Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004356.1 Hibiscus syriacus cultivar Beakdansim tig00009544_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 120639
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1363 original size:19 final size:19
Alignment explanation
Indices: 1341--1390 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1331 TTTTAAAAGT
1341 TTTATAAATAATTATTAAA
1 TTTATAAATAATTATTAAA
*
1360 TTTAATAAAT-A-TGTTAAA
1 TTT-ATAAATAATTATTAAA
*
1378 TTTTTAAA-AATTA
1 TTTATAAATAATTA
1391 ATAATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 4 0.16
20 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTATAAATAATTATTAAA
Found at i:3159 original size:18 final size:18
Alignment explanation
Indices: 3136--3171 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3126 AAATATATCA
3136 TCCTCCGTATATAAATCC
1 TCCTCCGTATATAAATCC
3154 TCCTCCGTATATAAATCC
1 TCCTCCGTATATAAATCC
3172 GCTGCCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.06, T:0.33
Consensus pattern (18 bp):
TCCTCCGTATATAAATCC
Found at i:5596 original size:2 final size:2
Alignment explanation
Indices: 5591--5615 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5581 ATATATATAT
5591 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5616 TCATGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20184 original size:77 final size:79
Alignment explanation
Indices: 20045--20195 Score: 209
Period size: 77 Copynumber: 1.9 Consensus size: 79
20035 ATATAGTAAG
** * *
20045 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAATTAATATTTAATTTGGAATAATTA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATTAATATTTAATTCGAAATAATTA
20110 AATAAGATTTTAAA
66 AATAAGATTTTAAA
* * *
20124 TAAACATT-AAAGATTGTAATTCAGATTATAAGTC-TTTAATGT-ATATTTAATTCGAAATAATT
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTTAAT-TAATATTTAATTCGAAATAATT
20186 AAATAAGATT
65 AAATAAGATT
20196 ATTTATTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
77 34 0.53
78 22 0.34
79 8 0.12
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATTAATATTTAATTCGAAATAATTA
AATAAGATTTTAAA
Found at i:20962 original size:17 final size:17
Alignment explanation
Indices: 20936--20982 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
20926 TAACATGTAC
20936 TTTG-AAATGTATATAT
1 TTTGTAAATGTATATAT
20952 TTTGTAAATGTATATAT
1 TTTGTAAATGTATATAT
20969 TTTGTAAATG-ATAT
1 TTTGTAAATGTATAT
20983 TCGTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.27
17 22 0.73
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (17 bp):
TTTGTAAATGTATATAT
Found at i:26027 original size:21 final size:21
Alignment explanation
Indices: 26003--26043 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25993 AGAGACACTT
* *
26003 ACCAAGGTACTTCATCTACTA
1 ACCAAAGTAATTCATCTACTA
26024 ACCAAAGTAATTCATCTACT
1 ACCAAAGTAATTCATCTACT
26044 TCCACTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (21 bp):
ACCAAAGTAATTCATCTACTA
Found at i:37884 original size:30 final size:30
Alignment explanation
Indices: 37828--37884 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
37818 TTTAAATTAC
* **
37828 ACTTTAGTCCATAAACTTTTTTAATTTTTT
1 ACTTTAGTCCATAAAATTTTAAAATTTTTT
37858 ACTTTAG-CCATTAAAATTTTAAAATTT
1 ACTTTAGTCCA-TAAAATTTTAAAATTT
37885 ACATTTTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.13
30 20 0.87
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (30 bp):
ACTTTAGTCCATAAAATTTTAAAATTTTTT
Found at i:47319 original size:23 final size:23
Alignment explanation
Indices: 47292--47335 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
47282 ACATTATATG
47292 GCACAAAATAGTACATGGTGCCT
1 GCACAAAATAGTACATGGTGCCT
*
47315 GCACAATATAGTACATGGTGC
1 GCACAAAATAGTACATGGTGC
47336 AATGTATTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (23 bp):
GCACAAAATAGTACATGGTGCCT
Found at i:50150 original size:18 final size:18
Alignment explanation
Indices: 50127--50188 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
50117 ATAAAATATA
50127 ACTTTTTCAAAAATTTTG
1 ACTTTTTCAAAAATTTTG
*
50145 ACTTTTTTAAAAAATTTTG
1 AC-TTTTTCAAAAATTTTG
50164 ACTTTTTCAAAAATTTTG
1 ACTTTTTCAAAAATTTTG
50182 ACTTTTT
1 ACTTTTT
50189 GGTCAAAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 24 0.59
19 17 0.41
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (18 bp):
ACTTTTTCAAAAATTTTG
Found at i:50157 original size:19 final size:19
Alignment explanation
Indices: 50129--50188 Score: 104
Period size: 19 Copynumber: 3.2 Consensus size: 19
50119 AAAATATAAC
50129 TTTTTCAAAAATTTTGACT
1 TTTTTCAAAAATTTTGACT
*
50148 TTTTTAAAAAATTTTGAC-
1 TTTTTCAAAAATTTTGACT
50166 TTTTTCAAAAATTTTGACT
1 TTTTTCAAAAATTTTGACT
50185 TTTT
1 TTTT
50189 GGTCAAAGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 17 0.45
19 21 0.55
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTTCAAAAATTTTGACT
Found at i:50207 original size:13 final size:13
Alignment explanation
Indices: 50189--50216 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
50179 TTGACTTTTT
50189 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
50202 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
50215 GG
1 GG
50217 CGATCAACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.29, T:0.14
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:51716 original size:32 final size:31
Alignment explanation
Indices: 51680--51756 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
51670 TCGGGCCACG
* *
51680 GGGCCTACCTAAGAATATATCTTAGGGCCGCA
1 GGGCCTACCTAAGAAT-GATCTAAGGGCCGCA
* **
51712 GGGCCTTCCCGAGAATGATCTAAGGGCCGCA
