Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 29
Found at i:6065125 original size:24 final size:24
Alignment explanation
Indices: 6065098--6065153 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
6065088 GAAAGCAAGA
6065098 AAAAAAATCAGAAA-AG-AAGCACTC
1 AAAAAAA--AGAAATAGAAAGCACTC
* *
6065122 AAAAACAAGAAATTGAAAGCACTC
1 AAAAAAAAGAAATAGAAAGCACTC
6065146 AAAAAAAA
1 AAAAAAAA
6065154 AAAAGTTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.19
23 1 0.04
24 21 0.78
ACGTcount: A:0.66, C:0.14, G:0.11, T:0.09
Consensus pattern (24 bp):
AAAAAAAAGAAATAGAAAGCACTC
Found at i:6065150 original size:25 final size:24
Alignment explanation
Indices: 6065114--6065170 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
6065104 ATCAGAAAAG
*
6065114 AAGCACTCAAAAACAAGAAA-TTGA
1 AAGCACTCAAAAA-AAAAAAGTTGA
*
6065138 AAGCACTCAAAAAAAAAAAAGTTGG
1 AAGCACTC-AAAAAAAAAAAGTTGA
6065163 AAGCACTC
1 AAGCACTC
6065171 GTCAACAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.56, C:0.18, G:0.14, T:0.12
Consensus pattern (24 bp):
AAGCACTCAAAAAAAAAAAGTTGA
Found at i:6070273 original size:28 final size:28
Alignment explanation
Indices: 6070233--6070290 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
6070223 AATGCCACTA
6070233 TAGTATTAATTCCTAATTGCAATTGGTC
1 TAGTATTAATTCCTAATTGCAATTGGTC
6070261 TAGTATTAATTCCTAATTGCAATTGGTC
1 TAGTATTAATTCCTAATTGCAATTGGTC
6070289 TA
1 TA
6070291 CAAAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (28 bp):
TAGTATTAATTCCTAATTGCAATTGGTC
Found at i:6083661 original size:49 final size:49
Alignment explanation
Indices: 6083536--6083670 Score: 150
Period size: 48 Copynumber: 2.8 Consensus size: 49
6083526 ATACCATGAG
* * * * * *
6083536 TGACATCTTTTATGCCGAAATGCATCGTTAGGCATTTAACTTTCATTAG
1 TGACATATTTTATTCCTAAATGCACCGTTATGCATTTAACTTTCATTAC
* * *
6083585 T-ATA-ACCTTTA-TGCTGAAATGCACCGTTATGCATTTAACTTTCATTAC
1 TGACATA-TTTTATTCCT-AAATGCACCGTTATGCATTTAACTTTCATTAC
6083633 TGACATATTTTATTCCTAAATGCACCGTTATGCATTTA
1 TGACATATTTTATTCCTAAATGCACCGTTATGCATTTA
6083671 TTTTAGCACA
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
47 1 0.01
48 36 0.52
49 28 0.41
50 4 0.06
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (49 bp):
TGACATATTTTATTCCTAAATGCACCGTTATGCATTTAACTTTCATTAC
Found at i:6086404 original size:18 final size:19
Alignment explanation
Indices: 6086369--6086405 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6086359 CACGGAATGT
6086369 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
6086389 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
6086406 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:6089118 original size:19 final size:19
Alignment explanation
Indices: 6089094--6089146 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
6089084 TAGGCTTTGG
*
6089094 AGTTTTGAAACTTCATAAA
1 AGTTTTGAAACTTCACAAA
* *
6089113 AGTTTTAAAACTTTCACAAG
1 AGTTTTGAAAC-TTCACAAA
*
6089133 ATTTTTGAAACTTC
1 AGTTTTGAAACTTC
6089147 CCTTATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (19 bp):
AGTTTTGAAACTTCACAAA
Found at i:6092075 original size:29 final size:30
Alignment explanation
Indices: 6092038--6092094 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6092028 AAATTTTCAA
* *
6092038 GGACTAAATTG-AATTTTGATTTAATTCTG
1 GGACCAAATTGAAATTTTGATTAAATTCTG
6092067 GGACCAAATTGAAATTTTGATTAAATTC
1 GGACCAAATTGAAATTTTGATTAAATTC
6092095 ATATTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (30 bp):
GGACCAAATTGAAATTTTGATTAAATTCTG
Found at i:6093090 original size:16 final size:16
Alignment explanation
Indices: 6093069--6093107 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
6093059 ACCGTTGATT
6093069 GTGGTAGACATACTCA
1 GTGGTAGACATACTCA
6093085 GTGGTAGACATACTCA
1 GTGGTAGACATACTCA
*
6093101 GTAGTAG
1 GTGGTAG
6093108 GCTTCCCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (16 bp):
GTGGTAGACATACTCA
Found at i:6094005 original size:28 final size:29
Alignment explanation
Indices: 6093951--6094005 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
6093941 ATAAATGTTT
* *
6093951 TATATGTTTTTCTACGGTATTTTGATACG
1 TATATGTTTTTATACAGTATTTTGATACG
6093980 TATATG-TTTTATACAGT-TTTCTGATA
1 TATATGTTTTTATACAGTATTT-TGATA
6094006 TATGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.13
28 14 0.61
29 6 0.26
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (29 bp):
TATATGTTTTTATACAGTATTTTGATACG
Found at i:6098329 original size:21 final size:21
Alignment explanation
Indices: 6098300--6098373 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
6098290 ATTCTGACTA
*
6098300 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCTAAT
*
6098321 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
*
6098342 TCGCAATGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
*
6098363 TCGCAATGCGA
1 TCGCATTGCGA
6098374 ATACGTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:6098388 original size:20 final size:20
Alignment explanation
Indices: 6098363--6098415 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
6098353 TTTTCCTAAT
6098363 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
6098383 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
6098403 TCGCAACGCGAAT
1 TCGCAATGCGAAT
6098416 TTGACTATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:6098425 original size:20 final size:20
Alignment explanation
Indices: 6098402--6098528 Score: 175
Period size: 20 Copynumber: 6.3 Consensus size: 20
6098392 GAATACGTAA
6098402 ATCGCAACGCGAATT-TGACT
1 ATCGCAACGCG-ATTCTGACT
* *
6098422 ATCGCAACACGATTCTAACT
1 ATCGCAACGCGATTCTGACT
* * *
6098442 ATCGTAATGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
6098462 ATCATAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
6098482 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
6098502 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
6098522 ATCGCAA
1 ATCGCAA
6098529 TACTGAATTT
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
19 3 0.03
20 91 0.97
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:6099397 original size:24 final size:24
Alignment explanation
Indices: 6099370--6099423 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6099360 GTATTCGAAA
6099370 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
6099394 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
6099418 TTTGAT
1 TTTGAT
6099424 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:6101868 original size:20 final size:19
Alignment explanation
Indices: 6101843--6101911 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 19
6101833 TAACGCGAAA
*
6101843 ATCGCAACGTGAATATGACT
1 ATCGCAACGCGAA-ATGACT
6101863 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
6101883 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
6101903 ATCACAACG
1 ATCGCAACG
6101912 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 42 0.93
21 3 0.07
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:6101971 original size:34 final size:33
Alignment explanation
Indices: 6101883--6101978 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
6101873 GAAAATGACT
* ** *
6101883 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
6101917 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
6101950 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
6101979 CAAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:6102207 original size:14 final size:14
Alignment explanation
Indices: 6102188--6102224 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6102178 CATCAATTAA
6102188 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
6102202 ACAAATCATCTTTT
1 ACAAATCAACATTT
6102216 ACAAATCAA
1 ACAAATCAA
6102225 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:6103702 original size:42 final size:42
Alignment explanation
Indices: 6103604--6103715 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
6103594 TCTAGAATGT
* * *
6103604 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGA
* **
6103646 TGGGAGGGGACTCTTGAGGGATGACAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
* *
6103688 TAGGGA-ATGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGACTCTTGAACGATGACAGG
6103716 TGATTCGGGC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
42 51 0.88
43 7 0.12
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:6104222 original size:20 final size:20
Alignment explanation
Indices: 6104199--6104283 Score: 118
Period size: 20 Copynumber: 4.2 Consensus size: 20
6104189 CTTAAAATCA
*
6104199 CAACGCGAAAATGACTATTG
1 CAACGCGAAAATGACTATCG
6104219 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
6104239 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
* * *
6104259 CAATGC-AAATTTGACTATCA
1 CAACGCGAAA-ATGACTATCG
6104279 CAACG
1 CAACG
6104284 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 3 0.05
20 56 0.95
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:6104319 original size:20 final size:20
Alignment explanation
Indices: 6104290--6104341 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
6104280 AACGAGAGAA
*
6104290 TCGCAATGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
6104310 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
6104330 TCGCGTTGCGAT
1 TCGCATTGCGAT
6104342 TTTGTTGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:6106413 original size:20 final size:20
Alignment explanation
Indices: 6106297--6106437 Score: 116
Period size: 20 Copynumber: 7.4 Consensus size: 20
6106287 GAAACTTAAA
**
6106297 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
6106317 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
**
6106337 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAAAATGACT
* *
