Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 7 of 145
Found at i:2991838 original size:85 final size:85
Alignment explanation
Indices: 2991707--2992115 Score: 310
Period size: 85 Copynumber: 4.7 Consensus size: 85
2991697 TTTGTGAAAT
* ** *
2991707 AAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCATTTTTGAAC-AAGCGCCGCTATAGAACATC
1 AAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TTCTAAGCGCCGCTAAAGAACATC
2991769 A-CTTTTAGAGACGTTT-TCTTCCA
63 ATC-TTTAGAGACGTTTAT-TTCCA
* *
2991792 AAGCGCCGCTAAAGAACTTGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATCATC
* * *
2991857 TTTAGCGGCGTTTATTTCCT
66 TTTAGAGACGTTTATTTCCA
* * * * **
2991877 TAGCGCCGCTAAAGAACATGATTTTTAGCGACGTTTATTTCTAAGCGCCGCTAAAGAACATGGTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATCATC
* * *
2991942 TTTAGTG-CTTTTATTTGTGGCTTTTATTTCT
66 TTTAGAGACGTTTA-TT-T--C--------CA
* * * * * * *
2991973 AAGCGCCGCTAAAGAACATGGTCTTTAGTGACGTTTATTTTTTTAGCGCCACTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTCTAAGCGCCGCTAAAGAACATCAT
* * * *
2992038 CTTTAGCGGCGTTT-TTTTCT
65 CTTTAGAGACGTTTATTTCCA
* *
2992058 AAGCGCCGCTAAAGAACATGATCTTTAGGGGCGTTTTTTTCTGTAAGCGCCGCAAAAG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC--TAAGCGCCGCTAAAG
2992116 TTTGCGACGT
Statistics
Matches: 267, Mismatches: 36, Indels: 41
0.78 0.10 0.12
Matches are distributed among these distances:
84 11 0.04
85 168 0.63
86 16 0.06
88 1 0.00
95 1 0.00
96 36 0.13
97 30 0.11
98 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATCATC
TTTAGAGACGTTTATTTCCA
Found at i:2991849 original size:42 final size:42
Alignment explanation
Indices: 2991706--2991946 Score: 258
Period size: 42 Copynumber: 5.7 Consensus size: 42
2991696 GTTTGTGAAA
* **
2991706 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCATTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TCC
* * * *
2991749 -AAGCGCCGCTATAGAACATCA-CTTTTAGAGACGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCC
* * *
2991791 AAAGCGCCGCTAAAGAACTTGATCTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
2991833 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCC
* * *
2991876 TTAGCGCCGCTAAAGAACATGATTTTTAGCGACGTTTATTT-C
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCC
*
2991918 TAAGCGCCGCTAAAGAACATGGTCTTTAG
1 TAAGCGCCGCTAAAGAACATGATCTTTAG
2991947 TGCTTTTATT
Statistics
Matches: 172, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 97 0.56
43 73 0.42
44 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:2992076 original size:42 final size:42
Alignment explanation
Indices: 2991963--2992115 Score: 198
Period size: 42 Copynumber: 3.5 Consensus size: 42
2991953 TATTTGTGGC
* * *
2991963 TTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGACG
1 TTTT-TTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG
* * *
2992006 TTTATTTTTTTAGCGCCACTAAAGAACATGATCTTTAGCGGCG
1 TTT-TTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG
*
2992049 TTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGGGGCG
1 TTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG
*
2992091 TTTTTTTCTGTAAGCGCCGCAAAAG
1 TTTTTTTC--TAAGCGCCGCTAAAG
2992116 TTTGCGACGT
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
42 43 0.45
43 38 0.40
44 15 0.16
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (42 bp):
TTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG
Found at i:2992083 original size:139 final size:138
Alignment explanation
Indices: 2991825--2992085 Score: 423
Period size: 139 Copynumber: 1.9 Consensus size: 138
2991815 TTTAGCGGCG
* *
2991825 TTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTCCTTAGCGCCGCTAAA
1 TTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTATTTCCTTAGCGCCACTAAA
* *
2991890 GAACATGATTTTTAGCGACGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGCTTTTA
66 GAACATGATCTTTAGCGACGTTTATTTCTAAGCGCCGCTAAAGAACATGATCTTTAGTGCTTTTA
2991955 TTTGTGGC
131 TTTGTGGC
* * **
2991963 TTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGACGTTTATTTTTTTAGCGCCACTAA
1 TTTT-TTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTATTTCCTTAGCGCCACTAA
* *
2992028 AGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAG
65 AGAACATGATCTTTAGCGACGTTTATTTCTAAGCGCCGCTAAAGAACATGATCTTTAG
2992086 GGGCGTTTTT
Statistics
Matches: 112, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
138 4 0.04
139 108 0.96
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.37
Consensus pattern (138 bp):
TTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTATTTCCTTAGCGCCACTAAA
GAACATGATCTTTAGCGACGTTTATTTCTAAGCGCCGCTAAAGAACATGATCTTTAGTGCTTTTA
TTTGTGGC
Found at i:3004276 original size:42 final size:42
Alignment explanation
Indices: 3004149--3004260 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
3004139 GATTGAACGT
* * *
3004149 CAGTATTCGGTTTGTCCCTCGAGAGCCTGGGTGATTGAAATG
1 CAGTATCCGGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
* *
3004191 CAGTATCTGGTTTGTCCTTGGAGAGCTTGGGTGATTGAAATG
1 CAGTATCCGGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
3004233 CAGTA-CCGGATTTGTCCTTGGAGAGCCT
1 CAGTATCCGG-TTTGTCCTTGGAGAGCCT
3004261 AGGTCGTTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 3 0.05
42 59 0.95
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (42 bp):
CAGTATCCGGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
Found at i:3004285 original size:42 final size:42
Alignment explanation
Indices: 3004159--3004289 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 42
3004149 CAGTATTCGG
* * * * ** *
3004159 TTTGTCCCTCGAGAGCCTGGGTGATTGAAATGCAGTATCTGG-
1 TTTGTCCTTGGAGAGCCTAGGTGATTCAAATGCACCA-CCGGA
* * * **
3004201 TTTGTCCTTGGAGAGCTTGGGTGATTGAAATGCAGTACCGGA
1 TTTGTCCTTGGAGAGCCTAGGTGATTCAAATGCACCACCGGA
*
3004243 TTTGTCCTTGGAGAGCCTAGGTCG-TTCAAATGCACCATCGGA
1 TTTGTCCTTGGAGAGCCTAGGT-GATTCAAATGCACCACCGGA
3004285 TTTGT
1 TTTGT
3004290 TCATGGGGAG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 3 0.04
42 73 0.95
43 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (42 bp):
TTTGTCCTTGGAGAGCCTAGGTGATTCAAATGCACCACCGGA
Found at i:3009149 original size:21 final size:20
Alignment explanation
Indices: 3009121--3009162 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3009111 ATCATATATT
3009121 GATTGATAAAAAATAAAGTA
1 GATTGATAAAAAATAAAGTA
**
3009141 GATTAGATATCAAATAAAGTA
1 GATT-GATAAAAAATAAAGTA
3009162 G
1 G
3009163 GCAGACCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.17, T:0.26
Consensus pattern (20 bp):
GATTGATAAAAAATAAAGTA
Found at i:3012263 original size:91 final size:92
Alignment explanation
Indices: 3012159--3012344 Score: 365
Period size: 91 Copynumber: 2.0 Consensus size: 92
3012149 TAAAAGATTT
3012159 ATCGAGTTGCATGGACGAAGTCAAAAAATCTTTTTAGGGGAGTCGAAATTAAATTATAATACCTT
1 ATCGAGTTGCATGGACGAAGTCAAAAAATCTTTTTAGGGGAGTCGAAATTAAATTATAATACCTT
3012224 ATATTTTTATAATTTTT-AAGAATTAA
66 ATATTTTTATAATTTTTAAAGAATTAA
3012250 ATCGAGTTGCATGGACGAAGTCAAAAAATCTTTTTAGGGGAGTCGAAATTAAATTATAATACCTT
1 ATCGAGTTGCATGGACGAAGTCAAAAAATCTTTTTAGGGGAGTCGAAATTAAATTATAATACCTT
3012315 ATATTTTTATAATTTTTAAAGAATTAA
66 ATATTTTTATAATTTTTAAAGAATTAA
3012342 ATC
1 ATC
3012345 AAAATTTTAT
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 82 0.87
92 12 0.13
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (92 bp):
ATCGAGTTGCATGGACGAAGTCAAAAAATCTTTTTAGGGGAGTCGAAATTAAATTATAATACCTT
ATATTTTTATAATTTTTAAAGAATTAA
