Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003190.1 Kokia drynarioides strain JFW-HI SEQ_115802, 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: 575368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 121 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:14091 original size:2 final size:2
Alignment explanation
Indices: 14084--14127 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
14074 TATCATTGCA
14084 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
14126 AT
1 AT
14128 GTTAAATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17411 original size:25 final size:23
Alignment explanation
Indices: 17383--17428 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
17373 GTTGAATCCA
17383 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
17408 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
17429 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:25137 original size:13 final size:13
Alignment explanation
Indices: 25119--25143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25109 TTCCTCCCAA
25119 TTCTTCTTCTTTT
1 TTCTTCTTCTTTT
25132 TTCTTCTTCTTT
1 TTCTTCTTCTTT
25144 ACCCCATTTC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCTTCTTCTTTT
Found at i:32415 original size:242 final size:238
Alignment explanation
Indices: 31990--32460 Score: 710
Period size: 242 Copynumber: 2.0 Consensus size: 238
31980 TAATAATAAT
*
31990 GATAAAATATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTTTTAG
1 GATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTTTTAG
* *
32055 GTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTCACTATAATTATTT
66 GTTTTTTTTAGGATTCTAAAATAGAATTAATTTCAAGAATTGAAGGTATTTCACTAGAATTATTT
* * *
32120 AAGTATCTTTTAGGGTTCTCGTTAGAAGTAAAAATCCCTAATTTAATTTTTAAATTAGATAAATG
131 AAGTATCCTTTAGGGTTCTCATTAGAAGTAAAAATCCCTAATTTAAGTTTTAAATTAGATAAATG
*
32185 TGGTGAACACGTCTTATTCAAGTTACAAGTAAATCAAATTAAG
196 TGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCAAATTAAG
* * **
32228 GATAAAAGATCGAATAAGTTGTAGTTGAATTTTAATATTTCTCTTAATTTATTAGTGATTTTTTT
1 GATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGT-A---ACTT
* * *
32293 TTAGGTTTTTTTTAGGATTCTAAAATAGAATTTATTTCAAGGATTGAAGGTATTTTACTAGAATT
62 TTAGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTCAAGAATTGAAGGTATTTCACTAGAATT
* * *
32358 ATTTAGGTATCCTTTAGGGTTCTTATTAAGAA-TAAAAATCTCTAATTTAAGTTTTAAATTAGAT
127 ATTTAAGTATCCTTTAGGGTTCTCATT-AGAAGTAAAAATCCCTAATTTAAGTTTTAAATTAGAT
* * *
32422 AAGTTTGGTGAACATGTCTTAGTCAAGTTACAAGTAAAT
191 AAATGTGGTGAACACGTCTTAGTCAAGTTACAAGTAAAT
32461 TGGAGGCATT
Statistics
Matches: 208, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
238 53 0.25
239 1 0.00
242 150 0.72
243 4 0.02
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (238 bp):
GATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTTTTAG
GTTTTTTTTAGGATTCTAAAATAGAATTAATTTCAAGAATTGAAGGTATTTCACTAGAATTATTT
AAGTATCCTTTAGGGTTCTCATTAGAAGTAAAAATCCCTAATTTAAGTTTTAAATTAGATAAATG
TGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCAAATTAAG
Found at i:32936 original size:21 final size:23
Alignment explanation
Indices: 32894--32939 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
32884 CGATTTTTAG
32894 TATTTGTGCATATTAGATTTATT
1 TATTTGTGCATATTAGATTTATT
32917 TATTTGTGCAT-TTA-ATTTATT
1 TATTTGTGCATATTAGATTTATT
32938 TA
1 TA
32940 ATTTTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 11 0.48
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (23 bp):
TATTTGTGCATATTAGATTTATT
Found at i:42118 original size:27 final size:26
Alignment explanation
Indices: 42087--42139 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
42077 AATTAAACCC
42087 AAATTATTAATGAAAT-ATTTTATATTT
1 AAATTATTAA--AAATAATTTTATATTT
*
42114 AAATTATTAAATATAATTTTATATTT
1 AAATTATTAAAAATAATTTTATATTT
42140 TATTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATTATTAAAAATAATTTTATATTT
Found at i:44096 original size:18 final size:18
Alignment explanation
Indices: 44069--44104 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44059 ACCCTCTTAT
44069 TAAACATAAAAATGAAAA
1 TAAACATAAAAATGAAAA
* *
44087 TAAACTTAAAATTGAAAA
1 TAAACATAAAAATGAAAA
44105 AAAATCCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (18 bp):
TAAACATAAAAATGAAAA
Found at i:52534 original size:20 final size:20
Alignment explanation
Indices: 52498--52543 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
52488 GTTTAAATCA
*
52498 AGAAAAAAAATACAAAAAGG
1 AGAAAAAAAAGACAAAAAGG
52518 AGAAGAAAAAAGA-AAAAAGG
1 AGAA-AAAAAAGACAAAAAGG
52538 A-AAAAA
1 AGAAAAA
52544 TAGAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.12
19 2 0.08
20 12 0.50
21 7 0.29
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (20 bp):
AGAAAAAAAAGACAAAAAGG
Found at i:53506 original size:42 final size:42
Alignment explanation
Indices: 52965--53488 Score: 757
Period size: 42 Copynumber: 12.5 Consensus size: 42
52955 AAAGAAAGCA
52965 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
53007 TTCATTGCATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
53049 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
53091 TTCATTACATTCAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
53133 TTCATTGCATTTAGAGGCCCAGGTGTGGAGATCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
53175 TTCATCGCATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
53217 TTCATCGCATTTAG-GGCTTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
53258 TTCATTGCATTTAGAGGCCCAGGT-TCGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGT-GGAGGTC-CATTTACTT
* *
53300 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * ** *
53342 TTCATTGCATTTAAAGGCCTAAGTGTATAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
53384 TTCATTGCATTTAGAGGCCTAGATGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
**
53426 TTCATTGCATTCGGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
53468 TTCATTGCAATTAGAGGCCTA
1 TTCATTGCATTTAGAGGCCTA
53489 AGCATAGAGG
Statistics
Matches: 431, Mismatches: 46, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
41 39 0.09
42 390 0.90
43 2 0.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
Found at i:53883 original size:3 final size:3
Alignment explanation
Indices: 53875--53903 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53865 GGCCCAAATT
53875 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
53904 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:53908 original size:3 final size:3
Alignment explanation
Indices: 53902--53934 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53892 CATCATCATC
53902 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53935 CTTTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56178 original size:244 final size:236
Alignment explanation
Indices: 55757--56226 Score: 710
Period size: 244 Copynumber: 2.0 Consensus size: 236
55747 AAAATAATAA
*
55757 TAATGATAAAAGATCAAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAAGATCAAATAAGTTGCAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
55822 TTAGGTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTCACTAGAATTAT
66 TTAGGTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTCACTAGAATTAT
*
55887 TTAAGTATCTTTTAGGGTTATCGTTAAAAGTAAAAATCCATAATTTAAGTTTTAAATTAGATAAA
131 TTAAGTATCTTTTAGGGTTATCATTAAAAGTAAAAATCCATAATTTAAGTTTTAAATTAGATAAA
55952 TGTGGTGAACACGTCTTAGTCAAGTTACAAGGAAGTCGGAT
196 TGTGGTGAACACGTCTTAGTCAAGTTACAAGGAAGTCGGAT
** *
55993 TAATGATAAAAGATTGAATAAGTTGCAGATGAATTTTCATATTTCTCTTAATTCATTAGTGATTT
1 TAATGATAAAAGATCAAATAAGTTGCAGATGAATTTTAATATTTCTCTTAATTCATTAGT-A---
** *
56058 TTTTTTTTAGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAA-AGATTGAAGGTATTTTAC
62 --ACTTTTAGG--TTTTTTAGGATTCTAAAATAGAATTAATTTTAAGA-ATTGAAGGTATTTCAC
* * * *
56122 TAGAATTATTTAGGTATCTTTTAGGGTTCTTATTAAGAGTAAAAATCTC-TAATTTAAGTTTTAA
122 TAGAATTATTTAAGTATCTTTTAGGGTTATCATTAAAAGTAAAAATC-CATAATTTAAGTTTTAA
* *
56186 ATTAGATAAGTTTGGTGAACACGTCTTAGTCAAGTTACAAG
186 ATTAGATAAATGTGGTGAACACGTCTTAGTCAAGTTACAAG
56227 TAAATTGGAG
Statistics
Matches: 210, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
236 56 0.27
237 1 0.00
242 7 0.03
243 1 0.00
244 144 0.69
245 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (236 bp):
TAATGATAAAAGATCAAATAAGTTGCAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAGGTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTCACTAGAATTAT
TTAAGTATCTTTTAGGGTTATCATTAAAAGTAAAAATCCATAATTTAAGTTTTAAATTAGATAAA
TGTGGTGAACACGTCTTAGTCAAGTTACAAGGAAGTCGGAT
Found at i:60598 original size:17 final size:17
Alignment explanation
Indices: 60576--60609 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
60566 CATTAACACT
60576 AAAATGCAATGACAATG
1 AAAATGCAATGACAATG
60593 AAAATGCAATGACAATG
1 AAAATGCAATGACAATG
60610 CTTACTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATG
Found at i:61744 original size:7 final size:8
Alignment explanation
Indices: 61727--61751 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
61717 AAACTTGAAC
61727 AAAAATAA
1 AAAAATAA
61735 AAAAATAA
1 AAAAATAA
61743 AAAAATAA
1 AAAAATAA
61751 A
1 A
61752 CACTTGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:62189 original size:38 final size:38
Alignment explanation
Indices: 62127--62215 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
62117 GAGTTCCTGT
*
62127 AGCGACAATTCTGGGCATGCTCATGCAGAGATAATTTTG
1 AGCG-CAATTCTGGGCATGCTCATGCAGAGACAATTTTG
* *
62166 AGCGCAATTTTGGGCAT-CGTCATGCAGTGACAATTTTG
1 AGCGCAATTCTGGGCATGC-TCATGCAGAGACAATTTTG
* *
62204 GGCGTAATTCTG
1 AGCGCAATTCTG
62216 AATAGACTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
37 1 0.02
38 38 0.88
39 4 0.09
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (38 bp):
AGCGCAATTCTGGGCATGCTCATGCAGAGACAATTTTG
Found at i:68638 original size:26 final size:26
Alignment explanation
Indices: 68605--68790 Score: 137
Period size: 26 Copynumber: 7.3 Consensus size: 26
68595 GGACATGCAA
* *
68605 TTACGCTCATCAACATGATTTTACGT
1 TTACGCTCATCAACATGAATATACGT
* * *
68631 TTATGCTCATCAGCATGATTATAC-T
1 TTACGCTCATCAACATGAATATACGT
* * *
68656 TTAACGCTCTTCAACTTGAATATATGT
1 TT-ACGCTCATCAACATGAATATACGT
* *
68683 TTACGCTCGTCAGCATGAATATACGT
1 TTACGCTCATCAACATGAATATACGT
* * * * *
68709 TTATGCTCATCAGCATCAATAAAAGT
1 TTACGCTCATCAACATGAATATACGT
* * * *
68735 TTACTCTCGTCAGCATGGATATACGT
1 TTACGCTCATCAACATGAATATACGT
* * *
68761 TTATGCTTATCAGCATG---ATACGT
1 TTACGCTCATCAACATGAATATACGT
68784 TTACGCT
1 TTACGCT
68791 ACTAGAGCTC
Statistics
Matches: 128, Mismatches: 30, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
23 12 0.09
25 3 0.02
26 110 0.86