6106357 ATCG-TA-ACG-CAA-GA--
1 ATCGCAACACGAAAATGACT
* **
6106371 ATCGCAACGCG-AAATGAAA
1 ATCGCAACACGAAAATGACT
6106390 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
** **
6106410 ATCGCAATGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
6106430 ATCGCAAC
1 ATCGCAAC
6106438 GCAAGAATCG
Statistics
Matches: 96, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
14 4 0.04
15 1 0.01
16 6 0.06
17 2 0.02
18 3 0.03
19 11 0.11
20 69 0.72
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:6106416 original size:73 final size:73
Alignment explanation
Indices: 6106296--6106470 Score: 305
Period size: 73 Copynumber: 2.4 Consensus size: 73
6106286 TGAAACTTAA
6106296 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAATTTGACTATCG
1 AATCGCAACACG-AAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAATTTGACTATCG
*
6106361 TAACGCAAG
65 CAACGCAAG
* **
6106370 AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACTATCGCAATGCGAATTTGACTATCGC
1 AATCGCAACACGAAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAATTTGACTATCGC
6106435 AACGCAAG
66 AACGCAAG
6106443 AATCGCAACACGAAATGAAAATCGCAAC
1 AATCGCAACACGAAATGAAAATCGCAAC
6106471 GACAGAATCG
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 85 0.89
74 11 0.11
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.15
Consensus pattern (73 bp):
AATCGCAACACGAAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAATTTGACTATCGC
AACGCAAG
Found at i:6106861 original size:22 final size:22
Alignment explanation
Indices: 6106799--6106864 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
6106789 TGACCGTGAA
* * *
6106799 TGATTTTGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
6106821 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
6106843 TGATTTCGTCGGACATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
6106865 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:6107085 original size:20 final size:20
Alignment explanation
Indices: 6107062--6107122 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
6107052 CGATAGTCAG
* *
6107062 ATTCGCGTTGCGATTAACGT
1 ATTCGCATTGCGATTTACGT
*
6107082 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
6107102 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
6107122 A
1 A
6107123 ACGCGAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:6112087 original size:23 final size:22
Alignment explanation
Indices: 6112057--6112119 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
6112047 CGATTCCCCT
6112057 AAGGGGGAATCGGTTCCCATTC
1 AAGGGGGAATCGGTTCCCATTC
* *
6112079 AAAGGGGGAATTGGTTCCCCTTC
1 -AAGGGGGAATCGGTTCCCATTC
* * *
6112102 ATGGGGGTATCGATTCCC
1 AAGGGGGAATCGGTTCCC
6112120 TCTGCCCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.25
Consensus pattern (22 bp):
AAGGGGGAATCGGTTCCCATTC
Found at i:6127539 original size:37 final size:37
Alignment explanation
Indices: 6127483--6127555 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
6127473 ACAGTGACTC
*
6127483 AACGTTTGACGCCAGCTTCGAAAACTTTTGTTCGCTT
1 AACGTTTGACGCCAGCTTCGAAAAATTTTGTTCGCTT
* *
6127520 AACGTTTGACGTCATCTTCGAAAAATTTTGTTCGCT
1 AACGTTTGACGCCAGCTTCGAAAAATTTTGTTCGCT
6127556 CAACAGAGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (37 bp):
AACGTTTGACGCCAGCTTCGAAAAATTTTGTTCGCTT
Found at i:6130134 original size:44 final size:46
Alignment explanation
Indices: 6130085--6130188 Score: 124
Period size: 46 Copynumber: 2.3 Consensus size: 46
6130075 CACATTGAAT
* *
6130085 GTGCATCGATGCA-CTC-TTTAAAGAAG-AAACATCGAATGCAATTG
1 GTGCATCGATGCATCCCTTTTAAA-AAGAAAACATCGAAGGCAATTG
* * *
6130129 GTGCATCGATGCATCCCTTTTAAAATGAAAACATCGAAGGTAATTT
1 GTGCATCGATGCATCCCTTTTAAAAAGAAAACATCGAAGGCAATTG
*
6130175 GTGTATCGATGCAT
1 GTGCATCGATGCAT
6130189 GGGTAGTGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 13 0.25
45 4 0.08
46 34 0.67
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (46 bp):
GTGCATCGATGCATCCCTTTTAAAAAGAAAACATCGAAGGCAATTG
Found at i:6130240 original size:20 final size:22
Alignment explanation
Indices: 6130195--6130252 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
6130185 GCATGGGTAG
6130195 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
6130219 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
6130239 TGCATCGATGCACT
1 TGCATCGATGCACT
6130253 TCAAGGAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:6131041 original size:18 final size:18
Alignment explanation
Indices: 6131018--6131069 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
6131008 GGGTTTACGC
6131018 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
6131036 GGTCCTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
6131054 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
6131070 TGTGTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:6135300 original size:109 final size:110
Alignment explanation
Indices: 6135106--6135546 Score: 640
Period size: 109 Copynumber: 4.0 Consensus size: 110
6135096 AAACGACATA
* * * * * * *
6135106 ATGTTTTCAAAAGAATTTTTAAAAAAACTAAACCTAATTTTCAAGGGTTTCTTGATGATGATTTC
1 ATGTTTTCAAATGAGTTTTT--AGAAACTAAGCCTGATTTTCAGGGGTTTCTTTATGATGATTTC
6135171 CAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTG
64 CAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTG
* *
6135218 ATGTTTTTAAATGAGTTTTTAGAAACTAAGTCTGATTTTCAGGGGTTT-TTTATGATGATTTCCA
1 ATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTTATGATGATTTCCA
6135282 ATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTG
66 ATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTG
**
6135327 ATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTTTGGGGGTTT-TTTATGATGATTTCC
1 ATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGA-TTTTCAGGGGTTTCTTTATGATGATTTCC
* * * *
6135391 AATGAATTTTTAAAAGAAGTTAAGTCTAATTTTTA-GGGTTT-TTT
65 AATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTG
*
6135435 ATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTTATGATTATTTCCA
1 ATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTTATGATGATTTCCA
* * * *
6135500 AAGAAT-TTTTAAAGAACCTAAGACTAATTTTTAGGGGTTTCTTG
66 ATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTG
6135544 ATG
1 ATG
6135547 ATAATTGAAA
Statistics
Matches: 299, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
107 34 0.11
108 63 0.21
109 104 0.35
110 81 0.27
112 17 0.06
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (110 bp):
ATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTTATGATGATTTCCA
ATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTG
Found at i:6135529 original size:217 final size:220
Alignment explanation
Indices: 6135150--6135546 Score: 649
Period size: 217 Copynumber: 1.8 Consensus size: 220
6135140 TAATTTTCAA
6135150 GGGTTTCTTGATGATGATTTCCAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTC
1 GGGTTTCTTGATGATGATTTCCAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTC
* *
6135215 TTGATGTTTTTAAATGAGTTTTTAGAAACTAAGTCTGATTTTCAGGGGTTTTTTATGATGATTTC
66 TTGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTTTTATGATGATTTC
* * *
6135280 CAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTT
131 CAAAGAATGTTTAAAAGAACCTAAGACTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTT
6135345 TTAGAAACTAAGCCTGATTTTTTGG
196 TTAGAAACTAAGCCTGATTTTTTGG
* * * *
6135370 GGGTTT-TTTATGATGATTTCCAATGAATTTTTAAAAGAAGTTAAGTCTAATTTTTA-GGGTTT-
1 GGGTTTCTTGATGATGATTTCCAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTC
* *
6135432 TTTATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTTATGATTATTT
66 TTGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTT-TTTATGATGATTT
*
6135497 CCAAAGAAT-TTTTAAAGAACCTAAGACTAATTTTTAGGGGTTTCTTGATG
130 CCAAAGAATGTTTAAAAGAACCTAAGACTAATTTTTAGGGGTTTCTTGATG
6135547 ATAATTGAAA
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
217 86 0.52
218 26 0.16
219 46 0.28
220 6 0.04
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (220 bp):
GGGTTTCTTGATGATGATTTCCAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTC
TTGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTTTTATGATGATTTC
CAAAGAATGTTTAAAAGAACCTAAGACTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTT
TTAGAAACTAAGCCTGATTTTTTGG
Found at i:6135676 original size:42 final size:41
Alignment explanation
Indices: 6135614--6135719 Score: 106
Period size: 41 Copynumber: 2.6 Consensus size: 41
6135604 AAGTACGTTG
* * *
6135614 TTCGGGCCAT-CAGTACGTCTTTCAAGCATGATGCTTAAATCC
1 TTCGGGCCATCCA-TAAGTCTTTCAAGCAAGATG-ATAAATCC
* * ** *
6135656 TTCGGGTCATCTATAAGTCTTTTGAGCAAGATGATAAGTCC
1 TTCGGGCCATCCATAAGTCTTTCAAGCAAGATGATAAATCC
*
6135697 TTCGGGCCATCCATAAGACTTTC
1 TTCGGGCCATCCATAAGTCTTTC
6135720 GGGCAGGATG
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 25 0.49
42 25 0.49
43 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (41 bp):
TTCGGGCCATCCATAAGTCTTTCAAGCAAGATGATAAATCC
Found at i:6136176 original size:22 final size:22
Alignment explanation
Indices: 6136146--6136235 Score: 95
Period size: 22 Copynumber: 4.3 Consensus size: 22
6136136 ACCAAATAAA
6136146 ACCCAAACCAAAACCCGAAATAG
1 ACCC-AACCAAAACCCGAAATAG
*
6136169 ACCCAACCAAACCCCGAAATAG
1 ACCCAACCAAAACCCGAAATAG
6136191 ACCCAACC-AAACCC---A-A-
1 ACCCAACCAAAACCCGAAATAG
*
6136207 ACCAAAACCAAAA-CCGAAATAG
1 ACC-CAACCAAAACCCGAAATAG
6136229 ACCCAAC
1 ACCCAAC
6136236 TAAAGCCCAG
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.05
17 7 0.12
18 4 0.07
20 1 0.02
21 9 0.16
22 28 0.50
23 4 0.07
ACGTcount: A:0.51, C:0.39, G:0.07, T:0.03
Consensus pattern (22 bp):
ACCCAACCAAAACCCGAAATAG
Found at i:6137763 original size:15 final size:15
Alignment explanation
Indices: 6137735--6137776 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