1 GGGCCTACCTAAGAATGATCTAAGGGCCGCA
*
51743 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
51757 GTCGCATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (31 bp):
GGGCCTACCTAAGAATGATCTAAGGGCCGCA
Found at i:56388 original size:32 final size:31
Alignment explanation
Indices: 56351--56427 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
56341 TGGGGCCACG
* *
56351 GGGCCTACCTAAGAACACATCTTAGGGCTGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
* **
56383 GGGCCTACCCAAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
56414 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
56428 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:60729 original size:45 final size:45
Alignment explanation
Indices: 60680--60769 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
60670 TACAAAGAAC
60680 ACATGCATGGACATTT-ATCTCATTTGCATTTCCATATTAAGAATG
1 ACATGCATGGACATTTAATCTCATTTGCATTTCC-TATTAAGAATG
60725 ACATGCATGGACATTTAATCTCATTTGCATTTCCTATTAAGAATG
1 ACATGCATGGACATTTAATCTCATTTGCATTTCCTATTAAGAATG
60770 TAAAAATTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 27 0.61
46 17 0.39
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (45 bp):
ACATGCATGGACATTTAATCTCATTTGCATTTCCTATTAAGAATG
Found at i:67819 original size:448 final size:448
Alignment explanation
Indices: 66799--68383 Score: 2408
Period size: 446 Copynumber: 3.5 Consensus size: 448
66789 TAGTGGACAA
* * *
66799 AAAGTATCGATACTTTATGTTAACGTATTTTTTCATTAAA-TCGTTATAATTTTACCTCTTACAT
1 AAAGTATCGATACTTTATGTTAACGTATTTTGTCATTAAACTCG-TATATTTTTACCGCTTACAT
*** *
66863 TGTAAATTTACCTATTACTTTAAAGTAATTTGTTTCAAAGTTTTAAGAATCAATACTTCTCGTAC
65 TGTAAATTTACCTATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATCGATACTTCTCGTAC
* * * *
66928 GTGCATCGATACTTTATAGGCGCAATTATGGAAATTGGTTTTGTTAATTTTGAACCTGTTAAGTT
130 GTGTATCGATACTTTATAGGCGCAATTATGGAAATCGGTTTTGTCAATTTTGAACCTATTAAGTT
* * **
66993 ATTTATATTTAATCGATACCATTACCCTTACTTAAGTACCAATACATTTTTGTATTATATCGATA
195 ATTTATATTTAATCGATACCATTACCCTTACTTAAGTATCAATACTTTTTTGTATGGTATCGATA
* * * *
67058 CTTTCGAGATATTTCTTTTTTTTTTTGTAAACTGATATCTTTTTACCTATTTTTTCATATTGAAA
260 CTTTCGAGATGTTTC--ATTTTTTTTGTAAACCGATATCTTTTTACCTATTTTGTCATATTGAAA
* * * * * * *
67123 CTGAATTTTTCAATTTTCAACATATTATATTGTCATGTATCAATACATGTGTATTAGGTATTGAT
323 CCGGATTTATCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTATTAGGTATCGAT
* * * *
67188 ACTTTCTGTGTGCATCTAGTTTGGGAAGCGTACTGG-ACAAAAGTATCGGTACATATACAC
388 ACTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGAAAAAAAGTATCGATACATATACAC
* * *
67248 AAAGTATCGATACATTATGTTAACGTATTTTTTCATTAAACTGGTATATTTTTACCGCTTACATT
1 AAAGTATCGATACTTTATGTTAACGTATTTTGTCATTAAACTCGTATATTTTTACCGCTTACATT
* * *
67313 TTAAATTTACCTATTACTTTAAAGTAATTCATTTCAAAGTTTTAAGAATCGATACTTCTCATACG
66 GTAAATTTACCTATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATCGATACTTCTCGTACG
** *
67378 TGTATCGATACTTTATAGTTGCAATTATGGAAATCGGTTTTGTCAGTTTTGAACCTATTAAGTTA
131 TGTATCGATACTTTATAGGCGCAATTATGGAAATCGGTTTTGTCAATTTTGAACCTATTAAGTTA
*
67443 TTTATATTTAATCGATACCATTACCCTTACTTAATTATCAATACTTTTTTGTATGGTATCGATAC
196 TTTATATTTAATCGATACCATTACCCTTACTTAAGTATCAATACTTTTTTGTATGGTATCGATAC
67508 TTTCGAGATGTTTCATTTTTTTTGTAAACCGATATCTTTTTACCTATTTTGTCATATTGAAACCG
261 TTTCGAGATGTTTCATTTTTTTTGTAAACCGATATCTTTTTACCTATTTTGTCATATTGAAACCG
* *
67573 GATTTATCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTATTAGGTATCAATATT
326 GATTTATCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTATTAGGTATCGATACT
* * * *
67638 TTCTACATGCATCTAGTTTGGGTAGCATACTGGAAAAAAAGTATCGATACATATACCC
391 TTCTGCGTGCATCTAGTTTGGGAAGCATACTGGAAAAAAAGTATCGATACATATACAC
67696 AAAGTATCGATACTTTATGTTAACGTATTTTGTCATTAAACTCGTATATTTTTACCGCTTACATT
1 AAAGTATCGATACTTTATGTTAACGTATTTTGTCATTAAACTCGTATATTTTTACCGCTTACATT
* * * ** *
67761 TTAAATTTACCTACTACTTTAAAGTAATCCGTTTTGAAGTTTCAAGAATCGATACTTCTCGTACG
66 GTAAATTTACCTATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATCGATACTTCTCGTACG
*
67826 TGTATCGATACTTTATAGGCGCAATTATGGAAA-CTGGTTTTGTCAATTTTGAACTTATTAAGTT
131 TGTATCGATACTTTATAGGCGCAATTATGGAAATC-GGTTTTGTCAATTTTGAACCTATTAAGTT
* * *
67890 ATTTATATTTAATCGATACCATTACCCTTACTTAAGTATCGATACTTTTTAGTAAGGTATCGATA
195 ATTTATATTTAATCGATACCATTACCCTTACTTAAGTATCAATACTTTTTTGTATGGTATCGATA
* * **
67955 CTTTTGAGACGTTTCA--TTTTTTGTAAACCGATATCTTTTTACCCGTTTTGTCATATTGAAACC
260 CTTTCGAGATGTTTCATTTTTTTTGTAAACCGATATCTTTTTACCTATTTTGTCATATTGAAACC
68018 -GATTTTATCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTATTAGGTATCGATA
325 GGA-TTTATCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTATTAGGTATCGATA
** * * *
68082 CTTTCTGCGTATATCTAGTTTGGGAAGCATACTGGACAAAAAGTATCAATACATATACAA
389 CTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGAAAAAAAGTATCGATACATATACAC
* * *
68142 AAAGTATCGATACTTTATGTTAACGTATTTTGTCATTAAACTGGTATATTATTACCGTTTACATT
1 AAAGTATCGATACTTTATGTTAACGTATTTTGTCATTAAACTCGTATATTTTTACCGCTTACATT
** *
68207 GTAAATTTACCTATTACTTTAAAGTAATCCATTTTGAAGTTTTAAGAGTCGATACTTCTCGTACG
66 GTAAATTTACCTATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATCGATACTTCTCGTACG
* * *
68272 TGTATCGATACTTTATAGGCGCAATTATGGAAACCAGTTTTGTCAATTTTGAACCTGTTAAGTTA
131 TGTATCGATACTTTATAGGCGCAATTATGGAAATCGGTTTTGTCAATTTTGAACCTATTAAGTTA
*
68337 TTTATATTTAATCGATACCATTACCCTTACTTAAGTATCGATACTTT
196 TTTATATTTAATCGATACCATTACCCTTACTTAAGTATCAATACTTT
68384 CGAGATGTTT
Statistics
Matches: 1045, Mismatches: 86, Indels: 13
0.91 0.08 0.01
Matches are distributed among these distances:
445 2 0.00
446 384 0.37
447 134 0.13
448 274 0.26
449 249 0.24