27 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (26 bp):
TTACGCTCATCAACATGAATATACGT
Found at i:68757 original size:78 final size:78
Alignment explanation
Indices: 68605--68778 Score: 188
Period size: 78 Copynumber: 2.2 Consensus size: 78
68595 GGACATGCAA
* * * * * * *
68605 TTACGCTCATCAACATGATTTTACGTTTATGCTCATCAGCATGATTATACTTTAACGCTCTTCAA
1 TTACGCTCATCAGCATGAATATACGTTTATGCTCATCAGCATAATAAAACTTTAACGCTCGTCAA
* *
68670 CTTGAATATATGT
66 CATGAATATACGT
* * *
68683 TTACGCTCGTCAGCATGAATATACGTTTATGCTCATCAGCATCAATAAAAGTTT-ACTCTCGTCA
1 TTACGCTCATCAGCATGAATATACGTTTATGCTCATCAGCAT-AATAAAACTTTAACGCTCGTCA
* *
68747 GCATGGATATACGT
65 ACATGAATATACGT
* *
68761 TTATGCTTATCAGCATGA
1 TTACGCTCATCAGCATGA
68779 TACGTTTACG
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
78 71 0.91
79 7 0.09
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (78 bp):
TTACGCTCATCAGCATGAATATACGTTTATGCTCATCAGCATAATAAAACTTTAACGCTCGTCAA
CATGAATATACGT
Found at i:79754 original size:19 final size:19
Alignment explanation
Indices: 79730--79767 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
79720 ATCTCTCCTA
79730 GGTATTTGGGAATTTAGTT
1 GGTATTTGGGAATTTAGTT
79749 GGTATTTGGGAATTTAGTT
1 GGTATTTGGGAATTTAGTT
79768 CGTGCTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (19 bp):
GGTATTTGGGAATTTAGTT
Found at i:80067 original size:25 final size:23
Alignment explanation
Indices: 80039--80084 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
80029 GTTGGATCCA
80039 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
80064 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
80085 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:81141 original size:14 final size:13
Alignment explanation
Indices: 81114--81155 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
81104 TCAGACATAT
81114 TTTTTATCTTTTTC
1 TTTTT-TCTTTTTC
81128 TTCTCTTT-TTTTTC
1 TT-T-TTTCTTTTTC
81142 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
81155 T
1 T
81156 AAATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.12
13 8 0.32
14 10 0.40
15 2 0.08
16 2 0.08
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:85025 original size:3 final size:3
Alignment explanation
Indices: 85001--85044 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
84991 TAAGAATGCA
* *
85001 AAT AAT AA- AAC AAA AAT AAAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
85045 AATGGCTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:96396 original size:12 final size:12
Alignment explanation
Indices: 96381--96405 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
96371 ATTAATTTAT
96381 TTTTATAAAATA
1 TTTTATAAAATA
96393 TTTTATAAAATA
1 TTTTATAAAATA
96405 T
1 T
96406 AATTAATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTATAAAATA
Found at i:97059 original size:24 final size:25
Alignment explanation
Indices: 97018--97075 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 25
97008 TTAGATGACT
*
97018 ATATAAAACAATTATTAATATTAAA
1 ATATATAACAATTATTAATATTAAA
*
97043 ATATATAA-AATTATTAATATTCAA
1 ATATATAACAATTATTAATATTAAA
97067 ATAATATAA
1 AT-ATATAA
97076 TATAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATATAACAATTATTAATATTAAA
Found at i:105494 original size:23 final size:23
Alignment explanation
Indices: 105464--106166 Score: 650
Period size: 23 Copynumber: 30.4 Consensus size: 23
105454 TCTTATATCC
*
105464 GTGCTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
* * *
105487 ATGATTAAATATTAACGTGATTT
1 GTGCTTAAATATTAATGTGATTT
105510 GTGCTTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105533 ATGCTTAAATATTAATGTAATTT
1 GTGCTTAAATATTAATGTGATTT
* **
105556 ATGCTTAAATATTAATACGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105579 GTGCTCAAATATTAATGTGAATT
1 GTGCTTAAATATTAATGTGATTT
* * *
105602 ATGCTCAAATATTAATGTGTTTT
1 GTGCTTAAATATTAATGTGATTT
105625 GTGCTTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
*
105648 GTGCTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105671 GTGCTTAAATATGAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105694 GTGCTCAAATATTAATGTAATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105717 ATGCTCAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105740 GTACTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105763 TTGATTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105786 GTACTTAAAGAATTAAGATGTGATATT
1 GTGCTTAAA-TATT-A-ATGTGAT-TT
* * * *
105813 GTGTATTTGGGAAT-TT-A-GAGA-TA
1 GTG--CTT--AAATATTAATGTGATTT
* * * * * *
105836 G-CCTAAAATCTTACTCTAAATTT
1 GTGCTTAAATATTAATGT-GATTT
* * ** * **
105859 CAAGTG--TAAGTGTTCTTAT-ATCC
1 ---GTGCTTAAATATTAATGTGATTT
* *
105882 GAGCTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
* **
105905 ATAATTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
*
105928 GTACTTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
105951 ATGTTTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
*
105974 GTGCTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
*
105997 GTGCTCAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
106020 ATGCTTAAATATTAATAAT-ATTT
1 GTGCTTAAATATTAAT-GTGATTT
* *
106043 ATGCTCAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
106066 GTGCTTAAATATTAATATGAGTT
1 GTGCTTAAATATTAATGTGATTT
*
106089 GTGCTCAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
*
106112 GTGCTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
106135 ATGATTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
106158 GTGCTTAAA
1 GTGCTTAAA
106167 GAATTAAGAT
Statistics
Matches: 550, Mismatches: 108, Indels: 44
0.78 0.15 0.06
Matches are distributed among these distances:
18 3 0.01
19 2 0.00
20 3 0.01
22 11 0.02
23 497 0.90
24 4 0.01
25 11 0.02
26 9 0.02
27 4 0.01
29 4 0.01
31 2 0.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (23 bp):
GTGCTTAAATATTAATGTGATTT
Found at i:110136 original size:71 final size:70
Alignment explanation
Indices: 109952--110136 Score: 158
Period size: 71 Copynumber: 2.7 Consensus size: 70
109942 TGAGTTTTCA
* ** * * ** *
109952 TTGCGGTACAAAGTTGGACAATTTCATGTCATTCAACTGGATT--AAAATCATATTTTAATTGAA
1 TTGCTGTACAAAACTGGACAATTACATATCATTCAGTTGAATTAAAAAATCATATTTTAATTGAA
110015 ATTAG
66 ATTAG
* * * * * ** * *
110020 TTGTTGTATAAAACTGGACAATTCCATATTATTCGGTTGGGTTAAAAAATCATGTTTTTATTTGA
1 TTGCTGTACAAAACTGGACAATTACATATCATTCAGTTGAATTAAAAAATCAT-ATTTTAATTGA
*
110085 AGTTAG
65 AATTAG
* * *
110091 TTGCTGTCCAAAGCTGGACAATTACATATCATTTAGTTGAATTAAA
1 TTGCTGTACAAAACTGGACAATTACATATCATTCAGTTGAATTAAA
110137 TTCATGTTCT
Statistics
Matches: 89, Mismatches: 25, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
68 31 0.35
70 8 0.09
71 50 0.56
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (70 bp):
TTGCTGTACAAAACTGGACAATTACATATCATTCAGTTGAATTAAAAAATCATATTTTAATTGAA
ATTAG
Found at i:110374 original size:56 final size:56
Alignment explanation
Indices: 110305--110437 Score: 153
Period size: 56 Copynumber: 2.4 Consensus size: 56
110295 TTGCTGTCAT
* * * *
110305 TTGTTATCTATTATTGGAATCAAATTGTCAAAAATGGGTGTTTAGT-TTGCTATT-CA
1 TTGTTATTTATTATTGGAATCAAACTGTCAAAAA-GGGTGTTTAATCCTGCT-TTCCA
* * * *
110361 TTGTTCTTTATTATTGGGATTAAGCTGTCAAAAAGGGTGTTTAATCGCTGCTTTCCA
1 TTGTTATTTATTATTGGAATCAAACTGTCAAAAAGGGTGTTTAATC-CTGCTTTCCA
110418 TTGTTATTTATTATTGGAAT
1 TTGTTATTTATTATTGGAAT
110438 TAGGCTATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
55 10 0.16
56 30 0.47
57 24 0.38
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.46
Consensus pattern (56 bp):
TTGTTATTTATTATTGGAATCAAACTGTCAAAAAGGGTGTTTAATCCTGCTTTCCA
Found at i:110433 original size:57 final size:55
Alignment explanation
Indices: 110305--110457 Score: 164
Period size: 57 Copynumber: 2.7 Consensus size: 55
110295 TTGCTGTCAT
* * ** * *
110305 TTGTTATCTATTATTGGAATCAAATTGTCAAAAATGGGTGTTTAGTTTGCTATTCA
1 TTGTTATTTATTATTGGAATTAAGCTGTCAAAAA-GGGTGTTTAATCTGCTATTCA
* *
110361 TTGTTCTTTATTATTGGGATTAAGCTGTCAAAAAGGGTGTTTAATCGCTGCT-TTCCA
1 TTGTTATTTATTATTGGAATTAAGCTGTCAAAAAGGGTGTTTAAT--CTGCTATT-CA
* * *
110418 TTGTTATTTATTATTGGAATTAGGCTATCAATAAGGGTGT
1 TTGTTATTTATTATTGGAATTAAGCTGTCAAAAAGGGTGT
110458 ATAAATCGTT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
55 10 0.12
56 30 0.37
57 41 0.51
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (55 bp):
TTGTTATTTATTATTGGAATTAAGCTGTCAAAAAGGGTGTTTAATCTGCTATTCA
Found at i:113710 original size:43 final size:43
Alignment explanation
Indices: 113647--114095 Score: 411
Period size: 43 Copynumber: 10.5 Consensus size: 43
113637 ACTTCGGTAA
* * *
113647 ATCCGATGATGCACTATGTGTGCTAGTATAGTTGCTTTGATTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* * *
113690 ATCCGATGGTGTACTGTGTGTGCCAATATAGTTGCTTCGATTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* * * * *
113733 ATCAGATGATGCATTGTGTGTGCCAGTTTAGTTGTTTCGGTTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* * * *
113776 ATTCGATGATGCATTGTATGTGCCAGTATAGTTACTTCGATTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* *
113819 ATCCGATGATACACTGTGTGTGTCAGTATAGTTGCTTC-AGTTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGA-TTT
* *
113862 ATCCGATGATGCA--ATGTGTGCCAGTATAGTTGCTTCAATTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* * * * * *
113903 ATCCAATGATGCACTGTGTGTGCCAATAAATTTTCTTTGATTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* * ** * ***
113946 ATTCGATGATGCACTATACGTGCTAGTATACAAGCTTCGATTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* * ** *
113989 ATACGATGATGCACTGTGTGTGCCAGTATATTTTTTTAG-TTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* * ** * ** * * *
114031 ATCTGGTGATGCACTGTACGTGCCAATATACATACTTCGGTAT
1 ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
* *
114074 ACCCGATGATGCACTATGTGTG
1 ATCCGATGATGCACTGTGTGTG
114096 TATGTTGGTT
Statistics
Matches: 321, Mismatches: 80, Indels: 10
0.78 0.19 0.02
Matches are distributed among these distances:
41 36 0.11
42 33 0.10
43 252 0.79
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (43 bp):
ATCCGATGATGCACTGTGTGTGCCAGTATAGTTGCTTCGATTT
Found at i:113923 original size:170 final size:170
Alignment explanation
Indices: 113647--114018 Score: 439
Period size: 170 Copynumber: 2.2 Consensus size: 170
113637 ACTTCGGTAA
* * * **
113647 ATCCGATGATGCACTATGTGTGCTAGTATAGTTGCTTTGATTTATCCGATGGTGTACTGTGTGTG
1 ATCCGATGATGCACTGTGTGTGC-AGTATAGTTGCTTAGATTTATCCGATGATG-ACAATGTGTG
* * * * * *
113712 CCAATATAGTTGCTTCGATTTATCAGATGATGCATTGTGTGTGCCAGTTTAGTTGT-TTCGGTTT
64 CCAATATAGTTGCTTCAATTTATCAGATGATGCACTGTGTGTGCCA-ATAAATTGTCTTCGATTT
* * * **
113776 ATTCGATGATGCATTGTATGTGCCAGTATAGTTA-CTTCGATTT
128 ATTCGATGATGCACTATACGTGCCAGTATA-CAAGCTTCGATTT
