Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold700
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: 259550
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:186598 original size:21 final size:20
Alignment explanation
Indices: 186552--186598 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
186542 GTAGCCAAAC
**
186552 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
186572 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACAC-AAAAAA
186592 TTGTATC
1 TTGTATC
186599 ATTACATTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 13 0.57
20 4 0.17
21 6 0.26
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:189457 original size:149 final size:148
Alignment explanation
Indices: 189129--189588 Score: 475
Period size: 149 Copynumber: 3.1 Consensus size: 148
189119 TTTTATATAA
* * * * *
189129 TTTTTAAGTCTATTAGGGTTACTGAGATACTTTTATGTCAAAGGTATACCC-TAAGGGTATTTTT
1 TTTTTAAGTCTTTTAGGGTTATTGAGATACTTTCATGTCAAAGGTATACCCAT-AGGGCATTTTC
* * * * * ** * *
189193 GTAA--TTCCAAGTACCAAGTTTTAACTTGTCACTAGGTCGCTTCTATGCC-AAGGGTACGTATT
65 ATAATTTTACTAGAACCGAGTCATAATTTGTCACTAGGTCACTTCTATGCCGAA-GGTACGTATT
*
189255 AGGCATAGG-TTGCTTTTCC
129 AGGCATAGGTTTTCTTTTCC
* * * * *
189274 TTTTTAAGTCTTTTAAGGTTATCGGGATATTTTCATGTCGAAGGTATACCCATCAGGGCATTTTC
1 TTTTTAAGTCTTTTAGGGTTATTGAGATACTTTCATGTCAAAGGTATACCCAT-AGGGCATTTTC
* * * * ** *
189339 ATAATTTTTCTAGAATCGAGTCCTAATTTGTAACCGGGTCACTTCTATGCCGAAAGTACGTATTA
65 ATAATTTTACTAGAACCGAGTCATAATTTGTCACTAGGTCACTTCTATGCCGAAGGTACGTATTA
189404 GGCATAGGTTTTCTTTTCC
130 GGCATAGGTTTTCTTTTCC
* *
189423 TTTTTAAGTCTTTTAGGGTTATTGAGATACTTTCATGTTTAAA-GTATGCCCATAGGGACATTTT
1 TTTTTAAGTCTTTTAGGGTTATTGAGATACTTTCATG-TCAAAGGTATACCCATAGGG-CATTTT
* ** *
189487 CATAATTTTACTAGAACCGAGTCATAATTTGTCACTAGGTTACTTCTATGTTGAGGGTACGTATT
64 CATAATTTTACTAGAACCGAGTCATAATTTGTCACTAGGTCACTTCTATGCCGAAGGTACGTATT
** *
189552 AGGTGTAGGTTCGT-TTTTCC
129 AGGCATAGGTT-TTCTTTTCC
* *
189572 TTTTTCAGTCCTTTAGG
1 TTTTTAAGTCTTTTAGG
189589 ATCATTGGGC
Statistics
Matches: 258, Mismatches: 49, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
145 43 0.17
146 13 0.05
148 55 0.21
149 143 0.55
150 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41
Consensus pattern (148 bp):
TTTTTAAGTCTTTTAGGGTTATTGAGATACTTTCATGTCAAAGGTATACCCATAGGGCATTTTCA
TAATTTTACTAGAACCGAGTCATAATTTGTCACTAGGTCACTTCTATGCCGAAGGTACGTATTAG
GCATAGGTTTTCTTTTCC
Found at i:200872 original size:44 final size:44
Alignment explanation
Indices: 200819--201156 Score: 271
Period size: 44 Copynumber: 7.7 Consensus size: 44
200809 TTCACCTTTG
***
200819 TTTTG-TTTGACGTACAATTACCACCCTAGTCAAATTTTTCTCA
1 TTTTGATTTGACGTATGGTTACCACCCTAGTCAAATTTTTCTCA
200862 TTTTGATTTGACGTATGGTTACCACCCT-GATCAAATTCTTT-TCA
1 TTTTGATTTGACGTATGGTTACCACCCTAG-TCAAATT-TTTCTCA
* * * *
200906 TTTTGATTTGATGTATGGTTACCACCCTGGTCAAA-TTTGC-CT
1 TTTTGATTTGACGTATGGTTACCACCCTAGTCAAATTTTTCTCA
* * *
200948 TTGTTCTATTTGACTGTATTGGTTACCACCCTGGTCAAACTTTTCTCA
1 TT-TT-GATTTGAC-GTA-TGGTTACCACCCTAGTCAAATTTTTCTCA
* * **** *
200996 TTTTGATCTGACGTATGGTTACCACCTTAGTCAAATCCACCTCT
1 TTTTGATTTGACGTATGGTTACCACCCTAGTCAAATTTTTCTCA
* * * * * *
201040 TTTCTG-TCTGACGTATGGTTAACACCCTGGTCAGATTCTTCTTA
1 TTT-TGATTTGACGTATGGTTACCACCCTAGTCAAATTTTTCTCA
* * * * *
201084 TTCTGATTTGACGTATGGTTGCCACCTTGGTCAAATCTTTT-TCC
1 TTTTGATTTGACGTATGGTTACCACCCTAGTCAAAT-TTTTCTCA
* *
201128 TTTT--TTTGATGTATAGTTACCACCCTAGT
1 TTTTGATTTGACGTATGGTTACCACCCTAGT
201157 TAAACCCTTC
Statistics
Matches: 237, Mismatches: 44, Indels: 29
0.76 0.14 0.09
Matches are distributed among these distances:
42 25 0.11
43 11 0.05
44 151 0.64
45 15 0.06
46 26 0.11
47 6 0.03
48 3 0.01
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.42
Consensus pattern (44 bp):
TTTTGATTTGACGTATGGTTACCACCCTAGTCAAATTTTTCTCA
Found at i:201056 original size:134 final size:132
Alignment explanation
Indices: 200836--201153 Score: 335
Period size: 134 Copynumber: 2.4 Consensus size: 132
200826 TGACGTACAA
* * * * *
200836 TTACCACCCTAGTCAAATTTTTCTCATTTTGATTTGACGTATGGTTACCACCCTGATCAAATTCT
1 TTACCACCCTGGTCAAACTTTTCTCATTTTGATCTGACGTATGGTTACCACCCTGATCAAATCCA
** * * * *
200901 TTTCATTTTGATTTGATGTATGGTTACCACCCTGGTCAAATTTGCCT-TTGTTCT-ATTTGACTG
66 CCTCATTTTGATCTGACGTATGGTTAACACCCTGGTCAAA-TT-CCTCTTATTCTGATTTGAC-G
200964 TATTGG
128 TA-TGG
*
200970 TTACCACCCTGGTCAAACTTTTCTCATTTTGATCTGACGTATGGTTACCA-CCTTAGTCAAATCC
1 TTACCACCCTGGTCAAACTTTTCTCATTTTGATCTGACGTATGGTTACCACCCTGA-TCAAATCC
* * *
201034 ACCTCTTTTCTG-TCTGACGTATGGTTAACACCCTGGTCAGATTCTTCTTATTCTGATTTGACGT
65 ACCTCATTT-TGATCTGACGTATGGTTAACACCCTGGTCAAATTCCTCTTATTCTGATTTGACGT
201098 ATGG
129 ATGG
* * * * * *
201102 TTGCCACCTTGGTCAAATCTTTT-TCCTTTT--TTTGATGTATAGTTACCACCCT
1 TTACCACCCTGGTCAAA-CTTTTCTCATTTTGATCTGACGTATGGTTACCACCCT
201154 AGTTAAACCC
Statistics
Matches: 157, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
130 15 0.10
131 3 0.02
132 26 0.17
133 20 0.13
134 91 0.58
135 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (132 bp):
TTACCACCCTGGTCAAACTTTTCTCATTTTGATCTGACGTATGGTTACCACCCTGATCAAATCCA
CCTCATTTTGATCTGACGTATGGTTAACACCCTGGTCAAATTCCTCTTATTCTGATTTGACGTAT
GG
Found at i:201605 original size:20 final size:20
Alignment explanation
Indices: 201580--201766 Score: 83
Period size: 20 Copynumber: 8.8 Consensus size: 20
201570 CTGCCAAGGA
201580 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
*
201600 AATGTATCGATACATCGA-TC
1 AATGTATCGATACAT-TATTC
**
201620 TTTGTATCGATACATCTAGGAAGTTTACCC
1 AATGTATCGATACAT-T----A--TT---C
201650 AGATGTATCGATACATT-TTGC
1 A-ATGTATCGATACATTATT-C
* * *
201671 ATTGTATCAATACATTGCTT-
1 AATGTATCGATACATT-ATTC
* **
201691 ATTGTATCGATACATTGCTC
1 AATGTATCGATACATTATTC
* * **
201711 ATTGTATCGATACATTGTAA
1 AATGTATCGATACATTATTC
* **
201731 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTATTC
201751 AATGTATCGATACATT
1 AATGTATCGATACATT
201767 CAGGCATTTT
Statistics
Matches: 136, Mismatches: 16, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.01
20 111 0.82
21 3 0.02
22 2 0.01
23 2 0.01
24 1 0.01
27 1 0.01
30 2 0.01
31 13 0.10
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:201746 original size:60 final size:60
Alignment explanation
Indices: 201653--201766 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
201643 TTTACCCAGA
* ** * * *
201653 TGTATCGATACATTTTGCATTGTATCAATACATTGCT-TATTGTATCGATACATTGCTCAT