450 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (448 bp):
AAAGTATCGATACTTTATGTTAACGTATTTTGTCATTAAACTCGTATATTTTTACCGCTTACATT
GTAAATTTACCTATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATCGATACTTCTCGTACG
TGTATCGATACTTTATAGGCGCAATTATGGAAATCGGTTTTGTCAATTTTGAACCTATTAAGTTA
TTTATATTTAATCGATACCATTACCCTTACTTAAGTATCAATACTTTTTTGTATGGTATCGATAC
TTTCGAGATGTTTCATTTTTTTTGTAAACCGATATCTTTTTACCTATTTTGTCATATTGAAACCG
GATTTATCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTATTAGGTATCGATACT
TTCTGCGTGCATCTAGTTTGGGAAGCATACTGGAAAAAAAGTATCGATACATATACAC
Found at i:68591 original size:19 final size:19
Alignment explanation
Indices: 68569--68606 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
68559 ATTTAATCAA
68569 TTTTGTAAAATTTTAACCG
1 TTTTGTAAAATTTTAACCG
*
68588 TTTTGTCAAATTTTAACCG
1 TTTTGTAAAATTTTAACCG
68607 GTTTAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (19 bp):
TTTTGTAAAATTTTAACCG
Found at i:70318 original size:230 final size:225
Alignment explanation
Indices: 69912--70365 Score: 649
Period size: 230 Copynumber: 2.0 Consensus size: 225
69902 AGTAAAACGG
*
69912 TTTCCTTCAAAAGAATCGAAATATTCTCTACTACAAGTATCGATACATTTATACAACCTACAATA
1 TTTCCTTCAAAAGAATCGAAATACTCTCTACTACAAGTATCGATACATTTATACAACCTACAATA
*
69977 TCATTTTCTACCTATAATATTATATACAAGTATCGATATTTATTTTCTACCTACAATATCACTTT
66 TCATTTTCTACCTATAATATTATATACAAGTATCAATATTTATTTTCTACCTACAATATCACTTT
* * * * *
70042 CTAGCTATAATCGGTCCCAAATTCTTCTTTGCATCGAAATCCCCAAACCCATAAACCCTAATCCC
131 CTACCTATAATCGGTCCCAAATGCTTCTTTACATCGAAAACCCCAAACCCATAAAACC---T--C
* *
70107 TATTTTCGATTACTGTAATACTAAAAAAACTAGGA
191 TATTTCCGATTACTGTAATAATAAAAAAACTAGGA
* * * * * *
70142 TTTCCTTTAAATGAATGGGAATACTCTCTACTACAAGTATCGGTACATTTATACAACCTACATTA
1 TTTCCTTCAAAAGAATCGAAATACTCTCTACTACAAGTATCGATACATTTATACAACCTACAATA
* * *
70207 TCATTTTCTACCTATAATATTTTATA-AGAGTGTCAATATTTATTTTCTACCTAGAATATCACTT
66 TCATTTTCTACCTATAATATTATATACA-AGTATCAATATTTATTTTCTACCTACAATATCACTT
* * *
70271 TCTACCTGTAATCGGTCTCAAATGCTTCTTTACTTCGAAAACCCCAAACCCATAAAACCTCTATT
130 TCTACCTATAATCGGTCCCAAATGCTTCTTTACATCGAAAACCCCAAACCCATAAAACCTCTATT
*
70336 TCCGATTATTGTAATAATAAAAAAACTAGG
195 TCCGATTACTGTAATAATAAAAAAACTAGG
70366 GTTTTGACAC
Statistics
Matches: 201, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
225 32 0.16
227 1 0.00
229 1 0.00
230 167 0.83
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.36
Consensus pattern (225 bp):
TTTCCTTCAAAAGAATCGAAATACTCTCTACTACAAGTATCGATACATTTATACAACCTACAATA
TCATTTTCTACCTATAATATTATATACAAGTATCAATATTTATTTTCTACCTACAATATCACTTT
CTACCTATAATCGGTCCCAAATGCTTCTTTACATCGAAAACCCCAAACCCATAAAACCTCTATTT
CCGATTACTGTAATAATAAAAAAACTAGGA
Found at i:74184 original size:22 final size:23
Alignment explanation
Indices: 74143--74185 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
74133 CTAAAATCCT
74143 TTAATAAAATCATTTTCATAAAC
1 TTAATAAAATCATTTTCATAAAC
74166 TTAATGAAAAT-A-TTTCATAA
1 TTAAT-AAAATCATTTTCATAA
74186 TGCGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAATAAAATCATTTTCATAAAC
Found at i:74919 original size:26 final size:24
Alignment explanation
Indices: 74873--74941 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 24
74863 TTTAATTATA
74873 TTTTTATTTAT-TTACTA-TATTCCTT
1 TTTTTATTTATATTA-TATTATT--TT
74898 TTTTTATTTATATTATATTATTTT
1 TTTTTATTTATATTATATTATTTT
*
74922 TTATTATATATATATTATAT
1 TT-TT-TATTTATATTATAT
74942 CATTATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 4 0.10
25 15 0.38
26 20 0.51
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTTATTTATATTATATTATTTT
Found at i:74921 original size:21 final size:21
Alignment explanation
Indices: 74897--74959 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
74887 CTATATTCCT
74897 TTTTTTATT-TATATTATATTA
1 TTTTTTATTATATA-TATATTA
74918 TTTTTTATTATATATATATTA
1 TTTTTTATTATATATATATTA
**
74939 TATCATTATATATATATATAT
1 T-TTTTTAT-TATATATATAT
74960 AGATGTATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.46
22 9 0.24
23 11 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTTATTATATATATATTA
Found at i:74954 original size:19 final size:18
Alignment explanation
Indices: 74924--74959 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
74914 ATTATTTTTT
74924 ATTATATATATATTATATC
1 ATTATATATATA-TATATC
74943 ATTATATATATATATAT
1 ATTATATATATATATAT
74960 AGATGTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATATATATATATATC
Found at i:75109 original size:44 final size:41
Alignment explanation
Indices: 75035--75122 Score: 108
Period size: 44 Copynumber: 2.1 Consensus size: 41
75025 TTTATACGTT
75035 TTTATATATATATTTTCTTACTATTCTATTTTTTT-TATTTA
1 TTTATATATATATTTTCTTACTATTCTATTTTTTTCTA-TTA
*
75076 TTTATATATATTATATTT-TTACTTTATTTTATTTTTTTCTATTA
1 TTTATATATA-TAT-TTTCTTAC--TATTCTATTTTTTTCTATTA
75120 TTT
1 TTT
75123 TTTTCTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
41 10 0.24
42 7 0.17
43 3 0.07
44 19 0.46
45 2 0.05
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (41 bp):
TTTATATATATATTTTCTTACTATTCTATTTTTTTCTATTA
Found at i:75112 original size:18 final size:18
Alignment explanation
Indices: 75067--75123 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
75057 ATTCTATTTT
* *
75067 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
75084 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
75102 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
75120 TTTT
1 TTTT
75124 TTTCTTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:75120 original size:13 final size:13
Alignment explanation
Indices: 75104--75128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75094 TTACTTTATT