*
113819 ATCCGATGATACACTGTGTGTGTCAGTATAGTTGCTTCAG-TTTATCCGATGATG-CAATGTGTG
1 ATCCGATGATGCACTGTGTGTG-CAGTATAGTTGCTT-AGATTTATCCGATGATGACAATGTGTG
* * *
113882 CCAGTATAGTTGCTTCAATTTATCCA-ATGATGCACTGTGTGTGCCAATAAATTTTCTTTGATTT
64 CCAATATAGTTGCTTCAATTTAT-CAGATGATGCACTGTGTGTGCCAATAAATTGTCTTCGATTT
*
113946 ATTCGATGATGCACTATACGTGCTAGTATACAAGCTTCGATTT
128 ATTCGATGATGCACTATACGTGCCAGTATACAAGCTTCGATTT
*
113989 ATACGATGATGCACTGTGTGTGCCAGTATA
1 ATCCGATGATGCACTGTGTGTG-CAGTATA
114019 TTTTTTTAGT
Statistics
Matches: 171, Mismatches: 24, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
169 6 0.04
170 115 0.67
171 2 0.01
172 46 0.27
173 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (170 bp):
ATCCGATGATGCACTGTGTGTGCAGTATAGTTGCTTAGATTTATCCGATGATGACAATGTGTGCC
AATATAGTTGCTTCAATTTATCAGATGATGCACTGTGTGTGCCAATAAATTGTCTTCGATTTATT
CGATGATGCACTATACGTGCCAGTATACAAGCTTCGATTT
Found at i:119368 original size:194 final size:195
Alignment explanation
Indices: 119039--119478 Score: 546
Period size: 194 Copynumber: 2.3 Consensus size: 195
119029 TACCAATACT
* * ** * * *
119039 CGATGCTGCTCACACGAGCTGTCAAGAATTCATAACATATGTGGTACACT-AGCCATCGTTACGG
1 CGATGCTGCTCACACGAGCTGTCAAGGACTCGCAACATATGTGGTAC-CTCAACCATCGATACAG
* * * *
119103 TATCTGTCTATAAATTGTCTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATTTAA
65 TATCTGTCTATAAACTGTCTCCCTAACGATGCTGCTCACACGAGCTATCCAGAATATGCACTTAA
* **
119168 GCATAAATCCCAACCATCGTAGGGCCTACACTCCATT-TAGAATTCATATCTC-TTTTTCGACTC
130 GCATAAATCCCAACCATCGTAGGGCCTACAATCCATTCTAGAATTCATATCTCATTTCCCGACTC
119231 A
195 A
* * * *
119232 CGATGCTACTCACACGAGCTATCAAGGACTCGCAACATATGCGGTACCTCAACCATCGATCCAGT
1 CGATGCTGCTCACACGAGCTGTCAAGGACTCGCAACATATGTGGTACCTCAACCATCGATACAGT
* * *
119297 ATTTGTGC-ATATAACTGTTTCCCTAACGATGCTGCTCATACGAGCTATCCAGAATATGCACTTA
66 ATCTGT-CTATA-AACTGTCTCCCTAACGATGCTGCTCACACGAGCTATCCAGAATATGCACTTA
* * * ** * * *
119361 TGCATAAATCCTAGCCATCGTAGGGCCTGTAATCCATTCTTGGATTCATTTCTCATTTCCCGACT
129 AGCATAAATCCCAACCATCGTAGGGCCTACAATCCATTCTAGAATTCATATCTCATTTCCCGACT
119426 CA
194 CA
* *
119428 CGATGCTGCTCACACAAGCTGTCGAGGACTCGCAACATATGTGGTACCTCA
1 CGATGCTGCTCACACGAGCTGTCAAGGACTCGCAACATATGTGGTACCTCA
119479 GTCATCGTGT
Statistics
Matches: 208, Mismatches: 34, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
192 2 0.01
193 59 0.28
194 79 0.38
195 12 0.06
196 56 0.27
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (195 bp):
CGATGCTGCTCACACGAGCTGTCAAGGACTCGCAACATATGTGGTACCTCAACCATCGATACAGT
ATCTGTCTATAAACTGTCTCCCTAACGATGCTGCTCACACGAGCTATCCAGAATATGCACTTAAG
CATAAATCCCAACCATCGTAGGGCCTACAATCCATTCTAGAATTCATATCTCATTTCCCGACTCA
Found at i:126497 original size:14 final size:15
Alignment explanation
Indices: 126472--126500 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
126462 ATTCATCAAA
126472 ATCTTAAAATAACAT
1 ATCTTAAAATAACAT
126487 ATCTT-AAATAACAT
1 ATCTTAAAATAACAT
126501 TTATTAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
ATCTTAAAATAACAT
Found at i:127086 original size:16 final size:16
Alignment explanation
Indices: 127041--127088 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
127031 GGGGAATGTG
127041 TAAATAAAACAT-AAATA
1 TAAAT-AAACATGAAA-A
*
127058 TAAATAGACATGAAAA
1 TAAATAAACATGAAAA
*
127074 TAAATAAAGATGAAA
1 TAAATAAACATGAAA
127089 TAAGAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:128123 original size:146 final size:144
Alignment explanation
Indices: 127669--128153 Score: 555
Period size: 146 Copynumber: 3.2 Consensus size: 144
127659 TTTTTAAAAC
* *
127669 AAAATCAGAACTTTTATTTCGAAATAATTAAAAAA-AATCAAATTTTGTTTAAAAA-TTAAACTT
1 AAAATCAAAACTTTTATTTCGAAATAGTTAAAAAATAA--AAA-TTTGTTTAAAAATTTAAA-TT
* *
127732 TTTCTTTTAAAATGTCTAAAAAATAGATTTTTTATTTTTAAAAATCTAAAATTTCTTCTTTTTTT
62 TTTC-TTTAAAATGACTAAAAAATATA-TTTTTATTTTTAAAAATCT-AAA-TT-TTC-----TT
* *
127797 TTTTTGAAAAAAAATCAACTATTTTACATA
117 TTTTT-AAAGAAAATC-ACTATTTTACTTA
* * *
127827 AAAATCAAAACTTTTATTTTGAAATAGTTAAAAAAATCAAAAATTTGTTTAAAATTTTAAACTTT
1 AAAATCAAAACTTTTATTTCGAAATAGTT-AAAAAAT-AAAAATTTGTTTAAAAATTTAAATTTT
* * * *
127892 T-TTTAAAATGATTAAAAAATATATTTTTATTTTTTTAAAATCTAAACTTTC-TTTTTTAATGAA
64 TCTTTAAAATGACTAAAAAATATATTTTTA-TTTTTAAAAATCTAAATTTTCTTTTTTTAAAGAA
*
127955 AATCACTACTTTACTTA
128 AATCACTATTTTACTTA
* *
127972 AAAATCCAAACTTTTATTTCTAAATAGTTAAAAAATAAAAACTTTGTTTAAAAATTTAAATTTTT
1 AAAATCAAAACTTTTATTTCGAAATAGTTAAAAAATAAAAA-TTTGTTTAAAAATTTAAA-TTTT
*
128037 TCTTTAAAAAGACTAAAAAATATATTTTTATTTTTAAAAATCTAAATTTTCTTTTTTTAAAGAAA
64 TCTTTAAAATGACTAAAAAATATATTTTTATTTTTAAAAATCTAAATTTTCTTTTTTTAAAGAAA
**
128102 ATCACTATTTTTGTTA
129 ATCACTATTTTACTTA
* *
128118 AAAATCAAAATTTTTATTTCGAAATTGTTAAGAAAA
1 AAAATCAAAACTTTTATTTCGAAATAGTTAA-AAAA
128154 GTCAAAACCT
Statistics
Matches: 286, Mismatches: 31, Indels: 31
0.82 0.09 0.09
Matches are distributed among these distances:
143 5 0.02
144 24 0.08
145 60 0.21
146 86 0.30
147 10 0.03
153 3 0.01
154 1 0.00
155 9 0.03
156 31 0.11
158 41 0.14
159 14 0.05
161 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (144 bp):
AAAATCAAAACTTTTATTTCGAAATAGTTAAAAAATAAAAATTTGTTTAAAAATTTAAATTTTTC
TTTAAAATGACTAAAAAATATATTTTTATTTTTAAAAATCTAAATTTTCTTTTTTTAAAGAAAAT
CACTATTTTACTTA
Found at i:128963 original size:16 final size:16
Alignment explanation
Indices: 128939--128969 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
128929 CTATGCATGC
*
128939 AAAATATAAAAGACAA
1 AAAACATAAAAGACAA
128955 AAAACATAAAAGACA
1 AAAACATAAAAGACA
128970 TAGTAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAACATAAAAGACAA
Found at i:130805 original size:18 final size:18
Alignment explanation
Indices: 130780--130839 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
130770 AGGTTTCTCA
130780 AAATGGAAACGGAAATGG
1 AAATGGAAACGGAAATGG
*
130798 AGATGGAAACGGAAATGG
1 AAATGGAAACGGAAATGG
*
130816 AAATGGAAATGGAAATGAG
1 AAATGGAAACGGAAATG-G
130835 AAATG
1 AAATG
130840 ATTCATTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
18 32 0.84
19 6 0.16
ACGTcount: A:0.50, C:0.03, G:0.33, T:0.13
Consensus pattern (18 bp):
AAATGGAAACGGAAATGG
Found at i:130840 original size:7 final size:6
Alignment explanation
Indices: 130780--130839 Score: 84
Period size: 6 Copynumber: 9.8 Consensus size: 6
130770 AGGTTTCTCA
* * *
130780 AAATGG AAACGG AAATGG AGATGG AAACGG AAATGG AAATGG AAATGG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
130828 AAATGAG AAATG
1 AAATG-G AAATG
130840 ATTCATTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
6 41 0.87
7 6 0.13
ACGTcount: A:0.50, C:0.03, G:0.33, T:0.13
Consensus pattern (6 bp):
AAATGG
Found at i:135807 original size:29 final size:29
Alignment explanation
Indices: 135765--135824 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
135755 CCCAGCTAGT
135765 TTGTTGAAGACGTTCTGCCTTCCTAATTC
1 TTGTTGAAGACGTTCTGCCTTCCTAATTC
135794 TTGTTGAAGACGTTCTGCCTTCCTAATTC
1 TTGTTGAAGACGTTCTGCCTTCCTAATTC
135823 TT
1 TT
135825 TGTTTTCTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (29 bp):
TTGTTGAAGACGTTCTGCCTTCCTAATTC
Found at i:141607 original size:53 final size:52
Alignment explanation
Indices: 141549--141659 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 52
141539 ATAGAAAAGG
* * * * *
141549 TGAAAATG-GATAAATGAGAAACATTTGTGAAATGATTATGGTTTTTTCCAAGA
1 TGAAAATGAGAGAAATGA-AAACATTTGT-AAATGAATATGATTTTCTCCAAAA
* * *
141602 TGAAAATGAGGGAAATGAAATCATTTGTAAATGAATGTGATTTTCTCCAAAA
1 TGAAAATGAGAGAAATGAAAACATTTGTAAATGAATATGATTTTCTCCAAAA
141654 TGAAAA
1 TGAAAA
141660 ATGAAAATGA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
52 25 0.51
53 17 0.35
54 7 0.14
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (52 bp):
TGAAAATGAGAGAAATGAAAACATTTGTAAATGAATATGATTTTCTCCAAAA
Found at i:143394 original size:3 final size:3
Alignment explanation
Indices: 143386--143414 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
143376 TATGACACCA
143386 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
143415 ACTCTATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:145046 original size:17 final size:18
Alignment explanation
Indices: 145018--145057 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
145008 CTATATTGAA
145018 TATTTTTAATATAATTAT
1 TATTTTTAATATAATTAT
145036 TATTTTT-ATATAATTAT
1 TATTTTTAATATAATTAT
145053 T-TTTT
1 TATTTT
145058 ATTTGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTTAATATAATTAT
Found at i:146398 original size:7 final size:8
Alignment explanation
Indices: 146383--146421 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
146373 AATTTTCTCA
146383 TTAAAAAT
1 TTAAAAAT
*
146391 TTAAAATT
1 TTAAAAAT
146399 TTAAAAAT
1 TTAAAAAT
146407 TTAAAAAT
1 TTAAAAAT
146415 TTAAAAA
1 TTAAAAA
146422 ATTTTCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TTAAAAAT
Found at i:146407 original size:9 final size:9
Alignment explanation
Indices: 146383--146426 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
146373 AATTTTCTCA
146383 TTAAAAA-T
1 TTAAAAATT
146391 TT-AAAATT
1 TTAAAAATT
146399 TTAAAAA-T
1 TTAAAAATT
146407 TTAAAAATT
1 TTAAAAATT
*
146416 TAAAAAATT
1 TTAAAAATT
146425 TT
1 TT
146427 CATTTTAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 4 0.13
8 13 0.42
9 14 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TTAAAAATT
Found at i:147986 original size:44 final size:43
Alignment explanation
Indices: 147938--148027 Score: 108
Period size: 44 Copynumber: 2.1 Consensus size: 43
147928 CTAAGGTAAA
147938 AAAAAAATAATATTATTTACTTCAAAATAAAAAATAAAATAATT
1 AAAAAAATAATATTATTTACTTCAAAAT-AAAAATAAAATAATT
** * * * * *
147982 AAAAATGTATTCTTATTTGCTTTAAAATAAAAATAATATAATT
1 AAAAAAATAATATTATTTACTTCAAAATAAAAATAAAATAATT
148025 AAA
1 AAA
148028 TTTAAAGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 17 0.44
44 22 0.56
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (43 bp):
AAAAAAATAATATTATTTACTTCAAAATAAAAATAAAATAATT
Found at i:148077 original size:113 final size:113
Alignment explanation
Indices: 147914--148153 Score: 430
Period size: 113 Copynumber: 2.1 Consensus size: 113
147904 CAATATATAT
147914 ATTAAAGTTTAAGTCTAAGGTAAAAAAAAAATAATATTATTTACTTCAAAATAAAAAATAAAATA
1 ATTAAAGTTTAAGTCTAAGGTAAAAAAAAAATAATATTATTTACTTCAAAATAAAAAATAAAATA
*
147979 ATTAAAAATGTATTCTTATTTGCTTTAAAATAAAAATAATATAATTAA
66 ATTAAAAATATATTCTTATTTGCTTTAAAATAAAAATAATATAATTAA
* *
148027 ATTTAAAGTTTAAGTCTAAGGT-GAAAAAAATTAATATTATTTACTTCAAAATAAAAAATAAAAT
1 A-TTAAAGTTTAAGTCTAAGGTAAAAAAAAAATAATATTATTTACTTCAAAATAAAAAATAAAAT
148091 AATTAAAAATATATTCTTATTTGCTTTAAAATAAAAATAATATAATTAA
65 AATTAAAAATATATTCTTATTTGCTTTAAAATAAAAATAATATAATTAA
148140 ATTAAA-TTTAAGTC
1 ATTAAAGTTTAAGTC
148154 GGGTCGAAGT
Statistics