6137725 GGTCCTCATA
6137735 TTTA-TGTTTATTATT
1 TTTATTGTTT-TTATT
6137750 TTTATTGTTTTTATT
1 TTTATTGTTTTTATT
6137765 TTTATT-TTTTTA
1 TTTATTGTTTTTA
6137777 AACTAGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.23
15 15 0.58
16 5 0.19
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTATTGTTTTTATT
Found at i:6139301 original size:18 final size:20
Alignment explanation
Indices: 6139265--6139301 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
6139255 CCATTATATT
6139265 AATATCTTTATTAACATTTA
1 AATATCTTTATTAACATTTA
*
6139285 AATAT-TTT-TTAATATTT
1 AATATCTTTATTAACATTT
6139302 TTTAATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 3 0.19
20 5 0.31
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATCTTTATTAACATTTA
Found at i:6146575 original size:22 final size:23
Alignment explanation
Indices: 6146538--6146584 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
6146528 AACCCTAAAT
6146538 AAGCCCAAAAATCGTATCTACTA
1 AAGCCCAAAAATCGTATCTACTA
* *
6146561 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTACTA
6146583 AA
1 AA
6146585 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTACTA
Found at i:6158858 original size:20 final size:20
Alignment explanation
Indices: 6158833--6158878 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
6158823 ATACATCTAG
6158833 GCAGATCCTTTTGAGAGACT
1 GCAGATCCTTTTGAGAGACT
6158853 GCAGATCCTTTTGAGAGACT
1 GCAGATCCTTTTGAGAGACT
6158873 GCAGAT
1 GCAGAT
6158879 TCCTCATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (20 bp):
GCAGATCCTTTTGAGAGACT
Found at i:6158891 original size:24 final size:20
Alignment explanation
Indices: 6158833--6158892 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
6158823 ATACATCTAG
*
6158833 GCAGATCCTTTTGAGAGACT
1 GCAGATCCTTATGAGAGACT
*
6158853 GCAGATCCTTTTGAGAGACT
1 GCAGATCCTTATGAGAGACT
*
6158873 GCAGATTCCTCATGATGAGA
1 GCAGA-TCCTTATGA-GAGA
6158893 AAGCTAATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 25 0.69
21 7 0.19
22 4 0.11
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (20 bp):
GCAGATCCTTATGAGAGACT
Found at i:6160363 original size:20 final size:20
Alignment explanation
Indices: 6160338--6160377 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6160328 AAAAGATATG
* *
6160338 GAATACATACGCCAAGCTCT
1 GAATACACACACCAAGCTCT
*
6160358 GAATACGCACACCAAGCTCT
1 GAATACACACACCAAGCTCT
6160378 TCCTTACTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (20 bp):
GAATACACACACCAAGCTCT
Found at i:6164137 original size:17 final size:14
Alignment explanation
Indices: 6164102--6164131 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6164092 GTTATTAGAT
6164102 AATTATTATTAAAA
1 AATTATTATTAAAA
6164116 AATTATTATTAAAA
1 AATTATTATTAAAA
6164130 AA
1 AA
6164132 CCATTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTATTATTAAAA
Found at i:6164416 original size:83 final size:83
Alignment explanation
Indices: 6164322--6164484 Score: 236
Period size: 83 Copynumber: 2.0 Consensus size: 83
6164312 CCGATAAATG
* * * * *
6164322 TAGTTGTTTGAACATAAAACCCTGAGTAACATTTATTTTTATTACTAAGACAACTTGATAGATTT
1 TAGTTGCTTGAACATAAAACCCTAAGTAACATTTATTTATATCACTAAGACAACTTAATAGATTT
6164387 CTCTAACCACATTTATAT
66 CTCTAACCACATTTATAT
* * * **
6164405 TAGTTGCTTGAACCTAAAACCCTAAGTAACATTTGTTTATATCACTAATACGGCTTAATAGATTT
1 TAGTTGCTTGAACATAAAACCCTAAGTAACATTTATTTATATCACTAAGACAACTTAATAGATTT
6164470 CTCTAACCACATTTA
66 CTCTAACCACATTTA
6164485 AAATATAGCG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (83 bp):
TAGTTGCTTGAACATAAAACCCTAAGTAACATTTATTTATATCACTAAGACAACTTAATAGATTT
CTCTAACCACATTTATAT
Found at i:6164856 original size:16 final size:18
Alignment explanation
Indices: 6164815--6164856 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
6164805 ATTTGGAGGC
*
6164815 TATTTCAAAAAATGTATA
1 TATTTAAAAAAATGTATA
6164833 TATATTAAAAAAAT-TATA
1 TAT-TTAAAAAAATGTATA
6164851 -ATTTAA
1 TATTTAA
6164857 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.18
17 2 0.09
18 7 0.32
19 9 0.41
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
TATTTAAAAAAATGTATA
Found at i:6164861 original size:2 final size:2
Alignment explanation
Indices: 6164856--6164905 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
6164846 TTATAATTTA
6164856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6164898 AT AT AT AT
1 AT AT AT AT
6164906 GTGTGTGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6168130 original size:41 final size:40
Alignment explanation
Indices: 6168009--6168130 Score: 97
Period size: 41 Copynumber: 3.0 Consensus size: 40
6167999 GCCGCTATAG
* * * *
6168009 TACTACTTTATTGTGGTGTTTGTTGAAAAACGTCACTATAGA
1 TACTACTATATTGCGGCGTTTGTTGAAAAACG-CACTA-AAA
* * * *
6168051 TGA--ACCATATTGGGGCATTTGTAT-AAAAACACCACTAAAA
1 T-ACTACTATATTGCGGCGTTTGT-TGAAAAAC-GCACTAAAA
6168091 TACTACTATATTGCGGCGTTTGTTGAAAAACGCAGCTAAA
1 TACTACTATATTGCGGCGTTTGTTGAAAAACGCA-CTAAA
6168131 GTTACCATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
39 1 0.02
40 6 0.10
41 52 0.84
42 2 0.03
43 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (40 bp):
TACTACTATATTGCGGCGTTTGTTGAAAAACGCACTAAAA
Found at i:6170418 original size:19 final size:18
Alignment explanation
Indices: 6170385--6170421 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6170375 TTAACAATTC
6170385 TTTAAAAAACACTCCCCT
1 TTTAAAAAACACTCCCCT
*
6170403 TTTAAAAACACTCTCCCCT
1 TTTAAAAA-ACACTCCCCT
6170422 CTCTCCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (18 bp):
TTTAAAAAACACTCCCCT
Found at i:6171355 original size:19 final size:18
Alignment explanation
Indices: 6171317--6171391 Score: 73
Period size: 19 Copynumber: 4.1 Consensus size: 18
6171307 TTGGACCTGA
*
6171317 AAAATAATTAAATAAAAT
1 AAAATAAATAAATAAAAT
6171335 AAAATAAATAAATAAAGAT
1 AAAATAAATAAATAAA-AT
*
6171354 AAAAATAGA-AAATAAAAAT
1 -AAAATAAATAAAT-AAAAT
*
6171373 AAAAATAGA-AAATAAAAT
1 -AAAATAAATAAATAAAAT
6171391 A
1 A
6171392 TATGTATTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
17 1 0.02
18 20 0.38
19 21 0.40
20 10 0.19
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (18 bp):
AAAATAAATAAATAAAAT
Found at i:6171367 original size:7 final size:6
Alignment explanation
Indices: 6171316--6171389 Score: 71
Period size: 6 Copynumber: 11.7 Consensus size: 6
6171306 CTTGGACCTG
*
6171316 AAAAAT AATTAAAT -AAAAT -AAAAT AAATAAAT AAAGAT AAAAAT AGAAAAT
1 AAAAAT AA--AAAT AAAAAT AAAAAT -AA-AAAT AAAAAT AAAAAT A-AAAAT
6171367 AAAAAT AAAAAT AGAAAAT AAAA
1 AAAAAT AAAAAT A-AAAAT AAAA
6171390 TATATGTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
5 9 0.15
6 26 0.44
7 16 0.27
8 8 0.14
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:6171596 original size:34 final size:34
Alignment explanation
Indices: 6171549--6171631 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 34
6171539 TTTTCCAAAA
6171549 TATGTTTTCAAAAACCA-TTTTTAAAACTATATAT
1 TATGTTTTCAAAAA-CATTTTTTAAAACTATATAT
6171583 TATGTGTTT-AAAAACATGTTTTTTAAAACTATACTA-
1 TATGT-TTTCAAAAACA--TTTTTTAAAACTATA-TAT
6171619 TA--TTTTCAAAAAC
1 TATGTTTTCAAAAAC
6171632 TATATATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
33 5 0.12
34 17 0.40
35 3 0.07
36 16 0.37
37 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (34 bp):
TATGTTTTCAAAAACATTTTTTAAAACTATATAT
Found at i:6175737 original size:21 final size:21
Alignment explanation
Indices: 6175713--6175766 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
6175703 TATCGCAAAT
6175713 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
6175734 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
6175755 TCGCGTTGCGAT
1 TCGCGTTGCGAT
6175767 TTTTCAGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:6175814 original size:22 final size:22
Alignment explanation
Indices: 6175755--6175814 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
6175745 TAGTTGAAAA
6175755 TCGCGTTGCGATTTT-T-CAGT
1 TCGCGTTGCGATTTTCTACAGT
**
6175775 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGATTTTCTACAGT
6175797 T-GTCGTTGCGATTTTCTA
1 TCG-CGTTGCGATTTTCTA
6175815 AATTCGTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 13 0.39
21 2 0.06
22 18 0.55
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.42
Consensus pattern (22 bp):
TCGCGTTGCGATTTTCTACAGT
Found at i:6176526 original size:22 final size:22
Alignment explanation
Indices: 6176501--6176555 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
6176491 TTTTTTTTTA
**
6176501 ACTATCACAATGACAACTGTAG
1 ACTATCACAACAACAACTGTAG
* *
6176523 ACTATCGCAACAATAACTGTAG
1 ACTATCACAACAACAACTGTAG
*
6176545 ACTATCGCAAC
1 ACTATCACAAC
6176556 GAATTTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (22 bp):
ACTATCACAACAACAACTGTAG
Found at i:6176572 original size:19 final size:19
Alignment explanation
Indices: 6176548--6176595 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
6176538 ACTGTAGACT
6176548 ATCGCAACGAATTT-GAAAA
1 ATCGCAACGAATTTAG-AAA
6176567 ATCGCAACGAATTTAGAAA
1 ATCGCAACGAATTTAGAAA
*
6176586 TTCGCAACGA
1 ATCGCAACGA
6176596 CAACTGTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTAGAAA
Found at i:6177365 original size:21 final size:21
Alignment explanation
Indices: 6177321--6177363 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
6177311 TGATAAAAAG
*
6177321 TTATATAAAAAATTATTATTT
1 TTATATAAAAAATTAATATTT
*
6177342 TTAT-TAAAATATTAATATTT
1 TTATATAAAAAATTAATATTT
6177362 TT
1 TT
6177364 TAATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATATAAAAAATTAATATTT
Found at i:6179341 original size:14 final size:14
Alignment explanation
Indices: 6179324--6179352 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6179314 TATTAAAGAG
6179324 ATTAAATTATTTAA
1 ATTAAATTATTTAA
6179338 ATTAAATTATTTAA