Found at i:3013537 original size:22 final size:24
Alignment explanation
Indices: 3013493--3013537 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
3013483 GCTTCATGTT
*
3013493 ATTTTTTATAAACTTTATATATAG
1 ATTTTTTATAAACTATATATATAG
*
3013517 ATTTTTTA-AAA-TATATTTATA
1 ATTTTTTATAAACTATATATATA
3013538 AGTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTTTTATAAACTATATATATAG
Found at i:3017451 original size:33 final size:33
Alignment explanation
Indices: 3017414--3017525 Score: 197
Period size: 33 Copynumber: 3.4 Consensus size: 33
3017404 GCCTGTAGAT
*
3017414 AAAAGGAATATATTTATAGTAGTACTACAAGCC
1 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
3017447 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
1 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
*
3017480 AAAAAGAATATATTTATAGTAGTAGTACAAGCC
1 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
*
3017513 AAAACGAATATAT
1 AAAAGGAATATAT
3017526 CATATCTAGG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (33 bp):
AAAAGGAATATATTTATAGTAGTAGTACAAGCC
Found at i:3022523 original size:184 final size:185
Alignment explanation
Indices: 3022319--3022688 Score: 733
Period size: 184 Copynumber: 2.0 Consensus size: 185
3022309 TTATTGCAAA
3022319 AATTATATTATTTAAATCTTAAAAAATTTTAAATTTATGGCCAAATTACGTTTTATAAAAATGTT
1 AATTATATTATTTAAATCTTAAAAAATTTTAAATTTATGGCCAAATTACGTTTTATAAAAATGTT
3022384 ATAATATATTTATTTATAAAAAATTATGGTCAAGTATAGACATAACTTAATTATGTGTCCATGCT
66 ATAATATATTTATTTATAAAAAATTATGGTCAAGTATAGACATAACTTAATTATGTGTCCATGCT
3022449 ATATATTATAAAAAATAATATATTTATTCATAAAAAAATGTTAC-TTTTTTTATC
131 ATATATTATAAAAAATAATATATTTATTCATAAAAAAATGTTACATTTTTTTATC
3022503 AATTATATTATTTAAATCTTAAAAAATTTTAAATTTATGGCCAAATTACGTTTTATAAAAATGTT
1 AATTATATTATTTAAATCTTAAAAAATTTTAAATTTATGGCCAAATTACGTTTTATAAAAATGTT
3022568 ATAATATATTTATTTATAAAAAATTATGGTCAAGTATAGACATAACTTAATTATGTGTCCATGCT
66 ATAATATATTTATTTATAAAAAATTATGGTCAAGTATAGACATAACTTAATTATGTGTCCATGCT
3022633 ATATATTATAAAAAATAATATATTTATTCATAAAAAAATGTTACATTTTTTTATC
131 ATATATTATAAAAAATAATATATTTATTCATAAAAAAATGTTACATTTTTTTATC
3022688 A
1 A
3022689 TAACTCATTA
Statistics
Matches: 185, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
184 174 0.94
185 11 0.06
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (185 bp):
AATTATATTATTTAAATCTTAAAAAATTTTAAATTTATGGCCAAATTACGTTTTATAAAAATGTT
ATAATATATTTATTTATAAAAAATTATGGTCAAGTATAGACATAACTTAATTATGTGTCCATGCT
ATATATTATAAAAAATAATATATTTATTCATAAAAAAATGTTACATTTTTTTATC
Found at i:3023961 original size:29 final size:29
Alignment explanation
Indices: 3023873--3023962 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
3023863 AATTGGTAAT
* * *
3023873 TAAATTATATTGTTTTTCACATCTTGATACT
1 TAAACTATATT-TTTTTCACA-ATTGATACC
* *
3023904 TAAACT-TTTTTTTTATCACAATTGGTACC
1 TAAACTATATTTTTT-TCACAATTGATACC
3023933 TAAACTATATTTTTTTC-CAAGTTGATACC
1 TAAACTATATTTTTTTCACAA-TTGATACC
3023962 T
1 T
3023963 TTATTAGTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.06
29 26 0.53
30 15 0.31
31 5 0.10
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (29 bp):
TAAACTATATTTTTTTCACAATTGATACC
Found at i:3036569 original size:3 final size:3
Alignment explanation
Indices: 3036554--3036587 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3036544 AGGAACTATT
* *
3036554 CTG CTG TTG CTG CTG CTG CGG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
3036588 GGAAAGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:3036588 original size:15 final size:15
Alignment explanation
Indices: 3036561--3036589 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3036551 ATTCTGCTGT
3036561 TGCTGCTGCTGCGGC
1 TGCTGCTGCTGCGGC
3036576 TGCTGCTGCTGCGG
1 TGCTGCTGCTGCGG
3036590 AAAGTGATGA
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:0.00, C:0.31, G:0.41, T:0.28
Consensus pattern (15 bp):
TGCTGCTGCTGCGGC
Found at i:3036622 original size:15 final size:15
Alignment explanation
Indices: 3036604--3036643 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3036594 TGATGAGGAG
*
3036604 GAGGGTGAGGAAAGC
1 GAGGGAGAGGAAAGC
*
3036619 GAGGGAGAGGAAAGT
1 GAGGGAGAGGAAAGC
*
3036634 GAAGGAGAGG
1 GAGGGAGAGG
3036644 GAGAGGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.55, T:0.05
Consensus pattern (15 bp):
GAGGGAGAGGAAAGC
Found at i:3036643 original size:21 final size:21
Alignment explanation
Indices: 3036619--3036659 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3036609 TGAGGAAAGC
*
3036619 GAGGGAGAGGAAAGTGAAGGA
1 GAGGGAGAGGAAAGGGAAGGA
*
3036640 GAGGGAGAGGAGAGGGAAGG
1 GAGGGAGAGGAAAGGGAAGG
3036660 GATGAAGAGA
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:0.39, C:0.00, G:0.59, T:0.02
Consensus pattern (21 bp):
GAGGGAGAGGAAAGGGAAGGA
Found at i:3053653 original size:96 final size:96
Alignment explanation
Indices: 3053541--3053731 Score: 373
Period size: 96 Copynumber: 2.0 Consensus size: 96
3053531 TTTAATAATA
*
3053541 ATTTGAATTGTTTGGAACTTGGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
1 ATTTGAATTGTTTGGAACTTAGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
3053606 TTGAATATGATGAATAGTAATTTGAGATATG
66 TTGAATATGATGAATAGTAATTTGAGATATG
3053637 ATTTGAATTGTTTGGAACTTAGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
1 ATTTGAATTGTTTGGAACTTAGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
3053702 TTGAATATGATGAATAGTAATTTGAGATAT
66 TTGAATATGATGAATAGTAATTTGAGATAT
3053732 TTAATGAATT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.32
Consensus pattern (96 bp):
ATTTGAATTGTTTGGAACTTAGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
TTGAATATGATGAATAGTAATTTGAGATATG
Found at i:3062638 original size:210 final size:210
Alignment explanation
Indices: 3062274--3063323 Score: 1665
Period size: 210 Copynumber: 5.0 Consensus size: 210
3062264 CAATCTATAA
* *
3062274 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCATGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* *
3062339 GTTCCCTCAGC-GAATTTTGCCAGTGAGCAGATGTTGCAAATCTTAGGGAAATCTTCTGATCCTG
66 GTTTCCTCA-CAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG
* * *
3062403 ACAATTTATCCC-ATTCTGGTTTATACATGAGTGATGAAATTCATGAAAATTCACAAGTGGAATC
130 ACAATTTA-CCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATC
*
3062467 TGTCATCAGTAATCCAT
194 TGTCATCAGTGATCCAT
* * *
3062484 TTGAATCCTCTGCCTCATCCAATATCATTTTAAGCGATGAGATCTCCACGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* * * *
3062549 GTTTCCTCGCAGAATTTTGCCAGTGAACATATGTTGCAAATCTCAGGGAAATCTTCTGATACTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* * *
3062614 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCACAAGGGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
3062679 TCATCAATGATCCAT
196 TCATCAGTGATCCAT
* *
3062694 TTGAATCCTCTGCCTCATCCAATATCATTACAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* *
3062759 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGCTGCAAATCTCAGGGAAATCTTCTGATCCTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* *
3062824 CAATTTTCCCTATACTGATTTATACATGAGTGGTGAAATTCATAAAAATTCACAAGTGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
3062889 TCATTAGTGATCCAT
196 TCATCAGTGATCCAT
3062904 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* * * *
3062969 GTTGCCTCACAGAATTTTGCCAGTGAACATATGTTGCAAATCTCAGGGAAATCTTCTGATACTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* *
