT-TTTCTTTTT
1 TTCTCTTTCTTTTT
6149868 TT
1 TT
6149870 TAAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTCTTTCTTTTT
Found at i:6156152 original size:18 final size:18
Alignment explanation
Indices: 6156110--6156146 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6156100 ATTCATATTC
*
6156110 ATATTCATATAAATATAA
1 ATATTAATATAAATATAA
*
6156128 ATATTAATATTAATATAA
1 ATATTAATATAAATATAA
6156146 A
1 A
6156147 ATTTAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATTAATATAAATATAA
Found at i:6160270 original size:16 final size:16
Alignment explanation
Indices: 6160245--6160278 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6160235 AAAACAAATG
*
6160245 AAATAAAAGAATAGAA
1 AAATAAAAGAACAGAA
*
6160261 AAATAGAAGAACAGAA
1 AAATAAAAGAACAGAA
6160277 AA
1 AA
6160279 GAAACAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.09
Consensus pattern (16 bp):
AAATAAAAGAACAGAA
Found at i:6161123 original size:20 final size:20
Alignment explanation
Indices: 6161098--6161137 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6161088 CGTAAAATGA
*
6161098 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
6161118 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
6161138 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:6161127 original size:34 final size:34
Alignment explanation
Indices: 6161084--6161149 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
6161074 AGTAAAATAT
*
6161084 TTTTCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGAAAAATATTTTAC
*
6161117 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGAAAAATATTTT
6161150 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:6162654 original size:280 final size:280
Alignment explanation
Indices: 6162153--6162712 Score: 976
Period size: 280 Copynumber: 2.0 Consensus size: 280
6162143 AAAATCTAAG
* *
6162153 ATTTTTATGCTTATGCAGCCTCAAATTTGGCAATTGGCATAATTGCCCATTTGACCCCTATTATT
1 ATTTTTATACTTATGCAGCCTCAAATTTGGCAATTGGCATAATTGCCCATTTGACCCATATTATT
*
6162218 TTCCTTTAATCTATAATTAAACTTTCACTTCTATTATAATTTAATCATTTTTACTAATTAATCTT
66 TTCCTTTAATCTATAATGAAACTTTCACTTCTATTATAATTTAATCATTTTTACTAATTAATCTT
*
6162283 AATTAGACTAAATTCACCTAATTAATACCTATTTAAGCACCAAACTAAATTCATAATTACTTCTA
131 AATTAGACTAAATTCACCTAATTAATACCTATTTAAGCACCAAACTAAATTCATAATTACGTCTA
* * * * *
6162348 ATAATTATTTTCGAACTCAATTTACTAAGACGGAGGCTCGATATTATATTTTTTCGATGCTCGTG
196 ATAATTATTTTCGAACTCAATTTACTAAAACGGAGGCCCGATATTATACTTTTCCGATGCCCGTG
6162413 AATTTTGGGTCATTACATTT
261 AATTTTGGGTCATTACATTT
* *
6162433 ATTTTTATACTTATGCCGCCTCAAATTTGGCAATTGGCATAATTGCCCATTTGACTCATATTATT
1 ATTTTTATACTTATGCAGCCTCAAATTTGGCAATTGGCATAATTGCCCATTTGACCCATATTATT
* *
6162498 TTCCTTTAATCTATAATGAAACTTTCACTTCTATTATAATTTAATCCTTTTTACTAATTACTCTT
66 TTCCTTTAATCTATAATGAAACTTTCACTTCTATTATAATTTAATCATTTTTACTAATTAATCTT
6162563 AATTAGACTAAATTCACCTAATTAATACCTATTTAAGCACCAAACTAAATTCATAATTACGTCTA
131 AATTAGACTAAATTCACCTAATTAATACCTATTTAAGCACCAAACTAAATTCATAATTACGTCTA
* *
6162628 ATAATTATTTTTGAACTCAATTTACTAAAACGGAGGCCCGATGTTATACTTTTCCGATGCCCGTG
196 ATAATTATTTTCGAACTCAATTTACTAAAACGGAGGCCCGATATTATACTTTTCCGATGCCCGTG
*
6162693 AATTTTGGGTCATTATATTT
261 AATTTTGGGTCATTACATTT
6162713 TAATTTCCAA
Statistics
Matches: 264, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
280 264 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (280 bp):
ATTTTTATACTTATGCAGCCTCAAATTTGGCAATTGGCATAATTGCCCATTTGACCCATATTATT
TTCCTTTAATCTATAATGAAACTTTCACTTCTATTATAATTTAATCATTTTTACTAATTAATCTT
AATTAGACTAAATTCACCTAATTAATACCTATTTAAGCACCAAACTAAATTCATAATTACGTCTA
ATAATTATTTTCGAACTCAATTTACTAAAACGGAGGCCCGATATTATACTTTTCCGATGCCCGTG
AATTTTGGGTCATTACATTT
Found at i:6162899 original size:24 final size:23
Alignment explanation
Indices: 6162819--6162903 Score: 66