75104 TTATTTTTTTCTA
1 TTATTTTTTTCTA
75117 TTATTTTTTTCT
1 TTATTTTTTTCT
75129 TAATATCATG
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:75259 original size:18 final size:17
Alignment explanation
Indices: 75227--75271 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
75217 TGTACACATT
75227 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
75244 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
75262 ATTTTTTTAC
1 ATTTTTTTAC
75272 TCCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:75269 original size:17 final size:17
Alignment explanation
Indices: 75225--75271 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
75215 TATGTACACA
75225 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
75242 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
75260 TTATTTTTTTAC
1 TTATTTTTTTAC
75272 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:75355 original size:18 final size:18
Alignment explanation
Indices: 75305--75356 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 18
75295 TGTGTCTTTG
* *
75305 TTTTTTAATATTTTATTCA
1 TTTTTTATTATTTT-TTAA
*
75324 TTTTGT-TTA-TTTTTAA
1 TTTTTTATTATTTTTTAA
75340 TTTTTTATTATTTTTTA
1 TTTTTTATTATTTTTTA
75357 CGTGTTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 8 0.30
19 5 0.19
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTTTATTATTTTTTAA
Found at i:79422 original size:10 final size:11
Alignment explanation
Indices: 79398--79423 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
79388 AGGGGCAATA
79398 TTTTCAAAACT
1 TTTTCAAAACT
79409 TTTTCAAAACT
1 TTTTCAAAACT
79420 TTTT
1 TTTT
79424 TAATTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTCAAAACT
Found at i:80055 original size:37 final size:37
Alignment explanation
Indices: 80003--80074 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
79993 TAAAAAGAAG
* *
80003 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAA
* *
80040 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
80075 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:80137 original size:36 final size:36
Alignment explanation
Indices: 80090--80315 Score: 216
Period size: 36 Copynumber: 6.4 Consensus size: 36
80080 ATTGAAAACA
*
80090 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
80126 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
80162 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * *
80191 TTTTATTTGAAATAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * ** *
80227 TTTCTTTTGGAACTACGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
*
80264 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
80300 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
80316 ATCTTTGAAT
Statistics
Matches: 153, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.02
29 17 0.11
30 2 0.01
35 1 0.01
36 98 0.64
37 32 0.21
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:80201 original size:101 final size:101
Alignment explanation
Indices: 80009--80279 Score: 346
Period size: 101 Copynumber: 2.7 Consensus size: 101
79999 GAAGATTTTA
* * *
80009 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
*
80074 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
66 A-AAACATTGAAAACATTTCACTTGAAATAAATTTCG
* * *
80111 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* * ** * *
80175 AAAATATTTGAATATGTTTTATTTGAAATAAATTTCG
66 AAAACA-TTGAAAACATTTCACTTGAAATAAATTTCG
** * * **
80212 TCTCCCTTGAGACAGTTTCTTTTGGAACTACGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
80277 AAA
66 AAA
80280 TTTCGTCTCT
Statistics
Matches: 147, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
100 4 0.03
101 82 0.56
102 61 0.41
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (101 bp):
TCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
AAAACATTGAAAACATTTCACTTGAAATAAATTTCG
Found at i:80261 original size:138 final size:138
Alignment explanation
Indices: 80110--80369 Score: 403
Period size: 138 Copynumber: 1.9 Consensus size: 138
80100 AATAAATTTC
* *
80110 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * ** * *
80175 AAAATATTTGAATATGTTTTATTTGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
80240 TACGTTTT
131 TACGTTTT
*
80248 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * *
80313 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCT
80370 CTTGAAACAC
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 109 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
TACGTTTT
Found at i:80377 original size:65 final size:65
Alignment explanation
Indices: 80273--80446 Score: 233
Period size: 65 Copynumber: 2.6 Consensus size: 65
80263 GTTTCTCTTG
* * * **
80273 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
*
80338 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
80403 TA
64 TA
* * *
80405 AAACAAAATTTTGTTTCCCTTGAGACAATTT-TCATGAAACAA
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
80447 CAGATATCTT
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
65 37 0.38
66 4 0.04
67 32 0.33
68 24 0.25
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:80443 original size:67 final size:67
Alignment explanation
Indices: 80273--80445 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 67
80263 GTTTCTCTTG
* * * * * **
80273 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
80336 TA
66 TA
* * *
80338 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
80403 TA
66 TA
*
80405 AAACAAAATTTTGTTTCCCTTGAGACAATTT-TCATGAAACA
1 AAAC-AAATTTTGTCTCCCTTGAGACAATTTCTCATGAAACA
80446 ACAGATATCT