Matches: 123, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
111 8 0.07
112 5 0.04
113 90 0.73
114 20 0.16
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (113 bp):
ATTAAAGTTTAAGTCTAAGGTAAAAAAAAAATAATATTATTTACTTCAAAATAAAAAATAAAATA
ATTAAAAATATATTCTTATTTGCTTTAAAATAAAAATAATATAATTAA
Found at i:148099 original size:43 final size:43
Alignment explanation
Indices: 148052--148140 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
148042 CTAAGGTGAA
148052 AAAAAT-TAATATTATTTACTTCAAAATAAAAAATAAAATAATT
1 AAAAATATAATATTATTTACTTCAAAAT-AAAAATAAAATAATT
* * * * *
148095 AAAAATATATTCTTATTTGCTTTAAAATAAAAATAATATAATT
1 AAAAATATAATATTATTTACTTCAAAATAAAAATAAAATAATT
148138 AAA
1 AAA
148141 TTAAATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 23 0.57
44 17 0.43
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (43 bp):
AAAAATATAATATTATTTACTTCAAAATAAAAATAAAATAATT
Found at i:151388 original size:44 final size:44
Alignment explanation
Indices: 151325--151413 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
151315 AAGAAAAATC
151325 GCGCCTAGTAAGTTAAGGTACAAATTTTCAAAACCCGGGATAAA
1 GCGCCTAGTAAGTTAAGGTACAAATTTTCAAAACCCGGGATAAA
151369 GCGCCTAGTAAGTTAAGGTACAAATTTTCAAAACCCGGGATAAA
1 GCGCCTAGTAAGTTAAGGTACAAATTTTCAAAACCCGGGATAAA
151413 G
1 G
151414 GAATATTGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (44 bp):
GCGCCTAGTAAGTTAAGGTACAAATTTTCAAAACCCGGGATAAA
Found at i:151858 original size:29 final size:29
Alignment explanation
Indices: 151826--152079 Score: 233
Period size: 28 Copynumber: 8.9 Consensus size: 29
151816 AAGTTTTAGG
*
151826 GGTAAAAATGTCA-TTTTGAGAGAGTTCGA
1 GGTAAAAATGTAATTTTTGAGA-AGTTCGA
* *
151855 GGTAAAAATGTAATTTTTGAGAAGTTTGG
1 GGTAAAAATGTAATTTTTGAGAAGTTCGA
* * *
151884 GGCAAAATATG--ATTTTTG-GAAGTTTGGG
1 GGTAAAA-ATGTAATTTTTGAGAAG-TTCGA
* * *
151912 GGCAAAAATGTAATTTTTG-GAAGATTAGG
1 GGTAAAAATGTAATTTTTGAGAAG-TTCGA
* *
151941 GGTAAAAATGTGATTTTCG-GAAGTTCGA
1 GGTAAAAATGTAATTTTTGAGAAGTTCGA
* *
151969 GGGT-AAAATGTGATTTTTGA-AAGTTCAA
1 -GGTAAAAATGTAATTTTTGAGAAGTTCGA
151997 GGGTAAAAATGTAATTTTTGA-AAGTTCGA
1 -GGTAAAAATGTAATTTTTGAGAAGTTCGA
*
152026 GGGAAAAATGTAATTTTT-AGAAGTTCGA
1 GGTAAAAATGTAATTTTTGAGAAGTTCGA
* *
152054 GGGAAAAATGTGATTTTT-AGAAGTTC
1 GGTAAAAATGTAATTTTTGAGAAGTTC
152080 AGGAGTAAAA
Statistics
Matches: 198, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.04
28 96 0.48
29 83 0.42
30 11 0.06
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
GGTAAAAATGTAATTTTTGAGAAGTTCGA
Found at i:151899 original size:57 final size:56
Alignment explanation
Indices: 151821--152079 Score: 217
Period size: 57 Copynumber: 4.5 Consensus size: 56
151811 TTGGAAAGTT
* *
151821 TTAGGGGTAAAAATGTCATTTTGAGAGAGTTCGAGGTAAAAATGTAATTTTTGAGAAG
1 TTAGGGG-AAAAATATGATTTTGAGA-AGTTCGAGGTAAAAATGTAATTTTTGAGAAG
* * * * *
151879 TTTGGGGCAAAATATGATTTTTG-GAAGTTTGGGGGCAAAAATGTAATTTTTG-GAAG
1 TTAGGGGAAAAATATGA-TTTTGAGAAG-TTCGAGGTAAAAATGTAATTTTTGAGAAG
* *
151935 ATTAGGGGTAAAAATGTGATTTTCG-GAAGTTCGAGGGT-AAAATGTGATTTTTGA-AAG
1 -TTAGGGG-AAAAATATGATTTT-GAGAAGTTCGA-GGTAAAAATGTAATTTTTGAGAAG
* * * *
151992 TTCAAGGGTAAAAATGTAATTTTTGA-AAGTTCGAGGGAAAAATGTAATTTTT-AGAAG
1 TT--AGGGGAAAAATATGA-TTTTGAGAAGTTCGAGGTAAAAATGTAATTTTTGAGAAG
* * *
152049 TTCGAGGGAAAAATGTGATTTTTAGAAGTTC
1 TTAG-GGGAAAAATATGATTTTGAGAAGTTC
152080 AGGAGTAAAA
Statistics
Matches: 164, Mismatches: 22, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
55 6 0.04
56 28 0.17
57 96 0.59
58 34 0.21
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (56 bp):
TTAGGGGAAAAATATGATTTTGAGAAGTTCGAGGTAAAAATGTAATTTTTGAGAAG
Found at i:153152 original size:3 final size:3
Alignment explanation
Indices: 153144--153193 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
153134 TTTTTGTTAT
153144 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
153192 TT
1 TT
153194 TATAAAACGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:153852 original size:17 final size:17
Alignment explanation
Indices: 153832--153894 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
153822 AATTAAATTT
153832 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
* *
153849 TAAATCTAAATTTAAAA
1 TAAATTTAAATTCAAAA
* *
153866 TAAATTTAAACTCAGAA
1 TAAATTTAAATTCAAAA
*
153883 TAAGTTTAAATT
1 TAAATTTAAATT
153895 TAAACTTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:153872 original size:34 final size:34
Alignment explanation
Indices: 153832--153898 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
153822 AATTAAATTT
*
153832 TAAATTTAAATTCAAAATAAATCTAAATTTAAAA
1 TAAATTTAAACTCAAAATAAATCTAAATTTAAAA
* * *
153866 TAAATTTAAACTCAGAATAAGTTTAAATTTAAA
1 TAAATTTAAACTCAAAATAAATCTAAATTTAAA
153899 CTTTAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (34 bp):
TAAATTTAAACTCAAAATAAATCTAAATTTAAAA
Found at i:153918 original size:24 final size:23
Alignment explanation
Indices: 153866--153915 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
153856 AAATTTAAAA
*
153866 TAAATTTAAACTCAGAATAAGTT
1 TAAATTTAAACTCAAAATAAGTT
*
153889 TAAATTTAAACTTTAAAATAA-TT
1 TAAATTTAAAC-TCAAAATAAGTT
153912 TAAA
1 TAAA
153916 ATTAGGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (23 bp):
TAAATTTAAACTCAAAATAAGTT
Found at i:155058 original size:6 final size:6
Alignment explanation
Indices: 155037--155098 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
155027 CAATGTAGGT
* * * * *
155037 TACTAA TACTAA TACTAC TACTAC TACTAA TAATAA TAATAA TAATAA
1 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
* *
155085 TAATAA TAATAA TA
1 TACTAA TACTAA TA
155099 ATAGAATTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (6 bp):
TACTAA
Found at i:155070 original size:3 final size:3
Alignment explanation
Indices: 155064--155101 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
155054 CTACTACTAC
155064 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
155102 GAATTTAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:160335 original size:6 final size:6
Alignment explanation
Indices: 160324--160358 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
160314 CATGAATTCA
160324 TCACTG TCACTG TCACTG TCACTG TCACTG TCACT
1 TCACTG TCACTG TCACTG TCACTG TCACTG TCACT
160359 CTCTCTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.34
Consensus pattern (6 bp):
TCACTG
Found at i:166717 original size:67 final size:66
Alignment explanation
Indices: 166615--166753 Score: 260
Period size: 67 Copynumber: 2.1 Consensus size: 66
166605 GTTTCCATGT
*
166615 TATTCTAAAATGTGGTATTATCGCAGATATATAAAACTTACTGTGTCTGTTAATGACTCAATTAT
1 TATTCTAAAATGTGGTATTATCGCAGATATATAAAACTTACCGTGTCTGTTAATGACTCAATTA-
166680 TC
65 TC
166682 TATTCTAAAATGTGGTATTATCGCAGATATATAAAACTTACCGTGTCTGTTAATGACTCAATTAT
1 TATTCTAAAATGTGGTATTATCGCAGATATATAAAACTTACCGTGTCTGTTAATGACTCAATTAT
166747 C
66 C
166748 TATTCT
1 TATTCT
166754 TTTGATTGAC
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
66 8 0.11
67 63 0.89
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (66 bp):
TATTCTAAAATGTGGTATTATCGCAGATATATAAAACTTACCGTGTCTGTTAATGACTCAATTAT
C
Found at i:177715 original size:55 final size:55
Alignment explanation
Indices: 177655--177765 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
177645 TAGATATAAG
177655 AAGCATACATAACATAAAAGACAACTTTTAATAAACATTAAAATCTTAAATGTAT
1 AAGCATACATAACATAAAAGACAACTTTTAATAAACATTAAAATCTTAAATGTAT
177710 AAGCATACATAACATAAAAGACAACTTTTAATAAACATTAAAATCTTAAATGTAT
1 AAGCATACATAACATAAAAGACAACTTTTAATAAACATTAAAATCTTAAATGTAT
177765 A
1 A
177766 TTAAATTTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (55 bp):
AAGCATACATAACATAAAAGACAACTTTTAATAAACATTAAAATCTTAAATGTAT
Found at i:185561 original size:19 final size:19
Alignment explanation
Indices: 185537--185605 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
185527 CAGTAATTTA
* *
185537 CTCTTACGAGTCAGTATCG
1 CTCTTACGAGCCTGTATCG
185556 CTCTTACGAGCCTGTATCG
1 CTCTTACGAGCCTGTATCG
185575 CTCTTACGAGCCTGTATCG
1 CTCTTACGAGCCTGTATCG
*
185594 CTCTTATGAGCC
1 CTCTTACGAGCC
185606 AATATGCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.32
Consensus pattern (19 bp):
CTCTTACGAGCCTGTATCG
Found at i:185641 original size:19 final size:19
Alignment explanation
Indices: 185537--185701 Score: 85
Period size: 19 Copynumber: 8.9 Consensus size: 19
185527 CAGTAATTTA
* *
185537 CTCTTACGAGTCAGTATCG
1 CTCTTAAGAGCCAGTATCG
* *
185556 CTCTTACGAGCCTGTATCG
1 CTCTTAAGAGCCAGTATCG
* *
185575 CTCTTACGAGCCTGTATCG
1 CTCTTAAGAGCCAGTATCG
* *
185594 CTCTTATGAGCCAATAT-G
1 CTCTTAAGAGCCAGTATCG
* *
185612 CT-TAAACGATCCAGTATCG
1 CTCTTAA-GAGCCAGTATCG
* * *
185631 CTTTTAAGATCGAGTAT-G
1 CTCTTAAGAGCCAGTATCG
* *
185649 CTC-AAACGAGCTAGTAT-G
1 CTCTTAA-GAGCCAGTATCG
185667 CTC--AAGTAAGCCAGTAT-G
1 CTCTTAAG--AGCCAGTATCG
* *
185685 CCCTTACGAGCCAGTAT
1 CTCTTAAGAGCCAGTAT
185702 TCTCAAGCGA
Statistics
Matches: 120, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
16 1 0.01
17 6 0.05
18 46 0.38
19 62 0.52
20 5 0.04
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (19 bp):
CTCTTAAGAGCCAGTATCG
Found at i:189244 original size:59 final size:61
Alignment explanation
Indices: 189167--189284 Score: 177
Period size: 62 Copynumber: 2.0 Consensus size: 61
189157 ATCACTTTAA
* * * *
189167 TATTAAATTAATATAATATTTATC-A-AGATACATATTAAATTAAATTTAATATTAAATCT
1 TATTAAAATAATAAAATATTTATCAACAGATAAACATTAAATTAAATTTAATATTAAATCT
189226 TATTAAAATAATAAAATATTTATCAACGAGATAAACATTAAATTAAATTTAATATTAAA
1 TATTAAAATAATAAAATATTTATCAAC-AGATAAACATTAAATTAAATTTAATATTAAA
189285 ATAATCACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
62 29 0.56
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (61 bp):
TATTAAAATAATAAAATATTTATCAACAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:197127 original size:15 final size:15
Alignment explanation
Indices: 197107--197150 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
197097 TTATTATTCT
197107 AATAAATAATTTTAA
1 AATAAATAATTTTAA
*
197122 AATAAAT-ATTATTTA
1 AATAAATAATT-TTAA
197137 AATAAATAAATTTT
1 AATAAAT-AATTTT
197151 TTTATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 17 0.68
16 2 0.08
17 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATAATTTTAA
Found at i:197494 original size:15 final size:15
Alignment explanation
Indices: 197474--197504 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
197464 TTCTGCTGAA
197474 GAAAAAGATATGCTT
1 GAAAAAGATATGCTT
197489 GAAAAAGATATGCTT
1 GAAAAAGATATGCTT
197504 G
1 G
197505 CTAACAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (15 bp):
GAAAAAGATATGCTT
Found at i:199281 original size:27 final size:28
Alignment explanation