1 ATTAAATTATTTAA
6179352 A
1 A
6179353 GACTTGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTAAATTATTTAA
Found at i:6185739 original size:15 final size:15
Alignment explanation
Indices: 6185719--6185749 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6185709 TATTAATATA
6185719 AATAGTAATATATTT
1 AATAGTAATATATTT
*
6185734 AATAGTAATGTATTT
1 AATAGTAATATATTT
6185749 A
1 A
6185750 TAAAAAAAAC
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:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (15 bp):
AATAGTAATATATTT
Found at i:6186166 original size:51 final size:51
Alignment explanation
Indices: 6186112--6186353 Score: 218
Period size: 51 Copynumber: 4.6 Consensus size: 51
6186102 AGATGTACAT
* * * *
6186112 ACTTGCACCGGTGTATGTATGTGTTAAGTAATACACTTTTTTATTTTATTT
1 ACTTACACTGGTGTAAGTATGTGTTAAGTAATACACTTTTTTATTTTATTC
*** *
6186163 ACTTACACCATTGTAAGTATGTGTTAAGTGTTATACTTTTAGCACTTATTTATTTTATTC
1 ACTTACACTGGTGTAAGTATGTGTTAA--G-TA-A----TA-CACTTTTTTATTTTATTC
* * * * *
6186223 ACGTACAGTGGTGT-AGTATGTGTTAAGTGCTATATA-TTTTTTGTTTTATTC
1 ACTTACACTGGTGTAAGTATGTGTTAAGT--AATACACTTTTTTATTTTATTC
* ** *
6186274 ACTTACACTGGTGTAAGTATGTATTAAGTGTTACACTTGTTTATTTTATTC
1 ACTTACACTGGTGTAAGTATGTGTTAAGTAATACACTTTTTTATTTTATTC
6186325 ACTTACACTGGTGTAAGTATGTGTTAAGT
1 ACTTACACTGGTGTAAGTATGTGTTAAGT
6186354 GCTATCTTTT
Statistics
Matches: 154, Mismatches: 24, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
50 3 0.02
51 89 0.58
52 14 0.09
53 3 0.02
54 2 0.01
55 1 0.01
56 1 0.01
57 2 0.01
59 14 0.09
60 25 0.16
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (51 bp):
ACTTACACTGGTGTAAGTATGTGTTAAGTAATACACTTTTTTATTTTATTC
Found at i:6186218 original size:60 final size:59
Alignment explanation
Indices: 6186145--6186256 Score: 143
Period size: 60 Copynumber: 1.9 Consensus size: 59
6186135 TTAAGTAATA
* * * * *
6186145 CACTTTTTTATTTTATTTACTTACACCATTGTAAGTATGTGTTAAGTGTTATACTTTTAG
1 CACTTATTTATTTTATTCACGTACACCAGTGT-AGTATGTGTTAAGTGCTATACTTTTAG
***
6186205 CACTTATTTATTTTATTCACGTACAGTGGTGTAGTATGTGTTAAGTGCTATA
1 CACTTATTTATTTTATTCACGTACACCAGTGTAGTATGTGTTAAGTGCTATA
6186257 TATTTTTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 19 0.43
60 25 0.57
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (59 bp):
CACTTATTTATTTTATTCACGTACACCAGTGTAGTATGTGTTAAGTGCTATACTTTTAG
Found at i:6188090 original size:29 final size:29
Alignment explanation
Indices: 6188002--6188105 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 29
6187992 AAAATTTAAG
* *
6188002 AAAATAAGTAATAACAAAAAGTTAAAG-GACT
1 AAAATAA--AATAACAGAAA-TTTAAGTGACT
* * *
6188033 AAAATGACAAA-AATAGAAACTTAAATGACT
1 AAAAT-A-AAATAACAGAAATTTAAGTGACT
6188063 AAAATAAAATAACAGAAATTTAAGTGACT
1 AAAATAAAATAACAGAAATTTAAGTGACT
6188092 AAAATAAAATAACA
1 AAAATAAAATAACA
6188106 TAAAGTAAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
28 3 0.05
29 34 0.56
30 15 0.25
31 7 0.11
32 1 0.02
33 1 0.02
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.20
Consensus pattern (29 bp):
AAAATAAAATAACAGAAATTTAAGTGACT
Found at i:6188116 original size:29 final size:29
Alignment explanation
Indices: 6188002--6188117 Score: 103
Period size: 29 Copynumber: 3.9 Consensus size: 29
6187992 AAAATTTAAG
*
6188002 AAAATAAGTAATAACAAAAAGTTAAAG-GACT
1 AAAATAA--AATAACAGAAAG-TAAAGTGACT
* *
6188033 AAAATGACAAA-AATAGAAACTTAAA-TGACT
1 AAAAT-A-AAATAACAGAAA-GTAAAGTGACT
* *
6188063 AAAATAAAATAACAGAAATTTAAGTGACT
1 AAAATAAAATAACAGAAAGTAAAGTGACT
*
6188092 AAAATAAAATAACATAAAGTAAAGTG
1 AAAATAAAATAACAGAAAGTAAAGTG
6188118 TCAAAATCAG
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
28 7 0.10
29 36 0.51
30 19 0.27
31 7 0.10
32 1 0.01
33 1 0.01
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.21
Consensus pattern (29 bp):
AAAATAAAATAACAGAAAGTAAAGTGACT
Found at i:6189307 original size:3 final size:3
Alignment explanation
Indices: 6189299--6189335 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
6189289 AGTGGTAAAT
*
6189299 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6189336 CTTTTTCGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:6190036 original size:127 final size:127
Alignment explanation
Indices: 6189530--6190046 Score: 691
Period size: 127 Copynumber: 4.1 Consensus size: 127
6189520 GGGTCGTCTA
* * * * *
6189530 AGGGTGACA-AGACTCCTACGTAATGAGGAGATCTAGTCAGGGGATGACACTGCTCATTTGTTAA
1 AGGGTGACACAG-CTCCTACGTGATGAGGAGATCTGGTCAGGTGATGACACTGCTCATCTGTTCA
* ** ** **
6189594 TGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTAC-GTGATAAGGACGGTTGGTTATCAA
65 TGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCC-ACTCTGATGGGGACGACTGGTTATCTG
* * * * * * *
6189657 ATGTTGAAACGGCTCCTATGTGATGAGGAGATCTGGTCGGGTGATGACATTGCTCATCTGTTCAT
1 AGGGTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGTGATGACACTGCTCATCTGTTCAT
*
6189722 GAGTCTTGGCCATCTAAGGGTGATAACACGGTTCTACTCTGATGGGGACGACTGGTTATCTG
66 GAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGATGGGGACGACTGGTTATCTG
* * * * * * * *
6189784 AAGTTGACACGGCTCCTACGTGATGAAGACATCAGGTCGGGTGATGACATTGCTCATCTGTTCAT
1 AGGGTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGTGATGACACTGCTCATCTGTTCAT
*
6189849 GAGTCTTGGCCATCTAATGGTGATAACACGGTTCCACTCTGATGGGGACGACTGGTTATCTG
66 GAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGATGGGGACGACTGGTTATCTG
*
6189911 AGGGTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGTGATGACACTACTCATCTGTTCAT
1 AGGGTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGTGATGACACTGCTCATCTGTTCAT
* *
6189976 GAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCT-ACTGGGGACGTCTAGTTATCT-
66 GAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGA-TGGGGACGACTGGTTATCTG
6190037 AGGGTGACAC
1 AGGGTGACAC
6190047 TACTCATTTG
Statistics
Matches: 347, Mismatches: 40, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
126 13 0.04
127 333 0.96
128 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (127 bp):
AGGGTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGTGATGACACTGCTCATCTGTTCAT
GAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGATGGGGACGACTGGTTATCTG
Found at i:6190222 original size:37 final size:38
Alignment explanation
Indices: 6190181--6190253 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
6190171 GATTCTTTTA
* * *
6190181 TGTCTCAAATGAGACAA-AATTTATTTTGAGAGAAAAT
1 TGTCTCAAACGAGAAAATAATTTATTTCGAGAGAAAAT
* *
6190218 TGTCTCAAGCGAGAAAATAATTTGTTTCGAGAGAAA
1 TGTCTCAAACGAGAAAATAATTTATTTCGAGAGAAA
6190254 CAACATCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 14 0.47
38 16 0.53
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (38 bp):
TGTCTCAAACGAGAAAATAATTTATTTCGAGAGAAAAT
Found at i:6190381 original size:32 final size:32
Alignment explanation
Indices: 6190333--6190419 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
6190323 TTTGCATCAG
* *
6190333 AATGTTGAATCCCCAAAGATGCCCCAATATTT
1 AATGTTGAATCTCCAAAGATGCCCCAACATTT
* * *
6190365 GATGTTGAATGTCCAAAGATACCCCAACATTT
1 AATGTTGAATCTCCAAAGATGCCCCAACATTT
* *
6190397 AATGTTGAATTTTCAAAGATGCC
1 AATGTTGAATCTCCAAAGATGCC
6190420 TTCATTGTTC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (32 bp):
AATGTTGAATCTCCAAAGATGCCCCAACATTT
Found at i:6191560 original size:19 final size:22
Alignment explanation
Indices: 6191523--6191562 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
6191513 TTTTTGCTTC
6191523 TTTTCTTTTTACTCTTTCGTTG
1 TTTTCTTTTTACTCTTTCGTTG
6191545 TTTT-TTTTT-CTC-TTCGTT
1 TTTTCTTTTTACTCTTTCGTT
6191563 TTGATTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 5 0.28
22 4 0.22
ACGTcount: A:0.03, C:0.17, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTCTTTTTACTCTTTCGTTG
Found at i:6193243 original size:8 final size:8
Alignment explanation
Indices: 6193232--6193371 Score: 67
Period size: 8 Copynumber: 17.8 Consensus size: 8
6193222 ACAAAAAAAT
*
6193232 AAAATATA
1 AAAATAAA
6193240 AAAA-AAA
1 AAAATAAA
6193247 AAAATAAA
1 AAAATAAA
*
6193255 TAAAATAAT
1 -AAAATAAA
**
6193264 AAACCAAA
1 AAAATAAA
*
6193272 AAAA-ATA
1 AAAATAAA
6193279 AAAATAAA
1 AAAATAAA
*
6193287 TAAATAAA
1 AAAATAAA
*
6193295 TAAATAAA
1 AAAATAAA
*
6193303 AAAGTCAAA
1 AAAAT-AAA
**
6193312 AGGA-AAA
1 AAAATAAA
*
6193319 AAATTAATA
1 AAAATAA-A
*
6193328 CAAAATTAA
1 -AAAATAAA
*
6193337 AGAA-AAA
1 AAAATAAA
*
6193344 ATAAT-AA
1 AAAATAAA
6193351 AAAAT-AA
1 AAAATAAA
6193358 AAAATAAA
1 AAAATAAA
*
6193366 ATAATA
1 AAAATA
6193372 TTAATAAAAT
Statistics
Matches: 99, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
7 34 0.34
8 47 0.47
9 13 0.13
10 5 0.05
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:6193262 original size:22 final size:22
Alignment explanation
Indices: 6193224--6193470 Score: 78
Period size: 22 Copynumber: 10.5 Consensus size: 22
6193214 ATCCAAGAAC
*
6193224 AAAAAAAT-AA-AATATAAAAA
1 AAAAAAATAAATAAAATAAAAA
6193244 AAAAAAATAAATAAAATAATAAA
1 AAAAAAATAAATAAAATAA-AAA
**
6193267 CCAAAAA-AAATAAAAATAAATAA
1 AAAAAAATAAAT-AAAATAAA-AA
*
6193290 ATAAATAAATAAA-AAAGTCAAAAGGA
1 A-AAA-AAATAAATAAAAT-AAAA--A
* *
6193316 AAAAAATTAATACAAAATTAAAGAA
1 AAAAAAATAA-ATAAAA-TAAA-AA
*
6193341 AAAATAAT-AA-AAAATAAAAA
1 AAAAAAATAAATAAAATAAAAA
*
6193361 ATAAAATAATATTAATAAAATAGATAA
1 A-AAAA-AATA--AATAAAATA-AAAA
* * *
6193388 ATAGAGATAAATAAAATTTAGTAAAA
1 AAAAAAATAAATAAAA--TA--AAAA
* *
6193414 TAATAATAAT-AATAATAATGAAAA
1 -AA-AAAAATAAATAA-AATAAAAA
* *
6193438 TAAAAAATAAAATAAACT-AAAA
1 AAAAAAAT-AAATAAAATAAAAA
*
6193460 TAAAAAATAAA
1 AAAAAAATAAA
6193471 AATGGTTAAA
Statistics
Matches: 172, Mismatches: 25, Indels: 59
0.67 0.10 0.23
Matches are distributed among these distances:
20 11 0.06
21 12 0.07
22 35 0.20
23 28 0.16
24 22 0.13
25 24 0.14
26 23 0.13
27 12 0.07
28 5 0.03