1 TGTATCGATACATTGTAAAATGTATCAATACATTG-TAAAATGTATCGATACATTGCTCAT
*
201713 TGTATCGATACATTGTAAAATGTATCGATACATTGTAAAATGTATCGATACATT
1 TGTATCGATACATTGTAAAATGTATCAATACATTGTAAAATGTATCGATACATT
201767 CAGGCATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 45 0.98
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (60 bp):
TGTATCGATACATTGTAAAATGTATCAATACATTGTAAAATGTATCGATACATTGCTCAT
Found at i:201757 original size:40 final size:39
Alignment explanation
Indices: 201652--201766 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 39
201642 GTTTACCCAG
* * *
201652 ATGTATCGATACATTTTGCATTGTATCAATACATTGCTTA
1 ATGTATCGATACATTGT-CATTGTATCGATACATTGCTAA
*
201692 TTGTATCGATACATTGCTCATTGTATCGATACATTG-TAAA
1 ATGTATCGATACATTG-TCATTGTATCGATACATTGCT-AA
* *
201732 ATGTATCGATACATTGTAAAATGTATCGATACATT
1 ATGTATCGATACATTGT-CATTGTATCGATACATT
201767 CAGGCATTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 2 0.03
40 62 0.95
41 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTGTCATTGTATCGATACATTGCTAA
Found at i:204170 original size:76 final size:76
Alignment explanation
Indices: 204042--204431 Score: 618
Period size: 76 Copynumber: 5.0 Consensus size: 76
204032 AAATTTTTAG
* * *
204042 ATTTTTCATCTCGGGGATACTCCAACCCCGTTATTTTCGAAGGGACACTCCAACCCCGGTTTTAT
1 ATTTTTCA--TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
204107 TTCTAAAACATCA
64 TTCTAAAACATCA
* * *
204120 ATTTTTCATCGGGGATACTCCAACCCCGTTATTCTCAAAGGGATACTCCAACCCCGATTTTATTT
1 ATTTTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTT
204185 CTAAAACATCA
66 CTAAAACATCA
* *
204196 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGATTTTA
1 ATTTTTC---ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
204261 TTTCTAAAACATCA
63 TTTCTAAAACATCA
204275 ATTTTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTT
1 ATTTTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTT
204340 CTAAAACATCA
66 CTAAAACATCA
*
204351 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTA
1 ATTTTTC---ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
*
204416 TTTCTAAAACACCA
63 TTTCTAAAACATCA
204430 AT
1 AT
204432 GCTCCACAAT
Statistics
Matches: 293, Mismatches: 13, Indels: 11
0.92 0.04 0.03
Matches are distributed among these distances:
76 145 0.49
78 8 0.03
79 140 0.48
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (76 bp):
ATTTTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTT
CTAAAACATCA
Found at i:204251 original size:79 final size:78
Alignment explanation
Indices: 204042--204456 Score: 640
Period size: 79 Copynumber: 5.3 Consensus size: 78
204032 AAATTTTTAG
* * * *
204042 ATTTTTCATCTCGGGGATACTCCAACCCCGTTATTTTCGAAGGGACACTCCAACCCCGGTTTTAT
1 ATTTTTCATATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
204107 TTCTAAAACATCA
66 TTCTAAAACATCA
* * *
204120 ATTTTTC--ATCGGGGATACTCCAACCCCGTTATTCTCAAAGGGATACTCCAACCCCGATTTTAT
1 ATTTTTCATATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
204183 TTCTAAAACATCA
66 TTCTAAAACATCA
* *
204196 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGATTTTA
1 ATTTTTCAT-ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
204261 TTTCTAAAACATCA
65 TTTCTAAAACATCA
204275 ATTTTTC--ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
1 ATTTTTCATATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
204338 TTCTAAAACATCA
66 TTCTAAAACATCA
*
204351 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTA
1 ATTTTTCAT-ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
*
204416 TTTCTAAAACACCA
65 TTTCTAAAACATCA
** * *
204430 ATGCTCCACAATCGGGGATACTCCAAC
1 ATTTTTCA-TATCGGGGATACTCCAAC
204457 TCCAATTTTA
Statistics
Matches: 312, Mismatches: 18, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
76 145 0.46
78 7 0.02
79 160 0.51
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (78 bp):
ATTTTTCATATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
TTCTAAAACATCA
Found at i:204334 original size:155 final size:155
Alignment explanation
Indices: 204042--204431 Score: 683
Period size: 155 Copynumber: 2.5 Consensus size: 155
204032 AAATTTTTAG
* * *
204042 ATTTTTCAT-CTCGGGGATACTCCAACCCCGTTATTTTCGAAGGGACACTCCAACCCCGGTTTTA
1 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGATTTTA
204106 TTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTCTCAAAGGGATACTCCAA
66 TTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTCTCAAAGGGATACTCCAA
204171 CCCCGATTTTATTTCTAAAACATCA
131 CCCCGATTTTATTTCTAAAACATCA
*
204196 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGATTTTA
1 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGATTTTA
* * *
204261 TTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA
66 TTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTCTCAAAGGGATACTCCAA
204326 CCCCGATTTTATTTCTAAAACATCA
131 CCCCGATTTTATTTCTAAAACATCA
* *
204351 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTA
1 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGATTTTA
*
204416 TTTCTAAAACACCAAT
66 TTTCTAAAACATCAAT
204432 GCTCCACAAT
Statistics
Matches: 224, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
154 9 0.04
155 215 0.96
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (155 bp):
ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGATTTTA
TTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTCTCAAAGGGATACTCCAA
CCCCGATTTTATTTCTAAAACATCA
Found at i:204468 original size:51 final size:51
Alignment explanation
Indices: 204392--204510 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
204382 TTATTTTTGA
*
204392 GGGGATACTCCAACCCCGATTTTA-TTTCTAAAACACCAATGCTCCACAATC
1 GGGGATACTCCAACCCCAATTTTATTTTC-AAAACACCAATGCTCCACAATC
* * ** *
204443 GGGGATACTCCAACTCCAATTTTATTTTCAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATGCTCCACAATC
* *
204494 GGAGATATTCCAACCCC
1 GGGGATACTCCAACCCC
204511 GTTATTTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 54 0.93
52 4 0.07
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATGCTCCACAATC
Found at i:204528 original size:28 final size:28
Alignment explanation
Indices: 204491--204567 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
204481 ATTTTTCACA
* *
204491 ATCGGAGATATTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
204519 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