Period size: 24 Copynumber: 3.7 Consensus size: 23
6162809 TGATTTGTAC
*
6162819 AAAAATGGACAGCATAATATCCTT
1 AAAAATGGACAGCATAATATAC-T
* * *
6162843 AAAAATGGATAGCAT-TTAAAC-
1 AAAAATGGACAGCATAATATACT
* * *
6162864 AACATTCGGACAGCATAATATGCT
1 AAAAAT-GGACAGCATAATATACT
6162888 AAAAAATGGACAGCAT
1 -AAAAATGGACAGCAT
6162904 TTTGTTATCA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
21 4 0.09
22 8 0.18
23 6 0.13
24 23 0.51
25 4 0.09
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.22
Consensus pattern (23 bp):
AAAAATGGACAGCATAATATACT
Found at i:6170043 original size:22 final size:21
Alignment explanation
Indices: 6170014--6170061 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
6170004 TATGCATTAG
6170014 TTAATAATAATAGTAAT-ATAT
1 TTAATAATAATA-TAATAATAT
6170035 TATAATAATAATATAATAATAT
1 T-TAATAATAATATAATAATAT
6170057 TTAAT
1 TTAAT
6170062 TCACAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAATAATAATATAATAATAT
Found at i:6170254 original size:16 final size:17
Alignment explanation
Indices: 6170218--6170254 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
6170208 TAATATAATT
6170218 TATAATATTTTAATTAA
1 TATAATATTTTAATTAA
*
6170235 -ATAATATTTTTA-TAA
1 TATAATATTTTAATTAA
6170250 TATAA
1 TATAA
6170255 ATCAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATTTTAATTAA
Found at i:6174595 original size:26 final size:26
Alignment explanation
Indices: 6174565--6174653 Score: 126
Period size: 26 Copynumber: 3.4 Consensus size: 26
6174555 GCAACTCTTA
* * *
6174565 TGAGCGTCCCG-TTATATGGCTCTTCG
1 TGAGCTTCCCGATTA-AAGGCTCTTTG
6174591 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTTG
*
6174617 TGAGCTTCTCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTTG
6174643 TGAGCTTCCCG
1 TGAGCTTCCCG
6174654 TTAGTGCTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 54 0.95
27 3 0.05
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.35
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTTTG
Found at i:6174736 original size:24 final size:24
Alignment explanation
Indices: 6174700--6174748 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
6174690 TGGTGCTTCT
*
6174700 CGTTAATTACTCTTCGGAGCTACC
1 CGTTAATTACTCTTCGAAGCTACC
* *
6174724 CGTTAATTGCTCTTTGAAGCTACC
1 CGTTAATTACTCTTCGAAGCTACC
6174748 C
1 C
6174749 ATTATAGGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (24 bp):
CGTTAATTACTCTTCGAAGCTACC
Found at i:6174794 original size:25 final size:25
Alignment explanation
Indices: 6174766--6174823 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
6174756 GCTCTTTGTG
*
6174766 AGCTTCCCGTTATATTACCCGGATA
1 AGCTTCCCGTTATATTACCCAGATA
* **
6174791 AGCTTTCCGTTATATTGTCCAGATA
1 AGCTTCCCGTTATATTACCCAGATA
6174816 AGCTTCCC
1 AGCTTCCC
6174824 ATTACAAGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (25 bp):
AGCTTCCCGTTATATTACCCAGATA
Found at i:6181684 original size:21 final size:21
Alignment explanation
Indices: 6181658--6181713 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
6181648 AACAACGGTG
*
6181658 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
6181679 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
6181700 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
6181714 AACAGCGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:6184798 original size:6 final size:6
Alignment explanation
Indices: 6184787--6184830 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
6184777 TTTGCAACCC
*
6184787 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
6184831 GAAGAAGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:6187204 original size:20 final size:20
Alignment explanation
Indices: 6187181--6187242 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 20