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
65 33 0.34
66 2 0.02
67 37 0.39
68 24 0.25
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:81321 original size:110 final size:110
Alignment explanation
Indices: 81120--81326 Score: 315
Period size: 110 Copynumber: 1.9 Consensus size: 110
81110 GTTTCCCAGT
* * *
81120 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGATAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
81185 CAACGAAGGGGCGACTGATTGCCAACAAACAACTTTTCAGTTTCA
66 CAACGAAGGGGAGACTGACTGCCAACAAACAACTTTTCAGTTTCA
* *
81230 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * * *
81295 CAGCGAAGGGGAGGCTGGCTGTCAACAAACAA
66 CAACGAAGGGGAGACTGACTGCCAACAAACAA
81327 TTTCCCAGTT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGAGACTGACTGCCAACAAACAACTTTTCAGTTTCA
Found at i:82378 original size:21 final size:21
Alignment explanation
Indices: 82298--82371 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 21
82288 CCTTTATATA
*
82298 TATATTTTAATTATATTTTTATT
1 TATATTAT-ATTAT-TTTTTATT
* *
82321 TATTTACTATATTCCTTTTTTATT
1 TA--TATTATATT-ATTTTTTATT
82345 TATATTATATTATTTTTTATTT
1 TATATTATATTATTTTTTA-TT
82367 TATAT
1 TATAT
82372 ATCTTATATC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 7 0.17
22 15 0.36
23 2 0.05
24 13 0.31
25 5 0.12
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (21 bp):
TATATTATATTATTTTTTATT
Found at i:82440 original size:2 final size:2
Alignment explanation
Indices: 82433--82457 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
82423 CTCCATTTAC
82433 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
82458 CTTAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82487 original size:36 final size:33
Alignment explanation
Indices: 82447--82546 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 33
82437 TATATATATA
82447 TATATATATATCTTAATATTATATTTTATACGTTTT
1 TATATATATATCTTAATATTATATTTT-T--GTTTT
*
82483 TATATATATATTTTCTTAATATTCTATTTTTGTTTT
1 TATATATATA---TCTTAATATTATATTTTTGTTTT
* * *
82519 TATTTATTTAT-ATATATATTATATTTTT
1 TATATATATATCTTA-ATATTATATTTTT
82547 ACTTTATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
32 2 0.04
33 13 0.24
36 23 0.42
38 1 0.02
39 16 0.29
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (33 bp):
TATATATATATCTTAATATTATATTTTTGTTTT
Found at i:82563 original size:18 final size:18
Alignment explanation
Indices: 82516--82579 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
82506 CTATTTTTGT
* *
82516 TTTTATTTATTTATATATA
1 TTTTATTTTTTTCTAT-TA
* *
82535 TATTATATTTTTACT-TTA
1 TTTTAT-TTTTTTCTATTA
82553 TTTTATTTTTTTCTATTA
1 TTTTATTTTTTTCTATTA
82571 TTTT-TTTTT
1 TTTTATTTTT
82580 CATAATATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 12 0.32
18 14 0.38
19 6 0.16
20 5 0.14
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTCTATTA
Found at i:82725 original size:17 final size:17
Alignment explanation
Indices: 82680--82726 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
82670 TGTGTACACA
82680 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
* *
82697 TAATTTCATTTACCTTTT
1 TTATTT-TTTTACCTTTT
82715 TTATTTTTTTAC
1 TTATTTTTTTAC
82727 TCCATTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:84271 original size:19 final size:20
Alignment explanation
Indices: 84247--84291 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
84237 AAAATGCCCT
* *
84247 AATTTC-ACATTCTAACATC
1 AATTTCAACACTCTAACATA
84266 AATTTCAACACTCTAACATA
1 AATTTCAACACTCTAACATA
84286 AATTTC
1 AATTTC
84292 CAGCATAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTCAACACTCTAACATA
Found at i:84765 original size:42 final size:42
Alignment explanation
Indices: 84707--84885 Score: 322
Period size: 42 Copynumber: 4.3 Consensus size: 42
84697 CATATTCGCA
*
84707 TTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
84749 TTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
84791 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
84833 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
84875 TTGCGATAGTC
1 TTGCGATAGTC
84886 CAAAATCGCA
Statistics
Matches: 130, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 130 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:84858 original size:21 final size:21
Alignment explanation
Indices: 84701--84888 Score: 131
Period size: 21 Copynumber: 9.0 Consensus size: 21
84691 GATTTACATA
* * *
84701 TTCGCATTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
84722 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
84745 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
84764 TTTGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
84787 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
84806 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
84829 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
84848 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
84871 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
84889 AATCGCAACG
Statistics
Matches: 133, Mismatches: 20, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
19 33 0.25
21 66 0.50
23 34 0.26
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:85701 original size:16 final size:16
Alignment explanation
Indices: 85677--85708 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
85667 ATTTGGAAAA
85677 TCGCATTGCAATAGTC
1 TCGCATTGCAATAGTC
*
85693 TCGCGTTGCAATAGTC
1 TCGCATTGCAATAGTC
85709 GAAGTTCGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (16 bp):
TCGCATTGCAATAGTC
Found at i:91396 original size:18 final size:19
Alignment explanation