***
204547 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
204568 GCTTTATTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:204598 original size:158 final size:157
Alignment explanation
Indices: 204361--204702 Score: 395
Period size: 158 Copynumber: 2.2 Consensus size: 157
204351 ATTTTTCATA
** * *
204361 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAC
* ** *
204426 ACCAATGCTCCACAATCGGGGATACTCCAACTCC-AATTTTATTT-TCAAAACACTAATTTTTCA
66 ACCAATGCTCCACAATCAGGGATACTCCAAC-CCTAACCTTATTTCT-AAAACACTAATTTCTCA
* *
204489 CAATCGGAGATATTCCAACCCCGTTATTT
129 CAATCGGAGACACTCCAACCCCGTTATTT
*
204518 CATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAA
1 -ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAA
* *** * * ** * * *
204583 TATTTAT-TTCTCACAATCAGGGATACTTCAACCCTGGCCTTATTTCTAAAATATTGATTTCTCA
65 CACCAATGCTC-CACAATCAGGGATACTCCAACCCTAACCTTATTTCTAAAACACTAATTTCTCA
*
204647 CAATCGGGGACACTCCAACCCCGTTATTT
129 CAATCGGAGACACTCCAACCCCGTTATTT
204676 -TCGAGGGGATACTCCAACCCCGTTATT
1 ATC--GGGGATACTCCAACCCCGTTATT
204703 ATCTCCAAAA
Statistics
Matches: 156, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
156 2 0.01
157 4 0.03
158 149 0.96
159 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (157 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAC
ACCAATGCTCCACAATCAGGGATACTCCAACCCTAACCTTATTTCTAAAACACTAATTTCTCACA
ATCGGAGACACTCCAACCCCGTTATTT
Found at i:204615 original size:51 final size:51
Alignment explanation
Indices: 204551--204669 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
204541 TATTTCCGAG
* *
204551 GGGATACTCCAACCCCGGCTTTATTTCCAAAATATTTATTTCTCACAATCA
1 GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCA
* * * *
204602 GGGATACTTCAACCCTGGCCTTATTTCTAAAATATTGATTTCTCACAATCG
1 GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCA
*
204653 GGGACACTCCAACCCCG
1 GGGATACTCCAACCCCG
204670 TTATTTTCGA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (51 bp):
GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCA
Found at i:205826 original size:42 final size:42
Alignment explanation
Indices: 205796--206204 Score: 214
Period size: 42 Copynumber: 9.7 Consensus size: 42
205786 TCTTACCTTC
* * *
205796 AGTCTGCCTGTCAACTTTGACTCTAAAGACTGCCTCGCCTCG
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCACCTCG
* * * **
205838 AGTCTACTTGTCAACTTTGA-CCTCGGAGACTTTCTCACCTC-
1 AGTCTGCCTGTCAACTTTGACCCT-AGAGACTGCCTCACCTCG
** * * *
205879 AGTCTGCCTGTCGGCTTTGACCCTGGAGGCTGCCTCACCTCA
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCACCTCG
** ** * *
205921 AGTCTGCCTGTCTGCTTTGACTATAAAGACCGCCTCACCTCG
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCACCTCG
* * ** *
205963 AGTCTGCCTATCGACTTTGACCCTAGAGACTTTCTTACCTTC-
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCACC-TCG
* *** * * * *
206005 AGTCTACCTGTTGGCTTTGACCTTGGAGAATGCCTCACCTCA
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCACCTCG
* * ** * * ** **
206047 AGTCTACCTATCGGCTTTGACCCTGGAAACTTTCTTTCCTTC-
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCACC-TCG
* ** * * * * * *
206089 AGTCTACCTGTCGGCTTTGACCTTGGAGACTACCTAATCTCA
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCACCTCG
* ** * * *
206131 AGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCTTACCCTCA
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCA-CCTCG
* * *
206174 AGTTTGCCTATCGACTTTGACCCTAGAGACT
1 AGTCTGCCTGTCAACTTTGACCCTAGAGACT
206205 TTTCCACCTT
Statistics
Matches: 290, Mismatches: 69, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
41 36 0.12
42 217 0.75
43 37 0.13
ACGTcount: A:0.19, C:0.32, G:0.18, T:0.32
Consensus pattern (42 bp):
AGTCTGCCTGTCAACTTTGACCCTAGAGACTGCCTCACCTCG
Found at i:205912 original size:83 final size:84
Alignment explanation
Indices: 205768--205925 Score: 210
Period size: 83 Copynumber: 1.9 Consensus size: 84
205758 TGCTTGTTGG
* * * *
205768 CTTTGAACTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCAACTTTGACTCTAAAGACTGCCTCG
1 CTTTGAACTCGGAGACTTTCTCACCTTCAGTCTGCCTGTCAACTTTGACCCTAAAGACTGCCTCA
*
205833 CCTCGAGTCTACTTGTCAA
66 CCTCAAGTCTACTTGTCAA
* ** ** *
205852 CTTTGACCTCGGAGACTTTCTCACC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGGCTGCCTCA
1 CTTTGAACTCGGAGACTTTCTCACCTTCAGTCTGCCTGTCAACTTTGACCCTAAAGACTGCCTCA
205916 CCTCAAGTCT
66 CCTCAAGTCT
205926 GCCTGTCTGC
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
83 41 0.65
84 22 0.35
ACGTcount: A:0.17, C:0.32, G:0.19, T:0.32
Consensus pattern (84 bp):
CTTTGAACTCGGAGACTTTCTCACCTTCAGTCTGCCTGTCAACTTTGACCCTAAAGACTGCCTCA
CCTCAAGTCTACTTGTCAA
Found at i:205980 original size:125 final size:126
Alignment explanation
Indices: 205796--206067 Score: 350
Period size: 125 Copynumber: 2.2 Consensus size: 126
205786 TCTTACCTTC
* * * * * *
205796 AGTCTGCCTGTCAACTTTGACTCTAAAGACTGCCTCGCCTCGAGTCTACTTGTCAACTTTGA-CC
1 AGTCTGCCTGTCAGCTTTGACTATAAAGACCGCCTCACCTCGAGTCTACCTATCAACTTTGACCC
* * **
205860 TCGGAGACTTTCTCACC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGGCTGCCTCACCTCA
66 T-AGAGACTTTCTCACCTTCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCA
* * *
205921 AGTCTGCCTGTCTGCTTTGACTATAAAGACCGCCTCACCTCGAGTCTGCCTATCGACTTTGACCC
1 AGTCTGCCTGTCAGCTTTGACTATAAAGACCGCCTCACCTCGAGTCTACCTATCAACTTTGACCC
* * *
205986 TAGAGACTTTCTTACCTTCAGTCTACCTGTTGGCTTTGACCTTGGAGAATGCCTCACCTCA
66 TAGAGACTTTCTCACCTTCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCA
* * *
206047 AGTCTACCTATCGGCTTTGAC
1 AGTCTGCCTGTCAGCTTTGAC
206068 CCTGGAAACT
Statistics
Matches: 126, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
125 66 0.52
126 60 0.48
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.31
Consensus pattern (126 bp):
AGTCTGCCTGTCAGCTTTGACTATAAAGACCGCCTCACCTCGAGTCTACCTATCAACTTTGACCC
TAGAGACTTTCTCACCTTCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCA
Found at i:206009 original size:84 final size:84
Alignment explanation
Indices: 205767--206169 Score: 359
Period size: 84 Copynumber: 4.8 Consensus size: 84
205757 CTGCTTGTTG
* ** * * ** * * *
205767 GCTTTGAACTTGGAGACTTTCTTACCTTC-AGTCTGCCTGTCAACTTTGACTCTAAAGACTGCCT
1 GCTTTGACCTTGGAGACTGCCTCACC-TCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCT
** * *
205831 CGCC-TCGAGTCTACTTGTCA
65 TACCTTC-AGTCTACCTGTCT
* * ** * * * * *
205851 ACTTTGACCTCGGAGACTTTCTCACCTC-AGTCTGCCTGTCGGCTTTGACCCTGGAGGCTGCCTC