3063034 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCACAAGTGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
3063099 TCATCAATGATCCAT
196 TCATCAGTGATCCAT
* * *
3063114 TTGAATCCTTTGCCTCATCCAATATCATTGCAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* *
3063179 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGCTGCAAATCTCAGGGAAATCTTCTGATCCTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* ** *
3063244 CAATATT-CCCTATACTGATTTATGCACAAGTGATGAAATTCATAAAATTTCACAAGTGGAATCT
131 CAAT-TTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCT
*
3063308 GTCATCAGTCATCCAT
195 GTCATCAGTGATCCAT
3063324 CATCATCCTC
Statistics
Matches: 771, Mismatches: 66, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
209 4 0.01
210 765 0.99
211 2 0.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (210 bp):
TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
TCATCAGTGATCCAT
Found at i:3076652 original size:32 final size:32
Alignment explanation
Indices: 3076586--3076655 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
3076576 AAAAACATTG
**
3076586 ATAG-TTCAGTGACTTAAATAAAAACTTTTGA
1 ATAGTTTCAGTGACTTAAATAAAAACTTTCAA
*
3076617 ATAGTTTC-GTGACTTAGAATGAAAACTTTCAA
1 ATAGTTTCAGTGACTTA-AATAAAAACTTTCAA
3076649 ATAGTTT
1 ATAGTTT
3076656 AGTAATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (32 bp):
ATAGTTTCAGTGACTTAAATAAAAACTTTCAA
Found at i:3081953 original size:48 final size:48
Alignment explanation
Indices: 3081882--3082016 Score: 225
Period size: 48 Copynumber: 2.8 Consensus size: 48
3081872 TAACAGAAGT
* * * * *
3081882 GATAAAATGAACATAAATTTCATTTCCATAACATAATTTGTGGTAATC
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
3081930 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
3081978 GATAAGATGAACATAAATTTCATTTTCATAACATAACTT
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTT
3082017 ATTACAATAG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (48 bp):
GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
Found at i:3086406 original size:741 final size:743
Alignment explanation
Indices: 3084972--3086423 Score: 2211
Period size: 745 Copynumber: 2.0 Consensus size: 743
3084962 TGAACTTTTT
* * * *
3084972 ACCTATATCAGTAACTTCAAGACTAAGCTACAGTATAATTTTTTAATAAAGATCAGCAATCTCAG
1 ACCTATATCAGTAACTTCAAGACTAAGCTACAATAAAATGTTTGAATAAAGATCAGCAATCTCAG
* *
3085037 CCAAAAGATGGTGAATATTTATATAATCATCATAAGACACATCAGGTTTGATGATTCATTTTCAT
66 CCAAAAGATGGTGAATATTTATATAATCATCATAACACAAATCAGGTTTGATGATTCATTTTCAT
*
3085102 AATAGATTGCAGCAACTGACAAAAAAAAGGAGGAAAAAAAAGTTATATCAATTAAAATTTGACCC
131 AATAGATTGCAGCAACTGACAAAAAAAAGGAGGAAAAAAAAGTTAAATCAATTAAAATTTGACCC
3085167 CAAATTCCCAGAAAATTAAACAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCA
196 CAAATTCCCAGAAAATTAAACAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCA
3085232 TCATTCAAATGCAGAAATGATGGATAAGCATCATCACACCTCCTTGCATATCTTAAGAAAATCAA
261 TCATTCAAATGCAGAAATGATGGATAAGCATCATCACACCTCCTTGCATATCTTAAGAAAATCAA
*
3085297 ATCCTATGAAGCATAAAAAAGTAGAACCATTAACTTATAGCAATTTCTGTTTGGCAAATTAACAA
326 ATCCTATGAAGCATAAAAAACTAGAACCATTAAC-TATAG-AATTTCTGTTTGGCAAATTAACAA
* *
3085362 ATTGAAAATAATCATAAAAAGAGAATATTTTACAGTTTACATCCCATTGGAGTAATGGTAAATGA
389 AATGAAAATAATCATAAAAAGAGAATATTTTACAGTTTACACCCCATTGGAGTAATGGTAAATGA
*
3085427 ATCAGATAGACGATCGCTAATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAAATGTCTATCT
454 ATCAGATAGACGATCGCTAATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAAATATCTATCT
3085492 TCATATCCACATTCAATCAAATTTTAAAAAAATAAGATTTTTAGAAAAAATGTTGCAAACAAGTG
519 TCATATCCACATTCAATCAAATTTTAAAAAAATAAGATTTTTAGAAAAAATGTTGCAAACAAGTG
*
3085557 AAGCTGCAGACAATAATTACAAGTGGAAATCAGATAAAAATGTCAATCACCAATTTTGCATATGA
584 AAGCTGCAGACAATAATTACAAGTGGAAATCAGATAAAAATGTCAATCACCAATTTTGCATACGA
*
3085622 AGACATTATTATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATGTTCCCTTTTTCCCT
649 AGACATTAATATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATGTTCCCTTTTTCCCT
3085687 TGAAAACCATAGCTCAAACAAAAACATTTG
714 TGAAAACCATAGCTCAAACAAAAACATTTG
* * * *
3085717 ACCTATATCATTAATTTCAGGACTGAGCTACAATAAAATGTTTGAATAAAGATCAGCAATCTCAG
1 ACCTATATCAGTAACTTCAAGACTAAGCTACAATAAAATGTTTGAATAAAGATCAGCAATCTCAG
* * * *
3085782 CCGAAAGATGGTGATTATTTATATAATCATCATAACATAAATCAGGTTTGATTATTCATTTTCAT
66 CCAAAAGATGGTGAATATTTATATAATCATCATAACACAAATCAGGTTTGATGATTCATTTTCAT
* ** * *
3085847 CATAGATTGCAGCAACTGAC-GGAAAAATGAGGCAAAAAACAA-TTAAATCAATTAAAATTTGCC
131 AATAGATTGCAGCAACTGACAAAAAAAAGGAGG-AAAAAA-AAGTTAAATCAATTAAAATTTGAC
* *
3085910 CCCCAATTCCCA-AAAATGGTAAAGAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTA
194 CCCAAATTCCCAGAAAAT--TAAACAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTA
** **
3085974 TTCATCATTCAAATGCAGAAATGATGGATAAGTTTCATCACACCTCCTTGCATATCTTTTGAAGA
257 TTCATCATTCAAATGCAGAAATGATGGATAAGCATCATCACACCTCCTTGCATATCTTAAGAA-A
* * * *
3086039 ATCAAATCTTATTAAGCAATAAAAAACTAG-AGC-TT-A-T-T-G-ATTT-T-TTT-TCAAA-TA
321 ATCAAATCCTATGAAGC-ATAAAAAACTAGAACCATTAACTATAGAATTTCTGTTTGGCAAATTA
*
3086093 A-AAGAAT-AAAATATAGTCA-ATAAAAGTGAATATTTTACAGTTTACACCCCTCATTGGAGTAA
385 ACAA-AATGAAAATA-A-TCATA-AAAAGAGAATATTTTACAGTTTACA-CCC-CATTGGAGTAA
* * * *
3086155 TGGTAGATGGATCAGATAGTCGATCGCTAATGTCTCAGCATATTGCAACTCAGACTGGGTGTCAA
444 TGGTAAATGAATCAGATAGACGATCGCTAATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAA
*
3086220 ATATCTATCTTCATATCCACATTCAATCAATTTTTTTAAAAAAAATAAGATTTTTA-AACAAAAT
509 ATATCTATCTTCATATCCACATTCAATCAA--ATTTT-AAAAAAATAAGATTTTTAGAA-AAAAT
* *
3086284 TTTGCAAACAAGTGAAGCTGCAGACAATAATTACATGTGGAAATCAGATAAAAATGTCAATCACC
570 GTTGCAAACAAGTGAAGCTGCAGACAATAATTACAAGTGGAAATCAGATAAAAATGTCAATCACC
*
3086349 AATTTTGCATACGAAGACATTAATATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATT
635 AATTTTGCATACGAAGACATTAATATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATG
3086414 TTCCCTTTTT
700 TTCCCTTTTT
3086424 TTCTCAAAAA
Statistics
Matches: 646, Mismatches: 45, Indels: 36
0.89 0.06 0.05
Matches are distributed among these distances:
734 8 0.01
735 7 0.01
736 31 0.05
737 5 0.01
738 102 0.16
739 4 0.01
740 6 0.01
741 159 0.25
742 1 0.00
743 1 0.00
744 14 0.02
745 172 0.27
746 107 0.17
747 18 0.03
748 11 0.02
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (743 bp):
ACCTATATCAGTAACTTCAAGACTAAGCTACAATAAAATGTTTGAATAAAGATCAGCAATCTCAG
CCAAAAGATGGTGAATATTTATATAATCATCATAACACAAATCAGGTTTGATGATTCATTTTCAT
AATAGATTGCAGCAACTGACAAAAAAAAGGAGGAAAAAAAAGTTAAATCAATTAAAATTTGACCC
CAAATTCCCAGAAAATTAAACAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCA
TCATTCAAATGCAGAAATGATGGATAAGCATCATCACACCTCCTTGCATATCTTAAGAAAATCAA
ATCCTATGAAGCATAAAAAACTAGAACCATTAACTATAGAATTTCTGTTTGGCAAATTAACAAAA
TGAAAATAATCATAAAAAGAGAATATTTTACAGTTTACACCCCATTGGAGTAATGGTAAATGAAT
CAGATAGACGATCGCTAATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAAATATCTATCTTC
ATATCCACATTCAATCAAATTTTAAAAAAATAAGATTTTTAGAAAAAATGTTGCAAACAAGTGAA
GCTGCAGACAATAATTACAAGTGGAAATCAGATAAAAATGTCAATCACCAATTTTGCATACGAAG
ACATTAATATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATGTTCCCTTTTTCCCTTG
AAAACCATAGCTCAAACAAAAACATTTG
Found at i:3087003 original size:30 final size:31
Alignment explanation
Indices: 3086967--3087034 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 31
3086957 TTTTTTTACA
3086967 TTCATTTTAGTCACTCAACTTTAAT-AAATT
1 TTCATTTTAGTCACTCAACTTTAATAAAATT
3086997 TTCATTTTAGTCACTCAACTTTAATAAAATT
1 TTCATTTTAGTCACTCAACTTTAATAAAATT
3087028 TT-ATTTT
1 TTCATTTT