Indices: 199250--199331 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 28
199240 TATCGTCCTG
199250 GCAGACTACCCCATTTTTATTGTCTCGA
1 GCAGACTACCCCATTTTTATTGTCTCGA
* * * *
199278 -CAGACTATCCCATGTTTATCGTC-CTA
1 GCAGACTACCCCATTTTTATTGTCTCGA
* ***
199304 GCGGACTACCCTGCTTTTATTGTCTCGA
1 GCAGACTACCCCATTTTTATTGTCTCGA
199332 TGGACTTCAT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
26 2 0.05
27 36 0.90
28 2 0.05
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (28 bp):
GCAGACTACCCCATTTTTATTGTCTCGA
Found at i:203401 original size:23 final size:22
Alignment explanation
Indices: 203276--203420 Score: 123
Period size: 23 Copynumber: 6.2 Consensus size: 22
203266 CTAGCGCGCT
* *
203276 CTCTGATTAGCACCGTGTGTGCT
1 CTCTGATTAGCA-CTTGTGTGCC
203299 CTCTGATTAGCACTGTGTGTGCC
1 CTCTGATTAGCACT-TGTGTGCC
* * *
203322 CTCTGTTTAGCA-TGTTTCATGCC
1 CTCTGATTAGCACT-TGT-GTGCC
*
203345 CTCT-ATTCAGCATTGTGTGTGCC
1 CTCTGATT-AGCACT-TGTGTGCC
203368 CTCTGTTATTAGCACTTCGTGTGCC
1 CTCTG--ATTAGCACTT-GTGTGCC
203393 CTCTGATTAGCACTTTGTGTGCC
1 CTCTGATTAGCAC-TTGTGTGCC
*
203416 TTCTG
1 CTCTG
203421 CTACCCAGCA
Statistics
Matches: 103, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
22 7 0.07
23 69 0.67
24 7 0.07
25 17 0.17
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.39
Consensus pattern (22 bp):
CTCTGATTAGCACTTGTGTGCC
Found at i:205193 original size:27 final size:28
Alignment explanation
Indices: 205142--205202 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
205132 AAAATGTGAT
*
205142 TTTTGGATACTCGGGGGCAAAATGGTAA
1 TTTTGGACACTCGGGGGCAAAATGGTAA
*
205170 TTTTGGACACTTGGGGG-AAAATGGTAA
1 TTTTGGACACTCGGGGGCAAAATGGTAA
205197 TTTTGG
1 TTTTGG
205203 GAAAGTTCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.26, C:0.08, G:0.33, T:0.33
Consensus pattern (28 bp):
TTTTGGACACTCGGGGGCAAAATGGTAA
Found at i:205256 original size:59 final size:58
Alignment explanation
Indices: 205187--205496 Score: 250
Period size: 59 Copynumber: 5.2 Consensus size: 58
205177 CACTTGGGGG
* * * *
205187 AAAATGGTAATTTTGGGAAAGTTCGTGGTCAAAAATAGAATATTT-GGAAGTTCAAAGGT
1 AAAATGGTAATTTTGGGAAAATTCG-GGTTAAAAATGGAAT-TTTAGGAAGTTCAAGGGT
* * * * *
205246 AAAATGGTAATTTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
1 AAAATGGTAA-TTTTGGGAAAATTCGGGTTAAAAATGGAATTTTAGGAAGTTCAAGGGT
* * * * **
205305 AAAATGGTATTTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTA-GAAATTCGGGGGT
1 AAAATGGTAATTTTGGGAAAATTCG-GGTTAAAAATGGAA-TTTTAGGAAGTTCAAGGGT
* * * * * *
205364 GAAATGGTAATTTTAGGAAAAATCGAGGTCAAAAAATGGAATTTTAGAAAGTTCGAGGGT
1 AAAATGGTAATTTTGGGAAAATTCG-GGT-TAAAAATGGAATTTTAGGAAGTTCAAGGGT
* * * * * * *
205424 AAAAAT-GTAATTTTTGGAAAGTTTAGGGTTAAAAATAGAATTTTAGAAAGTTTAGGGGT
1 -AAAATGGTAATTTTGGGAAA-ATTCGGGTTAAAAATGGAATTTTAGGAAGTTCAAGGGT
205483 AAAAAT-GTAATTTT
1 -AAAATGGTAATTTT
205497 AAAAAGTTTA
Statistics
Matches: 209, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
58 14 0.07
59 137 0.66
60 52 0.25
61 6 0.03
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGGAAAATTCGGGTTAAAAATGGAATTTTAGGAAGTTCAAGGGT
Found at i:205288 original size:30 final size:30
Alignment explanation
Indices: 205246--205496 Score: 128
Period size: 29 Copynumber: 8.4 Consensus size: 30
205236 GTTCAAAGGT
205246 AAAATGGTAATTTTTGGAAAAATTAGGGTTA
1 AAAATGG-AATTTTTGGAAAAATTAGGGTTA
* ** *
205277 AAAATGGAA-TTTTGGGAAGTTTAGGGGT-
1 AAAATGGAATTTTTGGAAAAATTAGGGTTA
* *
205305 AAAATGGTATTTTTTGGAAAAA-TCGAGGTTA
1 AAAATGG-AATTTTTGGAAAAATTAG-GGTTA
* * *
205336 AAAATGGAATTTTT--AGAAATTCGGGGGT-
1 AAAATGGAATTTTTGGAAAAATT-AGGGTTA
* * * *
205364 GAAATGGTAATTTTAGGAAAAA-TCGAGGTCAA
1 AAAATGG-AATTTTTGGAAAAATTAG-GGT-TA
* *
205396 AAAATGGAA-TTTTAG-AAAGTTCGAGGG-TA
1 AAAATGGAATTTTTGGAAAAATT--AGGGTTA
* **
205425 AAAATGTAATTTTTGGAAAGTTTAGGGTTA
1 AAAATGGAATTTTTGGAAAAATTAGGGTTA
* * ** *
205455 AAAATAGAA-TTTTAGAAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAAAATTAGGGTTA
*
205484 AAAATGTAATTTT
1 AAAATGGAATTTT
205497 AAAAAGTTTA
Statistics
Matches: 165, Mismatches: 36, Indels: 39
0.69 0.15 0.16
Matches are distributed among these distances:
28 17 0.10
29 70 0.42
30 45 0.27
31 26 0.16
32 7 0.04
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAAATTAGGGTTA
Found at i:205324 original size:118 final size:117
Alignment explanation
Indices: 205160--205472 Score: 303
Period size: 118 Copynumber: 2.6 Consensus size: 117
205150 ACTCGGGGGC
* * * * * *
205160 AAAATGGTAATTTTGGACACTT-GGGGGAAAATGGTAATTTTGGGAAAGTTCGTGGTCAAAAATA
1 AAAATGG-AATTTTAGAAAGTTAGGGGTAAAATGGTAATTTTTGGAAAGTTCG-GGTTAAAAATA
* * * *
205224 GAATATTTGGAAGTTCAAAGGTAAAATGGTAATTTTTGGAAAAATTAG-GGT-TA
64 GAATATTTAGAAATTCAAAGGTAAAATGGTAATTTTAGGAAAAA-TAGAGGTCAA
* * * ** *
205277 AAAATGGAATTTTGGGAAGTTTAGGGGTAAAATGGTATTTTTTGGAAAAATCGAGGTTAAAAATG
1 AAAATGGAATTTTAGAAAG-TTAGGGGTAAAATGGTAATTTTTGGAAAGTTCG-GGTTAAAAATA
* *** * *
205342 GAATTTTTAGAAATTCGGGGGTGAAATGGTAATTTTAGGAAAAATCGAGGTCAA
64 GAATATTTAGAAATTCAAAGGTAAAATGGTAATTTTAGGAAAAATAGAGGTCAA
* *
205396 AAAATGGAATTTTAGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAAGTTTAGGGTTAAAAAT
1 AAAATGGAATTTTAGAAAGTTAG-GGGT-AAAATGGTAATTTTTGGAAAG-TTCGGGTTAAAAAT
205460 AGAAT-TTTAGAAA
63 AGAATATTTAGAAA
205473 GTTTAGGGGT
Statistics
Matches: 160, Mismatches: 29, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
116 9 0.06
117 11 0.07
118 84 0.52
119 49 0.31
120 7 0.04
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (117 bp):
AAAATGGAATTTTAGAAAGTTAGGGGTAAAATGGTAATTTTTGGAAAGTTCGGGTTAAAAATAGA
ATATTTAGAAATTCAAAGGTAAAATGGTAATTTTAGGAAAAATAGAGGTCAA
Found at i:205511 original size:59 final size:59
Alignment explanation
Indices: 205246--205539 Score: 198
Period size: 59 Copynumber: 4.9 Consensus size: 59
205236 GTTCAAAGGT
* * *
205246 AAAATGGTAATTTTTGGAAAAA--TTAGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT-
1 AAAAT-GTAATTTTT--AAAAAGTTTAGGGTTAAAAATAGAATTTTAGAAAGTTTAGGGGTA
* ** * **
205305 AAAATGGTATTTTTTGGAAAAA-TCGA-GGTTAAAAATGGAATTTTTAGAAA-TTCGGGGGT-
1 AAAAT-GTAATTTTT--AAAAAGTTTAGGGTTAAAAATAGAA-TTTTAGAAAGTTTAGGGGTA
* * ** * * *
205364 GAAATGGTAA-TTTTAGGAAAAATCGA-GGTCAAAAAATGGAATTTTAGAAAG-TTCGAGGGTA
1 AAAAT-GTAATTTTTA--AAAAGTTTAGGGT-TAAAAATAGAATTTTAGAAAGTTTAG-GGGTA
**
205425 AAAATGTAATTTTTGGAAAGTTTAGGGTTAAAAATAGAATTTTAGAAAGTTTAGGGGTA
1 AAAATGTAATTTTTAAAAAGTTTAGGGTTAAAAATAGAATTTTAGAAAGTTTAGGGGTA
* *
205484 AAAATGTAA-TTTTAAAAAGTTTAAGGGTT-AAAATATGATTTTTAGACAGTTTAGGG
1 AAAATGTAATTTTTAAAAAGTTT-AGGGTTAAAAATA-GAATTTTAGAAAGTTTAGGG
205540 ACCTTCAGGG
Statistics
Matches: 196, Mismatches: 25, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
56 1 0.01
58 25 0.13
59 130 0.66
60 32 0.16
61 8 0.04
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (59 bp):
AAAATGTAATTTTTAAAAAGTTTAGGGTTAAAAATAGAATTTTAGAAAGTTTAGGGGTA
Found at i:205527 original size:30 final size:28
Alignment explanation
Indices: 205395--205539 Score: 157
Period size: 29 Copynumber: 4.9 Consensus size: 28
205385 ATCGAGGTCA
*
205395 AAAAATGGAATTTTAGAAAGTTCGAGGG-T
1 AAAAAT-GAATTTTAGAAAGTT-TAGGGTT
*
205424 AAAAATGTAATTTTTGGAAAGTTTAGGGTT
1 AAAAATG-AA-TTTTAGAAAGTTTAGGGTT
*
205454 AAAAATAGAATTTTAGAAAGTTTAGGGGT
1 AAAAAT-GAATTTTAGAAAGTTTAGGGTT
*
205483 AAAAATGTAATTTTAAAAAGTTTAAGGGTT
1 AAAAATG-AATTTTAGAAAGTTT-AGGGTT
* *
205513 AAAATATGATTTTTAGACAGTTTAGGG
1 AAAA-ATGAATTTTAGAAAGTTTAGGG
205540 ACCTTCAGGG
Statistics
Matches: 100, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
28 2 0.02
29 53 0.53
30 41 0.41
31 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.34
Consensus pattern (28 bp):
AAAAATGAATTTTAGAAAGTTTAGGGTT
Found at i:207386 original size:17 final size:17
Alignment explanation
Indices: 207366--207413 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
207356 TCAATTTAAA
*
207366 TTTAAAATAAATTTTAG
1 TTTAAAATAAATTTGAG
* *
207383 TTTAAATTAAATTTGAT
1 TTTAAAATAAATTTGAG
207400 TTTAAAATAAATTT
1 TTTAAAATAAATTT
207414 AAATTCAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTAAAATAAATTTGAG
Found at i:207413 original size:12 final size:11
Alignment explanation
Indices: 207400--207438 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
207390 TAAATTTGAT
207400 TTTAAAATAAA
1 TTTAAAATAAA
*
207411 TTTAAATTCAAA
1 TTTAAAAT-AAA
*
207423 CTTAAAATAAA
1 TTTAAAATAAA
207434 TTTAA
1 TTTAA
207439 TTAAAGATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (11 bp):
TTTAAAATAAA
Found at i:208282 original size:98 final size:98
Alignment explanation
Indices: 208117--208300 Score: 224
Period size: 98 Copynumber: 1.9 Consensus size: 98
208107 AGGTTCGTCA
* * * * * * * *
208117 TTGCGACTTAAACCCTTCCCTTTGTGTCTTCGTGGTACTGGATCCACCGTTGTGGCTTAGATATT
1 TTGCGACTTAAACCCTTCCCCTCGCGTCTTCATGGTACTGGATCCACCGTTGCGACTAAAATATT
208182 TCCCTTCATGTCTCTGCGGTACAAGGTTCACTG
66 TCCCTTCATGTCTCTGCGGTACAAGGTTCACTG
* ** ** *
208215 TTGCGACTTAAACCCTTCCCCTCGCGTCTTCATGGTATTGTTTTTACCGTTGCGACTAAAATCTT
1 TTGCGACTTAAACCCTTCCCCTCGCGTCTTCATGGTACTGGATCCACCGTTGCGACTAAAATATT
* *
208280 TCCCTTCATGTTTTTGCGGTA
66 TCCCTTCATGTCTCTGCGGTA
208301 GTAGATCCGT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
98 70 1.00
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.39
Consensus pattern (98 bp):
TTGCGACTTAAACCCTTCCCCTCGCGTCTTCATGGTACTGGATCCACCGTTGCGACTAAAATATT
TCCCTTCATGTCTCTGCGGTACAAGGTTCACTG
Found at i:208315 original size:49 final size:50
Alignment explanation
Indices: 208262--208537 Score: 149
Period size: 49 Copynumber: 5.6 Consensus size: 50
208252 TTGTTTTTAC
* * *
208262 CGTTGCGACTAAAATCTTTCCCTTCATGT-TTTTGCGGTAGTA-GATCCGT
1 CGTTGCGACTAAAATCTTTCCCTTAATGTCTTTTGAGGTACTAGGAT-CGT
* * * *
208311 CGTTGCGGCTTAGATCTTTCCCTTAATGTCTTTTGAGGTACTAGGATTGT
1 CGTTGCGACTAAAATCTTTCCCTTAATGTCTTTTGAGGTACTAGGATCGT
* * * * *
208361 CATTGCGAC-ATAAACCTTTCCCTT-GTGTC-TTTGTGGTACT-GGATCTGC
1 CGTTGCGACTA-AAATCTTTCCCTTAATGTCTTTTGAGGTACTAGGATC-GT
* * * ** * * * *
208409 CGTTGCGGCTTAGATCTTTCCCTCCATG-CTTCTGAGATACTAGGTTCGC
1 CGTTGCGACTAAAATCTTTCCCTTAATGTCTTTTGAGGTACTAGGATCGT
* * * * * * *
208458 CATTGCGACTTAAACCTTTCCCTT-GTGTC-TTTGTGGTAC-CGGATCCGC
1 CGTTGCGACTAAAATCTTTCCCTTAATGTCTTTTGAGGTACTAGGAT-CGT
* * * * *
208506 CGTTGCGGCTTAGATATTTCCCTTCATGTCTT
1 CGTTGCGACTAAAATCTTTCCCTTAATGTCTT
208538 ATAGTGCTGA
Statistics
Matches: 171, Mismatches: 44, Indels: 23
0.72 0.18 0.10
Matches are distributed among these distances:
47 7 0.04
48 60 0.35
49 65 0.38
50 36 0.21
51 3 0.02
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (50 bp):
CGTTGCGACTAAAATCTTTCCCTTAATGTCTTTTGAGGTACTAGGATCGT
Found at i:208474 original size:97 final size:98
Alignment explanation
Indices: 208264--208537 Score: 363
Period size: 97 Copynumber: 2.8 Consensus size: 98