1 GCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCTT
*
205915 ACC-TCAAGTCTGCCTGTCT
66 ACCTTC-AGTCTACCTGTCT
** * * * *
205934 GCTTTGA-CTATAAAGACCGCCTCACCTCGAGTCTGCCTATCGACTTTGACCCTAGAGACTTTCT
1 GCTTTGACCT-TGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCT
205998 TACCTTCAGTCTACCTGT-T
65 TACCTTCAGTCTACCTGTCT
* * * * *
206017 GGCTTTGACCTTGGAGAATGCCTCACCTCAAGTCTACCTATCGGCTTTGACCCTGGAAACTTTCT
1 -GCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCT
* *
206082 TTCCTTCAGTCTACCTGTCG
65 TACCTTCAGTCTACCTGTCT
* * *
206102 GCTTTGACCTTGGAGACTACCTAATCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCTT
1 GCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCTT
206167 ACC
66 ACC
206170 CTCAAGTTTG
Statistics
Matches: 263, Mismatches: 50, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
82 2 0.01
83 65 0.25
84 192 0.73
85 4 0.02
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.32
Consensus pattern (84 bp):
GCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCTT
ACCTTCAGTCTACCTGTCT
Found at i:206064 original size:126 final size:125
Alignment explanation
Indices: 205810--206067 Score: 338
Period size: 126 Copynumber: 2.1 Consensus size: 125
205800 TGCCTGTCAA
* * * * * *
205810 CTTTGACTCTAAAGACTGCCTCGCCTCGAGTCTACTTGTCAACTTTGACCTCGGAGACTTTCTCA
1 CTTTGACTATAAAGACCGCCTCACCTCGAGTCTACCTATCAACTTTGACCTCAGAGACTTTCTCA
* ** * * *
205875 CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGGCTGCCTCACCTCAAGTCTGCCTGTCTG
66 CCTCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCAAGTCTACCTATCGG
* * *
205935 CTTTGACTATAAAGACCGCCTCACCTCGAGTCTGCCTATCGACTTTGACC-CTAGAGACTTTCTT
1 CTTTGACTATAAAGACCGCCTCACCTCGAGTCTACCTATCAACTTTGACCTC-AGAGACTTTCTC
* *
205999 ACCTTCAGTCTACCTGTTGGCTTTGACCTTGGAGAATGCCTCACCTCAAGTCTACCTATCGG
65 ACC-TCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCAAGTCTACCTATCGG
206061 CTTTGAC
1 CTTTGAC
206068 CCTGGAAACT
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
124 1 0.01
125 56 0.49
126 57 0.50
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.31
Consensus pattern (125 bp):
CTTTGACTATAAAGACCGCCTCACCTCGAGTCTACCTATCAACTTTGACCTCAGAGACTTTCTCA
CCTCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCAAGTCTACCTATCGG
Found at i:206118 original size:126 final size:125
Alignment explanation
Indices: 205810--206195 Score: 337
Period size: 126 Copynumber: 3.1 Consensus size: 125
205800 TGCCTGTCAA
* * * * *
205810 CTTTGACTC-TAAAGACTGCCTCGCCTCGAGTCTACTTGTCAACTTTGACCTCGGAGACTTTCTC
1 CTTTGAC-CATAAAGACCGCCTCACCTCGAGTCTACCTGTCGACTTTGACCTTGGAGACTTTCTC
* ** * * *
205874 ACCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGGCTGCCTCACCTCAAGTCTGCCTGTCTG
65 ACCTCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCAAGTCTACCTATCGG
* * * * * *
205935 CTTTGACTATAAAGACCGCCTCACCTCGAGTCTGCCTATCGACTTTGACCCTAGAGACTTTCTTA
1 CTTTGACCATAAAGACCGCCTCACCTCGAGTCTACCTGTCGACTTTGACCTTGGAGACTTTCTCA
* *
206000 CCTTCAGTCTACCTGTTGGCTTTGACCTTGGAGAATGCCTCACCTCAAGTCTACCTATCGG
66 CC-TCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCAAGTCTACCTATCGG
* * *** ** * **
206061 CTTTGACCCTGGAA-ACTTTCTTTCCTTC-AGTCTACCTGTCGGCTTTGACCTTGGAGACTACCT
1 CTTTGACCAT-AAAGACCGCCTCACC-TCGAGTCTACCTGTCGACTTTGACCTTGGAGACTTTCT
* * * * * * * * * * *
206124 AATCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCCTTACCCTCAAGTTTGCCTATCGA
64 CACCTC-AGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCA-CCTCAAGTCTACCTATCGG
206188 CTTTGACC
1 CTTTGACC
206196 CTAGAGACTT
Statistics
Matches: 208, Mismatches: 47, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
125 57 0.27
126 123 0.59
127 28 0.13
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (125 bp):
CTTTGACCATAAAGACCGCCTCACCTCGAGTCTACCTGTCGACTTTGACCTTGGAGACTTTCTCA
CCTCAGTCTACCTGTCGGCTTTGACCCTGGAGAATGCCTCACCTCAAGTCTACCTATCGG
Found at i:206725 original size:13 final size:13
Alignment explanation
Indices: 206707--206750 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 13
206697 TAATTAATTA
206707 AAAAATAAAAAAT
1 AAAAATAAAAAAT
206720 AAAAATAAATAAAT
1 AAAAATAAA-AAAT
206734 AATATAATAACAAAAT
1 AA-A-AATAA-AAAAT
206750 A
1 A
206751 GTATCAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
15 1 0.04
16 10 0.37
17 1 0.04
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:207850 original size:31 final size:33
Alignment explanation
Indices: 207787--207850 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
207777 GAAACAACTT
* *
207787 GATTGTAGCAAGAAGAAGAAATGAAGCTGCTGCC
1 GATTGCAGCAAGAAGAAGAAATGAA-CAGCTGCC
207821 GATTGCAGCAAGAAGAAGAAAT-AA-AGCTGC
1 GATTGCAGCAAGAAGAAGAAATGAACAGCTGC
207851 AGTTGTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.18
33 2 0.07
34 21 0.75
ACGTcount: A:0.42, C:0.14, G:0.28, T:0.16
Consensus pattern (33 bp):
GATTGCAGCAAGAAGAAGAAATGAACAGCTGCC
Found at i:210953 original size:21 final size:22
Alignment explanation
Indices: 210927--210970 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
210917 TTTAGTATAA
* *
210927 TTCCATGCA-GTATTGATACTT
1 TTCCATGCATATATTAATACTT
210948 TTCCATGCATATATTAATACTT
1 TTCCATGCATATATTAATACTT
210970 T
1 T
210971 GATTTACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (22 bp):
TTCCATGCATATATTAATACTT
Found at i:212820 original size:20 final size:21
Alignment explanation
Indices: 212787--212826 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
212777 CTTAGTGTCA
212787 ATACATTCACTTA-TGTATCG
1 ATACATTCACTTATTGTATCG
* *
212807 ATACATTTATTTATTGTATC
1 ATACATTCACTTATTGTATC
212827 AGTACAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
ATACATTCACTTATTGTATCG
Found at i:220164 original size:51 final size:52
Alignment explanation
Indices: 220046--220164 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 52
220036 ATTTGCCTGC
** * * *
220046 ATGTATCGATACATTTAGGTCAAATTCTAAGAATATATCGATACAGTGAAGA
1 ATGTATCGATACATTTAGGTCAAAACCCAAGAATATATCGATACAATGAAAA
* * * *
220098 TTGTATCGATACATTTGGGTCAAAACCCAA-AATGTATTGATACAATGAAAA
1 ATGTATCGATACATTTAGGTCAAAACCCAAGAATATATCGATACAATGAAAA
*
220149 ATGTATCGATGCATTT
1 ATGTATCGATACATTT
220165 TCATTCCAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 31 0.55
52 25 0.45
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (52 bp):
ATGTATCGATACATTTAGGTCAAAACCCAAGAATATATCGATACAATGAAAA
Found at i:220267 original size:21 final size:20
Alignment explanation