Indices: 91363--91398 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
91353 AAAGATCTAG
*
91363 ACTTGGTTTGATGTGAAAT
1 ACTTGCTTTGATGTGAAAT
91382 ACTTGCTTT-ATGTGAAA
1 ACTTGCTTTGATGTGAAA
91399 GAATTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (19 bp):
ACTTGCTTTGATGTGAAAT
Found at i:97610 original size:20 final size:20
Alignment explanation
Indices: 97585--97622 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
97575 TTCATATTAT
97585 TTTATATTATTTTAAGTTTA
1 TTTATATTATTTTAAGTTTA
*
97605 TTTATATTATTTTGAGTT
1 TTTATATTATTTTAAGTT
97623 GTTATAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (20 bp):
TTTATATTATTTTAAGTTTA
Found at i:99162 original size:33 final size:33
Alignment explanation
Indices: 99117--99186 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
99107 CTTTACAAAC
* * *
99117 TCCCTAGTTTTTCACGGGCTAAACTAGAATCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
* *
99150 TCCCTAGCTTTTCACGGGATCAGCTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
99183 TCCC
1 TCCC
99187 CTTTATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
Found at i:99491 original size:21 final size:22
Alignment explanation
Indices: 99466--99519 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
99456 TCCATAACAG
*
99466 GGGGTATC-AGTACCCCTTTAA
1 GGGGTATCGAGTACCCCTTCAA
*
99487 GGGGTATCGGGGTACCCCTTCAA
1 GGGGTATC-GAGTACCCCTTCAA
99510 GGGGTATCGA
1 GGGGTATCGA
99520 TACTATCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.29
22 1 0.04
23 19 0.68
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.24
Consensus pattern (22 bp):
GGGGTATCGAGTACCCCTTCAA
Found at i:99505 original size:23 final size:23
Alignment explanation
Indices: 99475--99518 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
99465 GGGGGTATCA
*
99475 GTACCCCTTTAAGGGGTATCGGG
1 GTACCCCTTCAAGGGGTATCGGG
99498 GTACCCCTTCAAGGGGTATCG
1 GTACCCCTTCAAGGGGTATCG
99519 ATACTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (23 bp):
GTACCCCTTCAAGGGGTATCGGG
Found at i:99639 original size:33 final size:35
Alignment explanation
Indices: 99576--99641 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
99566 GGAGCCAGGG
99576 GGTATTGATACCCACACAGGGGTATCGGTACCCAA
1 GGTATTGATACCCACACAGGGGTATCGGTACCCAA
* *
99611 GGTATTGATA-CC-CATAGGGGTATTGGTACCC
1 GGTATTGATACCCACACAGGGGTATCGGTACCC
99642 TTTTTGCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 17 0.59
34 2 0.07
35 10 0.34
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (35 bp):
GGTATTGATACCCACACAGGGGTATCGGTACCCAA
Found at i:101905 original size:20 final size:20
Alignment explanation
Indices: 101880--101949 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 20
101870 CGTTGGAGCT
*
101880 CAGGGGTATTGATACCCATG
1 CAGGGGTATCGATACCCATG
101900 CAGGGGTATCGATACCCA--
1 CAGGGGTATCGATACCCATG
101918 -A--GGTATCGATACCCAT-
1 CAGGGGTATCGATACCCATG
*
101934 -AGGGGTATCGGTACCC
1 CAGGGGTATCGATACCC
101950 TTTTTGAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
15 14 0.31
16 1 0.02
17 1 0.02
18 12 0.27
20 17 0.38
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (20 bp):
CAGGGGTATCGATACCCATG
Found at i:101924 original size:15 final size:15
Alignment explanation
Indices: 101904--101932 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
101894 CCCATGCAGG
101904 GGTATCGATACCCAA
1 GGTATCGATACCCAA
101919 GGTATCGATACCCA
1 GGTATCGATACCCA
101933 TAGGGGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (15 bp):
GGTATCGATACCCAA
Found at i:101943 original size:33 final size:34
Alignment explanation
Indices: 101884--101949 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
101874 GGAGCTCAGG
*
101884 GGTATTGATACCCATGCAGGGGTATCGATACCCAA
1 GGTATCGATACCCAT-CAGGGGTATCGATACCCAA
*
101919 GGTATCGATACCCAT-AGGGGTATCGGTACCC
1 GGTATCGATACCCATCAGGGGTATCGATACCC
101950 TTTTTGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 15 0.52
35 14 0.48
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (34 bp):
GGTATCGATACCCATCAGGGGTATCGATACCCAA
Found at i:102022 original size:22 final size:22
Alignment explanation
Indices: 101975--102023 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
101965 TTTAAGCCTT
* *
101975 CATAGGGGTATTGATACCCAGT
1 CATAGGGGTATCGATACCCAGG
101997 CATAGGGGTATCGATA-CCAGGG
1 CATAGGGGTATCGATACCCA-GG
102019 CATAG
1 CATAG
102024 ATACCCATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (22 bp):
CATAGGGGTATCGATACCCAGG
Found at i:102083 original size:99 final size:96
Alignment explanation
Indices: 101881--102094 Score: 218
Period size: 99 Copynumber: 2.2 Consensus size: 96
101871 GTTGGAGCTC
* * *
101881 AGGGGTATTGATACCCATGCAGGGGTATCGATACCCAAGGTATCGATACCCATAGGGGTATCGGT
1 AGGGGTATTGATACCCATGCAGGGGTATCGATACCCAAGGCATAGATACCCATAGGGGAATCGGT
** * * *
101946 ACCCTTTTTGAATTCGATGTTTAAGCCTTCAT
66 ACCCTTCAT-AATTCGATATTGAACCCTTCAT
*
101978 AGGGGTATTGATACCCA-GTCATAGGGGTATCGATA-CCAGGGCATAGATACCCATAGGGGAATC
1 AGGGGTATTGATACCCATG-C--AGGGGTATCGATACCCAAGGCATAGATACCCATAGGGGAATC
* * *
102041 GGTACCCATTCAT-ATTGGGTATTGACACCCATTTAT
63 GGTACCC-TTCATAATTCGATATTGA-ACCC-TTCAT
* *
102077 AGGGGTATCGGTACCCAT
1 AGGGGTATTGATACCCAT
102095 TTGCATTTTT
Statistics
Matches: 96, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
96 1 0.01
97 26 0.27
98 34 0.35
99 35 0.36
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (96 bp):
AGGGGTATTGATACCCATGCAGGGGTATCGATACCCAAGGCATAGATACCCATAGGGGAATCGGT
ACCCTTCATAATTCGATATTGAACCCTTCAT
Found at i:102092 original size:22 final size:22
Alignment explanation
Indices: 102030--102096 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