208254 GTTTTTACCG
* * * * * * * *
208264 TTGCGACTAAAATCTTTCCCTTCATGTTTTTGCGGTAGTAGATCCGTCGTTGCGGCTTAGATCTT
1 TTGCGACTTAAACCTTTCCCTT-GTGTCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTT
* * * *
208329 TCCCTTAATGTCTTTTGAGGTACTAGGATTGTCA
65 TCCCTTCATGTCTTCTGAGATACTAGGATTGCCA
* *
208363 TTGCGACATAAACCTTTCCCTTGTGTCTTTGTGGTACTGGATCTGCCGTTGCGGCTTAGATCTTT
1 TTGCGACTTAAACCTTTCCCTTGTGTCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTT
*
208428 CCCTCCATG-CTTCTGAGATACTAGG-TTCGCCA
66 CCCTTCATGTCTTCTGAGATACTAGGATT-GCCA
* *
208460 TTGCGACTTAAACCTTTCCCTTGTGTCTTTGTGGTACCGGATCCGCCGTTGCGGCTTAGATATTT
1 TTGCGACTTAAACCTTTCCCTTGTGTCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTT
208525 CCCTTCATGTCTT
66 CCCTTCATGTCTT
208538 ATAGTGCTGA
Statistics
Matches: 153, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
96 2 0.01
97 86 0.56
98 46 0.30
99 19 0.12
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (98 bp):
TTGCGACTTAAACCTTTCCCTTGTGTCTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTT
CCCTTCATGTCTTCTGAGATACTAGGATTGCCA
Found at i:220251 original size:29 final size:29
Alignment explanation
Indices: 220183--220514 Score: 142
Period size: 29 Copynumber: 11.4 Consensus size: 29
220173 TATTTGGGGG
* **
220183 AAATGGTAATTTTGGAAAGTTCGAGGTTTA
1 AAATGGTAATTTTAGAAAGTTC-AGGGGTA
* *
220213 AAAT-GAAATTGTTAG-AAGTTCGGGGGTA
1 AAATGGTAATT-TTAGAAAGTTCAGGGGTA
*
220241 AAATGGTAATTTTTAGAAAGATT-AGGGTTA
1 AAATGGTAA-TTTTAGAAAG-TTCAGGGGTA
* *
220271 GAATGG-AATTTTA-AGAAGTTTAGGGGTA
1 AAATGGTAATTTTAGA-AAGTTCAGGGGTA
* * *
220299 AAATGGTAATTTTTGGAAAATT-AGGGTTA
1 AAATGGTAA-TTTTAGAAAGTTCAGGGGTA
** * *
220328 AAATGG-AATTTTTTAAAATTC-GATGGTA
1 AAATGGTAATTTTAGAAAGTTCAG-GGGTA
* * *
220356 AAATGGCAATTTTTTGAAAAATT-A-GGGTCA
1 AAATGGTAA-TTTTAG-AAAGTTCAGGGGT-A
*
220386 AAATGG-AATTTT-GAAAAGTTC-GAGTGTAA
1 AAATGGTAATTTTAG-AAAGTTCAG-GGGT-A
* *
220415 AAAT-GTAATCTTTA-AATAGTTTAGGGTTAA
1 AAATGGTAAT-TTTAGAA-AGTTCAGGGGT-A
* * *
220445 AAAT-GAAATTTTATAAAGTTTAGGGGTA
1 AAATGGTAATTTTAGAAAGTTCAGGGGTA
* *
220473 AAAT-GTAATTTTTAGAAAGTTTAAGGGTTA
1 AAATGGTAA-TTTTAGAAAG-TTCAGGGGTA
220503 AAAT-GTAATTTT
1 AAATGGTAATTTT
220515 GAATAAGTTT
Statistics
Matches: 242, Mismatches: 32, Indels: 57
0.73 0.10 0.17
Matches are distributed among these distances:
27 21 0.09
28 51 0.21
29 81 0.33
30 79 0.33
31 10 0.04
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (29 bp):
AAATGGTAATTTTAGAAAGTTCAGGGGTA
Found at i:220251 original size:58 final size:56
Alignment explanation
Indices: 220183--220514 Score: 251
Period size: 58 Copynumber: 5.7 Consensus size: 56
220173 TATTTGGGGG
*
220183 AAATGGTAA-TTTTGGAAAGTTCGAGGTTTAAAATGAAATTGTTAGAAGTTCGGGGGTA
1 AAATGGTAATTTTTGGAAAGTT--AGGGTTAAAATGAAATT-TTAGAAGTTCGGGGGTA
* * * **
220241 AAATGGTAATTTTTAGAAAGATTAGGGTTAGAATGGAATTTTAAGAAGTTTAGGGGTA
1 AAATGGTAATTTTTGGAAAG-TTAGGGTTAAAATGAAATTTT-AGAAGTTCGGGGGTA
* * * **
220299 AAATGGTAATTTTTGGAAAATTAGGGTTAAAATGGAATTTTTTA-AAATTCGATGGTA
1 AAATGGTAATTTTTGGAAAGTTAGGGTTAAAAT-GAA-ATTTTAGAAGTTCGGGGGTA
* * * * * * * *
220356 AAATGGCAATTTTTTGAAAAATTAGGGTCAAAATGGAATTTTGAAAAGTTCGAGTGTAA
1 AAATGGTAA-TTTTTGGAAAGTTAGGGTTAAAATGAAATTTT-AGAAGTTCGGGGGT-A
* * * **
220415 AAAT-GTAATCTTT-AAATAGTTTAGGGTTAAAAATGAAATTTTATAAAGTTTAGGGGTA
1 AAATGGTAATTTTTGGAA-AG-TTAGGGTT-AAAATGAAATTTTA-GAAGTTCGGGGGTA
* *
220473 AAAT-GTAATTTTTAGAAAGTTTAAGGGTTAAAATGTAATTTT
1 AAATGGTAATTTTTGGAAAG-TT-AGGGTTAAAATGAAATTTT
220515 GAATAAGTTT
Statistics
Matches: 223, Mismatches: 36, Indels: 30
0.77 0.12 0.10
Matches are distributed among these distances:
56 7 0.03
57 38 0.17
58 129 0.58
59 47 0.21
60 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (56 bp):
AAATGGTAATTTTTGGAAAGTTAGGGTTAAAATGAAATTTTAGAAGTTCGGGGGTA
Found at i:220293 original size:28 final size:29
Alignment explanation
Indices: 220239--220514 Score: 162
Period size: 29 Copynumber: 9.5 Consensus size: 29
220229 AGTTCGGGGG
220239 TAAAATGGTAATTTTTAGAAAGATTAGGGT
1 TAAAATGGTAATTTTTAG-AAGATTAGGGT
* * * *
220269 TAGAATGG-AATTTTAAGAAGTTTAGGGG
1 TAAAATGGTAATTTTTAGAAGATTAGGGT
* *
220297 TAAAATGGTAATTTTTGGAAAATTAGGGT
1 TAAAATGGTAATTTTTAGAAGATTAGGGT
*
220326 TAAAATGG-AATTTTTTA-AA-ATTCGATGG-
1 TAAAATGGTAA-TTTTTAGAAGATT--AGGGT
* * *
220354 TAAAATGGCAATTTTTTGAAAAATTAGGGT
1 TAAAATGGTAATTTTTAG-AAGATTAGGGT
* * * *
220384 CAAAATGG-AATTTTGAAAAG-TTCGAGTGT
1 TAAAATGGTAATTTTTAGAAGATT--AGGGT
* * * *
220413 AAAAAT-GTAATCTTTAAATAGTTTAGGGT
1 TAAAATGGTAATTTTTAGA-AGATTAGGGT
* * *
220442 TAAAAAT-GAAATTTTATA-AAGTTTAGGGG
1 T-AAAATGGTAATTTT-TAGAAGATTAGGGT
*
220471 TAAAAT-GTAATTTTTAGAAAGTTTAAGGGT
1 TAAAATGGTAATTTTTAG-AAGATT-AGGGT
220501 TAAAAT-GTAATTTT
1 TAAAATGGTAATTTT
220515 GAATAAGTTT
Statistics
Matches: 197, Mismatches: 30, Indels: 38
0.74 0.11 0.14
Matches are distributed among these distances:
27 7 0.04
28 48 0.24
29 87 0.44
30 48 0.24
31 7 0.04
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (29 bp):
TAAAATGGTAATTTTTAGAAGATTAGGGT
Found at i:220540 original size:29 final size:29
Alignment explanation
Indices: 220236--220553 Score: 144
Period size: 29 Copynumber: 10.9 Consensus size: 29
220226 AGAAGTTCGG
* *
220236 GGGTAAAATGGTAATTTTTAGAAAGATT-A
1 GGGTAAAAT-GTAATTTTGAGAAAGTTTAA
* * * *
220265 GGGTTAGAATGGAATTTTAAG-AAGTTTAG
1 GGG-TAAAATGTAATTTTGAGAAAGTTTAA
*
220294 GGGTAAAATGGTAATTTTTG-GAAA-ATT-A
1 GGGTAAAAT-GTAA-TTTTGAGAAAGTTTAA
* * **
220322 GGGTTAAAATGGAATTTTTTA-AAA-TTCGA
1 GGG-TAAAATGTAA-TTTTGAGAAAGTTTAA
* * ** **
220351 TGGTAAAATGGCAATTTTTTGAAAAATT-A
1 GGGTAAAAT-GTAATTTTGAGAAAGTTTAA
* **
220380 GGGTCAAAATGGAATTTTGA-AAAGTTCGA
1 GGGT-AAAATGTAATTTTGAGAAAGTTTAA
*
220409 GTGTAAAAATGTAATCTTT-A-AATAGTTT-A
1 GGGT-AAAATGTAAT-TTTGAGAA-AGTTTAA
* * *
220438 GGGTTAAAAATGAAATTTT-ATAAAGTTTAG
1 GGG-T-AAAATGTAATTTTGAGAAAGTTTAA
*
220468 GGGTAAAATGTAATTTTTAGAAAGTTTAA
1 GGGTAAAATGTAATTTTGAGAAAGTTTAA
220497 GGGTTAAAATGTAATTTTGA-ATAAGTTTAA
1 GGG-TAAAATGTAATTTTGAGA-AAGTTTAA
* *
220527 GGGTCAAATATAATTTT-AGTAAAGTTT
1 GGGTAAAATGTAATTTTGAG-AAAGTTT
220554 GGGGGTCAAA
Statistics
Matches: 227, Mismatches: 39, Indels: 46
0.73 0.12 0.15
Matches are distributed among these distances:
28 53 0.23
29 107 0.47
30 67 0.30
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
GGGTAAAATGTAATTTTGAGAAAGTTTAA
Found at i:220559 original size:29 final size:29
Alignment explanation
Indices: 220432--220587 Score: 122
Period size: 29 Copynumber: 5.3 Consensus size: 29
220422 ATCTTTAAAT
*
220432 AGTTTAGGGTTAAAA-ATGAAATTTTA-TAA
1 AGTTTAGGGGTAAAATAT--AATTTTAGTAA
*
220461 AGTTTAGGGGTAAAATGTAATTTTTAG-AA
1 AGTTTAGGGGTAAAATATAA-TTTTAGTAA
* * *
220490 AGTTTAAGGGTTAAAATGTAATTTT-GAATA
1 AGTTT-AGGGGTAAAATATAATTTTAGTA-A
* *
220520 AGTTTAAGGGTCAAATATAATTTTAGTAA
1 AGTTTAGGGGTAAAATATAATTTTAGTAA
* * * * *
220549 AGTTTGGGGGTCAAAATATGATTTTTGGAC
1 AGTTTAGGGGT-AAAATATAATTTTAGTAA
220579 AGTTTAGGG
1 AGTTTAGGG
220588 ACCTCTAGAG
Statistics
Matches: 103, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
28 3 0.03
29 56 0.54
30 44 0.43
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (29 bp):
AGTTTAGGGGTAAAATATAATTTTAGTAA
Found at i:220565 original size:59 final size:58
Alignment explanation
Indices: 220236--220565 Score: 176
Period size: 58 Copynumber: 5.7 Consensus size: 58
220226 AGAAGTTCGG
* * * * * *
220236 GGGTAAAATGGTAATTTTTAGAAAGATT-AGGGTTAGAATGGAATTTTA-AGAAGTTTAG
1 GGGTAAAAT-ATAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTATA-AAGTTTAA
* * * * * * * **
220294 GGGTAAAATGGTAATTTTTGGAAA-ATT-AGGGTTAAAATGGAATTTTTTAAAATTCGA
1 GGGTAAAAT-ATAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTATAAAGTTTAA
* ** * ** * **
220351 TGGTAAAATGGCAATTTTTTGAAAAATT-AGGGTCAAAATGGAATTTTGA-AAAGTTCGA
1 GGGTAAAAT-ATAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTT-ATAAAGTTTAA
* * * * *
220409 GTGTAAAAATGTAATCTTTA-AATAGTTT-AGGGTTAAAAATGAAATTTTATAAAGTTTAG
1 GGGT-AAAATATAATTTTTAGAA-AGTTTAAGGG-TCAAAATGAAATTTTATAAAGTTTAA
* * *
220468 GGGTAAAATGTAATTTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTGA-ATAAGTTTAA
1 GGGTAAAATATAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTT-ATA-AAGTTTAA
* **
220527 GGGTCAAATATAA-TTTTAGTAAAGTTTGGGGGTCAAAAT
1 GGGTAAAATATAATTTTTAG-AAAGTTTAAGGGTCAAAAT
220566 ATGATTTTTG
Statistics
Matches: 225, Mismatches: 35, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
57 48 0.21
58 109 0.48
59 68 0.30
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (58 bp):
GGGTAAAATATAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTATAAAGTTTAA
Found at i:220573 original size:59 final size:59
Alignment explanation
Indices: 220379--220573 Score: 143
Period size: 59 Copynumber: 3.3 Consensus size: 59
220369 TTGAAAAATT
** ** * * *
220379 AGGGTCAAAATGGAATTTTGAA-AAGTTCGAGTGTAAAAATGTAATCTTTA-AATAGTTT-
1 AGGGTCAAAATATAATTTTGAATAAGTTTAAGGGT-AAAATATAATTTTTAGAA-AGTTTA
* * *
220437 AGGGTTAAAA-ATGAAATTTT--ATAAAGTTTAGGGGTAAAATGTAATTTTTAGAAAGTTTA
1 AGGGTCAAAATAT--AATTTTGAAT-AAGTTTAAGGGTAAAATATAATTTTTAGAAAGTTTA
* * * *
220496 AGGGTTAAAATGTAATTTTGAATAAGTTTAAGGGTCAAATATAA-TTTTAGTAAAGTTTG
1 AGGGTCAAAATATAATTTTGAATAAGTTTAAGGGTAAAATATAATTTTTAG-AAAGTTTA
* *
220555 GGGGTCAAAATATGATTTT
1 AGGGTCAAAATATAATTTT
220574 TGGACAGTTT
Statistics
Matches: 110, Mismatches: 17, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
57 1 0.01
58 40 0.36
59 66 0.60
60 3 0.03
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (59 bp):
AGGGTCAAAATATAATTTTGAATAAGTTTAAGGGTAAAATATAATTTTTAGAAAGTTTA
Found at i:222445 original size:30 final size:30
Alignment explanation
Indices: 222411--222473 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
222401 TAATTCGACT
*
222411 TTTTAATCTTCAATTTGAATTTAAAATAAA
1 TTTTAATCTTAAATTTGAATTTAAAATAAA
* *
222441 TTTTAGTTTTAAATTTGAATTTAAAATAAA
1 TTTTAATCTTAAATTTGAATTTAAAATAAA
222471 TTT
1 TTT
222474 AAATTCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (30 bp):
TTTTAATCTTAAATTTGAATTTAAAATAAA
Found at i:222470 original size:17 final size:17
Alignment explanation
Indices: 222422--222478 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
222412 TTTAATCTTC
222422 AATTTGAATTTAAAATA
1 AATTTGAATTTAAAATA
* *
222439 AATTTTAGTTT----TA
1 AATTTGAATTTAAAATA
222452 AATTTGAATTTAAAATA
1 AATTTGAATTTAAAATA
*
222469 AATTTAAATT
1 AATTTGAATT
222479 CAAACTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
13 11 0.35
17 20 0.65
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATTTGAATTTAAAATA
Found at i:222474 original size:11 final size:11
Alignment explanation
Indices: 222458--222498 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
222448 TTTAAATTTG