Indices: 220207--220273 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
220197 TCCTGGATCA
220207 ATACATTTCAC-ACATGTATCG
1 ATACA-TTCACTA-ATGTATCG
*
220228 AGACATTCACTAATGTATCG
1 ATACATTCACTAATGTATCG
* * *
220248 ATACATTACCCTATTGTATCA
1 ATACATT-CACTAATGTATCG
220269 ATACA
1 ATACA
220274 ATTTATTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 19 0.49
21 20 0.51
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (20 bp):
ATACATTCACTAATGTATCG
Found at i:232008 original size:31 final size:31
Alignment explanation
Indices: 231973--232060 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
231963 AAAAATCACA
**
231973 TTTTTACCCAGATGTATCGATACATTCTGTC
1 TTTTTACCCAGATGTATCGATACATTCAATC
*
232004 TTTTTACCTAGATGTATCGATACATTCAATC
1 TTTTTACCCAGATGTATCGATACATTCAATC
* *
232035 CTTTTACCCTGATGTATCGATACATT
1 TTTTTACCCAGATGTATCGATACATT
232061 TTTCAATGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (31 bp):
TTTTTACCCAGATGTATCGATACATTCAATC
Found at i:235296 original size:51 final size:50
Alignment explanation
Indices: 235192--235303 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 50
235182 TTCTAAGAAA
* *
235192 ATACTCCAACCTCAGTTTTATTTCTAAAACACCAATTTTCCACAATTAGGG
1 ATACTCCAA-CTCAGTTTTATTTCCAAAACACCAATTTTCCACAATGAGGG
* * * *
235243 ATACTCCAACTCCGATTTTATTTCCAAAACACCATTTTTTCATAATCGA-GG
1 ATACTCCAACTCAG-TTTTATTTCCAAAACACCAATTTTCCACAAT-GAGGG
*
235294 ATACACCAAC
1 ATACTCCAAC
235304 CTCGTTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 4 0.08
51 47 0.90
52 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (50 bp):
ATACTCCAACTCAGTTTTATTTCCAAAACACCAATTTTCCACAATGAGGG
Found at i:235398 original size:79 final size:78
Alignment explanation
Indices: 235315--235518 Score: 284
Period size: 79 Copynumber: 2.6 Consensus size: 78
235305 TCGTTATTTC
* * *
235315 ATCGGAGATACTCCAACCCCATTATTTCCGAGGGGATACTTCAACCCCAGCTTTATTTCTAAAAT
1 ATCGG-GATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACCCCAGCTATATTTCTAAAAT
235380 ATTGATTTCTCACA
65 ATTGATTTCTCACA
* *
235394 ATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATAC-TCTAACCCCGGCTATATTTCTAAAA
1 ATC-GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTC-AACCCCAGCTATATTTCTAAAA
*
235458 TTTTGATTTCTCACA
64 TATTGATTTCTCACA
* * *
235473 ATCAGGGATACTCCAACCCTGTTATTTTCGAAGGGATACTCCAACC
1 ATC-GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACC
235519 TCGATTTTAT
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
78 2 0.02
79 106 0.95
80 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (78 bp):
ATCGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACCCCAGCTATATTTCTAAAATA
TTGATTTCTCACA
Found at i:235545 original size:79 final size:78
Alignment explanation
Indices: 235315--235564 Score: 272
Period size: 79 Copynumber: 3.2 Consensus size: 78
235305 TCGTTATTTC
* * * * * *
235315 ATCGGAGATACTCCAACCCCATTATTTCCGAGGGGATACTTCAACCCCAGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCGA-CTTTATTTCTAAAAT
235380 ATTGATTTCTCACA
65 ATTGATTTCTCACA
* * *
235394 ATCGGGGATACTCCAACCCCGTTATTTTCG-AGAGGATACTCTAACCCCGGCTATATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAAG-GGATACTCCAA-CCCGACTTTATTTCTAAAA
*
235458 TTTTGATTTCTCACA
64 TATTGATTTCTCACA
* * *
235473 ATCAGGGATACTCCAACCCTGTTATTTTCGAAGGGATACTCCAACCTCGATTTTATTT-TCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACC-CGACTTTATTTCT-AAAA
* ** *
235537 CACCGATTT-TCTATA
64 TATTGATTTCTC-ACA
235552 ATCGGGGATACTC
1 ATCGGGGATACTC
235565 TGGCCTCGTT
Statistics
Matches: 143, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
78 6 0.04
79 132 0.92
80 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCGACTTTATTTCTAAAATA
TTGATTTCTCACA
Found at i:243465 original size:14 final size:14
Alignment explanation
Indices: 243429--243465 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
243419 CAATCAAAAG
*
243429 ACAAAAAAAACAAC
1 ACAAAAAAAACAAA
*
243443 ACACAAAAAACAAA
1 ACAAAAAAAACAAA
243457 ACAAAAAAA
1 ACAAAAAAA
243466 GGTGCAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (14 bp):
ACAAAAAAAACAAA
Found at i:243722 original size:15 final size:15
Alignment explanation
Indices: 243702--243732 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
243692 GTTATTTTCT
243702 AAAAAAAAGAAACAA
1 AAAAAAAAGAAACAA
243717 AAAAAAAAGAAACAA
1 AAAAAAAAGAAACAA
243732 A
1 A
243733 CAAACAAAAA
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:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAACAA
Found at i:243733 original size:19 final size:20
Alignment explanation
Indices: 243702--243747 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
243692 GTTATTTTCT
*
243702 AAAAA-AAAGAAACAAA-AA
1 AAAAAGAAACAAACAAACAA
243720 AAAAAGAAACAAACAAACAA
1 AAAAAGAAACAAACAAACAA
243740 AAAAAGAA
1 AAAAAGAA
243748 GAAAGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.20
19 10 0.40
20 10 0.40
ACGTcount: A:0.85, C:0.09, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAGAAACAAACAAACAA
Found at i:244769 original size:32 final size:31
Alignment explanation
Indices: 244698--244884 Score: 177
Period size: 30 Copynumber: 6.0 Consensus size: 31
244688 AAATACCTTC
*
244698 TCAAAGCCCACGACTCAGTGGCAT-TTTGTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTT-TCT
*
244728 TCAAAGTCCATGACTCAGTGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCAT-CTTTTCT
244760 TCAAAGTCCACGACTCAGTGGCAT-TTTGTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTT-TCT
* *
244790 TCAAAGTCCACAACTCAGTGGGATCTTTTCCTT
1 TCAAAGTCCACGACTCAGTGGCATCTTTT-C-T
* * *
244823 TCAAAGTCCACAACTCCGTGGCACCTTCTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTT-TTCT
* * * *
244854 TCAAAGCCCACAATTCTGTGGCACTCTTTTC
1 TCAAAGTCCACGACTCAGTGGCA-TCTTTTC
244885 CCCTTTTAAA
Statistics
Matches: 134, Mismatches: 12, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
30 48 0.36
31 31 0.23
32 29 0.22
33 24 0.18
34 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (31 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTCT
Found at i:244795 original size:62 final size:63
Alignment explanation
Indices: 244693--244900 Score: 226
Period size: 62 Copynumber: 3.2 Consensus size: 63
244683 TCGTCAAATA
* **
244693 CCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTCAAAGTCCATGACTCAGTGGCATCCTTTT
1 CCTT-TCAAAGTCCACGACTCAGTGGCATTTTGTCTCAAAGTCCACAACTCAGTGGCAT-CTTTT