102020 ATAGATACCC
* *
102030 ATAGGGGAATCGGTACCCATTC
1 ATAGGGGTATCGGTACCCATTT
* * **
102052 ATATTGGGTATTGACACCCATTT
1 ATA-GGGGTATCGGTACCCATTT
102075 ATAGGGGTATCGGTACCCATTT
1 ATAGGGGTATCGGTACCCATTT
102097 GCATTTTTTC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (22 bp):
ATAGGGGTATCGGTACCCATTT
Found at i:111340 original size:72 final size:72
Alignment explanation
Indices: 111198--111535 Score: 336
Period size: 72 Copynumber: 4.7 Consensus size: 72
111188 GGGATTGAAT
* * * * * * * * *
111198 CAGTTGAAGAGGAAGCCAATGTGGTTTCTCAAAGCCAAGTAGAAGCCGAAACAGAGGATGGGGAA
1 CAGTTGAAGAGGAAGCAAATATGGTTCCTGAAAGTCAAGTACAAGCAGAAGCAGAAGA-GGGGAA
111263 A-AGGAAA
65 ACAGGAAA
* * * * **
111270 CAGTTGAACAGGAAGCAAATGTCGTTCCTGAAAGTCAAGTACAAGCAGAAGTAGCGGAGGGGAAA
1 CAGTTGAAGAGGAAGCAAATATGGTTCCTGAAAGTCAAGTACAAGCAGAAGCAGAAGAGGGGAAA
111335 CAGGAAA
66 CAGGAAA
* * * ** * *
111342 TAGTTGAAGAGGAAACAAATATGGCTCCTGAAAGTCGTGTACAAGCAGAACCAGAAGAGGGGAAG
1 CAGTTGAAGAGGAAGCAAATATGGTTCCTGAAAGTCAAGTACAAGCAGAAGCAGAAGAGGGGAAA
111407 CAGGAAA
66 CAGGAAA
* * * *** * * * * *
111414 CAGTTGAAGAGGAAACAAATATGGATCCTAAAAGTTGTGTACAAGCAGAAGAAGCACAAGGGAAG
1 CAGTTGAAGAGGAAGCAAATATGGTTCCTGAAAGTCAAGTACAAGCAGAAGCAGAAGAGGGGAAA
*
111479 CAAGAAA
66 CAGGAAA
* *
111486 CAGTTGAAGAGGAAGCAAATATGGTCCCTGAAAGTCAAGAACAAGCAGAA
1 CAGTTGAAGAGGAAGCAAATATGGTTCCTGAAAGTCAAGTACAAGCAGAA
111536 TCAGCAAACG
Statistics
Matches: 223, Mismatches: 42, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
71 7 0.03
72 216 0.97
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (72 bp):
CAGTTGAAGAGGAAGCAAATATGGTTCCTGAAAGTCAAGTACAAGCAGAAGCAGAAGAGGGGAAA
CAGGAAA
Found at i:111459 original size:144 final size:144
Alignment explanation
Indices: 111264--111566 Score: 349
Period size: 144 Copynumber: 2.1 Consensus size: 144
111254 GATGGGGAAA
* * * * * * ** *
111264 AGGAAACAGTTGAACAGGAAGCAAATGTCGTTCCTGAAAGTCAAGTACAAGCAGAAGTAGCGGAG
1 AGGAAACAGTTGAAGAGGAAACAAATATCGATCCTAAAAGTCAAGTACAAGCAGAAGAAGCACAA
* * ** *
111329 GGGAAACAGGAAATAGTTGAAGAGGAAACAAATATGG-CTCCTGAAAGTCGTGTACAAGCAGAAC
66 GGGAAACAAGAAACAGTTGAAGAGGAAACAAATATGGTC-CCTGAAAGTCAAGAACAAGCAGAAC
*
111393 CAG-AAGAGGGGAAGC
130 CAGCAA-ACGGGAAGC
* ***
111408 AGGAAACAGTTGAAGAGGAAACAAATATGGATCCTAAAAGTTGTGTACAAGCAGAAGAAGCACAA
1 AGGAAACAGTTGAAGAGGAAACAAATATCGATCCTAAAAGTCAAGTACAAGCAGAAGAAGCACAA
* * *
111473 GGGAAGCAAGAAACAGTTGAAGAGGAAGCAAATATGGTCCCTGAAAGTCAAGAACAAGCAGAATC
66 GGGAAACAAGAAACAGTTGAAGAGGAAACAAATATGGTCCCTGAAAGTCAAGAACAAGCAGAACC
*
111538 AGCAAACGGGAAGG
131 AGCAAACGGGAAGC
* *
111552 AAGAAAAAGTTGAAG
1 AGGAAACAGTTGAAG
111567 TGGGTGCAGA
Statistics
Matches: 132, Mismatches: 25, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
144 129 0.98
145 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.29, T:0.13
Consensus pattern (144 bp):
AGGAAACAGTTGAAGAGGAAACAAATATCGATCCTAAAAGTCAAGTACAAGCAGAAGAAGCACAA
GGGAAACAAGAAACAGTTGAAGAGGAAACAAATATGGTCCCTGAAAGTCAAGAACAAGCAGAACC
AGCAAACGGGAAGC
Found at i:111549 original size:72 final size:72
Alignment explanation
Indices: 111266--111566 Score: 297
Period size: 72 Copynumber: 4.2 Consensus size: 72
111256 TGGGGAAAAG
* * * * * **
111266 GAAACAGTTGAACAGGAAGCAAATGTCGTTCCTGAAAGTCAAGTACAAGCAGAAGT-AGCGGAGG
1 GAAACAGTTGAAGAGGAAACAAATATGGTCCCTGAAAGTCAAGTACAAGCAGAA-TCAGCAAAGG
* *
111330 GGAAACAG
65 GGAAGCAA
* ** *
111338 GAAATAGTTGAAGAGGAAACAAATATGG-CTCCTGAAAGTCGTGTACAAGCAGAACCAG-AAGAG
1 GAAACAGTTGAAGAGGAAACAAATATGGTC-CCTGAAAGTCAAGTACAAGCAGAATCAGCAA-AG
*
111401 GGGAAGCAG
64 GGGAAGCAA
* *** **
111410 GAAACAGTTGAAGAGGAAACAAATATGGAT-CCTAAAAGTTGTGTACAAGCAGAAGAAGCACAA-
1 GAAACAGTTGAAGAGGAAACAAATATGG-TCCCTGAAAGTCAAGTACAAGCAGAATCAGCA-AAG
111473 GGGAAGCAA
64 GGGAAGCAA
* * *
111482 GAAACAGTTGAAGAGGAAGCAAATATGGTCCCTGAAAGTCAAGAACAAGCAGAATCAGCAAACGG
1 GAAACAGTTGAAGAGGAAACAAATATGGTCCCTGAAAGTCAAGTACAAGCAGAATCAGCAAAGGG
*
111547 GAAGGAA
66 GAAGCAA
*
111554 GAAAAAGTTGAAG
1 GAAACAGTTGAAG
111567 TGGGTGCAGA
Statistics
Matches: 192, Mismatches: 28, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
71 3 0.02
72 186 0.97
73 2 0.01
74 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.29, T:0.13
Consensus pattern (72 bp):
GAAACAGTTGAAGAGGAAACAAATATGGTCCCTGAAAGTCAAGTACAAGCAGAATCAGCAAAGGG
GAAGCAA
Found at i:111790 original size:51 final size:51
Alignment explanation
Indices: 111689--111792 Score: 165
Period size: 51 Copynumber: 2.0 Consensus size: 51
111679 TACAGAGAGG
*
111689 AAGGGCAGCGTGAGAGCATTGGTTGGGGCATTTGAATCCCATGGCAAAAGC
1 AAGGGCAGCGTGAGAGCATTGGTTGGGGCATTTGAATCCCATAGCAAAAGC
* *
111740 AAGGGCAGGGTGAGAGCATTGGTTGGGGCATTTGAATCTCATAG-ATAAAGC
1 AAGGGCAGCGTGAGAGCATTGGTTGGGGCATTTGAATCCCATAGCA-AAAGC
111791 AA
1 AA
111793 ACTTCAATGC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
50 1 0.02
51 48 0.98
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (51 bp):
AAGGGCAGCGTGAGAGCATTGGTTGGGGCATTTGAATCCCATAGCAAAAGC
Found at i:113463 original size:140 final size:139
Alignment explanation
Indices: 113302--113598 Score: 393
Period size: 140 Copynumber: 2.1 Consensus size: 139
113292 TAAAATTTAG
*
113302 GCTCTAATTATTAATCCTAACCGATTTTAACGAATTATGGAATCGAATAATTGAAATGGAACCTC
1 GCTCTAATTATTAATCCTAACCAATTTTAACGAATTATGGAATCGAATAATTGAAATGGAACCTC
* * * *
113367 GGGCA-AAAATATGAGGA-CTAAATAAAAAATTCACCTAAAGTTAAAGGACTAGAGTGAAATTTA
66 AGGCATAAAA-ATGAGGATC-AAATAAAAAATTCAACTAAA-TTAAAGGACTAAAGTGAAATTAA
*
113430 TCTAAAATAGAA
128 ACTAAAATAGAA
* * *
113442 GCTCTAATTATTAATCCTAACCAATTTTAATGAATTATTGAATCGAATAATTGAAATTGAACCTC