222458 AATTTAAAATA
1 AATTTAAAATA
*
222469 AATTTAAATTCA
1 AATTTAAAAT-A
*
222481 AACTTAAAATA
1 AATTTAAAATA
222492 AATTTAA
1 AATTTAA
222499 TTAAAGATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTTAAAATA
Found at i:227809 original size:24 final size:26
Alignment explanation
Indices: 227782--227829 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
227772 AGAGAAATGT
227782 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
227806 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
227830 CCCATGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:228011 original size:48 final size:47
Alignment explanation
Indices: 227900--228042 Score: 168
Period size: 48 Copynumber: 3.0 Consensus size: 47
227890 GCGCTCTCTA
* *
227900 ATTAGCACTGTGTGTGCTCTCTGATTAGCATTGTGTGTGCTCTCTG-T
1 ATTAGCACT-TGTGTGCCCTCTGATTAGCATTGTGTGTGCCCTCTGTT
*
227947 -TTAGCACATT-TCGTGCCCTCT-ATTCAGCACTGTGTGTGCCCTCTGTT
1 ATTAGCAC-TTGT-GTGCCCTCTGATT-AGCATTGTGTGTGCCCTCTGTT
* *
227994 ATTAGCACTTCGTGTGCCCTCTGATTAGCATTTTGTGTGCCTTCTGTT
1 ATTAGCACTT-GTGTGCCCTCTGATTAGCATTGTGTGTGCCCTCTGTT
228042 A
1 A
228043 AGTACTTCGA
Statistics
Matches: 82, Mismatches: 6, Indels: 15
0.80 0.06 0.15
Matches are distributed among these distances:
45 4 0.05
46 34 0.41
47 4 0.05
48 36 0.44
49 4 0.05
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (47 bp):
ATTAGCACTTGTGTGCCCTCTGATTAGCATTGTGTGTGCCCTCTGTT
Found at i:228034 original size:23 final size:23
Alignment explanation
Indices: 227895--228039 Score: 136
Period size: 23 Copynumber: 6.2 Consensus size: 23
227885 CTAGCGCGCT
* *
227895 CTCTAATTAGCACTGTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCC
* *
227918 CTCTGATTAGCATTGTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCC
*
227941 CTCTGTTTAGCACAT-T-TCGTGCC
1 CTCTGATTAGCAC-TGTGT-GTGCC
227964 CTCT-ATTCAGCACTGTGTGTGCC
1 CTCTGATT-AGCACTGTGTGTGCC
227987 CTCTGTTATTAGCACT-TCGTGTGCC
1 CTCTG--ATTAGCACTGT-GTGTGCC
* *
228012 CTCTGATTAGCATTTTGTGTGCC
1 CTCTGATTAGCACTGTGTGTGCC
*
228035 TTCTG
1 CTCTG
228040 TTAAGTACTT
Statistics
Matches: 104, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.04
23 75 0.72
24 4 0.04
25 18 0.17
26 3 0.03
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (23 bp):
CTCTGATTAGCACTGTGTGTGCC
Found at i:230304 original size:21 final size:21
Alignment explanation
Indices: 230278--230320 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
230268 TTCTTGCCAT
*
230278 GTCAACAAGGAAGCTCATCCA
1 GTCAACAAGGAAGCTCACCCA
230299 GTCAACAAGGAAGCTCACCCA
1 GTCAACAAGGAAGCTCACCCA
230320 G
1 G
230321 CTGGACGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.30, G:0.21, T:0.12
Consensus pattern (21 bp):
GTCAACAAGGAAGCTCACCCA
Found at i:231709 original size:18 final size:18
Alignment explanation
Indices: 231686--231725 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
231676 AACCCTTTTA
* *
231686 AAAAACCATAACCCTACC
1 AAAAACCATAAACCTAAC
*
231704 AAAAACCTTAAACCTAAC
1 AAAAACCATAAACCTAAC
231722 AAAA
1 AAAA
231726 TTGAAAACCT
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:0.57, C:0.30, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAACCATAAACCTAAC
Found at i:232529 original size:2 final size:2
Alignment explanation
Indices: 232522--232554 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
232512 AACTGTAAAC
232522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
232555 GACTTATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:233161 original size:10 final size:10
Alignment explanation
Indices: 233143--233173 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
233133 ATACTAACAT
*
233143 AGCATGCAGG
1 AGCACGCAGG
233153 AGCACGCAGG
1 AGCACGCAGG
233163 AGCACGCAGG
1 AGCACGCAGG
233173 A
1 A
233174 TGACCTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.26, G:0.39, T:0.03
Consensus pattern (10 bp):
AGCACGCAGG
Found at i:233579 original size:5 final size:5
Alignment explanation
Indices: 233564--233592 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
233554 CAATGCGTAT
233564 TGGGG -GGGG TGGGG TGGGG TGGGG TGGGG
1 TGGGG TGGGG TGGGG TGGGG TGGGG TGGGG
233593 GAGTATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.83, T:0.17
Consensus pattern (5 bp):
TGGGG
Found at i:233812 original size:28 final size:28
Alignment explanation
Indices: 233768--233827 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
233758 AAAATTATAT
*
233768 TATATTATTTTAATATTTAATAA-TTTTA
1 TATATTATTTTAATATTGAA-AATTTTTA
*
233796 TATATT-TTTTATTTATTGAAAATTTTTA
1 TATATTATTTTA-ATATTGAAAATTTTTA
233824 TATA
1 TATA
233828 ATCATCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TATATTATTTTAATATTGAAAATTTTTA
Found at i:233825 original size:26 final size:26
Alignment explanation
Indices: 233758--233826 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 26
233748 TTTAAAAAAA
*
233758 AAAATTATATTATATTATTTTAATATTT
1 AAAATT-T-TTATATTATTTTAATATTG
*
233786 AATAATTTTATATATT-TTTTATTTATTG
1 AA-AATTTT-TATATTATTTTA-ATATTG
233814 AAAATTTTTATAT
1 AAAATTTTTATAT
233827 AATCATCTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
26 5 0.14
27 12 0.33
28 15 0.42
29 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (26 bp):
AAAATTTTTATATTATTTTAATATTG
Found at i:235258 original size:22 final size:18
Alignment explanation
Indices: 235232--235295 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
235222 TATTAAAAAA
235232 TAAAAAATTCAAAATATTATT
1 TAAAAAATT-AAAA-ATTA-T
*
235253 TTAAAAATTAAAAATTAT
1 TAAAAAATTAAAAATTAT
235271 TAAAAAATATAAAAATTA-
1 TAAAAAAT-TAAAAATTAT
235289 TAAAAAA
1 TAAAAAA
235296 GTAGTTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 15 0.38
19 13 0.32
20 4 0.10
21 8 0.20
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAATTAAAAATTAT
Found at i:235271 original size:19 final size:19
Alignment explanation
Indices: 235232--235289 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
235222 TATTAAAAAA
235232 TAAAAAATTCAAAATATTATT
1 TAAAAAATT-AAAA-ATTATT
*
235253 TTAAAAATTAAAAATTA-T
1 TAAAAAATTAAAAATTATT
235271 TAAAAAATATAAAAATTAT
1 TAAAAAAT-TAAAAATTAT
235290 AAAAAAGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 8 0.24
19 13 0.39
20 4 0.12
21 8 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAATTAAAAATTATT
Found at i:235274 original size:10 final size:9
Alignment explanation
Indices: 235261--235294 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
235251 TTTTAAAAAT
235261 TAAAAATTA
1 TAAAAATTA
*
235270 TTAAAAAATA
1 -TAAAAATTA
235280 TAAAAATTA
1 TAAAAATTA
235289 TAAAAA
1 TAAAAA
235295 AGTAGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:235294 original size:19 final size:18
Alignment explanation
Indices: 235255--235295 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
235245 ATATTATTTT
*
235255 AAAAATTAAAAATTATTA
1 AAAAATTAAAAATTATAA
235273 AAAAATATAAAAATTATAA
1 AAAAAT-TAAAAATTATAA
235292 AAAA
1 AAAA
235296 GTAGTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATTAAAAATTATAA
Found at i:239477 original size:18 final size:17
Alignment explanation
Indices: 239454--239491 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
239444 CTTTACTTTT
*
239454 ATTTTATTTTACCAATGA
1 ATTTTATTTTAACAAT-A
239472 ATTTTATTTTAACAATA
1 ATTTTATTTTAACAATA
239489 ATT
1 ATT
239492 CTAGTCACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTTATTTTAACAATA
Found at i:240027 original size:3 final size:3
Alignment explanation
Indices: 240019--240067 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
240009 AATTGAGGAG
*
240019 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
240067 T
1 T
240068 TAAGAAGTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:240387 original size:26 final size:26
Alignment explanation
Indices: 240357--240429 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
240347 TATTTTGGAG
240357 ATATTTTTTATTAATCA-ATTAGC-TAA
1 ATATTTTTTATTAAT-ATATTA-CTTAA
* *
240383 ATATTATTTTATTAATATTTTACTTAG
1 ATATT-TTTTATTAATATATTACTTAA
240410 ATATTTTTTATTAATATATT
1 ATATTTTTTATTAATATATT
240430 TAAAAAATGG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 21 0.51
27 20 0.49
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (26 bp):
ATATTTTTTATTAATATATTACTTAA
Found at i:241201 original size:12 final size:12
Alignment explanation
Indices: 241184--241215 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
241174 TTTCATATGG
241184 AAGAAACAGTGA
1 AAGAAACAGTGA
241196 AAGAAACAGTGA
1 AAGAAACAGTGA
241208 AAGAAACA
1 AAGAAACA
241216 AAATTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.09, G:0.22, T:0.06
Consensus pattern (12 bp):
AAGAAACAGTGA
Found at i:243468 original size:22 final size:23
Alignment explanation
Indices: 243436--243478 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
243426 AGTTAGGTGT
243436 CATTTGTTTAGTAACCTTTTAAA
1 CATTTGTTTAGTAACCTTTTAAA
* *
243459 CATTT-TTTAGTTACGTTTTA
1 CATTTGTTTAGTAACCTTTTA
243479 GTCTCACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (23 bp):
CATTTGTTTAGTAACCTTTTAAA
Found at i:247966 original size:149 final size:155
Alignment explanation
Indices: 247749--248099 Score: 446
Period size: 160 Copynumber: 2.3 Consensus size: 155
247739 ATTTAAATAA
* *
247749 TTTGAAATTGACAATGAGAAAGTGTTTACGATATACCTGTGATTCAGTTATGTTAGGCTGAATGC
1 TTTGGAATTGACAATGAGAAAGTGTTTACGATATACTTGTGATTCAGTTATGTTAGGCTGAATGC
* * * *
247814 ATGGT-G-G-TG-TTC-TGTTGGGTTGTAGTTCTTATACTCATACTAGACTAGGACCAAAAAAAT
66 ATGGTGGTGTTGATTCTTGTTGGGTTGTAGTTCTCATACTCATACCACACTAAGACCAAAAAAAT
* * * *
247874 TAGAATCGAAATTAGATTATTATAT
131 CAAAACCAAAATTAGATTATTATAT
* *
247899 TTTGGAATTGACAATGAGAAAGTGTTT-CGATATTCTTGTGA-TCTAGTTGTGTTAGGCTGAATG
1 TTTGGAATTGACAATGAGAAAGTGTTTACGATATACTTGTGATTC-AGTTATGTTAGGCTGAATG
* *
247962 CATGGTGGTGTTTTGTCATTCTTTTTTTGGGTTGTAGTTCTCATACTCGTACCACACTAAGACCA
65 CATGGTGGTG--TTG--ATTC--TTGTTGGGTTGTAGTTCTCATACTCATACCACACTAAGACCA
248027 AAAAAATCAAAACCAAAATTAGATTATTATAT
124 AAAAAATCAAAACCAAAATTAGATTATTATAT
* *
248059 TTTGGAATTGATAATGATAAAGTGTTTACGATATACTTGTG
1 TTTGGAATTGACAATGAGAAAGTGTTTACGATATACTTGTG
248100 TTCCCTTTGT
Statistics
Matches: 171, Mismatches: 17, Indels: 15
0.84 0.08 0.07
Matches are distributed among these distances:
148 2 0.01
149 36 0.21
150 27 0.16
151 1 0.01
154 2 0.01
157 3 0.02
160 88 0.51
161 12 0.07
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (155 bp):
TTTGGAATTGACAATGAGAAAGTGTTTACGATATACTTGTGATTCAGTTATGTTAGGCTGAATGC
ATGGTGGTGTTGATTCTTGTTGGGTTGTAGTTCTCATACTCATACCACACTAAGACCAAAAAAAT
CAAAACCAAAATTAGATTATTATAT
Found at i:256003 original size:56 final size:55
Alignment explanation
Indices: 255920--256070 Score: 248