*
244758 -C-TTCAAAGTCCACGACTCAGTGGCATTTTGTCTCAAAGTCCACAACTCAGTGGGATCTTTT
1 CCTTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCAAAGTCCACAACTCAGTGGCATCTTTT
* * * * *
244819 CCTTTCAAAGTCCACAACTCCGTGGCACCTTCTT-T-TCAAAGCCCACAATTCTGTGGCACTCTT
1 CCTTTCAAAGTCCACGACTCAGTGGCA--TT-TTGTCTCAAAGTCCACAACTCAGTGGCA-TCTT
244882 TT
62 TT
*
244884 CCCCTTTTAAAGTCCAC
1 --CCTTTCAAAGTCCAC
244901 AACCCCGTGG
Statistics
Matches: 124, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
61 5 0.04
62 51 0.41
63 23 0.19
64 20 0.16
65 9 0.07
66 2 0.02
67 14 0.11
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (63 bp):
CCTTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCAAAGTCCACAACTCAGTGGCATCTTTT
Found at i:244832 original size:33 final size:33
Alignment explanation
Indices: 244693--245439 Score: 261
Period size: 36 Copynumber: 23.0 Consensus size: 33
244683 TCGTCAAATA
* *
244693 CCTTCTCAAAGCCCACGACTCAGTGGCAT-TTTGT
1 CCTT-TCAAAGTCCACAACTCAGTGGCATCTTT-T
**
244727 -C--TCAAAGTCCATGACTCAGTGGCATCCTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCAT-CTTTT
*
244758 -C-TTCAAAGTCCACGACTCAGTGGCAT-TTTGT
1 CCTTTCAAAGTCCACAACTCAGTGGCATCTTT-T
*
244789 -C--TCAAAGTCCACAACTCAGTGGGATCTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCATCTTTT
* *
244819 CCTTTCAAAGTCCACAACTCCGTGGCA-C-CTT
1 CCTTTCAAAGTCCACAACTCAGTGGCATCTTTT
* * * *
244850 CTTTTCAAAGCCCACAATTCTGTGGCACTCTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCA-TCTTTT
* * * *
244884 CCCCTTTTAAAGTCCACAACCCCGTGGCACCTTATT
1 --CCTTTCAAAGTCCACAACTCAGTGGCATCTT-TT
* * * * *
244920 CCTTT-TAAGTCCACGACTCCGTAGCA-C-CTT
1 CCTTTCAAAGTCCACAACTCAGTGGCATCTTTT
** * * * * *
244950 CCTTTCAAAGTCTGCGATTCCGTGGGA-C-CTT
1 CCTTTCAAAGTCCACAACTCAGTGGCATCTTTT
* * *
244981 CTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCA-TC-TTTT
* * *
245016 CCCTTTTAAAGCCCACAACTTC-GTGGCACTTTTTTT
1 -CCTTTCAAAGTCCACAAC-TCAGTGGCA--TCTTTT
* *
245052 CCCTTTTAAAGCCCACAACTTC-GTGGCACTCTTTTT
1 -CCTTTCAAAGTCCACAAC-TCAGTGGCA-TC-TTTT
* * *
245088 CCCTTTTAAAATCCACAACTCCGTGGCA-C----
1 -CCTTTCAAAGTCCACAACTCAGTGGCATCTTTT
* * * *
245117 CCTTT-TAAGCCCACAACTCCGTGGCACTTTTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCA--TCTTTT
* *
245151 CC-TTCTAAGTCCACAACTCCGTGGCA-C----
1 CCTTTCAAAGTCCACAACTCAGTGGCATCTTTT
* *
245178 CCTATT--AAGCCCACAACTCCGTGGCACTCTTTTT
1 CCT-TTCAAAGTCCACAACTCAGTGGCA-TC-TTTT
* *
245212 CC-TTCTAAGTCCACAACTCCGTGGCA-C----
1 CCTTTCAAAGTCCACAACTCAGTGGCATCTTTT
* * *
245239 CCTTT-TAAGCCCACAACTCTGTGGCACTCTTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCA-TC-TTTT
* * *
245273 CC-TTCTAAGTCCACAACTCCGTGGCACCTTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCATC-TTTT
* * * * *
245306 CTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCA--TCTTTT
* *
245341 CC-TTCTAAGTCCACAACTCCGTGGCACTCTTTTT
1 CCTTTCAAAGTCCACAACTCAGTGGCA-TC-TTTT
* * ** *
245375 CCCTTTTAAAGCCCACAACTCCTTGGCACCTTGTT
1 -CCTTTCAAAGTCCACAACTCAGTGGCATCTT-TT
*
245410 -CTTT-TAAGTCCACAACTTC-GTGGCATCTTT
1 CCTTTCAAAGTCCACAAC-TCAGTGGCATCTTT
245440 CACCCTTTCT
Statistics
Matches: 572, Mismatches: 81, Indels: 123
0.74 0.10 0.16
Matches are distributed among these distances:
27 60 0.10
28 7 0.01
29 4 0.01
30 55 0.10
31 73 0.13
32 49 0.09
33 59 0.10
34 120 0.21
35 18 0.03
36 124 0.22
37 3 0.01
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
CCTTTCAAAGTCCACAACTCAGTGGCATCTTTT
Found at i:244901 original size:36 final size:35
Alignment explanation
Indices: 244792--245459 Score: 452
Period size: 36 Copynumber: 20.3 Consensus size: 35
244782 ATTTTGTCTC
* * * *
244792 AAAGTCCACAACTCAGTGGGA-TCTTTT-CCTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
*
244825 AAAGTCCACAACTCCGTGGCAC-C--TT--CTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
* *
244855 CAAAGCCCACAATTCTGTGGCACTCTTTTCCCCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTT-CCCTTTT
* *
244892 AAAGTCCACAACCCCGTGGCAC-CTTATT-CCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTT-TTCCCTTTT
* * * *
244926 -AAGTCCACGACTCCGTAGCAC-C--TT-CCTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
* ** * * *
244956 AAAGTCTGCGATTCCGTGGGAC-C--TT--CTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
244986 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 -AAAGCCCACAACTCCGTGGCACTC-TTTTCCCTTTT
* *
245023 AAAGCCCACAACTTCGTGGCACTTTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-TCTTTTCCCTTTT
*
245059 AAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTC-TTTTCCCTTTT
**
245095 AAAATCCACAACTCCGTGGCA-------CCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
* * *
245123 -AAGCCCACAACTCCGTGGCACTTTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
* *
245157 -AAGTCCACAACTCCGTGGCA-------CCCTATT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
* *
245184 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
*
245218 -AAGTCCACAACTCCGTGGCA-------CCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
* * *
245245 -AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
* * *
245279 -AAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
* * *
245312 AAAGCCCACAACTCCGTGGCACTTTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
*
245347 -AAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTC-TTTTCCCTTTT
*
245382 AAAGCCCACAACTCCTTGGCAC-CTTGTT--CTTTT
1 AAAGCCCACAACTCCGTGGCACTCTT-TTCCCTTTT
* * *
245415 -AAGTCCACAACTTCGTGGCA-TCTTTCACCCTTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTT-TCCCTTT-T
245450 AAAGCCCACA
1 AAAGCCCACA
245460 CAAGTCGGTG
Statistics
Matches: 514, Mismatches: 70, Indels: 99
0.75 0.10 0.14
Matches are distributed among these distances:
27 64 0.12
28 7 0.01
30 15 0.03
31 57 0.11
32 22 0.04
33 54 0.11
34 126 0.25
35 28 0.05
36 130 0.25
37 11 0.02
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (35 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTCCCTTTT
Found at i:244954 original size:30 final size:32
Alignment explanation
Indices: 244816--244961 Score: 93
Period size: 31 Copynumber: 4.5 Consensus size: 32
244806 AGTGGGATCT
* * *
244816 TTTCCTTTCAAAGTCCACAACTCCGTGGCACC
1 TTTCCTTTTAAAGTCCACAACCCCGTAGCACC
* ** * *
244848 -TT-CTTTTCAAAGCCCACAATTCTGTGGCACTC
1 TTTCCTTTT-AAAGTCCACAACCCCGTAGCAC-C
*
244880 TTTTCCCCTTTTAAAGTCCACAACCCCGTGGCACC
1 -TTT--CCTTTTAAAGTCCACAACCCCGTAGCACC