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (22 bp):
AAAAAAATAAATAAAATAAAAA
Found at i:6193265 original size:32 final size:32
Alignment explanation
Indices: 6193224--6193473 Score: 105
Period size: 32 Copynumber: 7.9 Consensus size: 32
6193214 ATCCAAGAAC
*
6193224 AAAAAAATAAAATATAAAAAAA-AAAAATAAAT
1 AAAATAATAAAA-ATAAAAAAATAAAAATAAAT
*
6193256 AAAATAATAAACCA-AAAAAAATAAAAATAAAT
1 AAAATAATAAA-AATAAAAAAATAAAAATAAAT
* * **
6193288 -AAATAA-ATAAATAAAAAAGTCAAAAGGAAA-
1 AAAATAATAAAAATAAAAAAAT-AAAAATAAAT
* *
6193318 AAAATTAATACAAAAT-TAAAGA-AAAAAT-AAT
1 AAAA-TAATA-AAAATAAAAAAATAAAAATAAAT
* * *
6193349 AAAA-AAT-AAAA-AATAAAAT-AATATTAAT
1 AAAATAATAAAAATAAAAAAATAAAAATAAAT
* * * * * * *
6193377 AAAATAGATAAATAGAGATAAATAAAATTTAGT
1 AAAATA-ATAAAAATAAAAAAATAAAAATAAAT
* * *
6193410 AAAATAATAATAATAATAATAATGAAAATAAAAAAT
1 AAAATAATAAAAATAA-AAAAAT--AAA-AATAAAT
6193446 AAAATAA-ACTAAAAT-AAAAAATAAAAAT
1 AAAATAATA--AAAATAAAAAAATAAAAAT
6193474 GGTTAAATAT
Statistics
Matches: 158, Mismatches: 37, Indels: 46
0.66 0.15 0.19
Matches are distributed among these distances:
27 11 0.07
28 7 0.04
29 5 0.03
30 13 0.08
31 34 0.22
32 37 0.23
33 23 0.15
34 4 0.03
35 9 0.06
36 11 0.07
37 4 0.03
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (32 bp):
AAAATAATAAAAATAAAAAAATAAAAATAAAT
Found at i:6193321 original size:39 final size:38
Alignment explanation
Indices: 6193239--6193379 Score: 95
Period size: 39 Copynumber: 3.5 Consensus size: 38
6193229 AATAAAATAT
* * *
6193239 AAAAAAAAAAAATAAATAAAATAATAAACCAAAAAAAATA
1 AAAATAAATAAATAAAT-AAATAAAAAACCAAAAAAAA-A
* **
6193279 AAAATAAATAAATAAATAAATAAAAAAGTCAAAAGGAAA
1 AAAATAAATAAATAAATAAATAAAAAA-CCAAAAAAAAA
* * * **
6193318 AAAATTAATACAA-AATTAAAGAAAAAATAATAAAAAATAA
1 AAAATAAATA-AATAAATAAATAAAAAACCA-AAAAAA-AA
*
6193358 AAAATAAAATAATATTAATAAA
1 AAAAT-AAATAA-ATAAATAAA
6193380 ATAGATAAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
38 2 0.03
39 35 0.44
40 32 0.41
41 5 0.06
42 5 0.06
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (38 bp):
AAAATAAATAAATAAATAAATAAAAAACCAAAAAAAAA
Found at i:6193366 original size:6 final size:7
Alignment explanation
Indices: 6193225--6193371 Score: 84
Period size: 7 Copynumber: 19.1 Consensus size: 7
6193215 TCCAAGAACA
6193225 AAAAAAT
1 AAAAAAT
*
6193232 AAAATAT
1 AAAAAAT
6193239 AAAAAA-
1 AAAAAAT
6193245 AAAAAAT
1 AAAAAAT
6193252 AAATAAAAT
1 -AA-AAAAT
*
6193261 AATAAACCAA
1 AA-AAA--AT
6193271 AAAAAAT
1 AAAAAAT
6193278 -AAAAAT
1 AAAAAAT
6193284 AAATAAAT
1 AAA-AAAT
6193292 AAATAAAT
1 AAA-AAAT
6193300 AAAAAAGT
1 AAAAAA-T
*
6193308 CAAAAGGAAA
1 -AAAA--AAT
6193318 AAAATTAAT
1 AAAA--AAT
*
6193327 ACAAAATT
1 A-AAAAAT
6193335 AAAGAAA-
1 AAA-AAAT
*
6193342 AAATAAT
1 AAAAAAT
6193349 AAAAAAT
1 AAAAAAT
6193356 AAAAAAT
1 AAAAAAT
6193363 AAAATAAT
1 AAAA-AAT
6193371 A
1 A
6193372 TTAATAAAAT
Statistics
Matches: 113, Mismatches: 12, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
6 14 0.12
7 39 0.35
8 33 0.29
9 19 0.17
10 6 0.05
11 2 0.02
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:6193375 original size:50 final size:49
Alignment explanation
Indices: 6193229--6193403 Score: 125
Period size: 47 Copynumber: 3.6 Consensus size: 49
6193219 AGAACAAAAA
* * **
6193229 AATAAAATATAAA-AAA-AAA-AAATAAATAAAATAATAAACCAAAAAA--
1 AATAAAA-ATAAAGAAATAAATAAATAAA-AAAGTAAAAAAGAAAAAAATT
* * *
6193275 AATAAAAATAAATAAATAAATAAATAAAAAAGTCAAAAGGAAAAAAATT
1 AATAAAAATAAAGAAATAAATAAATAAAAAAGTAAAAAAGAAAAAAATT
*
6193324 AATACAAAATTAAAGAAA-AAAT-AATAAAAAA-TAAAAAATAAAATAATATT
1 AATA-AAAA-TAAAGAAATAAATAAATAAAAAAGTAAAAAAGAAAA-AA-ATT
* *
6193374 AAT-AAAATAGATAAATAGAGATAAATAAAA
1 AATAAAAATAAAGAAATA-A-ATAAATAAAA
6193404 TTTAGTAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
45 5 0.05
46 10 0.10
47 22 0.21
48 21 0.20
49 16 0.15
50 16 0.15
51 14 0.13
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (49 bp):
AATAAAAATAAAGAAATAAATAAATAAAAAAGTAAAAAAGAAAAAAATT
Found at i:6193376 original size:28 final size:27
Alignment explanation
Indices: 6193345--6193472 Score: 70
Period size: 28 Copynumber: 4.6 Consensus size: 27
6193335 AAAGAAAAAA
6193345 TAATAAAAAATAAAAAATAAAATAATAT
1 TAATAAAAAATAAAAAAT-AAATAATAT
*
6193373 TAATAAAATAGATAAATAGAGATAAATAAAAT
1 TAATAAAA-A-ATAAA-A-A-ATAAATAATAT
* * *
6193405 T--TAGTAAAAT-AATAAT-AATAATAA
1 TAATA-AAAAATAAAAAATAAATAATAT
*
6193429 TAAT-GAAAATAAAAAATAAAATAA-ACT
1 TAATAAAAAATAAAAAAT-AAATAATA-T
*
6193456 AAAATAAAAAATAAAAA
1 -TAATAAAAAATAAAAA
6193473 TGGTTAAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 27
0.67 0.09 0.24
Matches are distributed among these distances:
24 12 0.16
25 7 0.09
26 3 0.04
27 5 0.07
28 13 0.17
29 13 0.17
30 8 0.11
31 3 0.04
32 10 0.13
33 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (27 bp):
TAATAAAAAATAAAAAATAAATAATAT
Found at i:6193459 original size:56 final size:54
Alignment explanation
Indices: 6193355--6193460 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 54
6193345 TAATAAAAAA
* * *
6193355 TAAAAAATAAAATAATATTAATAAAATAGATAAATAGAGATAAATAAAATTTAG
1 TAAAAAATAAAATAATAATAATAAAATAGAAAAATAGAAATAAATAAAATTTAG
6193409 TAAAATAATAATAATAATAATAATGAAAATA-AAAAATA-AAATAAACTAAAAT
1 TAAAA-AATAA-AATAATAATAAT-AAAATAGAAAAATAGAAATAAA-TAAAAT
6193461 AAAAAATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
54 5 0.11
55 11 0.24
56 23 0.51
57 6 0.13
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (54 bp):
TAAAAAATAAAATAATAATAATAAAATAGAAAAATAGAAATAAATAAAATTTAG
Found at i:6195421 original size:85 final size:84
Alignment explanation
Indices: 6195275--6195595 Score: 394
Period size: 85 Copynumber: 3.8 Consensus size: 84
6195265 TGTCGTCGAC
* * ** * * *
6195275 CTGAATGGAATCGAACTCGATA-GTGTTTGTTGACAGATAGCTTTTCTCGACTTAAGCTATGCTA
1 CTGAATGTAATCGAACTCGA-AGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTG
*
6195339 TAAATTTGACATGTCC-TTGAG
64 TAAATTTGATATG-CCTTTGAG
* * * *
6195360 CTGAATGTAATCGAACTCGTAGGTATTTATTGACATATAACCCTTCTCGCCTTGAGTTATGCTGT
1 CTGAATGTAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
6195425 AAATTTGATATGCCTTTGAG
65 AAATTTGATATGCCTTTGAG
* * * *
6195445 CTGAATGTAATCGAACTCGAAGGTCTTGGTTGATAGATAACCCTTCTTGCCTTGAGCTATGTTGT
1 CTGAATGTAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
*
6195510 AAATTTGATATGCCTTTGAA
65 AAATTTGATATGCCTTTGAG
* * *
6195530 CTGAATGTAATCGAACTCAAAGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGTTGT
1 CTGAATGTAATCGAACTCGAAGGTTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
6195595 A
65 A
6195596 CTTGGTTGGG
Statistics
Matches: 205, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
84 5 0.02
85 200 0.98
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (84 bp):
CTGAATGTAATCGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTA
AATTTGATATGCCTTTGAG
Found at i:6195911 original size:64 final size:65
Alignment explanation
Indices: 6195724--6195966 Score: 327
Period size: 64 Copynumber: 3.8 Consensus size: 65
6195714 GTGAAGTTGA
* * * *
6195724 GCTTTGAGTTGGATATCCTTCGCTGTGAAGTTGAAATCCAA---GGA-T-TGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
* * * * *
6195784 GTTTTGAGTTGGATATCCTTCATCGTGAAGTTAAAATCCAATCTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
* *
6195849 GCTTTGAGTTGGATATCATTCGTTGTG-ATTTGAAATCCGATCTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
* *
6195913 GCTTTGAGTTAGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGTGTAAGTT
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTT
6195967 GCGTTATTTT
Statistics
Matches: 159, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
60 36 0.23
63 2 0.01
64 61 0.38
65 60 0.38
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (65 bp):
GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
Found at i:6196084 original size:126 final size:126
Alignment explanation
Indices: 6195939--6196173 Score: 404
Period size: 126 Copynumber: 1.9 Consensus size: 126
6195929 CATTCGTTGT
* *
6195939 GAAGTTGAAATCCAATCTTGTGTAAGTTGCGTTATTTT-GAGTCCAATATCCTTTGCTGTGAAGT
1 GAAGTTGAAATCCAATCTTGTGTAAGTTGCATT-TTTTCGAGTCCAATATCCTTCGCTGTGAAGT
6196003 TGAA-ATTGACTCTGAATGAAACTGGAA-AGTTGTTTGTTGACAGACGCTCATTCGTTGTGAAG
65 T-AATATTGACTCTGAATGAAACTGGAACA-TTGTTTGTTGACAGACGCTCATTCGTTGTGAAG
6196065 GAAGTTGAAATCCAATCTTGTGTAAGTTGCATTTTTTCGAGTCCAATATCCTTCGCTGTGAAGTT
1 GAAGTTGAAATCCAATCTTGTGTAAGTTGCATTTTTTCGAGTCCAATATCCTTCGCTGTGAAGTT
6196130 AATATTGACTCTGAATGAAACTGGAACATTGTTTGTTGACAGAC
66 AATATTGACTCTGAATGAAACTGGAACATTGTTTGTTGACAGAC
6196174 AGTTTTTCTC
Statistics
Matches: 104, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
125 6 0.06
126 97 0.93
127 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (126 bp):
GAAGTTGAAATCCAATCTTGTGTAAGTTGCATTTTTTCGAGTCCAATATCCTTCGCTGTGAAGTT
AATATTGACTCTGAATGAAACTGGAACATTGTTTGTTGACAGACGCTCATTCGTTGTGAAG
Found at i:6197864 original size:19 final size:16
Alignment explanation
Indices: 6197833--6197916 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 16
6197823 TTTTCTTCGC
* *
6197833 TTTTTCCTTTATTTTT
1 TTTTTTCTTTTTTTTT
* *
6197849 GTTTATCTTTTTTATTT
1 TTTTTTCTTTTTT-TTT
6197866 TCTCTTTTCTTTTTCTTTGTT
1 T-T-TTTTC-TTTT-TTT-TT
6197887 TTTTTTCTTTTTTTCTT
1 TTTTTTCTTTTTTT-TT
6197904 TTTTTCTCTTTTT
1 TTTTT-TCTTTTT
6197917 GTTCTGATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
16 9 0.17
17 13 0.24
18 12 0.22
19 9 0.17
20 6 0.11
21 5 0.09
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTT
Found at i:6197873 original size:7 final size:6
Alignment explanation
Indices: 6197844--6197916 Score: 53
Period size: 6 Copynumber: 11.8 Consensus size: 6
6197834 TTTTCCTTTA
* * *
6197844 TTTTTG TTTATC TTTTT- TATTTTC TCTTTTC TTTTTC TTTGTTT TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC T-TTTTC TTTTTC TTT-TTC TTTTTC