3087035 GATCACTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 30 0.81
31 7 0.19
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (31 bp):
TTCATTTTAGTCACTCAACTTTAATAAAATT
Found at i:3087473 original size:21 final size:21
Alignment explanation
Indices: 3087449--3087522 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
3087439 ATAAGGGAAA
3087449 ACTTGGGTTTTCCGGTGAACT
1 ACTTGGGTTTTCCGGTGAACT
** *
3087470 ACTTGGGTTTTAAAAGG-GAA-A
1 ACTTGGGTTTT--CCGGTGAACT
3087491 ACTTGGGTTTTCCGGTGAACT
1 ACTTGGGTTTTCCGGTGAACT
*
3087512 ACTTGGATTTT
1 ACTTGGGTTTT
3087523 AAAAGTTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 3 0.07
21 32 0.76
22 3 0.07
23 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.38
Consensus pattern (21 bp):
ACTTGGGTTTTCCGGTGAACT
Found at i:3087500 original size:42 final size:42
Alignment explanation
Indices: 3087441--3087527 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
3087431 TCTTGATAAT
*
3087441 AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGGTTTTAA
1 AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGATTTTAA
3087483 AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGATTTTAA
1 AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGATTTTAA
3087525 AAG
1 AAG
3087528 TTTCATCACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32
Consensus pattern (42 bp):
AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGATTTTAA
Found at i:3092176 original size:38 final size:38
Alignment explanation
Indices: 3092125--3092203 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
3092115 TGTTATAAAC
3092125 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
1 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
*
3092163 ACATAGGCATGCATACAAAAGAACTGTAGCAAAGCATG
1 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
3092201 ACA
1 ACA
3092204 ATGCCCAGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (38 bp):
ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
Found at i:3099145 original size:193 final size:193
Alignment explanation
Indices: 3098816--3099202 Score: 774
Period size: 193 Copynumber: 2.0 Consensus size: 193
3098806 CACTATTATT
3098816 TAAATCCACTGCAAGTGATCTCCATTATAGTTGACACAACAAACACATGGTTAGAGTAGTGCATT
1 TAAATCCACTGCAAGTGATCTCCATTATAGTTGACACAACAAACACATGGTTAGAGTAGTGCATT
3098881 TGCATGATTTATTATGATATTTAAATTTAAATCACAACCACTTGCACTATAGCTACTAGAATAGG
66 TGCATGATTTATTATGATATTTAAATTTAAATCACAACCACTTGCACTATAGCTACTAGAATAGG
3098946 AGGTCAAGTTTGTGACATAAAATATTGTTTCATTAAAAAAATTCAAATTTAACATTACATAGA
131 AGGTCAAGTTTGTGACATAAAATATTGTTTCATTAAAAAAATTCAAATTTAACATTACATAGA
3099009 TAAATCCACTGCAAGTGATCTCCATTATAGTTGACACAACAAACACATGGTTAGAGTAGTGCATT
1 TAAATCCACTGCAAGTGATCTCCATTATAGTTGACACAACAAACACATGGTTAGAGTAGTGCATT
3099074 TGCATGATTTATTATGATATTTAAATTTAAATCACAACCACTTGCACTATAGCTACTAGAATAGG
66 TGCATGATTTATTATGATATTTAAATTTAAATCACAACCACTTGCACTATAGCTACTAGAATAGG
3099139 AGGTCAAGTTTGTGACATAAAATATTGTTTCATTAAAAAAATTCAAATTTAACATTACATAGA
131 AGGTCAAGTTTGTGACATAAAATATTGTTTCATTAAAAAAATTCAAATTTAACATTACATAGA
3099202 T
1 T
3099203 TGCGGTTTAT
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 194 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (193 bp):
TAAATCCACTGCAAGTGATCTCCATTATAGTTGACACAACAAACACATGGTTAGAGTAGTGCATT
TGCATGATTTATTATGATATTTAAATTTAAATCACAACCACTTGCACTATAGCTACTAGAATAGG
AGGTCAAGTTTGTGACATAAAATATTGTTTCATTAAAAAAATTCAAATTTAACATTACATAGA
Found at i:3099898 original size:23 final size:23
Alignment explanation
Indices: 3099871--3100133 Score: 140
Period size: 23 Copynumber: 11.5 Consensus size: 23
3099861 TTGTACACCA
* * *
3099871 CAATTTGCAGCACTTAAACTCTT
1 CAATTTACAGCAATTAAACACTT
* * * * *
3099894 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCAATTAAACACTT
3099917 CAATTTACAGCAATTAAACACTT
1 CAATTTACAGCAATTAAACACTT
* * *
3099940 CAATTTACATCATTTAAACACCT
1 CAATTTACAGCAATTAAACACTT
* * * * *
3099963 CAACTTACAACACTTTAACA-TCC
1 CAATTTACAGCAATTAAACACT-T
* * * * *
3099986 CAATTAACAACATTTATACACCT
1 CAATTTACAGCAATTAAACACTT
*
3100009 CAA-TTACAGCGA-TAAACA-TCT
1 CAATTTACAGCAATTAAACACT-T
*
3100030 CAATTT-CTAGCAACTAAAACACTT
1 CAATTTAC-AGCAA-TTAAACACTT
* *
3100054 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCAATTAAACACTT
* *** *
3100077 CAATTTGCAGTGCTTTAACACTT
1 CAATTTACAGCAATTAAACACTT
* * * * *
3100100 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCAATTAAACACTT
3100123 CAATTTACAGC
1 CAATTTACAGC
3100134 NNNNNNNNNN
Statistics
Matches: 177, Mismatches: 54, Indels: 18
0.71 0.22 0.07
Matches are distributed among these distances:
21 10 0.06
22 11 0.06
23 139 0.79
24 15 0.08
25 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.32
Consensus pattern (23 bp):
CAATTTACAGCAATTAAACACTT
Found at i:3099962 original size:46 final size:46
Alignment explanation
Indices: 3099865--3100131 Score: 179
Period size: 46 Copynumber: 5.8 Consensus size: 46
3099855 ACTCATTTGT
* * * * *
3099865 ACACCACAATTTGCAGCACTTAAACTCTTCAATTTACATCATTTGA
1 ACACCTCAATTTACAGCAATTAAACACTTCAATTTACATCATTTAA
*
3099911 GCACCTCAATTTACAGCAATTAAACACTTCAATTTACATCATTTAA
1 ACACCTCAATTTACAGCAATTAAACACTTCAATTTACATCATTTAA
* * * * * * * *
3099957 ACACCTCAACTTACAACACTTTAACA-TCCCAATTAACAACATTTAT
1 ACACCTCAATTTACAGCAATTAAACACT-TCAATTTACATCATTTAA
* * * *
3100003 ACACCTCAA-TTACAGCGA-TAAACA-TCTCAATTT-CTAGCAACTAAA
1 ACACCTCAATTTACAGCAATTAAACACT-TCAATTTAC-ATC-ATTTAA
* * * *
3100048 ACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGTGC-TTT-A
1 ACACCTCAATTTACAGCAATTAAACACTTCAATTTACA-T-CATTTAA
* * * * * *
3100094 ACACTTCAATTTACATCATTTGAGCACCTCAATTTACA
1 ACACCTCAATTTACAGCAATTAAACACTTCAATTTACA
3100132 GCNNNNNNNN
Statistics
Matches: 175, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
43 1 0.01
44 14 0.08
45 18 0.10
46 124 0.71
47 15 0.09
48 2 0.01
49 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (46 bp):
ACACCTCAATTTACAGCAATTAAACACTTCAATTTACATCATTTAA
Found at i:3100104 original size:114 final size:114
Alignment explanation
Indices: 3099915--3100133 Score: 266
Period size: 114 Copynumber: 1.9 Consensus size: 114
3099905 ATTTGAGCAC
* *
3099915 CTCAATTTACAGCAATTAAACACTTCAATTTACATCATTTAAACACCTCAACTTACAACACTTTA
1 CTCAATTTACAGCAATAAAACACTTCAATTTACAACATTTAAACACCTCAACTTACAACACTTTA
3099980 ACATCCCAATTAACAACATTT-ATACACCTCAA-TTACAGCGATAAACAT
66 ACATCCCAATTAACAACATTTGA-ACACCTCAATTTACAGCGATAAACAT
* * * ***
3100028 CTCAATTT-CTAGCAACTAAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGTGCTT
1 CTCAATTTAC-AGCAA-TAAAACACTTCAATTTACAACATTTAAACACCTCAACTTACAACACTT
* * * *
3100092 TAACA-CTTCAATTTACATCATTTGAGCACCTCAATTTACAGC
64 TAACATC-CCAATTAACAACATTTGAACACCTCAATTTACAGC
3100134 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
112 1 0.01
113 14 0.16
114 66 0.74
115 8 0.09
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.32
Consensus pattern (114 bp):
CTCAATTTACAGCAATAAAACACTTCAATTTACAACATTTAAACACCTCAACTTACAACACTTTA
ACATCCCAATTAACAACATTTGAACACCTCAATTTACAGCGATAAACAT
Found at i:3103518 original size:23 final size:23
Alignment explanation
Indices: 3103492--3104290 Score: 420
Period size: 23 Copynumber: 35.0 Consensus size: 23
3103482 GGCCATTACA
* *
3103492 TTACATCATTTAAACACCTCAAC
1 TTACAGCATTTAAACACCTCAAT
*
3103515 TTACAACACTTT-AACATCC-CAAT
1 TTACAGCA-TTTAAACA-CCTCAAT
* * *
3103538 TAACAACATTTATACACCTCAA-
1 TTACAGCATTTAAACACCTCAAT
*
3103560 TTACAGCGA--TAAACATCTCAAT
1 TTACAGC-ATTTAAACACCTCAAT
* ** *