Period size: 56 Copynumber: 2.7 Consensus size: 55
255910 TCGAGACCTT
* *
255920 TCAATTTAAATTAAAAAACATAAGTAAGTCTGTTGTCAATATACTAAGTTTGTTG
1 TCAATTTAAATTAAAAAACATAAGTAAGTCTGTTGTCAATATACTAAGTTTGCTA
* *
255975 TTAATTTAAATTAAAAAAACATAAGTAAGTCTATTGTCAATATACTAAGTTTGCTA
1 TCAATTTAAATT-AAAAAACATAAGTAAGTCTGTTGTCAATATACTAAGTTTGCTA
*
256031 TCAATTTAAATTAAAAAATATAAGTAAGTCTGTTGTCAAT
1 TCAATTTAAATTAAAAAACATAAGTAAGTCTGTTGTCAAT
256071 TTAAATTTAA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
55 37 0.42
56 51 0.58
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (55 bp):
TCAATTTAAATTAAAAAACATAAGTAAGTCTGTTGTCAATATACTAAGTTTGCTA
Found at i:256105 original size:35 final size:35
Alignment explanation
Indices: 256020--256105 Score: 127
Period size: 35 Copynumber: 2.5 Consensus size: 35
256010 GTCAATATAC
*
256020 TAAGTTTGCTATCAATTTAAATTAAAAAATATAAG
1 TAAGTTTGCTATCAATTTAAATTAAAAAACATAAG
* * * *
256055 TAAGTCTGTTGTCAATTTAAATTTAAAAACATAAG
1 TAAGTTTGCTATCAATTTAAATTAAAAAACATAAG
256090 TAAGTTTGCTATCAAT
1 TAAGTTTGCTATCAAT
256106 ATACTAAGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (35 bp):
TAAGTTTGCTATCAATTTAAATTAAAAAACATAAG
Found at i:256110 original size:90 final size:91
Alignment explanation
Indices: 255964--256169 Score: 288
Period size: 90 Copynumber: 2.3 Consensus size: 91
255954 GTCAATATAC
* * * * *
255964 TAAGTTTGTTGTTAATTTAAATTAAAAAAACATAAGTAAGTCTATTGTCAATATACTAAGTTTGC
1 TAAGTCTGTTGTCAATTTAAATTAAAAAAACATAAGTAAGTCTACTATCAATATACTAAGTCTGC
*
256029 TATCAATTTAAATTAAAAAATATAAG
66 TATCAATTTAAATTAAAAAACATAAG
* * * *
256055 TAAGTCTGTTGTCAATTTAAATT-TAAAAACATAAGTAAGTTTGCTATCAATATACTAAGTCTGT
1 TAAGTCTGTTGTCAATTTAAATTAAAAAAACATAAGTAAGTCTACTATCAATATACTAAGTCTGC
* *
256119 TGTCAATTTAAATTTAAAAACATAAG
66 TATCAATTTAAATTAAAAAACATAAG
*
256145 TAAGTCTGCTGTCAATTTAAATTAA
1 TAAGTCTGTTGTCAATTTAAATTAA
256170 TAGTATTAGT
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 79 0.79
91 21 0.21
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (91 bp):
TAAGTCTGTTGTCAATTTAAATTAAAAAAACATAAGTAAGTCTACTATCAATATACTAAGTCTGC
TATCAATTTAAATTAAAAAACATAAG
Found at i:256114 original size:55 final size:55
Alignment explanation
Indices: 256055--256160 Score: 194
Period size: 55 Copynumber: 1.9 Consensus size: 55
256045 AAAATATAAG
*
256055 TAAGTCTGTTGTCAATTTAAATTTAAAAACATAAGTAAGTTTGCTATCAATATAC
1 TAAGTCTGTTGTCAATTTAAATTTAAAAACATAAGTAAGTCTGCTATCAATATAC
*
256110 TAAGTCTGTTGTCAATTTAAATTTAAAAACATAAGTAAGTCTGCTGTCAAT
1 TAAGTCTGTTGTCAATTTAAATTTAAAAACATAAGTAAGTCTGCTATCAAT
256161 TTAAATTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (55 bp):
TAAGTCTGTTGTCAATTTAAATTTAAAAACATAAGTAAGTCTGCTATCAATATAC
Found at i:257422 original size:45 final size:45
Alignment explanation
Indices: 257314--257424 Score: 168
Period size: 45 Copynumber: 2.5 Consensus size: 45
257304 TTGCCTAGCT
* *
257314 TCTTGAAGCTCCTCATCAGCATCACCACCTAATAAGTAAATATCA
1 TCTTGAAGCTCCTCATCATCATCACCACATAATAAGTAAATATCA
* * * *
257359 TCTTGAAACTCCTCATCATCATCACCATATGATAAGTTAATATCA
1 TCTTGAAGCTCCTCATCATCATCACCACATAATAAGTAAATATCA
257404 TCTTGAAGCTCCTCATCATCA
1 TCTTGAAGCTCCTCATCATCA
257425 CTACCTCCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (45 bp):
TCTTGAAGCTCCTCATCATCATCACCACATAATAAGTAAATATCA
Found at i:257568 original size:87 final size:87
Alignment explanation
Indices: 257438--257601 Score: 240
Period size: 87 Copynumber: 1.9 Consensus size: 87
257428 CCTCCATCAC
* * *
257438 TAACAGCAACATCAACACCCTTCACACCTAAACTACTAGCAACCAAACCCTTACCTGAACCCTCA
1 TAACAGCAACATCAACACCCTCCACACCTAAACTACCAGCAACCAAACCCTTACCCGAACCCTCA
257503 CCA-CTACCCTCATCACCTTCAA
66 CCACCT-CCCTCATCACCTTCAA
* * * **
257525 TAACAGTAACATCAACACCCTCCACACCTAAACTGCCATCAACCTCACCCTTACCCGAACCCTCA
1 TAACAGCAACATCAACACCCTCCACACCTAAACTACCAGCAACCAAACCCTTACCCGAACCCTCA
257590 CCACCTCCCTCA
66 CCACCTCCCTCA
257602 CCCTCACCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
87 66 0.97
88 2 0.03
ACGTcount: A:0.34, C:0.45, G:0.04, T:0.18
Consensus pattern (87 bp):
TAACAGCAACATCAACACCCTCCACACCTAAACTACCAGCAACCAAACCCTTACCCGAACCCTCA
CCACCTCCCTCATCACCTTCAA
Found at i:257604 original size:18 final size:18
Alignment explanation
Indices: 257583--257619 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
257573 CCTTACCCGA
*
257583 ACCCTCACCACCTCCCTC
1 ACCCTCACCACCACCCTC
257601 ACCCTCACCACCACCCTC
1 ACCCTCACCACCACCCTC
257619 A
1 A
257620 AAACCTTCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.65, G:0.00, T:0.14
Consensus pattern (18 bp):
ACCCTCACCACCACCCTC
Found at i:257659 original size:105 final size:105
Alignment explanation
Indices: 257496--257706 Score: 332
Period size: 105 Copynumber: 2.0 Consensus size: 105
257486 CCTTACCTGA
* ** *
257496 ACCCTCACCACTACCCTCATCACCTTCAATAACAGTAACATCAACACCCTCCACACCTAAACTGC
1 ACCCTCACCACCACCCTCAAAACCTTCAATAACAGCAACATCAACACCCTCCACACCTAAACTGC
* *
257561 CATCAACCTCACCCTTACCCGAACCCTCACCACCTCCCTC
66 CAGCAACCTCACCCTTACCCGAACCCTCACCACCACCCTC
** *
257601 ACCCTCACCACCACCCTCAAAACCTTCGCTAACAGCAACATCAACACCCTGCACACCTAAACTGC
1 ACCCTCACCACCACCCTCAAAACCTTCAATAACAGCAACATCAACACCCTCCACACCTAAACTGC
*
257666 CAGCAACCTCACCCTTACCCGAACCCTCACCATCACCCTC
66 CAGCAACCTCACCCTTACCCGAACCCTCACCACCACCCTC
257706 A
1 A
257707 ACACCTTTAC
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 96 1.00
ACGTcount: A:0.30, C:0.49, G:0.04, T:0.16
Consensus pattern (105 bp):
ACCCTCACCACCACCCTCAAAACCTTCAATAACAGCAACATCAACACCCTCCACACCTAAACTGC
CAGCAACCTCACCCTTACCCGAACCCTCACCACCACCCTC
Found at i:257676 original size:87 final size:87
Alignment explanation
Indices: 257601--257789 Score: 234
Period size: 87 Copynumber: 2.2 Consensus size: 87
257591 CACCTCCCTC
* * *
257601 ACCCTCACCACCACCCTCAAAACCTTCGCTAACAGCAACATCAACACCCTGCACACCTAAACTGC
1 ACCCTCACCACCACCCTCAAAACCTTCACTAACAACAACATCAACACCCTCCACACCTAAACTGC
* *
257666 CAGCAACCTCACCCTTACCCGA
66 CAACAACCTCACCCCTACCCGA
* * * * * * *
257688 ACCCTCACCATCACCCTCAACACCTTTACTAACAACAACATCAACATCGTCCACATCTAAATTGC
1 ACCCTCACCACCACCCTCAAAACCTTCACTAACAACAACATCAACACCCTCCACACCTAAACTGC
* *
257753 TAACAACCTCACCCTTACCCGA
66 CAACAACCTCACCCCTACCCGA
* *
257775 ACTCTCACCATCACC
1 ACCCTCACCACCACC
257790 ACCTTCAACA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.33, C:0.45, G:0.05, T:0.17
Consensus pattern (87 bp):
ACCCTCACCACCACCCTCAAAACCTTCACTAACAACAACATCAACACCCTCCACACCTAAACTGC
CAACAACCTCACCCCTACCCGA
Found at i:257764 original size:192 final size:192
Alignment explanation
Indices: 257437--257784 Score: 518
Period size: 192 Copynumber: 1.8 Consensus size: 192
257427 ACCTCCATCA
* * *
257437 CTAACAGCAACATCAACACCCTTCACACCTAAACTACTAGCAACCAAACCCTTACCTGAACCCTC
1 CTAACAGCAACATCAACACCCTGCACACCTAAACTACCAGCAACCAAACCCTTACCCGAACCCTC
* ** *
257502 ACCACTACCCTCATCACCTTCAATAACAGTAACATCAACACCCTCCACACCTAAACTGCCATCAA
66 ACCACTACCCTCAACACCTTCAATAACAACAACATCAACACCCTCCACACCTAAACTGCCAACAA
257567 CCTCACCCTTACCCGAACCCTCACCACCTCCCTCACCCTCACCACCACCCTCAAAACCTTCG
131 CCTCACCCTTACCCGAACCCTCACCACCTCCCTCACCCTCACCACCACCCTCAAAACCTTCG
* **
257629 CTAACAGCAACATCAACACCCTGCACACCTAAACTGCCAGCAACCTCACCCTTACCCGAACCCTC
1 CTAACAGCAACATCAACACCCTGCACACCTAAACTACCAGCAACCAAACCCTTACCCGAACCCTC
* * * * * * *
257694 ACCA-TCACCCTCAACACCTTTACTAACAACAACATCAACATCGTCCACATCTAAATTGCTAACA
66 ACCACT-ACCCTCAACACCTTCAATAACAACAACATCAACACCCTCCACACCTAAACTGCCAACA
*
257758 ACCTCACCCTTACCCGAACTCTCACCA
130 ACCTCACCCTTACCCGAACCCTCACCA
257785 TCACCACCTT
Statistics
Matches: 137, Mismatches: 18, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
191 1 0.01
192 136 0.99
ACGTcount: A:0.33, C:0.45, G:0.04, T:0.18
Consensus pattern (192 bp):
CTAACAGCAACATCAACACCCTGCACACCTAAACTACCAGCAACCAAACCCTTACCCGAACCCTC
ACCACTACCCTCAACACCTTCAATAACAACAACATCAACACCCTCCACACCTAAACTGCCAACAA
CCTCACCCTTACCCGAACCCTCACCACCTCCCTCACCCTCACCACCACCCTCAAAACCTTCG
Found at i:257839 original size:23 final size:24
Alignment explanation
Indices: 257779--257852 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
257769 ACCCGAACTC
* ** *
257779 TCACCATCACCACCTTCAACACCC
1 TCACCATCACCACCTTTATTACCA
*
257803 TCACCATCATCACCTTTATT-CCA
1 TCACCATCACCACCTTTATTACCA
*
257826 TCACCCTCACCACCTTTATTACCA
1 TCACCATCACCACCTTTATTACCA
257850 TCA
1 TCA
257853 GCATAATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 20 0.48
24 22 0.52
ACGTcount: A:0.27, C:0.46, G:0.00, T:0.27
Consensus pattern (24 bp):
TCACCATCACCACCTTTATTACCA
Found at i:261793 original size:72 final size:72
Alignment explanation
Indices: 261676--261822 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
261666 AGAAAATTGG
261676 GTTGGTGCTTCAAAATAGATTTGGTGTAACAAAAATCATTCAAGAGATGTAGAAAACATATTTTT
1 GTTGGTGCTTCAAAATAGATTTGGTGTAACAAAAATCATTCAAGAGATGTAGAAAACATATTTTT
261741 CTCTCTT
66 CTCTCTT
*
261748 GTTGGTGCTTCAAAATTGATTTGGTGTAACAAAAATCATTCAAGAGATGTAGAAAACATATTTTT
1 GTTGGTGCTTCAAAATAGATTTGGTGTAACAAAAATCATTCAAGAGATGTAGAAAACATATTTTT
261813 CTCTCTT
66 CTCTCTT
261820 GTT
1 GTT
261823 TGGGTGTTTG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (72 bp):
GTTGGTGCTTCAAAATAGATTTGGTGTAACAAAAATCATTCAAGAGATGTAGAAAACATATTTTT
CTCTCTT
Found at i:269331 original size:17 final size:18
Alignment explanation
Indices: 269299--269334 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
269289 AGAGATAACT
269299 ACTCAAAAAATCAAGAAG
1 ACTCAAAAAATCAAGAAG
*
269317 ACTCTAAAAAT-AAGAAG
1 ACTCAAAAAATCAAGAAG
269334 A
1 A
269335 AAACCCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.61, C:0.14, G:0.11, T:0.14
Consensus pattern (18 bp):
ACTCAAAAAATCAAGAAG
Found at i:270047 original size:26 final size:26
Alignment explanation
Indices: 269983--270047 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
269973 TTCTGGATTT
* *
269983 TTTTTATTTTATGTATTTTTATAATG
1 TTTTTATTTTTTGTATTTTTATAATA
* *
270009 TTTTTATAATTTTGTA-TTTTATTACTA
1 TTTTTAT-TTTTTGTATTTTTA-TAATA
270036 TTTTTATTTTTT
1 TTTTTATTTTTT
270048 TAATCTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
26 16 0.50
27 16 0.50
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTTTATTTTTTGTATTTTTATAATA
Found at i:270048 original size:27 final size:26
Alignment explanation
Indices: 269961--270048 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 26
269951 TTTCTTCAGA
*
269961 TTTTTGTATTTTTT-CTGGATTTTTTTT
1 TTTTTGTATTTTTTACT--ATTTTTATT
* * *
269988 ATTTTATGTATTTTTATAATGTTTTTATA
1 -TTTT-TGTATTTTT-TACTATTTTTATT
*
270017 ATTTTGTATTTTATTACTATTTTTATT
1 TTTTTGTATTTT-TTACTATTTTTATT
270044 TTTTT
1 TTTTT
270049 AATCTTTTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
27 22 0.47
28 8 0.17
29 15 0.32
30 1 0.02
31 1 0.02
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (26 bp):
TTTTTGTATTTTTTACTATTTTTATT
Done.