* *
244915 TTATTCCTTTT-AAGTCCACGACTCCGTAGCACC
1 -T-TTCCTTTTAAAGTCCACAACCCCGTAGCACC
*
244948 -TTCCTTTCAAAGTC
1 TTTCCTTTTAAAGTC
244962 TGCGATTCCG
Statistics
Matches: 93, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
30 11 0.12
31 26 0.28
32 1 0.01
33 19 0.20
34 8 0.09
35 3 0.03
36 20 0.22
37 5 0.05
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (32 bp):
TTTCCTTTTAAAGTCCACAACCCCGTAGCACC
Found at i:245048 original size:34 final size:33
Alignment explanation
Indices: 244988--245459 Score: 374
Period size: 34 Copynumber: 14.3 Consensus size: 33
244978 CTTCTTTTCA
244988 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCA--CTTTTTCCCTTTT
*
245023 AAAGCCCACAACTTCGTGGCACTTTTTTTCCCTTTT
1 -AAGCCCACAACTCCGTGGCAC--TTTTTCCCTTTT
*
245059 AAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTT
1 -AAGCCCACAACTCCGTGGCA--CTTTTTCCCTTTT
**
245095 AAAATCCACAACTCCGTGGCA------CCCTTTT
1 -AAGCCCACAACTCCGTGGCACTTTTTCCCTTTT
* *
245123 AAGCCCACAACTCCGTGGCACTTTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCAC-TTTTTCCCTTTT
* *
245157 AAGTCCACAACTCCGTGGCA------CCCTATT
1 AAGCCCACAACTCCGTGGCACTTTTTCCCTTTT
* *
245184 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACT-TTTTCCCTTTT
*
245218 AAGTCCACAACTCCGTGGCA------CCCTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTCCCTTTT
* * *
245245 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACT-TTTTCCCTTTT
* *
245279 AAGTCCACAACTCCGTGGCACCTTTTT-CTTTTT
1 AAGCCCACAACTCCGTGGCA-CTTTTTCCCTTTT
* *
245312 AAAGCCCACAACTCCGTGGCACTTTTTTTCCTTCT
1 -AAGCCCACAACTCCGTGGCAC-TTTTTCCCTTTT
*
245347 AAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCA--CTTTTTCCCTTTT
* *
245382 AAAGCCCACAACTCCTTGGCACCTTGTT--CTTTT
1 -AAGCCCACAACTCCGTGGCA-CTTTTTCCCTTTT
* * **
245415 AAGTCCACAACTTCGTGGCATCTTTCACCCTTTCT
1 AAGCCCACAACTCCGTGGCA-CTTTTTCCCTTT-T
245450 AAAGCCCACA
1 -AAGCCCACA
245460 CAAGTCGGTG
Statistics
Matches: 355, Mismatches: 45, Indels: 72
0.75 0.10 0.15
Matches are distributed among these distances:
27 64 0.18
28 7 0.02
32 20 0.06
33 10 0.03
34 122 0.34
35 22 0.06
36 109 0.31
38 1 0.00
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.33
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACTTTTTCCCTTTT
Found at i:245135 original size:27 final size:27
Alignment explanation
Indices: 245100--245271 Score: 155
Period size: 27 Copynumber: 5.9 Consensus size: 27
245090 CTTTTAAAAT
245100 CCACAACTCCGTGGCACCCTTTTAAGC
1 CCACAACTCCGTGGCACCCTTTTAAGC
* *
245127 CCACAACTCCGTGGCACTTTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCAC-------CCTTTTAAGC
*
245161 CCACAACTCCGTGGCACCCTATTAAGC
1 CCACAACTCCGTGGCACCCTTTTAAGC
* *
245188 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCA--C-----CCTTTTAAGC
245222 CCACAACTCCGTGGCACCCTTTTAAGC
1 CCACAACTCCGTGGCACCCTTTTAAGC
* *
245249 CCACAACTCTGTGGCACTCTTTT
1 CCACAACTCCGTGGCACCCTTTT
245272 TCCTTCTAAG
Statistics
Matches: 119, Mismatches: 12, Indels: 28
0.75 0.08 0.18
Matches are distributed among these distances:
27 69 0.58
29 1 0.01
32 1 0.01
34 48 0.40
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.29
Consensus pattern (27 bp):
CCACAACTCCGTGGCACCCTTTTAAGC
Found at i:245347 original size:68 final size:67
Alignment explanation
Indices: 244792--245439 Score: 588
Period size: 61 Copynumber: 9.9 Consensus size: 67
244782 ATTTTGTCTC
* * * *
244792 AAAGTCCACAACTCAGTGGGA-TC-TTTTCCTTTCAAAGTCCACAACTCCGTGGCACC---TTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCC-TTCTAAGTCCACAACTCCGTGGCACCTTTTTCT
244852 TTT
65 TTT
* * * * *
244855 CAAAGCCCACAATTCTGTGGCACTCTTTTCCCCTTTTAAAGTCCACAACCCCGTGGCACCTTATT
1 -AAAGCCCACAACTCCGTGGCACTCTTTT-TCCTTCT-AAGTCCACAACTCCGTGGCACCTT-TT
*
244920 CCTTTT
62 TCTTTT
* * * * ** * * *
244926 -AAGTCCACGACTCCGTAGCAC-C---TTCCTTTCAAAGTCTGCGATTCCGTGGGACC---TTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCC-TTCTAAGTCCACAACTCCGTGGCACCTTTTTCT
244983 TTT
65 TTT
* * * *
244986 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTTCGTGGCACTTTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTCT-AAGTCCACAACTCCGTGGCAC-CTTTT
245051 TCCCTTTT
62 T--CTTTT
* * *
245059 AAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTTAAAATCCACAACTCCGTGGCACC-----C
1 AAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTCT-AAGTCCACAACTCCGTGGCACCTTTTTC
245119 TTTT
64 TTTT
* *
245123 -AAGCCCACAACTCCGTGGCACTTTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----CTA
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTT
245182 TT
66 TT
245184 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----CTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTT
245243 TT
66 TT
*
245245 -AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTC-T
245309 TTT
65 TTT
*
245312 AAAGCCCACAACTCCGTGGCACTTTTTTTCCTTCTAAGTCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCAC-CTTTTT--
245377 CTTTT
63 CTTTT
* * * * *
245382 AAAGCCCACAACTCCTTGGCAC-CTTGTT-CTTTTAAGTCCACAACTTCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTT
245440 CACCCTTTCT
Statistics
Matches: 493, Mismatches: 58, Indels: 63
0.80 0.09 0.10
Matches are distributed among these distances:
60 6 0.01
61 139 0.28
62 23 0.05
63 27 0.05
64 40 0.08
65 5 0.01
66 10 0.02
67 47 0.10
68 77 0.16
69 26 0.05
70 25 0.05
71 9 0.02
72 54 0.11
73 5 0.01
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (67 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTT
TT
Found at i:245489 original size:33 final size:33
Alignment explanation
Indices: 245443--245799 Score: 492
Period size: 33 Copynumber: 10.9 Consensus size: 33
245433 CATCTTTCAC
*
245443 CCTT-TCTAAAGCCCACACAAGTCGGTGGTAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
*
245475 CCTTCTCTAAAGCCCACACAAGTCAGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
**
245508 CCGCCTCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
*
245541 CCGTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
** *
245574 CCGCCTTTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
245607 CCTTCTCTAAAGCCCACACAAGTCGGTGGC-AA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
245639 CTTTCTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTC-TCTAAAGCCCACACAAGTCGGTGGCAAA
245673 CCTTCTC-AAAGCCCACACAAGTCGGTGGC-AA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