6197894 TTTTT- TTCTTT- TTTTCTC TTTTT
1 TTTTTC TT-TTTC TTTT-TC TTTTT
6197917 GTTCTGATTG
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
5 5 0.09
6 34 0.62
7 16 0.29
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:6197873 original size:13 final size:11
Alignment explanation
Indices: 6197844--6197908 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 11
6197834 TTTTCCTTTA
*
6197844 TTTTTGTTTATC
1 TTTTT-TTTTTC
6197856 TTTTTTATTTTC
1 TTTTTT-TTTTC
6197868 TCTTTTCTTTTTC
1 T-TTTT-TTTTTC
*
6197881 TTTGTTTTTT-
1 TTTTTTTTTTC
*
6197891 TTCTTTTTTTC
1 TTTTTTTTTTC
6197902 TTTTTTT
1 TTTTTTT
6197909 CTCTTTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
10 8 0.18
11 12 0.27
12 13 0.30
13 10 0.23
14 1 0.02
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:6197873 original size:25 final size:26
Alignment explanation
Indices: 6197845--6197904 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
6197835 TTTCCTTTAT
*
6197845 TTTTGTTTATCTTT-TTTATTTTCTC
1 TTTTCTTTATCTTTGTTTATTTTCTC
* * *
6197870 TTTTCTTTTTCTTTGTTTTTTTTCTTT
1 TTTTCTTTATCTTTGTTTATTTTC-TC
6197897 TTTTCTTT
1 TTTTCTTT
6197905 TTTTCTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 12 0.41
26 8 0.28
27 9 0.31
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (26 bp):
TTTTCTTTATCTTTGTTTATTTTCTC
Found at i:6197880 original size:42 final size:42
Alignment explanation
Indices: 6197832--6197915 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
6197822 TTTTTCTTCG
6197832 CTTTTTCCTTTATTTTTGTTT-ATCTTTT-TTATTTTCTCTTTT
1 CTTTTT-CTTTATTTTT-TTTCATCTTTTCTTATTTTCTCTTTT
* * * *
6197874 CTTTTTCTTTGTTTTTTTTCTTTTTTTCTTTTTTTCTCTTTT
1 CTTTTTCTTTATTTTTTTTCATCTTTTCTTATTTTCTCTTTT
6197916 TGTTCTGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 3 0.08
41 14 0.39
42 19 0.53
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (42 bp):
CTTTTTCTTTATTTTTTTTCATCTTTTCTTATTTTCTCTTTT
Found at i:6197899 original size:8 final size:8
Alignment explanation
Indices: 6197886--6197916 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
6197876 TTTTCTTTGT
6197886 TTTTTTTC
1 TTTTTTTC
6197894 TTTTTTTC
1 TTTTTTTC
6197902 TTTTTTTC
1 TTTTTTTC
*
6197910 TCTTTTT
1 TTTTTTT
6197917 GTTCTGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:6197915 original size:27 final size:27
Alignment explanation
Indices: 6197870--6197921 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
6197860 TTATTTTCTC
* *
6197870 TTTTCTTTTTCTTTGTTTTTTTTCTTT
1 TTTTCTTTTTCTTTCTTTTTGTTCTTT
6197897 TTTTCTTTTT-TTCTCTTTTTGTTCT
1 TTTTCTTTTTCTT-TCTTTTTGTTCT
6197922 GATTGGATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (27 bp):
TTTTCTTTTTCTTTCTTTTTGTTCTTT
Found at i:6197916 original size:11 final size:10
Alignment explanation
Indices: 6197858--6197916 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
6197848 TGTTTATCTT
6197858 TTTTATTTTCTC
1 TTTT-TTTT-TC
6197870 TTTTCTTTTTC
1 TTTT-TTTTTC
6197881 TTTGTTTTTT-
1 TTT-TTTTTTC
6197891 TTCTTTTTTTC
1 TT-TTTTTTTC
*
6197902 TTTTTTTCTC
1 TTTTTTTTTC
6197912 TTTTT
1 TTTTT
6197917 GTTCTGATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 20 0.48
11 13 0.31
12 9 0.21
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:6200886 original size:13 final size:13
Alignment explanation
Indices: 6200870--6200899 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6200860 TTTAATTGCG
6200870 AAAATTAAAAATT
1 AAAATTAAAAATT
*
6200883 AAAATTAAAATTT
1 AAAATTAAAAATT
6200896 AAAA
1 AAAA
6200900 ACCCGATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:6201128 original size:11 final size:12
Alignment explanation
Indices: 6201114--6201247 Score: 56
Period size: 12 Copynumber: 9.8 Consensus size: 12
6201104 AATTAAAGAC
*
6201114 AAATAACAAA-A
1 AAATAAAAAATA
6201125 AAATAAAAAATA
1 AAATAAAAAATA
*
6201137 AAATAATAATATTA
1 AAATAA-AA-AATA
6201151 AAATAAATAAAATAGA
1 AAAT-AA-AAAAT--A
6201167 TAAATAGAGATAAATA
1 -AAATA-A-A-AAATA
*
6201183 AAATTTAGTAAAATA
1 AAA--TA-AAAAATA
6201198 ATAATAATAATAATGA
1 A-AATAA-AA-AAT-A
6201214 AAATAAAAAATA
1 AAATAAAAAATA
6201226 AAATAAAATAA-A
1 AAATAAAA-AATA
6201238 AAATGAAAAA
1 AAAT-AAAAA
6201248 GGGTTAAATA
Statistics
Matches: 100, Mismatches: 6, Indels: 33
0.72 0.04 0.24
Matches are distributed among these distances:
11 9 0.09
12 22 0.22
13 11 0.11
14 15 0.15
15 22 0.22
16 8 0.08
17 9 0.09
18 4 0.04
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:6201158 original size:23 final size:23
Alignment explanation
Indices: 6201132--6201186 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
6201122 AAAAAATAAA
6201132 AAATAAAATA-ATAATATTA-AAAT
1 AAATAAAATAGATAA-A-TAGAAAT
*
6201155 AAATAAAATAGATAAATAGAGAT
1 AAATAAAATAGATAAATAGAAAT
6201178 AAATAAAAT
1 AAATAAAAT
6201187 TTAGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 23 0.79
24 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (23 bp):
AAATAAAATAGATAAATAGAAAT
Found at i:6201225 original size:53 final size:55
Alignment explanation
Indices: 6201135--6201238 Score: 126
Period size: 53 Copynumber: 1.9 Consensus size: 55
6201125 AAATAAAAAA
* *
6201135 TAAAATAATAATATTAAAATAAATAAAATAGATAAATAGAGAT-AAATAAAATTTAG
1 TAAAATAATAATA-TAAAATAAATAAAATAGAAAAATA-AAATAAAATAAAATTTAG
*
6201191 TAAAATAATAATA-ATAAT-AATGAAAATA-AAAAATAAAATAAAATAAAA
1 TAAAATAATAATATAAAATAAAT-AAAATAGAAAAATAAAATAAAATAAAA
6201239 AATGAAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
52 3 0.07
53 17 0.40
54 10 0.23
56 13 0.30
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (55 bp):
TAAAATAATAATATAAAATAAATAAAATAGAAAAATAAAATAAAATAAAATTTAG
Found at i:6201297 original size:4 final size:4
Alignment explanation
Indices: 6201288--6201314 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6201278 AATGTTACGA
6201288 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
6201315 AGGGATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:6204346 original size:37 final size:37
Alignment explanation
Indices: 6204296--6204367 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
6204286 GGTGGCATGG
6204296 ATAACGGTTACTGATGTGGTTTGTCACTCCAAAACAA
1 ATAACGGTTACTGATGTGGTTTGTCACTCCAAAACAA
6204333 ATAACGGTTACTGATGTGGTTTGTCACTCCAAAAC
1 ATAACGGTTACTGATGTGGTTTGTCACTCCAAAAC
6204368 GATTTTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (37 bp):
ATAACGGTTACTGATGTGGTTTGTCACTCCAAAACAA
Found at i:6214678 original size:128 final size:128
Alignment explanation
Indices: 6214450--6214712 Score: 508
Period size: 128 Copynumber: 2.0 Consensus size: 128
6214440 CCGTCTGTAA
*
6214450 TTAAGGCTACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
1 TTAAGGCCACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
6214515 GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
66 GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
6214578 TTAAGGCCACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
1 TTAAGGCCACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
6214643 GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
66 GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
6214706 TCTAAGG
1 T-TAAGG
6214713 AAATATGGGA
Statistics
Matches: 133, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
128 128 0.96
129 5 0.04
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.38
Consensus pattern (128 bp):
TTAAGGCCACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
Found at i:6221755 original size:12 final size:12
Alignment explanation
Indices: 6221738--6221762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6221728 TCAGTTTGGC
6221738 ATTGTTTTTTAA
1 ATTGTTTTTTAA
6221750 ATTGTTTTTTAA
1 ATTGTTTTTTAA
6221762 A
1 A
6221763 AGTTCGATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
ATTGTTTTTTAA
Found at i:6224291 original size:22 final size:20
Alignment explanation
Indices: 6224241--6224312 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 20
6224231 GTAAAAATGA
6224241 TATCGATACCAT-G-ATAGGG
1 TATCGATACCATAGTA-AGGG
*
6224260 TATC-AGTACCATAGTATGGTAG
1 TATCGA-TACCATAGTAAGG--G
*
6224282 TATCGATACCATGGTAAGGG
1 TATCGATACCATAGTAAGGG
6224302 TATCGATACCA
1 TATCGATACCA
6224313 GGAAACATCG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.02
19 10 0.23
20 15 0.34
21 1 0.02
22 16 0.36
23 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (20 bp):
TATCGATACCATAGTAAGGG
Found at i:6224868 original size:27 final size:27
Alignment explanation
Indices: 6224830--6224897 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
6224820 ATGCATTAAG
*
6224830 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATGCCATAATTGAAAAT
6224857 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCCATAATTGAAAAT
*
6224884 CCATGAAAGGATGC
1 GCATGAAAGGATGC
6224898 ATTAAGGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.22
Consensus pattern (27 bp):
GCATGAAAGGATGCCATAATTGAAAAT
Found at i:6224908 original size:47 final size:47
Alignment explanation
Indices: 6224857--6225131 Score: 401
Period size: 47 Copynumber: 5.9 Consensus size: 47
6224847 AATTGAAAAT
* *
6224857 GCATGAAAGGATGCCATAATTGAAAATCCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATGCATTAAG
* * *
6224904 GCATGAAAAGATGTCATAATTGAAAATGCATGAAAGGATACATAAAG
1 GCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATGCATTAAG
* * *
6224951 GCATGAAAGGATGTCATAATTTAAAATGCATGAAAGGGTGCATTACG
1 GCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATGCATTAAG
* * * * *
6224998 ACATGAAATGATGCCATAATTTAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATGCATTAAG
6225045 GCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATGCATTAAG
6225092 GCATGAAAGGATGTCATAAGTT-AAAATGCAT-AAATGGATG