6187171 TATAAAATTA
*
6187181 TAAAAAAAATTAATTATTTT
1 TAAAAAAAATTAAATATTTT
**
6187201 TAAAGTAAA-TAAAT-TTTT
1 TAAAAAAAATTAAATATTTT
*
6187219 TATAAAAAATTAAATATATTT
1 TAAAAAAAATTAAATAT-TTT
6187240 TAA
1 TAA
6187243 TAATTTCATA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 10 0.31
19 9 0.28
20 8 0.25
21 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAAAAAAATTAAATATTTT
Found at i:6187232 original size:19 final size:19
Alignment explanation
Indices: 6187184--6187240 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
6187174 AAAATTATAA
6187184 AAAAAATT-AATTATTTTT
1 AAAAAATTAAATTATTTTT
6187202 AAAGTAAA-TAAATT-TTTTAT
1 AAA--AAATTAAATTATTTT-T
6187222 AAAAAATTAAATATATTTT
1 AAAAAATTAAAT-TATTTT
6187241 AATAATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
18 6 0.19
19 10 0.31
20 12 0.38
21 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AAAAAATTAAATTATTTTT
Found at i:6191707 original size:140 final size:138
Alignment explanation
Indices: 6191449--6191728 Score: 366
Period size: 140 Copynumber: 2.0 Consensus size: 138
6191439 TATAACAAAA
* * * *
6191449 GTCGACATAGTGTTGGACAAAACTGACTTTTATTTAAGCGTTGCCTTAAGCATGCATATCCCGAC
1 GTCGACATAGTGTTGGACAAAACAGACTCTTATTTAAGCGTTGCCTCAAGCATGCATATCCCAAC
* * * * *
6191514 CCTTATACAAAGAGTTGGCTAAAGCATATATTGACAATTCTATCTCAAAACTTAGGAAAGTTTTG
66 CCTTATACAAAGAGTTGGCCAAAGCATACATCGACAATTCTATCCCAAAACTTA--AAAGTGTTG
6191579 GCCCAAAAGT
129 GCCCAAAAGT
* *
6191589 GTCGGCATAGTGTTGGACAAAACAGACTCTTATTTAA-CGGTTGCCTCAAGCATGGATATCCCAA
1 GTCGACATAGTGTTGGACAAAACAGACTCTTATTTAAGC-GTTGCCTCAAGCATGCATATCCCAA
* * * * *
6191653 CTCTTATACAAAGAGTTTGCCAAAGCGTACATCGGCAAGTT-TATCCCAACACTTAAAAGTGTTG
65 CCCTTATACAAAGAGTTGGCCAAAGCATACATCGACAA-TTCTATCCCAAAACTTAAAAGTGTTG
6191717 GCCCAAAAGT
129 GCCCAAAAGT
6191727 GT
1 GT
6191729 TGTCTTAGGA
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
138 20 0.16
139 1 0.01
140 99 0.81
141 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (138 bp):
GTCGACATAGTGTTGGACAAAACAGACTCTTATTTAAGCGTTGCCTCAAGCATGCATATCCCAAC
CCTTATACAAAGAGTTGGCCAAAGCATACATCGACAATTCTATCCCAAAACTTAAAAGTGTTGGC
CCAAAAGT
Found at i:6201657 original size:21 final size:21
Alignment explanation
Indices: 6201633--6201672 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6201623 AAGTTTATAG
6201633 ATTTTCAGGGAAGGACATAAA
1 ATTTTCAGGGAAGGACATAAA
6201654 ATTTTCAGGGAAGGACATA
1 ATTTTCAGGGAAGGACATA
6201673 GGATCTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (21 bp):
ATTTTCAGGGAAGGACATAAA
Found at i:6208334 original size:23 final size:23
Alignment explanation
Indices: 6208308--6208446 Score: 176
Period size: 23 Copynumber: 6.2 Consensus size: 23
6208298 GTTATTTATT
*
6208308 AGTGGTAACTACGGCTACATATC
1 AGTGGTAGCTACGGCTACATATC
* *
6208331 AGTGGTAGCTTCGGCTACATTTC
1 AGTGGTAGCTACGGCTACATATC
*
6208354 AGTAGTAGCTACGGCTACATATC
1 AGTGGTAGCTACGGCTACATATC
* * *
6208377 AGTGGAAGCTTCGG---CATTTC
1 AGTGGTAGCTACGGCTACATATC
*
6208397 AGTGGTAGCTACGGCTACGTATC
1 AGTGGTAGCTACGGCTACATATC
*
6208420 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTACGGCTACATATC
6208443 AGTG
1 AGTG
6208447 TGGCACTTAT
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.18
23 80 0.82
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.29
Consensus pattern (23 bp):
AGTGGTAGCTACGGCTACATATC
Found at i:6208409 original size:43 final size:43
Alignment explanation
Indices: 6208308--6208434 Score: 191
Period size: 43 Copynumber: 2.9 Consensus size: 43
6208298 GTTATTTATT
*
6208308 AGTGGTAACTACGGCTACATATCAGTGGTAGCTTCGGCTACATTTC
1 AGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGG---CATTTC
* *
6208354 AGTAGTAGCTACGGCTACATATCAGTGGAAGCTTCGGCATTTC
1 AGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCATTTC
*
6208397 AGTGGTAGCTACGGCTACGTATCAGTGGTAGCTTCGGC
1 AGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGC
6208435 TACATATCAG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
43 41 0.55
46 34 0.45
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (43 bp):
AGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCATTTC
Found at i:6210359 original size:28 final size:28
Alignment explanation
Indices: 6210313--6210369 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
6210303 TATAGTTTTT
6210313 ATAATATTTATAAAGGTTATAATAATAA
1 ATAATATTTATAAAGGTTATAATAATAA
**
6210341 ATAATATATTATAAA-GTTATTCTAATAA
1 ATAATAT-TTATAAAGGTTATAATAATAA
6210369 A
1 A
6210370 AACAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (28 bp):
ATAATATTTATAAAGGTTATAATAATAA
Found at i:6211526 original size:64 final size:64
Alignment explanation
Indices: 6211442--6211589 Score: 226
Period size: 64 Copynumber: 2.3 Consensus size: 64
6211432 ATATATATTT
* * *
6211442 AAAGTTCTTGAGTTGCATTTAAGGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAAGGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
* * *
6211506 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAGTATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAAGGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
6211570 AAA-TTCTTTGAGCTGAATTT
1 AAAGTTC-TTGAGCTGAATTT
6211590 TAATGTTGTA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 3 0.04
64 74 0.96
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.41
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAAGGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
Found at i:6211797 original size:41 final size:42
Alignment explanation
Indices: 6211738--6211854 Score: 134
Period size: 41 Copynumber: 2.8 Consensus size: 42
6211728 ATCTGAGATT
*
6211738 TTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTG-AAT-TAA
1 TTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAAATGT-A
* *
6211779 TTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGTA
1 TTCAGGCTTTATGCCTAGCAGGC-TTGATGCCGGTGAAATGTA
* * *
6211821 -TCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTG
6211855 TTTTATACAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
40 2 0.03
41 54 0.84
42 7 0.11
43 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (42 bp):
TTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAAATGTA
Found at i:6212549 original size:14 final size:15
Alignment explanation
Indices: 6212525--6212559 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6212515 TATTTTAATC
6212525 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
6212540 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
6212555 ATGGT
1 ATGGT
6212560 AATGTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:6214633 original size:14 final size:15
Alignment explanation
Indices: 6214609--6214643 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6214599 TATTTTAATC
6214609 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
6214624 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
6214639 ATGGT
1 ATGGT
6214644 AATGTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:6216056 original size:2 final size:2
Alignment explanation
Indices: 6215984--6216041 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
6215974 TTGCATAGAT
*
6215984 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6216026 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
6216042 GCCGAATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6216509 original size:41 final size:40
Alignment explanation
Indices: 6216464--6216608 Score: 218
Period size: 41 Copynumber: 3.5 Consensus size: 40
6216454 GACTTTAAGT
* *