245704 CCCTCTCTAAAGCCCACACAAGTTGGTGGC-AA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
** *
245736 CCCCCTCTAAAGGCCACACAAGTCGGTGGC-AA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* * *
245768 CCTTCTTCAAAAGCCCACACAAATTGGTGGCA
1 CCTTC-TCTAAAGCCCACACAAGTCGGTGGCA
245800 TCTACCTTTA
Statistics
Matches: 293, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
31 7 0.02
32 87 0.30
33 194 0.66
34 5 0.02
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.18
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
Found at i:245858 original size:49 final size:49
Alignment explanation
Indices: 245805--246137 Score: 323
Period size: 43 Copynumber: 6.9 Consensus size: 49
245795 TGGCATCTAC
*
245805 CTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTTGCACCTTCAT
1 CTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * *
245854 CTTTAAGTCCAGTGTAGCTGGCCTTGAATCAGCACATT-G---C--CAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
245897 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
245946 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
245989 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CAT
* * * *
246041 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC----T-TCAT
* * * * *
246096 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
246138 TCTTTATCAC
Statistics
Matches: 236, Mismatches: 28, Indels: 34
0.79 0.09 0.11
Matches are distributed among these distances:
43 76 0.32
44 1 0.00
45 2 0.01
47 1 0.00
48 2 0.01
49 73 0.31
50 1 0.00
52 38 0.16
53 2 0.01
55 39 0.17
56 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
Found at i:245962 original size:92 final size:92
Alignment explanation
Indices: 245803--246088 Score: 464
Period size: 92 Copynumber: 3.1 Consensus size: 92
245793 GGTGGCATCT
* * *
245803 ACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTTGCACCTTCATCTTTAAGTCCAGTG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
245868 TAGCTGGCCTTGAATCAGCACATTGCC
66 TAGCTGGCCTTGAATCAGCACATTGAC
*
245895 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
245960 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGAC
* *
245987 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCA
246052 ATGTAGCTGGCCTTGAATCAGCACATTGAC
63 ATGTAGCTGGCCTTGAATCAGCACATTGAC
246082 ATCCTTT
1 A-CCTTT
246089 TTCTCATCTT
Statistics
Matches: 181, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
92 132 0.73
94 2 0.01
95 42 0.23
96 5 0.03
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (92 bp):
ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGAC
Found at i:246067 original size:52 final size:53
Alignment explanation
Indices: 245989--246142 Score: 193
Period size: 52 Copynumber: 2.9 Consensus size: 53
245979 ACATTGGCAC
245989 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
246041 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * *
246096 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
246143 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 6 0.07
55 36 0.42
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:246200 original size:67 final size:68
Alignment explanation
Indices: 246092--246218 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 68
246082 ATCCTTTTTC
* *
246092 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
246156 TCT
66 TCT
* * * *
246159 TCATCTTTAAGTCCAATAT-TTCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGT-TGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
246219 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
66 1 0.02
67 47 0.90
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:246906 original size:13 final size:13
Alignment explanation
Indices: 246888--246912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
246878 CATAAAGTGT
246888 TGTATCGATACAA
1 TGTATCGATACAA
246901 TGTATCGATACA
1 TGTATCGATACA
246913 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:246928 original size:32 final size:33
Alignment explanation
Indices: 246869--246933 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
246859 TTTGTCCAAG
246869 GTATCGATACATAAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAAGTGTTGTATCGATACAAT
*
246902 GTATCGATACAT-AAGTTTTGTATCGATACAAT
1 GTATCGATACATAAAGTGTTGTATCGATACAAT
246934 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
GTATCGATACATAAAGTGTTGTATCGATACAAT
Found at i:246992 original size:13 final size:13
Alignment explanation
Indices: 246974--246998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
246964 ATTACTCAAA
246974 TGTATCGATACAT
1 TGTATCGATACAT
246987 TGTATCGATACA
1 TGTATCGATACA
246999 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:259247 original size:52 final size:51
Alignment explanation
Indices: 259169--259285 Score: 191
Period size: 52 Copynumber: 2.3 Consensus size: 51
259159 AAGTTGCTTG
*
259169 CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTA
1 CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTGCCTA
*
259221 CATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAATTGCCTG
1 CATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAATTGCCTA
259272 CATGTATCGATACA
1 CATGTATCGATACA
259286 AAGATCAGTG
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 20 0.32
52 37 0.60
53 5 0.08
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (51 bp):
CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTA
Found at i:259312 original size:13 final size:13
Alignment explanation
Indices: 259294--259318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259284 CAAAGATCAG
259294 TGTATCGATACAA
1 TGTATCGATACAA
259307 TGTATCGATACA
1 TGTATCGATACA
259319 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:259396 original size:33 final size:33
Alignment explanation
Indices: 259359--259425 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
259349 AGTAGCTTAA
259359 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
259392 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
259425 A
1 A
259426 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:259399 original size:13 final size:13
Alignment explanation
Indices: 259381--259405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259371 CAAAAAAATA
259381 TGTATCGATACAT
1 TGTATCGATACAT
259394 TGTATCGATACA
1 TGTATCGATACA
259406 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.