1 GCTCTAATTATTAATCCTAACCAATTTTAACGAATTATGGAATCGAATAATTGAAATGGAACCTC
* * * *
113507 AGGCATAAAAGTGAGGATCAAATCAAATATTCAACTAAATTAAAGGAGTAAAGTGAAATTAAACT
66 AGGCATAAAAATGAGGATCAAATAAAAAATTCAACTAAATTAAAGGACTAAAGTGAAATTAAACT
* * *
113572 TAAGTTGAA
131 AAAATAGAA
*
113581 GCTCTAA-TATTAACCCTA
1 GCTCTAATTATTAATCCTA
113599 GTTATTTTTA
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
138 10 0.07
139 35 0.25
140 88 0.64
141 5 0.04
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (139 bp):
GCTCTAATTATTAATCCTAACCAATTTTAACGAATTATGGAATCGAATAATTGAAATGGAACCTC
AGGCATAAAAATGAGGATCAAATAAAAAATTCAACTAAATTAAAGGACTAAAGTGAAATTAAACT
AAAATAGAA
Found at i:113642 original size:138 final size:138
Alignment explanation
Indices: 113302--113688 Score: 359
Period size: 140 Copynumber: 2.8 Consensus size: 138
113292 TAAAATTTAG
* * ** * **
113302 GCTCTAATTATTAATCCTAACCGATTTTAACGAATTATGGAATCGAATAATTGAAATGGAACCTC
1 GCTCTAATTATTAACCCTAACCAATTTTAATAAATTATTGAATCGAATAATCCAAATGGAACCTC
* * * * * * * *
113367 GGGCA-AAAATATGAGGACTAAATAAAAAATTCACCTAAAGTTAAAGGACTAGAGTGAAATTTAT
66 AGGCATAAAA-GTGAGGAC-AAATCAAATATTCAACTAAA-TTAAAGGACTAAAGTGAAATTAAA
113431 CTAAAATAGAA
128 CTAAAATAGAA
* * ** *
113442 GCTCTAATTATTAATCCTAACCAATTTTAATGAATTATTGAATCGAATAATTGAAATTGAACCTC
1 GCTCTAATTATTAACCCTAACCAATTTTAATAAATTATTGAATCGAATAATCCAAATGGAACCTC
*
113507 AGGCATAAAAGTGAGGATCAAATCAAATATTCAACTAAATTAAAGGAGTAAAGTGAAATTAAACT
66 AGGCATAAAAGTGAGGA-CAAATCAAATATTCAACTAAATTAAAGGACTAAAGTGAAATTAAACT
* * *
113572 TAAGTTGAA
130 AAAATAGAA
*** * * *
113581 GCTCTAA-TATTAACCCT-AGTTATTTTTATCAAATTATTGAGTCTAATAATCCAAATGGAACCT
1 GCTCTAATTATTAACCCTAACCAATTTTAAT-AAATTATTGAATCGAATAATCCAAATGGAACCT
* * * * * *
113644 -TGAGTATAGAAGAGAGGACCAAAGCGAATATTCAACTAAATTAAA
65 CAG-GCATAAAAGTGAGGA-CAAATCAAATATTCAACTAAATTAAA
113689 AAGTTCAGCG
Statistics
Matches: 209, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
137 9 0.04
138 72 0.34
139 35 0.17
140 88 0.42
141 5 0.02
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (138 bp):
GCTCTAATTATTAACCCTAACCAATTTTAATAAATTATTGAATCGAATAATCCAAATGGAACCTC
AGGCATAAAAGTGAGGACAAATCAAATATTCAACTAAATTAAAGGACTAAAGTGAAATTAAACTA
AAATAGAA
Found at i:113831 original size:14 final size:14
Alignment explanation
Indices: 113814--113879 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 14
113804 TACAGATAAA
113814 TAAATACTAAAATT
1 TAAATACTAAAATT
* *
113828 TAAAGGACTAAAATG
1 TAAA-TACTAAAATT
* *
113843 TAAATGC-AAGAAAT
1 TAAATACTAA-AATT
113857 TAAATAACTAAAATT
1 TAAAT-ACTAAAATT
*
113872 AAAATACT
1 TAAATACT
113880 TGAAAAATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
13 2 0.05
14 15 0.38
15 20 0.51
16 2 0.05
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (14 bp):
TAAATACTAAAATT
Found at i:116212 original size:116 final size:115
Alignment explanation
Indices: 116039--116419 Score: 391
Period size: 116 Copynumber: 3.3 Consensus size: 115
116029 TCATCGTTTG
* * * *
116039 AGTTTTTCTCATTATGAAC-CCTTCCATTGGTAATAC-GA-ATCCACCTCATTCTGTGATGGATG
1 AGTTCTTCTCATTATGAACTCC-TCCATTGGAAATACTGATAT--ACATCTTTCTGTGATGGATG
* * * *
116101 AGCCAAAATTGATCAGGTTCTTCTCATTATGAACTTCTTCTCCTTCTCTGGATA
63 AGCCAAAGTTGAACA-GTTCTTCTCATTATGAACTTCTTCTCCTTCTATGGACA
* *
116155 AGTTCTTCTCATTATGAACTCCTCCATTGAAAATACTGATATACATCTTTCTCTGATGGATGAGC
1 AGTTCTTCTCATTATGAACTCCTCCATTGGAAATACTGATATACATCTTTCTGTGATGGATGAGC
* * * *
116220 TAAAGTTGAACAATCTCTTCTTATTATGAACTTCTTCTTCC-TCTTTGGACA
66 CAAAGTTGAACAGT-TCTTCTCATTATGAACTTCTTC-TCCTTCTATGGACA
** * * *
116271 AGTTAATCTCATTATGAACTCATTCATTGGAAATGA-TGAT-T-CATCTCCTTTTGTGATGGATG
1 AGTTCTTCTCATTATGAACTCCTCCATTGGAAAT-ACTGATATACATCT--TTCTGTGATGGATG
* * *
116333 GGCCAAGGTTGAACAAGTTCTTCTCGTTATGAACATT-TTCTCCTTCTATGGACA
63 AGCCAAAGTTGAAC-AGTTCTTCTCATTATGAAC-TTCTTCTCCTTCTATGGACA
* *
116387 AGTTCTTCTCATTATGAACTCGTCAATTGGAAA
1 AGTTCTTCTCATTATGAACTCCTCCATTGGAAA
116420 CACTAATTAA
Statistics
Matches: 222, Mismatches: 32, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
114 5 0.02
115 5 0.02
116 198 0.89
117 12 0.05
118 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (115 bp):
AGTTCTTCTCATTATGAACTCCTCCATTGGAAATACTGATATACATCTTTCTGTGATGGATGAGC
CAAAGTTGAACAGTTCTTCTCATTATGAACTTCTTCTCCTTCTATGGACA
Found at i:116367 original size:20 final size:20
Alignment explanation
Indices: 116342--116405 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
116332 GGGCCAAGGT
*
116342 TGAACAAGTTCTTCTCGTTA
1 TGAACAAGTTCTTCTCATTA
*
116362 TGAAC-A-TT-TTCTCCTTCTA
1 TGAACAAGTTCTTCT-CAT-TA
*
116381 TGGACAAGTTCTTCTCATTA
1 TGAACAAGTTCTTCTCATTA
116401 TGAAC
1 TGAAC
116406 TCGTCAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 4 0.11
18 4 0.11
19 7 0.20
20 12 0.34
21 4 0.11
22 4 0.11
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (20 bp):
TGAACAAGTTCTTCTCATTA
Found at i:116949 original size:17 final size:17
Alignment explanation
Indices: 116914--116952 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
116904 TCTTTCTAAC
*
116914 TTTTTCATTTTTCTATT
1 TTTTTAATTTTTCTATT
116931 TTTTTAATTTTTC-ATT
1 TTTTTAATTTTTCTATT
116947 TTTTTA
1 TTTTTA
116953 CAACAGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTAATTTTTCTATT
Found at i:119008 original size:20 final size:20
Alignment explanation
Indices: 118965--119020 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
118955 ATCAGTATAT
*
118965 GTATCGATACTTTTA-ACAA
1 GTATCGATACTATTATACAA
**
118984 GTATCGATACTATTATAGTA
1 GTATCGATACTATTATACAA
*
119004 GTATCGATACTACTATA
1 GTATCGATACTATTATA
119021 TTTAAAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (20 bp):
GTATCGATACTATTATACAA
Done.