6216464 CTAGCAGGCTAAGTGCCGATGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
*
6216505 CTAGCAGGATAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
* *
6216546 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA-C
6216587 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
6216609 ATATGTTAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 2 0.02
41 93 0.98
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (40 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAC
Found at i:6219148 original size:23 final size:23
Alignment explanation
Indices: 6219096--6219183 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
6219086 CTTGATCAAT
*
6219096 ATACGACACAT-AAGTGCTTG-A
1 ATACGACACATAAAGTGCCTGAA
*
6219117 A-ACGACACATGAAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
6219139 ATACGACACATAAAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
6219162 ATACAACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
6219184 TCGGTAAAGC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
20 9 0.15
21 9 0.15
22 2 0.03
23 41 0.67
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:6219880 original size:13 final size:13
Alignment explanation
Indices: 6219862--6219888 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6219852 TAATTACAAC
6219862 AATAATTTAATAT
1 AATAATTTAATAT
6219875 AATAATTTAATAT
1 AATAATTTAATAT
6219888 A
1 A
6219889 TGTCTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATTTAATAT
Found at i:6219943 original size:149 final size:150
Alignment explanation
Indices: 6219711--6219989 Score: 325
Period size: 149 Copynumber: 1.8 Consensus size: 150
6219701 TTAAATTAAT
*
6219711 TAATTTAATATAATAATAATTAAAATAAATATCTATTTAATATCAAATGCATGTATTACAATTGT
1 TAATTTAATATAATAAT-ATT-AAATAAATATCTATTTAATATCAAAT-CATGTATTACAAGTGT
* ** * *
6219776 ACACTTACATATTATTACACATGTGTTTTATCATCACCCTACATTTGTCATAATTCAATTTATTT
63 ACAATTACATATTATTACACATGTACTATATCATCACCATACATTTGTCATAATTCAATTTATTT
6219841 GATAATTTTAATAATTACAACAA
128 GATAATTTTAATAATTACAACAA
* * *
6219864 TAATTTAATATAATAAT-TT-AATATATGTCTATTTAATAATCAATAT-ATTTATTACAAGTGTA
1 TAATTTAATATAATAATATTAAATAAATATCTATTTAAT-ATCAA-ATCATGTATTACAAGTGTA
* ** ** *
6219926 -ATATTACTTA-TATTTACACATGTACTATATCATCATTATACATTTGTCATGTTTTAATTTATT
64 CA-ATTACATATTA-TTACACATGTACTATATCATCACCATACATTTGTCATAATTCAATTTATT
6219989 T
127 T
6219990 ATCACATAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
148 3 0.03
149 78 0.73
150 5 0.05
151 4 0.04
153 17 0.16
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (150 bp):
TAATTTAATATAATAATATTAAATAAATATCTATTTAATATCAAATCATGTATTACAAGTGTACA
ATTACATATTATTACACATGTACTATATCATCACCATACATTTGTCATAATTCAATTTATTTGAT
AATTTTAATAATTACAACAA
Found at i:6220053 original size:28 final size:29
Alignment explanation
Indices: 6220021--6220090 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
6220011 ATAATTATTT
*
6220021 AATAATAAATATCT-TTTACTT-AATAATA
1 AATAATAAATATCTATTTAATTAAATAA-A
6220049 AATAATAAATATCTATTTAATTAAATAAA
1 AATAATAAATATCTATTTAATTAAATAAA
6220078 AAGTAATTAAATA
1 AA-TAA-TAAATA
6220091 AATCTATTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 14 0.38
29 9 0.24
30 8 0.22
31 6 0.16
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (29 bp):
AATAATAAATATCTATTTAATTAAATAAA
Found at i:6236487 original size:258 final size:258
Alignment explanation
Indices: 6236030--6236504 Score: 914
Period size: 258 Copynumber: 1.8 Consensus size: 258
6236020 ATTATGAGTT
6236030 TCTGGTTATGCCGTTTGGGTTGACTAATGCACCTGCAGTATTCATGGATTTGATGAACCGGATAT
1 TCTGGTTATGCCGTTTGGGTTGACTAATGCACCTGCAGTATTCATGGATTTGATGAACCGGATAT
6236095 TCAGACCGTATCTAGATAGGTTTGTAGTAGTTTTCATTGATGACATTTTAGTCTATTCTCGGGAT
66 TCAGACCGTATCTAGATAGGTTTGTAGTAGTTTTCATTGATGACATTTTAGTCTATTCTCGGGAT
* *