3103582 TTCCAGCAACTAAACGA-TTCAAT
1 TTACAGCATTTAAAC-ACCTCAAT
* * *
3103605 TTACAGTACTTAAAACACTTCAAT
1 TTACAGCA-TTTAAACACCTCAAT
* *
3103629 TTACAACATTTAAACACTTCAAT
1 TTACAGCATTTAAACACCTCAAT
* **
3103652 TTGCAGCACCTAAACA-CTCCAAT
1 TTACAGCATTTAAACACCT-CAAT
* * *
3103675 TTACATCATTTGAGCACCTCAAT
1 TTACAGCATTTAAACACCTCAAT
* * *
3103698 TTATAGCAATTAAACACTTCAAT
1 TTACAGCATTTAAACACCTCAAT
* *
3103721 TTACAGCATTTAAACGCCTCAAC
1 TTACAGCATTTAAACACCTCAAT
*
3103744 TTACAACACTTT-AACATCCT-AAT
1 TTACAGCA-TTTAAACA-CCTCAAT
* * *
3103767 TAACACCATTTATACACCTCAA-
1 TTACAGCATTTAAACACCTCAAT
*
3103789 TTACAGCGA--TAAACATCTCAAT
1 TTACAGC-ATTTAAACACCTCAAT
* ** * *
3103811 TTCCAGCAACTAAAGGA-TTCAAT
1 TTACAGCATTTAAA-CACCTCAAT
* * * *
3103834 TTGCAGTACTTAAAACACTTCAAT
1 TTACAGCA-TTTAAACACCTCAAT
* * *
3103858 TTACAACATTTAAATACTTCAAT
1 TTACAGCATTTAAACACCTCAAT
* ** *
3103881 TTGCAGCACCTAAACACTTCAAT
1 TTACAGCATTTAAACACCTCAAT
* * *
3103904 TTACATCATTTGAGCACCTCAAT
1 TTACAGCATTTAAACACCTCAAT
* * *
3103927 TTATAGCAATTAAACACTTCAAT
1 TTACAGCATTTAAACACCTCAAT
*
3103950 TTACAGCATTTAAACACCTCAAC
1 TTACAGCATTTAAACACCTCAAT
*
3103973 TTACAACACTTT-AACATCCT-AAT
1 TTACAGCA-TTTAAACA-CCTCAAT
* * *
3103996 TAACACCATTTATACACCTCAA-
1 TTACAGCATTTAAACACCTCAAT
* *
3104018 TTACAGCGA--TAAACATCTCAGT
1 TTACAGC-ATTTAAACACCTCAAT
** **
3104040 TT-CAGCAACTAAACAATTCAAT
1 TTACAGCATTTAAACACCTCAAT
* * * *
3104062 TTGCAGTACTTAAAACACTTCAAT
1 TTACAGCA-TTTAAACACCTCAAT
* *
3104086 TTACAACATTTAAACACTTCAAT
1 TTACAGCATTTAAACACCTCAAT
* *
3104109 TTGCAGCACTTT-AACACTTCAAT
1 TTACAGCA-TTTAAACACCTCAAT
* * *
3104132 TCACAACATTTAAATACCTCAAT
1 TTACAGCATTTAAACACCTCAAT
* *
3104155 TTGCAGCACTTT-AACACTTCAAT
1 TTACAGCA-TTTAAACACCTCAAT
* *
3104178 TTACAACATTTAAACACTTCAAT
1 TTACAGCATTTAAACACCTCAAT
* * *
3104201 TTGCAGCACTTT-AACATCTCTAT
1 TTACAGCA-TTTAAACACCTCAAT
* * * *
3104224 TAACAACATTTATACACCTTAA-
1 TTACAGCATTTAAACACCTCAAT
* * * *
3104246 TTACAACAATAAAACATCTCAAT
1 TTACAGCATTTAAACACCTCAAT
* ** *
3104269 TTTCAGCAACTAAACACTTCAA
1 TTACAGCATTTAAACACCTCAA
3104291 ATTGCAGTAC
Statistics
Matches: 589, Mismatches: 146, Indels: 82
0.72 0.18 0.10
Matches are distributed among these distances:
20 1 0.00
21 35 0.06
22 84 0.14
23 393 0.67
24 76 0.13
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (23 bp):
TTACAGCATTTAAACACCTCAAT
Found at i:3103677 original size:46 final size:46
Alignment explanation
Indices: 3103492--3104247 Score: 506
Period size: 46 Copynumber: 16.5 Consensus size: 46
3103482 GGCCATTACA
* * * *
3103492 TTACATCATTTAAACACCTCAACTTACAACACTTTAACA-TCCCAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACT-CCAAT
* *
3103538 TAACAACATTTATACACCTCAA-TTACAGCGA--TAAACA-TCTCAAT
1 TTACAACATTTAAACACCTCAATTTACAGC-ACTTAAACACTC-CAAT
* * ** * * *
3103582 TTCCAGCAACTAAACGA-TTCAATTTACAGTACTTAAAACACTTCAAT
1 TTACAACATTTAAAC-ACCTCAATTTACAGCACTT-AAACACTCCAAT
* * *
3103629 TTACAACATTTAAACACTTCAATTTGCAGCACCTAAACACTCCAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCCAAT
* * * * * *
3103675 TTACATCATTTGAGCACCTCAATTTATAGCAATTAAACACTTCAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCCAAT
* * * * *
3103721 TTACAGCATTTAAACGCCTCAACTTACAACACTTTAACA-TCCTAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCC-AAT
* * *
3103767 TAACACCATTTATACACCTCAA-TTACAGCGA--TAAACA-TCTCAAT
1 TTACAACATTTAAACACCTCAATTTACAGC-ACTTAAACACTC-CAAT
* * ** * * * * *
3103811 TTCCAGCAACTAAAGGA-TTCAATTTGCAGTACTTAAAACACTTCAAT
1 TTACAACATTTAAA-CACCTCAATTTACAGCACTT-AAACACTCCAAT
* * * * *
3103858 TTACAACATTTAAATACTTCAATTTGCAGCACCTAAACACTTCAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCCAAT
* * * * * *
3103904 TTACATCATTTGAGCACCTCAATTTATAGCAATTAAACACTTCAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCCAAT
* * * *
3103950 TTACAGCATTTAAACACCTCAACTTACAACACTTTAACA-TCCTAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCC-AAT
* * * *
3103996 TAACACCATTTATACACCTCAA-TTACAGCGA--TAAACA-TCTCAGT
1 TTACAACATTTAAACACCTCAATTTACAGC-ACTTAAACACTC-CAAT
* ** ** * * *
3104040 TT-CAGCAACTAAACAATTCAATTTGCAGTACTTAAAACACTTCAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTT-AAACACTCCAAT
* * * *
3104086 TTACAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCCAAT
* * * * *
3104132 TCACAACATTTAAATACCTCAATTTGCAGCACTTTAACACTTCAAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCCAAT
* * * *
3104178 TTACAACATTTAAACACTTCAATTTGCAGCACTTTAACA-TCTCTAT
1 TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTC-CAAT
* * *
3104224 TAACAACATTTATACACCTTAATT
1 TTACAACATTTAAACACCTCAATT
3104248 ACAACAATAA
Statistics
Matches: 563, Mismatches: 118, Indels: 58
0.76 0.16 0.08
Matches are distributed among these distances:
43 15 0.03
44 62 0.11
45 39 0.07
46 350 0.62
47 95 0.17
48 2 0.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (46 bp):
TTACAACATTTAAACACCTCAATTTACAGCACTTAAACACTCCAAT
Found at i:3103906 original size:229 final size:229
Alignment explanation
Indices: 3103492--3104305 Score: 1292
Period size: 229 Copynumber: 3.6 Consensus size: 229
3103482 GGCCATTACA
* *
3103492 TTACATCATTTAAACACCTCAACTTACAACACTTTAACATCCCAATTAACAACATTTATACACCT
1 TTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTTATACACCT
*
3103557 CAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACGATTCAATTTACAGTACTTAAAACA
66 CAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACGATTCAATTTGCAGTACTTAAAACA
*
3103622 CTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACCTAAACACTCCAATTTACATCATTTG
131 CTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACCTAAACACTTCAATTTACATCATTTG
3103687 AGCACCTCAATTTATAGCAATTAAACACTTCAAT
196 AGCACCTCAATTTATAGCAATTAAACACTTCAAT
* *
3103721 TTACAGCATTTAAACGCCTCAACTTACAACACTTTAACATCCTAATTAACACCATTTATACACCT
1 TTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTTATACACCT
*
3103786 CAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAAGGATTCAATTTGCAGTACTTAAAACA
66 CAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACGATTCAATTTGCAGTACTTAAAACA
*
3103851 CTTCAATTTACAACATTTAAATACTTCAATTTGCAGCACCTAAACACTTCAATTTACATCATTTG
131 CTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACCTAAACACTTCAATTTACATCATTTG
3103916 AGCACCTCAATTTATAGCAATTAAACACTTCAAT
196 AGCACCTCAATTTATAGCAATTAAACACTTCAAT
*
3103950 TTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACACCATTTATACACCT
1 TTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTTATACACCT
* *
3104015 CAATTACAGCGATAAACATCTCAGTTT-CAGCAACTAAACAATTCAATTTGCAGTACTTAAAACA
66 CAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACGATTCAATTTGCAGTACTTAAAACA
* * * * *
3104079 CTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATTTA
131 CTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACCTAAACACTTCAATTTACATCATTTG
** ** * *
3104144 AATACCTCAATTTGCAGCACTTTAACACTTCAAT
196 AGCACCTCAATTTATAGCAATTAAACACTTCAAT
* * * * *
3104178 TTACAACATTTAAACACTTCAATTTGCAGCACTTTAACATCTCT-ATTAACAACATTTATACACC
1 TTACAGCATTTAAACACCTCAACTTACAACACTTTAACATC-CTAATTAACAACATTTATACACC
* * * * *
3104242 TTAATTACAACAATAAAACATCTCAATTTTCAGCAACTAAAC-ACTTCAAATTGCAGTACTTAAA
65 TCAATTACAGCGAT-AAACATCTCAATTTCCAGCAACTAAACGA-TTCAATTTGCAGTACTTAAA
3104306 CAGGGCTTTA
Statistics
Matches: 546, Mismatches: 35, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
228 188 0.34
229 327 0.60
230 31 0.06
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (229 bp):
TTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTTATACACCT
CAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACGATTCAATTTGCAGTACTTAAAACA
CTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACCTAAACACTTCAATTTACATCATTTG
AGCACCTCAATTTATAGCAATTAAACACTTCAAT
Found at i:3115518 original size:100 final size:100
Alignment explanation
Indices: 3115345--3115544 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
3115335 AACCAAAGAG
3115345 TAGCCATTTTTTTCCTTATTTACAACTATTTCTTCAAATTTCCAACATGATTTATTTGCTCCTAA
1 TAGCCATTTTTTTCCTTATTTACAACTATTTCTTCAAATTTCCAACATGATTTATTTGCTCCTAA
3115410 TCGAAAATCAACAGTAGCTAATTGACAGTTTAATC
66 TCGAAAATCAACAGTAGCTAATTGACAGTTTAATC
3115445 TAGCCATTTTTTTCCTTATTTACAACTATTTCTTCAAATTTCCAACATGATTTATTTGCTCCTAA
1 TAGCCATTTTTTTCCTTATTTACAACTATTTCTTCAAATTTCCAACATGATTTATTTGCTCCTAA
3115510 TCGAAAATCAACAGTAGCTAATTGACAGTTTAATC
66 TCGAAAATCAACAGTAGCTAATTGACAGTTTAATC
3115545 ATAAAATTCA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (100 bp):
TAGCCATTTTTTTCCTTATTTACAACTATTTCTTCAAATTTCCAACATGATTTATTTGCTCCTAA
TCGAAAATCAACAGTAGCTAATTGACAGTTTAATC
Found at i:3132223 original size:23 final size:23
Alignment explanation
Indices: 3132173--3132235 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
3132163 ATTGACAAGT
*
3132173 ATTTTATAAATATATA--ATAAG
1 ATTTTAAAAATATATATGATAAG
*
3132194 ATATTAAAAATATATATGATGAA-
1 ATTTTAAAAATATATATGAT-AAG
* *
3132217 ATTTTAAAATTATTTATGA
1 ATTTTAAAAATATATATGA
3132236 AATAAAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.41
23 18 0.53
24 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
ATTTTAAAAATATATATGATAAG
Found at i:3132326 original size:20 final size:21
Alignment explanation
Indices: 3132292--3132340 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
3132282 ATAGATGCGA
*
3132292 ATATATGTATATACT-AATGTT
1 ATATAT-TGTATACTAAATGTT
*
3132313 ATATATTGTATACTGAAATTTT
1 ATATATTGTATACT-AAATGTT
3132335 ATATAT
1 ATATAT
3132341 ACAGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (21 bp):
ATATATTGTATACTAAATGTT
Found at i:3139195 original size:38 final size:38
Alignment explanation
Indices: 3139152--3139227 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
3139142 TTTAAGTATG
*
3139152 TCAAGAAA-ACTGGTGAGCATATAGGTATTTAAGGCAAT
1 TCAAGAAACA-TGATGAGCATATAGGTATTTAAGGCAAT
* *
3139190 TCAAGAAACATTATGAGCATATAGGTATTTGAGGCAAT
1 TCAAGAAACATGATGAGCATATAGGTATTTAAGGCAAT
3139228 CCAGATGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (38 bp):
TCAAGAAACATGATGAGCATATAGGTATTTAAGGCAAT
Found at i:3146014 original size:1 final size:1
Alignment explanation
Indices: 3146008--3146032 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3145998 ATTGAGAACC
3146008 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
3146033 AGGATGGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3153002 original size:17 final size:18
Alignment explanation
Indices: 3152976--3153010 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3152966 CATGTTTTTA
*
3152976 TTTAATAATTTGATTAAT
1 TTTAATAATTAGATTAAT
3152994 TTTAA-AATTAGATTAAT
1 TTTAATAATTAGATTAAT
3153011 ATAATATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTAATAATTAGATTAAT
Found at i:3153073 original size:24 final size:24
Alignment explanation
Indices: 3153026--3153073 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3153016 ATTCTGTACC
* *
3153026 TATATTTAATTTTAGTGTTTAATT
1 TATATTTAATTTTAGTCTTAAATT
**
3153050 TATATTTAATTTTTTTCTTAAATT
1 TATATTTAATTTTAGTCTTAAATT
3153074 CGCCGATGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
TATATTTAATTTTAGTCTTAAATT
Found at i:3153958 original size:29 final size:28
Alignment explanation
Indices: 3153904--3153958 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
3153894 ATTTTAAGTT
*
3153904 AATAATGATAAAATTATATTTTACCTAA
1 AATAATGATAAAATTATATTTAACCTAA
3153932 AATAATGATAAAAATT-TAATTTAACCT
1 AATAATGAT-AAAATTAT-ATTTAACCT
3153959 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (28 bp):
AATAATGATAAAATTATATTTAACCTAA
Found at i:3158246 original size:29 final size:29
Alignment explanation
Indices: 3158186--3158247 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
3158176 TTTGTAAATT
* *
3158186 TTTCATTTTTCATTTTAATTTTTAAAGCC
1 TTTCATTTTTCATATTAATTTTTAAAGAC
*
3158215 TTTCATTTTTCATATT-ATTTATTATAGAC
1 TTTCATTTTTCATATTAATTT-TTAAAGAC
3158244 TTTC
1 TTTC
3158248 CAGATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTCATTTTTCATATTAATTTTTAAAGAC
Found at i:3166544 original size:13 final size:14
Alignment explanation
Indices: 3166526--3166558 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3166516 TTTTTTTCTT
3166526 AATAATT-AATATC
1 AATAATTAAATATC
*
3166539 AATAATTAAATATG
1 AATAATTAAATATC
3166553 AATAAT
1 AATAAT
3166559 CACTTATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
AATAATTAAATATC
Found at i:3175148 original size:1 final size:1
Alignment explanation
Indices: 3175098--3175129 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
3175088 TTTGCTCCTC
3175098 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3175130 GTTTAAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3193099 original size:23 final size:21
Alignment explanation
Indices: 3193073--3193124 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 21
3193063 AAAAAGCTTT
3193073 TAAACTATTATATTTT-GTTTAAA
1 TAAACTATT-T-TTTTAG-TTAAA
3193096 TAAATCCTATTTTTTTAGTTAAA
1 TAAA--CTATTTTTTTAGTTAAA
3193119 TAAACT
1 TAAACT
3193125 CTTAACTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 2 0.08
23 17 0.65
24 2 0.08
25 5 0.19
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (21 bp):
TAAACTATTTTTTTAGTTAAA
Found at i:3199617 original size:20 final size:20
Alignment explanation
Indices: 3199583--3199630 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
3199573 AATGACAGCA
*
3199583 AAAAAACAACAATAATGATAG-
1 AAAAAATAACAATAAT-A-AGT
3199604 AAAAAATAAC-ATAATAAGT
1 AAAAAATAACAATAATAAGT
3199623 AAAAAATA
1 AAAAAATA
3199631 TGAGCACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 5 0.20
21 9 0.36
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (20 bp):
AAAAAATAACAATAATAAGT
Found at i:3199628 original size:21 final size:21
Alignment explanation
Indices: 3199582--3199628 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3199572 TAATGACAGC
*
3199582 AAAAAAACAACAATAATGATA
1 AAAAAAACAACAATAATAATA
* *
3199603 GAAAAAATAAC-ATAATAAGTA
1 AAAAAAACAACAATAATAA-TA
3199624 AAAAA
1 AAAAA
3199629 TATGAGCACT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAAAAACAACAATAATAATA
Found at i:3202173 original size:15 final size:17
Alignment explanation
Indices: 3202153--3202189 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
3202143 ATAAATTCAA
3202153 TAATTTA-ATTTAAAT-
1 TAATTTACATTTAAATG
*
3202168 TAATTTACTTTTAAATG
1 TAATTTACATTTAAATG
3202185 TAATT
1 TAATT
3202190 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TAATTTACATTTAAATG
Found at i:3208196 original size:34 final size:34
Alignment explanation
Indices: 3208153--3208217 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
3208143 CATGGATTGT
* *
3208153 AAAACGTAAATTGTTAAGTGTATGAGCATGTTGA
1 AAAACGTAAATTGTCAAGCGTATGAGCATGTTGA
*
3208187 AAAACGTAAATTGTCATGCGTATGAGCATGT
1 AAAACGTAAATTGTCAAGCGTATGAGCATGT
3208218 ATGGTGTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (34 bp):
AAAACGTAAATTGTCAAGCGTATGAGCATGTTGA
Found at i:3226018 original size:33 final size:33