1 GCATGAAAGGATGTCATAA-TTGAAAATGCATGAAA-GGATG
6225132 TGTTAATACG
Statistics
Matches: 204, Mismatches: 22, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
46 3 0.01
47 199 0.98
48 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (47 bp):
GCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATGCATTAAG
Found at i:6224918 original size:74 final size:74
Alignment explanation
Indices: 6224797--6225085 Score: 318
Period size: 74 Copynumber: 4.0 Consensus size: 74
6224787 AAATCGAATT
6224797 CATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAATGCATG
1 CATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAATGCATG
6224862 AAAGGATGC
66 AAAGGATGC
* * *
6224871 CATAATTGAAAATCCATGAAAGGATGCATTAAGGCATGAAAAGATGTCATAATTGAAAATGCATG
1 CATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAATGCATG
6224936 AAAGGAT--
66 AAAGGATGC
* * * * **
6224943 -A-CA--T-AAAGGCATGAAAGGATGTCATAATTTAAAATGCATGAAAGGGTG-C---ATT-ACG
1 CATAATTTAAAATGCATGAAAGGATG-C---A-TT--AAGGCATGAAAGGATGTCATAATTGAAA
*
6224998 A--CATGAAATGATGC
59 ATGCATGAAAGGATGC
*
6225012 CATAATTTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAATGCATG
1 CATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAATGCATG
6225077 AAAGGATGC
66 AAAGGATGC
6225086 ATTAAGGCAT
Statistics
Matches: 173, Mismatches: 21, Indels: 42
0.73 0.09 0.18
Matches are distributed among these distances:
67 39 0.23
68 2 0.01
69 4 0.02
70 6 0.03
71 6 0.03
72 4 0.02
73 3 0.02
74 109 0.63
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (74 bp):
CATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAATGCATG
AAAGGATGC
Found at i:6224936 original size:27 final size:26
Alignment explanation
Indices: 6224830--6225122 Score: 117
Period size: 27 Copynumber: 12.2 Consensus size: 26
6224820 ATGCATTAAG
*
6224830 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAAGATGTCATAATT-AAAAT
* *
6224857 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAAGATGTCATAATT-AAAAT
* * *
6224884 CCATGAAAGGATG-C---ATT--AAG
1 GCATGAAAAGATGTCATAATTAAAAT
6224904 GCATGAAAAGATGTCATAATTGAAAAT
1 GCATGAAAAGATGTCATAATT-AAAAT
*
6224931 GCATG-AAAG--G--ATACA-T-AAAG
1 GCATGAAAAGATGTCATA-ATTAAAAT
*
6224951 GCATGAAAGGATGTCATAATTTAAAAT
1 GCATGAAAAGATGTCATAA-TTAAAAT
* * **
6224978 GCATGAAAGGGTG-C---ATTACGA-
1 GCATGAAAAGATGTCATAATTAAAAT
* *
6224999 -CATGAAATGATGCCATAATTTAAAAT
1 GCATGAAAAGATGTCATAA-TTAAAAT
* *
6225025 GCATGAAATGATG-C---ATT--AAG
1 GCATGAAAAGATGTCATAATTAAAAT
*
6225045 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAAGATGTCATAATT-AAAAT
* *
6225072 GCATGAAAGGATG-C---ATT--AAG
1 GCATGAAAAGATGTCATAATTAAAAT
*
6225092 GCATGAAAGGATGTCATAAGTTAAAAT
1 GCATGAAAAGATGTCATAA-TTAAAAT
6225119 GCAT
1 GCAT
6225123 AAATGGATGT
Statistics
Matches: 208, Mismatches: 21, Indels: 74
0.69 0.07 0.24
Matches are distributed among these distances:
20 60 0.29
21 7 0.03
22 10 0.05
23 10 0.05
24 10 0.05
25 9 0.04
26 9 0.04
27 93 0.45
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (26 bp):
GCATGAAAAGATGTCATAATTAAAAT
Found at i:6225064 original size:141 final size:141
Alignment explanation
Indices: 6224858--6225122 Score: 458
Period size: 141 Copynumber: 1.9 Consensus size: 141
6224848 ATTGAAAATG
6224858 CATGAAAGGATGCCATAATTGAAAATCCATGAAAGGATGCATTAAGGCATGAAAAGATGTCATAA
1 CATGAAAGGATGCCATAATTGAAAATCCATGAAAGGATGCATTAAGGCATGAAAAGATGTCATAA
*
6224923 TTGAAAATGCATGAAAGGATACATAAAGGCATGAAAGGATGTCATAATTTAAAATGCATGAAAGG
66 TTGAAAATGCATGAAAGGATACATAAAGGCATGAAAGGATGTCATAAGTTAAAATGCATGAAAGG
6224988 GTGCATTACGA
131 GTGCATTACGA
* * * * *
6224999 CATGAAATGATGCCATAATTTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAA
1 CATGAAAGGATGCCATAATTGAAAATCCATGAAAGGATGCATTAAGGCATGAAAAGATGTCATAA
* *
6225064 TTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAAGTTAAAATGCAT
66 TTGAAAATGCATGAAAGGATACATAAAGGCATGAAAGGATGTCATAAGTTAAAATGCAT
6225123 AAATGGATGT
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 116 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (141 bp):
CATGAAAGGATGCCATAATTGAAAATCCATGAAAGGATGCATTAAGGCATGAAAAGATGTCATAA
TTGAAAATGCATGAAAGGATACATAAAGGCATGAAAGGATGTCATAAGTTAAAATGCATGAAAGG
GTGCATTACGA
Found at i:6225111 original size:20 final size:20
Alignment explanation
Indices: 6224885--6225104 Score: 80
Period size: 20 Copynumber: 9.6 Consensus size: 20
6224875 ATTGAAAATC
6224885 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
* *
6224905 CATGAAAAGATGTCATAATTGAAAATG
1 CATGAAAGGATG-C---ATT---AAGG
* *
6224932 CATGAAAGGATACATAAAGG
1 CATGAAAGGATGCATTAAGG
*
6224952 CATGAAAGGATGTCATAATTTAAAATG
1 CATGAAAGGATG-C---A-TT--AAGG
* * *
6224979 CATGAAAGGGTGCATTACGA
1 CATGAAAGGATGCATTAAGG
* *
6224999 CATGAAATGATGCCATAATTTAAAATG
1 CATGAAAGGATG-C---A-TT--AAGG
*
6225026 CATGAAATGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
6225046 CATGAAAGGATGTCATAATTGAAAATG
1 CATGAAAGGATG-C---ATT---AAGG
6225073 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
6225093 CATGAAAGGATG
1 CATGAAAGGATG
6225105 TCATAAGTTA
Statistics
Matches: 150, Mismatches: 22, Indels: 56
0.66 0.10 0.25
Matches are distributed among these distances:
20 65 0.43
21 4 0.03
22 4 0.03
23 7 0.05
24 8 0.05
25 3 0.02
26 4 0.03
27 55 0.37
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGG
Found at i:6231151 original size:28 final size:28
Alignment explanation
Indices: 6231111--6231171 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
6231101 GTTTTTCCCT
6231111 ATTATTGTTCTTTTGCATTATCTAACAC
1 ATTATTGTTCTTTTGCATTATCTAACAC
*
6231139 ATTATTGTTCTTTTTCATTATCTAACAC
1 ATTATTGTTCTTTTGCATTATCTAACAC
6231167 ATTAT
1 ATTAT
6231172 CTAACTCTTT
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:0.26, C:0.16, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTATTGTTCTTTTGCATTATCTAACAC
Found at i:6237206 original size:47 final size:48
Alignment explanation
Indices: 6237132--6237273 Score: 216
Period size: 47 Copynumber: 3.0 Consensus size: 48
6237122 TAAATCGAAA
* *
6237132 TCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
*
6237180 T-ATAATTGAAATTGCATGAAATGATGCATTAAGGCATGAAAGGATG-
1 TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
* * *
6237226 TCATAATTGAAAACGCATGAAATGATGCATTTAGGCATGAAATGATGC
1 TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
6237274 ATTTAGGCAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 1 0.01
47 83 0.98
48 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.26
Consensus pattern (48 bp):
TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
Found at i:6237311 original size:27 final size:26
Alignment explanation
Indices: 6237280--6237451 Score: 101
Period size: 27 Copynumber: 7.2 Consensus size: 26
6237270 ATGCATTTAG
6237280 GCATGAAAGGATGCCATAATTTAAAAT
1 GCATGAAAGGATG-CATAATTTAAAAT
*
6237307 GCATGAAAGGATGC----TTT--AAG
1 GCATGAAAGGATGCATAATTTAAAAT
* *
6237327 GCATGAAAAGATGTCATAATTAAAAAT
1 GCATGAAAGGATG-CATAATTTAAAAT
* *
6237354 GCATGAAATGATGC---A-TT--AAG
1 GCATGAAAGGATGCATAATTTAAAAT
*
6237374 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATG-CATAATTTAAAAT
* *
6237401 GCATGAAAGGAT--A-CA-TT--AAG
1 GCATGAAAGGATGCATAATTTAAAAT
*
6237421 GCATGAAAGGATGTCATAAATTAAAAT
1 GCATGAAAGGATG-CATAATTTAAAAT
6237448 GCAT
1 GCAT
6237452 AAATGAATAT
Statistics
Matches: 109, Mismatches: 15, Indels: 42
0.66 0.09 0.25
Matches are distributed among these distances:
20 42 0.39
21 2 0.02
22 5 0.05
23 3 0.03
24 3 0.03
25 5 0.05
26 2 0.02
27 47 0.43
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (26 bp):
GCATGAAAGGATGCATAATTTAAAAT
Found at i:6237311 original size:47 final size:47
Alignment explanation
Indices: 6237260--6237457 Score: 299
Period size: 47 Copynumber: 4.2 Consensus size: 47
6237250 ATGCATTTAG
* *
6237260 GCATGAAATGATGCATTTAGGCATGAAAGGATGCCATAATTTAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTTAAAAT
* * * *
6237307 GCATGAAAGGATGCTTTAAGGCATGAAAAGATGTCATAATTAAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTTAAAAT
*
6237354 GCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTTAAAAT
* * *
6237401 GCATGAAAGGATACATTAAGGCATGAAAGGATGTCATAAATTAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTTAAAAT
6237448 GCAT-AAATGA
1 GCATGAAATGA
6237458 ATATGTTAAT
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
46 5 0.04
47 131 0.96
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (47 bp):
GCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTTAAAAT
Found at i:6237311 original size:94 final size:90
Alignment explanation
Indices: 6237237--6237438 Score: 257
Period size: 94 Copynumber: 2.2 Consensus size: 90
6237227 CATAATTGAA
* *
6237237 AACGCATGAAATGATG-CAT-TT-AGGCATGAAATGATGCATTTAGGCATGAAAGGATGCCATAA
1 AACGCATGAAAAGATGTCATATTAAGGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAA
*
6237299 TTTAAAATGCATGAAAGGATGCTTT
66 TTGAAAATGCATGAAAGGATGCTTT
* * *
6237324 AAGGCATGAAAAGATGTCATAATTAAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTC
1 AACGCATGAAAAGATGTCAT-ATT---AAGGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* *
6237389 ATAATTGAAAATGCATGAAAGGATACATT
62 ATAATTGAAAATGCATGAAAGGATGCTTT
* *
6237418 AAGGCATGAAAGGATGTCATA
1 AACGCATGAAAAGATGTCATA
6237439 AATTAAAATG
Statistics
Matches: 99, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
87 14 0.14
88 3 0.03
90 2 0.02
93 1 0.01
94 79 0.80
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (90 bp):
AACGCATGAAAAGATGTCATATTAAGGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAA
TTGAAAATGCATGAAAGGATGCTTT
Found at i:6237346 original size:114 final size:114
Alignment explanation
Indices: 6237146--6237386 Score: 383
Period size: 114 Copynumber: 2.1 Consensus size: 114
6237136 AATTAAAAAT
* * *