6236160 GAAACTGAGCATACAGAACATTTGACAATTGTGTTGCAAATTCTGCGTGAAAAGAAACTTTATGC
131 GAAACTGAACATACAGAACATTTGACAATAGTGTTGCAAATTCTGCGTGAAAAGAAACTTTATGC
6236225 TAAATTCAGTAAATGTGAATTTACTGACTAATGCAAATTCTGGTTATGCCGTTTGGGTTTAGG
196 TAAATTCAGTAAATGTGAATTTACTGACTAATGCAAATTCTGGTTATGCCGTTTGGGTTTAGG
6236288 TCTGGTTATGCCGTTTGGGTTGACTAATGCACCTGCAGTATTCATGGATTTGATGAACCGGATAT
1 TCTGGTTATGCCGTTTGGGTTGACTAATGCACCTGCAGTATTCATGGATTTGATGAACCGGATAT
6236353 TCAGACCGTATCTAGATAGGTTTGTAGTAGTTTTCATTGATGACATTTTAGTCTATTCTCGGGAT
66 TCAGACCGTATCTAGATAGGTTTGTAGTAGTTTTCATTGATGACATTTTAGTCTATTCTCGGGAT
* *
6236418 GAAACTGAACATGCAGAACATTTGAGAATAGTGTTGCAAATTCTGCGTGAAAAGAAACTTTATGC
131 GAAACTGAACATACAGAACATTTGACAATAGTGTTGCAAATTCTGCGTGAAAAGAAACTTTATGC
6236483 TAAATTCAGTAAATGTGAATTT
196 TAAATTCAGTAAATGTGAATTT
6236505 TGGCTTCGAG
Statistics
Matches: 213, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
258 213 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (258 bp):
TCTGGTTATGCCGTTTGGGTTGACTAATGCACCTGCAGTATTCATGGATTTGATGAACCGGATAT
TCAGACCGTATCTAGATAGGTTTGTAGTAGTTTTCATTGATGACATTTTAGTCTATTCTCGGGAT
GAAACTGAACATACAGAACATTTGACAATAGTGTTGCAAATTCTGCGTGAAAAGAAACTTTATGC
TAAATTCAGTAAATGTGAATTTACTGACTAATGCAAATTCTGGTTATGCCGTTTGGGTTTAGG
Found at i:6239348 original size:13 final size:13
Alignment explanation
Indices: 6239330--6239361 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6239320 TTTCCAGCAA
6239330 TTATGAATTTATT
1 TTATGAATTTATT
6239343 TTATGAATTTATT
1 TTATGAATTTATT
*
6239356 TGATGA
1 TTATGA
6239362 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:6239568 original size:50 final size:50
Alignment explanation
Indices: 6239456--6239697 Score: 322
Period size: 50 Copynumber: 4.7 Consensus size: 50
6239446 ATTTGGGTAA
* * *
6239456 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC----GA-GATG
*
6239512 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* * *
6239562 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* *
6239612 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
**
6239662 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
6239698 TTTGCATGTT
Statistics
Matches: 168, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 96 0.57
51 31 0.18
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:6239648 original size:100 final size:103
Alignment explanation
Indices: 6239456--6239697 Score: 382
Period size: 100 Copynumber: 2.3 Consensus size: 103
6239446 ATTTGGGTAA
6239456 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TAAGATCA--AGAGGTCCC
*
6239521 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* * *
6239562 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAGATC-AGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATCAAGAGGTCCCCTA
6239624 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
*
6239662 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGC
6239698 TTTGCATGTT
Statistics
Matches: 129, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
100 51 0.40
101 31 0.24
103 5 0.04
105 2 0.02
106 40 0.31
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATCAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:6244901 original size:43 final size:44
Alignment explanation
Indices: 6244838--6244923 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 44
6244828 TTTTGTGGCG
* *
6244838 TTTGTAAAGAAAAGCGCCGCTAAATATCATGTTCTATAACGGCA
1 TTTGTAAAGAAAAGCACCGCTAAAGATCATGTTCTATAACGGCA
* *
6244882 TTTGT-AATAAAAGCACCGCTAAAGATCATGTTCTATAGCGGC
1 TTTGTAAAGAAAAGCACCGCTAAAGATCATGTTCTATAACGGC
6244924 GTTTTCTCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 33 0.87
44 5 0.13
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
TTTGTAAAGAAAAGCACCGCTAAAGATCATGTTCTATAACGGCA
Done.