Alignment explanation
Indices: 3225955--3226018 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
3225945 TTTTATTAAA
* *
3225955 ATAATATTTTAATTACCTATTATTTTATTTTAGG
1 ATAATATTTTAATTA-CTAGTAGTTTATTTTAGG
3225989 ATAATACTTTTAATT-CTAGTAGTTTATTTT
1 ATAATA-TTTTAATTACTAGTAGTTTATTTT
3226019 TTATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 13 0.48
34 6 0.22
35 8 0.30
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (33 bp):
ATAATATTTTAATTACTAGTAGTTTATTTTAGG
Found at i:3232085 original size:2 final size:2
Alignment explanation
Indices: 3232078--3232103 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3232068 CCTCTTCATT
3232078 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3232104 ACTGCCTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3242897 original size:35 final size:35
Alignment explanation
Indices: 3242858--3242928 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3242848 CTATGAGTAT
3242858 GGCAACCTCATACTATCTCAACAATAGGAATATTA
1 GGCAACCTCATACTATCTCAACAATAGGAATATTA
3242893 GGCAACCTCATACTATCTCAACAATAGGAATATTA
1 GGCAACCTCATACTATCTCAACAATAGGAATATTA
3242928 G
1 G
3242929 AGAAAGTACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (35 bp):
GGCAACCTCATACTATCTCAACAATAGGAATATTA
Found at i:3252033 original size:18 final size:18
Alignment explanation
Indices: 3252012--3252046 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3252002 GGTGGGGGTG
3252012 ATGGTCATGGCCATGGTC
1 ATGGTCATGGCCATGGTC
*
3252030 ATGGTGATGGCCATGGT
1 ATGGTCATGGCCATGGT
3252047 GATTATTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.37, T:0.29
Consensus pattern (18 bp):
ATGGTCATGGCCATGGTC
Found at i:3252039 original size:12 final size:12
Alignment explanation
Indices: 3252008--3252049 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3251998 TGGTGGTGGG
3252008 GGTGATGGTCAT
1 GGTGATGGTCAT
**
3252020 GGCCATGGTCAT
1 GGTGATGGTCAT
*
3252032 GGTGATGGCCAT
1 GGTGATGGTCAT
3252044 GGTGAT
1 GGTGAT
3252050 TATTGGAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (12 bp):
GGTGATGGTCAT
Found at i:3257149 original size:23 final size:23
Alignment explanation
Indices: 3257123--3257167 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3257113 TAAACATTAA
3257123 AAAATGTTAA-AAAAACTATATAC
1 AAAATGTTAATAAAAA-TATATAC
*
3257146 AAAATTTTAATAAAAATATATA
1 AAAATGTTAATAAAAATATATA
3257168 TAATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATGTTAATAAAAATATATAC
Found at i:3258356 original size:36 final size:36
Alignment explanation
Indices: 3258309--3258380 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3258299 CCGAATCATG
3258309 TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
1 TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
3258345 TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
1 TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
3258381 CTAACTACGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (36 bp):
TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
Found at i:3260259 original size:97 final size:97
Alignment explanation
Indices: 3260140--3260332 Score: 379
Period size: 96 Copynumber: 2.0 Consensus size: 97
3260130 TTAATATTTT
3260140 TAATGTATTTAATCTATATTTTTTAAATTTTATTTTTATATCGAAATAATAATATAAAAAATTAA
1 TAATGTATTTAATCTATATTTTTTAAATTTTATTTTTATATCGAAATAATAATATAAAAAATTAA
3260205 TATGAGCGTGCTAGACCTAACTCAAATTTTAA
66 TATGAGCGTGCTAGACCTAACTCAAATTTTAA
3260237 TAATGTATTT-ATCTATATTTTTTAAATTTTATTTTTATATCGAAATAATAATATAAAAAATTAA
1 TAATGTATTTAATCTATATTTTTTAAATTTTATTTTTATATCGAAATAATAATATAAAAAATTAA
3260301 TATGAGCGTGCTAGACCTAACTCAAATTTTAA
66 TATGAGCGTGCTAGACCTAACTCAAATTTTAA
3260333 AGTTTTTATT
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 86 0.90
97 10 0.10
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (97 bp):
TAATGTATTTAATCTATATTTTTTAAATTTTATTTTTATATCGAAATAATAATATAAAAAATTAA
TATGAGCGTGCTAGACCTAACTCAAATTTTAA
Found at i:3267887 original size:16 final size:17
Alignment explanation
Indices: 3267866--3267901 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
3267856 CTTCGCGTGG
3267866 GGACATTTGA-ATCTAT
1 GGACATTTGATATCTAT
3267882 GGACATTTGATTATCTAT
1 GGACATTTGA-TATCTAT
3267900 GG
1 GG
3267902 GTTGCTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
18 8 0.44
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (17 bp):
GGACATTTGATATCTAT
Found at i:3270287 original size:25 final size:25
Alignment explanation
Indices: 3270256--3270305 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3270246 TAGAAAGCAA
3270256 ATAAATATTTAAAAACACAGACAAT
1 ATAAATATTTAAAAACACAGACAAT
*
3270281 ATAAATATTTAAAAACCCAGACAAT
1 ATAAATATTTAAAAACACAGACAAT
3270306 CTTTTACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.58, C:0.14, G:0.04, T:0.24
Consensus pattern (25 bp):
ATAAATATTTAAAAACACAGACAAT
Found at i:3270324 original size:18 final size:18
Alignment explanation
Indices: 3270301--3270338 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3270291 AAAAACCCAG
*
3270301 ACAATCTTTTACTTATCT
1 ACAATCTTTTACTTACCT
3270319 ACAATCTTTTACTTACCT
1 ACAATCTTTTACTTACCT
3270337 AC
1 AC
3270339 GAGAATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (18 bp):
ACAATCTTTTACTTACCT
Found at i:3275765 original size:277 final size:278
Alignment explanation
Indices: 3275260--3275814 Score: 1103
Period size: 277 Copynumber: 2.0 Consensus size: 278
3275250 GAACTTTAAA
3275260 ATTTTAAAATAATAAAAACAAAATTATATTTAAACTTTTTTTTTTATAATTCTATAATTTAATTT
1 ATTTTAAAATAATAAAAACAAAATTATATTTAAACTTTTTTTTTTATAATTCTATAATTTAATTT
3275325 TGACCTACAAATATAAAATTGTAGCTTCATCAGTCATTATAAATTAGAATTTTTTAGAAAGAGTG
66 TGACCTACAAATATAAAATTGTAGCTTCATCAGTCATTATAAATTAGAATTTTTTAGAAAGAGTG
3275390 GGCATAATTTAAAAGCAAAAAAATATTTTATGCTTAAAATTTGTCTTCCGATATCAAAGGTAAGA
131 GGCATAATTTAAAAGCAAAAAAATATTTTATGCTTAAAATTTGTCTTCCGATATCAAAGGTAAGA
3275455 TCCGGCACTTGTGTGTTGTGACATTCACTTGATGGGCATGGAATCGTTAAGAAAATTGAGATGTC
196 TCCGGCACTTGTGTGTTGTGACATTCACTTGATGGGCATGGAATCGTTAAGAAAATTGAGATGTC
3275520 ATAATCCCTCACTAGCTT
261 ATAATCCCTCACTAGCTT
3275538 ATTTTAAAAT-ATAAAAACAAAATTATATTTAAACTTTTTTTTTTATAATTCTATAATTTAATTT
1 ATTTTAAAATAATAAAAACAAAATTATATTTAAACTTTTTTTTTTATAATTCTATAATTTAATTT
3275602 TGACCTACAAATATAAAATTGTAGCTTCATCAGTCATTATAAATTAGAATTTTTTAGAAAGAGTG
66 TGACCTACAAATATAAAATTGTAGCTTCATCAGTCATTATAAATTAGAATTTTTTAGAAAGAGTG
3275667 GGCATAATTTAAAAGCAAAAAAATATTTTATGCTTAAAATTTGTCTTCCGATATCAAAGGTAAGA
131 GGCATAATTTAAAAGCAAAAAAATATTTTATGCTTAAAATTTGTCTTCCGATATCAAAGGTAAGA
3275732 TCCGGCACTTGTGTGTTGTGACATTCACTTGATGGGCATGGAATCGTTAAGAAAATTGAGATGTC
196 TCCGGCACTTGTGTGTTGTGACATTCACTTGATGGGCATGGAATCGTTAAGAAAATTGAGATGTC
3275797 ATAATCCCTCACTAGCTT
261 ATAATCCCTCACTAGCTT
3275815 TCAAGCACAA
Statistics
Matches: 277, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
277 267 0.96
278 10 0.04
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (278 bp):
ATTTTAAAATAATAAAAACAAAATTATATTTAAACTTTTTTTTTTATAATTCTATAATTTAATTT
TGACCTACAAATATAAAATTGTAGCTTCATCAGTCATTATAAATTAGAATTTTTTAGAAAGAGTG
GGCATAATTTAAAAGCAAAAAAATATTTTATGCTTAAAATTTGTCTTCCGATATCAAAGGTAAGA
TCCGGCACTTGTGTGTTGTGACATTCACTTGATGGGCATGGAATCGTTAAGAAAATTGAGATGTC
ATAATCCCTCACTAGCTT
Found at i:3280723 original size:21 final size:21
Alignment explanation
Indices: 3280673--3280725 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
3280663 TTTTTTAACC
*
3280673 TAAAAT-TTAGACCCTAAATT
1 TAAAATCTTAAACCCTAAATT