6237146 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAATTGAAATTGCATGAAATGATGCATTA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTA
* * *
6237211 AGGCATGAAAGGATGTCATAATTGAAAACGCATGAAATGATGCATTTAG
66 AGGCATGAAAAGATGTCATAATTAAAAACGCATGAAATGATGCATTAAG
* * * *
6237260 GCATGAAATGATGCATTTAGGCATGAAAGGATGCCATAATTTAAAATGCATGAAAGGATGCTTTA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTA
*
6237325 AGGCATGAAAAGATGTCATAATTAAAAATGCATGAAATGATGCATTAAG
66 AGGCATGAAAAGATGTCATAATTAAAAACGCATGAAATGATGCATTAAG
6237374 GCATGAAAGGATG
1 GCATGAAAGGATG
6237387 TCATAATTGA
Statistics
Matches: 115, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (114 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTA
AGGCATGAAAAGATGTCATAATTAAAAACGCATGAAATGATGCATTAAG
Found at i:6237359 original size:161 final size:161
Alignment explanation
Indices: 6237133--6237433 Score: 496
Period size: 161 Copynumber: 1.9 Consensus size: 161
6237123 AAATCGAAAT
* * *
6237133 CATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAATTGAAATTGCATG
1 CATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCTATAATTAAAAATGCATG
* * *
6237198 AAATGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAACGCATGAAATGATGCATTTAGGCA
66 AAATGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAACGCATGAAAGGATACATTAAGGCA
*
6237263 TGAAATGATGCATTTAGGCATGAAAGGATGC
131 TGAAAGGATGCATTTAGGCATGAAAGGATGC
* *
6237294 CATAATTTAAAATGCATGAAAGGATGCTTTAAGGCATGAAAAGATG-TCATAATTAAAAATGCAT
1 CATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCT-ATAATTAAAAATGCAT
*
6237358 GAAATGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATACATTAAGGC
65 GAAATGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAACGCATGAAAGGATACATTAAGGC
6237423 ATGAAAGGATG
130 ATGAAAGGATG
6237434 TCATAAATTA
Statistics
Matches: 129, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
160 1 0.01
161 128 0.99
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (161 bp):
CATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCTATAATTAAAAATGCATG
AAATGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAACGCATGAAAGGATACATTAAGGCA
TGAAAGGATGCATTTAGGCATGAAAGGATGC
Found at i:6240324 original size:13 final size:13
Alignment explanation
Indices: 6240306--6240330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6240296 AGTCAGTCAA
6240306 CATAATCAATATT
1 CATAATCAATATT
6240319 CATAATCAATAT
1 CATAATCAATAT
6240331 GCAATAGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAATCAATATT
Found at i:6242482 original size:20 final size:21
Alignment explanation
Indices: 6242435--6242487 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
6242425 ATTGTATGAA
*
6242435 TAGTATCGATACTCATTCAAG
1 TAGTATCGATACTCATGCAAG
* *
6242456 CAGTATCGATACT-ATGCTAG
1 TAGTATCGATACTCATGCAAG
6242476 TAGTATCGATAC
1 TAGTATCGATAC
6242488 CTAGTAAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (21 bp):
TAGTATCGATACTCATGCAAG
Found at i:6248256 original size:24 final size:23
Alignment explanation
Indices: 6248229--6248307 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
6248219 CTGTCCAGGG
*
6248229 AGTATCGATACTACTTTGTGCAGT
1 AGTATCGATACTAC-TTGTACAGT
*
6248253 AGTATCGATAC--C--GTCCAGT
1 AGTATCGATACTACTTGTACAGT
*
6248272 GAGTATCGATACTACTATGTAAAGT
1 -AGTATCGATACTACT-TGTACAGT
6248297 AGTATCGATAC
1 AGTATCGATAC
6248308 CTAACATGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 6 0.13
20 11 0.24
22 2 0.04
24 22 0.48
25 5 0.11
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (23 bp):
AGTATCGATACTACTTGTACAGT
Found at i:6248261 original size:44 final size:44
Alignment explanation
Indices: 6248210--6248308 Score: 153
Period size: 44 Copynumber: 2.2 Consensus size: 44
6248200 GCAAACCAAC
* * **
6248210 GTATCGATACTGTCCAGGGAGTATCGATACTACTTTGTGCAGTA
1 GTATCGATACCGTCCAGGGAGTATCGATACTACTATGTAAAGTA
*
6248254 GTATCGATACCGTCCAGTGAGTATCGATACTACTATGTAAAGTA
1 GTATCGATACCGTCCAGGGAGTATCGATACTACTATGTAAAGTA
6248298 GTATCGATACC
1 GTATCGATACC
6248309 TAACATGGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
GTATCGATACCGTCCAGGGAGTATCGATACTACTATGTAAAGTA
Found at i:6248278 original size:20 final size:20
Alignment explanation
Indices: 6248210--6248283 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
6248200 GCAAACCAAC
* *
6248210 GTATCGATACTGTCCAGGGA
1 GTATCGATACCGTCCAGTGA
*
6248230 GTATCGATACTACTTTGTGCAGT-A
1 GTATCGATAC--C---GTCCAGTGA
6248254 GTATCGATACCGTCCAGTGA
1 GTATCGATACCGTCCAGTGA
6248274 GTATCGATAC
1 GTATCGATAC
6248284 TACTATGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
19 6 0.14
20 21 0.48
22 1 0.02
24 11 0.25
25 5 0.11
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (20 bp):
GTATCGATACCGTCCAGTGA
Found at i:6262579 original size:18 final size:18
Alignment explanation
Indices: 6262541--6262580 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6262531 GCCCTCCATT
**
6262541 TTCTTTGCCACCTTTTGA
1 TTCTTTGCCACCTTTAAA
*
6262559 TTCTTTGCCGCCTTTAAA
1 TTCTTTGCCACCTTTAAA
6262577 TTCT
1 TTCT
6262581 CCTCCTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.28, G:0.10, T:0.50
Consensus pattern (18 bp):
TTCTTTGCCACCTTTAAA
Found at i:6262783 original size:60 final size:60
Alignment explanation
Indices: 6262690--6262873 Score: 199
Period size: 60 Copynumber: 3.1 Consensus size: 60
6262680 CCACCAGGCG
* * * *
6262690 CACCCGGAAACC-CGAATCCACCTGTGACAGTTCCAAACCCACCTGGCATTTTTCCAAGCC
1 CACCC-GAAACCACGAATCCACCTGTAATAGTTCCAAACCCACCTAGTATTTTTCCAAGCC
* * * * * *
6262750 CACCCGGAACTATGAATCCACCTGCAATAGTTCCGAACCCACCTAGTACTTTTCCAAGCC
1 CACCCGAAACCACGAATCCACCTGTAATAGTTCCAAACCCACCTAGTATTTTTCCAAGCC
* * * * * * *
6262810 CGCCCGAAACCCCGAATCCGCCGGTAATAATTCCAAACCCACCTAGTGTTTTACCAAGCC
1 CACCCGAAACCACGAATCCACCTGTAATAGTTCCAAACCCACCTAGTATTTTTCCAAGCC
6262870 CACC
1 CACC
6262874 ACAAGCAATA
Statistics
Matches: 99, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
59 4 0.04
60 95 0.96
ACGTcount: A:0.28, C:0.39, G:0.14, T:0.19
Consensus pattern (60 bp):
CACCCGAAACCACGAATCCACCTGTAATAGTTCCAAACCCACCTAGTATTTTTCCAAGCC
Found at i:6275151 original size:21 final size:22
Alignment explanation
Indices: 6275127--6275170 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6275117 GATTACAAAG
*
6275127 AGGGTACCGAT-TCCCTGCTAC
1 AGGGTACCGATACCCCTGCTAC
*
6275148 AGGGTATCGATACCCCTGCTAC
1 AGGGTACCGATACCCCTGCTAC
6275170 A
1 A
6275171 ATACTGCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.23
Consensus pattern (22 bp):
AGGGTACCGATACCCCTGCTAC
Found at i:6278425 original size:24 final size:24
Alignment explanation
Indices: 6278393--6278438 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
6278383 TAGTGGTCTT
6278393 CTAGAAGCGGGTTAACCTAACCTG
1 CTAGAAGCGGGTTAACCTAACCTG
6278417 CTAGAAGCGGGTTAACCTAACC
1 CTAGAAGCGGGTTAACCTAACC
6278439 AGCTGACCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (24 bp):
CTAGAAGCGGGTTAACCTAACCTG
Found at i:6279667 original size:2 final size:2
Alignment explanation
Indices: 6279660--6279704 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
6279650 TCTGATGTTG
*
6279660 AT AT AT AT AT AT AT AT AT -T AT ACC AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
6279701 AT AT
1 AT AT
6279705 TGTATTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.92
3 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6280996 original size:21 final size:22
Alignment explanation
Indices: 6280953--6280996 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
6280943 GTATTTTTCA
*
6280953 AAACCAACAATGAGTTAGGTCT
1 AAACCAACAATGAATTAGGTCT
6280975 AAACCAACAACT-AATT-GGTCT
1 AAACCAACAA-TGAATTAGGTCT
6280996 A
1 A
6280997 GTGGGATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 13 0.65
23 1 0.05
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (22 bp):
AAACCAACAATGAATTAGGTCT
Found at i:6292560 original size:16 final size:16
Alignment explanation
Indices: 6292539--6292584 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
6292529 GAGCCAGACC
*
6292539 GTTGACTTTCACAAGA
1 GTTGACTTTGACAAGA
* *
6292555 GTTGACTTTGACCAGC
1 GTTGACTTTGACAAGA
6292571 GTTGACTTTGACAA
1 GTTGACTTTGACAA
6292585 AAAACCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (16 bp):
GTTGACTTTGACAAGA
Found at i:6294602 original size:31 final size:32
Alignment explanation
Indices: 6294567--6294632 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
6294557 TACTCCTTTG
* *
6294567 GGTAGGCTCTAAGGCTTAAAGGTATTTC-TTA
1 GGTAGGCTCTAAGGCCTAAAGGTATTCCATTA
*
6294598 GGTAGGCTCTAAGGCCTCAAGGTATTCCATTA
1 GGTAGGCTCTAAGGCCTAAAGGTATTCCATTA
6294630 GGT
1 GGT
6294633 TGGCACCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (32 bp):
GGTAGGCTCTAAGGCCTAAAGGTATTCCATTA
Found at i:6299457 original size:23 final size:23
Alignment explanation
Indices: 6299427--6299476 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
6299417 CTCATATAAA
*
6299427 TGCACCGAAGTGCCACGTAGATT
1 TGCACCGAAGTGCCACGTAGAAT
*
6299450 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
6299473 TGCA
1 TGCA
6299477 TCGTAGTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:6303633 original size:2 final size:2
Alignment explanation
Indices: 6303626--6303655 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6303616 GAATTTTTCA
6303626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6303656 TAATTGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6308339 original size:19 final size:19
Alignment explanation
Indices: 6308315--6308355 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
6308305 TTCTCTTCCC
6308315 TCTAATAATATATATATTT
1 TCTAATAATATATATATTT
6308334 TCTAATAATATATATATTT
1 TCTAATAATATATATATTT
6308353 TCT
1 TCT
6308356 CTACTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTAATAATATATATATTT
Done.