* * * *
3280693 CAAGACCTTAAACCTTAAATT
1 TAAAATCTTAAACCCTAAATT
3280714 TAAAATCTTAAA
1 TAAAATCTTAAA
3280726 TTACAGTCCT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (21 bp):
TAAAATCTTAAACCCTAAATT
Found at i:3280967 original size:76 final size:77
Alignment explanation
Indices: 3280871--3281028 Score: 309
Period size: 76 Copynumber: 2.1 Consensus size: 77
3280861 TGATAAATGA
3280871 TATAAAATGATATAATTATACAATCTTCTCCCTAACTTTTATGTTTATTTGAAATGAATTTAATT
1 TATAAAATGATATAATTATACAATCTTCTCCCTAACTTTTATGTTTATTTGAAATGAATTTAATT
3280936 TTCTTATTATTT
66 TTCTTATTATTT
3280948 TATAAAATGA-ATAATTATACAATCTTCTCCCTAACTTTTATGTTTATTTGAAATGAATTTAATT
1 TATAAAATGATATAATTATACAATCTTCTCCCTAACTTTTATGTTTATTTGAAATGAATTTAATT
3281012 TTCTTATTATTT
66 TTCTTATTATTT
3281024 TATAA
1 TATAA
3281029 TTTAAATATT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 71 0.88
77 10 0.12
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (77 bp):
TATAAAATGATATAATTATACAATCTTCTCCCTAACTTTTATGTTTATTTGAAATGAATTTAATT
TTCTTATTATTT
Found at i:3281025 original size:38 final size:38
Alignment explanation
Indices: 3280907--3281026 Score: 97
Period size: 38 Copynumber: 3.2 Consensus size: 38
3280897 TCTCCCTAAC
3280907 TTTTATGTTTATTTGAAATGAATTTAATTTTCTTATTA
1 TTTTATGTTTATTTGAAATGAATTTAATTTTCTTATTA
* ** * ** *
3280945 TTTTA---TAAAATG-AAT-AATTATACAATCTTCTCCCTAA
1 TTTTATGTTTATTTGAAATGAATT-T--AATTTTCT-TATTA
3280982 CTTTTATGTTTATTTGAAATGAATTTAATTTTCTTATTA
1 -TTTTATGTTTATTTGAAATGAATTTAATTTTCTTATTA
3281021 TTTTAT
1 TTTTAT
3281027 AATTTAAATA
Statistics
Matches: 58, Mismatches: 14, Indels: 20
0.63 0.15 0.22
Matches are distributed among these distances:
33 4 0.07
34 4 0.07
35 4 0.07
36 7 0.12
37 2 0.03
38 16 0.28
39 2 0.03
40 7 0.12
41 4 0.07
42 4 0.07
43 4 0.07
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.55
Consensus pattern (38 bp):
TTTTATGTTTATTTGAAATGAATTTAATTTTCTTATTA
Found at i:3282884 original size:15 final size:17
Alignment explanation
Indices: 3282863--3282903 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
3282853 TACTTTTTCA
3282863 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
3282879 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
3282895 AAAATTATA
1 AAAATTATA
3282904 TTATTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:3282918 original size:22 final size:22
Alignment explanation
Indices: 3282863--3282925 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
3282853 TACTTTTTCA
*
3282863 AAAATTATAAAAATATAAATTATT
1 AAAATTAT-AAAAT-TATATTATT
*
3282887 AAAATAATAAAATTATATTATT
1 AAAATTATAAAATTATATTATT
** *
3282909 ACTATTATAAAAATATA
1 AAAATTATAAAATTATA
3282926 AAATTTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 21 0.64
23 5 0.15
24 7 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTATAAAATTATATTATT
Found at i:3283889 original size:14 final size:14
Alignment explanation
Indices: 3283870--3283911 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
3283860 TGGTGTTTGG
3283870 ATTATGAGTTTTCA
1 ATTATGAGTTTTCA
3283884 ATTATGAGTGGTGTTCA
1 ATTATGAGT--T-TTCA
3283901 ATTATG-GTTTT
1 ATTATGAGTTTT
3283912 GTCTGCCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
16 3 0.12
17 10 0.40
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (14 bp):
ATTATGAGTTTTCA
Found at i:3293458 original size:20 final size:20
Alignment explanation
Indices: 3293433--3293470 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3293423 TTTTGAAGAT
3293433 AAAATA-TACTTATTAAAATC
1 AAAATATTA-TTATTAAAATC
3293453 AAAATATTATTATTAAAA
1 AAAATATTATTATTAAAA
3293471 GTAAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATTATTATTAAAATC
Found at i:3294727 original size:29 final size:29
Alignment explanation
Indices: 3294692--3294749 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3294682 TATTTAAAAT
3294692 TGTTTCAGATGTGAATATGAATATTTGAA
1 TGTTTCAGATGTGAATATGAATATTTGAA
3294721 TGTTTCAGATGTGAATATGAATATTTGAA
1 TGTTTCAGATGTGAATATGAATATTTGAA
3294750 CATTGATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.41
Consensus pattern (29 bp):
TGTTTCAGATGTGAATATGAATATTTGAA
Found at i:3306066 original size:20 final size:20
Alignment explanation
Indices: 3306024--3306090 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
3306014 TATATTCTTT
*
3306024 ATTTTTTTAATAT-TTTTATA
1 ATTTTTTTAAAATATTTTA-A
*
3306044 ATTTTTTTAAAATATTTTGA
1 ATTTTTTTAAAATATTTTAA
*
3306064 A--TTTTAAAAATTATTTTAA
1 ATTTTTTTAAAA-TATTTTAA
3306083 ATTTTTTT
1 ATTTTTTT
3306091 GTAATTTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.21
19 8 0.21
20 14 0.37
21 8 0.21
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
ATTTTTTTAAAATATTTTAA
Found at i:3306068 original size:18 final size:19
Alignment explanation
Indices: 3306047--3306088 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3306037 TTTTATAATT
*
3306047 TTTTTAAAA-TATTTTGAA
1 TTTTTAAAATTATTTTAAA
*
3306065 TTTTAAAAATTATTTTAAA
1 TTTTTAAAATTATTTTAAA
3306084 TTTTT
1 TTTTT
3306089 TTGTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTAAAATTATTTTAAA
Found at i:3309461 original size:18 final size:18
Alignment explanation
Indices: 3309425--3309467 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3309415 TTTCTCCTTC
*
3309425 TCTCTCCCCTTCCTCTTTT
1 TCTCT-CCCATCCTCTTTT
*
3309444 TCTCTCCCATCCTTTTTT
1 TCTCTCCCATCCTCTTTT
*
3309462 TTTCTC
1 TCTCTC
3309468 TCTGAGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTCTCCCATCCTCTTTT
Found at i:3320912 original size:32 final size:33
Alignment explanation
Indices: 3320857--3320922 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
3320847 ATTTGGCAAG
*
3320857 TTTAAGTATCAAATTAAGAAAAAAATG-TTAAA
1 TTTAAGTATCAAATTAAGAAAAAAAAGATTAAA
* *
3320889 TTTAGGTATCAAATT-CGATAAAAAAAGATTAAA
1 TTTAAGTATCAAATTAAGA-AAAAAAAGATTAAA
3320922 T
1 T
3320923 ATCAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 2 0.07
32 21 0.72
33 6 0.21
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.32
Consensus pattern (33 bp):
TTTAAGTATCAAATTAAGAAAAAAAAGATTAAA
Found at i:3322018 original size:24 final size:24
Alignment explanation
Indices: 3321991--3322061 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 24
3321981 TTTACAAAAA
3321991 TAAAATATTTTCTTAAAAATTAAT
1 TAAAATATTTTCTTAAAAATTAAT
* * * *
3322015 T-AAA-ATGTGCAT-ATAA--AA-
1 TAAAATATTTTCTTAAAAATTAAT
3322033 TAAAATATTTTCTTAAAAATTAAT
1 TAAAATATTTTCTTAAAAATTAAT
3322057 TAAAA
1 TAAAA
3322062 ATATAATAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 1 0.03
19 5 0.15
20 5 0.15
21 6 0.18
22 5 0.15
23 5 0.15
24 6 0.18
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (24 bp):
TAAAATATTTTCTTAAAAATTAAT
Found at i:3327870 original size:9 final size:10
Alignment explanation
Indices: 3327858--3327916 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
3327848 TATTATTCTA
3327858 ATTTTTTTA-
1 ATTTTTTTAT
3327867 ATTTTTTTA-
1 ATTTTTTTAT
*
3327876 ACTTTCTTTAT
1 A-TTTTTTTAT
*
3327887 ATATTTTTTAG
1 AT-TTTTTTAT
*
3327898 ATTTTGTTAT
1 ATTTTTTTAT
*
3327908 ACTTTTTTA
1 ATTTTTTTA
3327917 GAAAATATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
9 10 0.25
10 21 0.52
11 9 0.22
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:3333591 original size:78 final size:79
Alignment explanation
Indices: 3333490--3333647 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 79
3333480 TGTTTTATTT
3333490 TATCTTTTACTTTTAAAAATTATTTATATATTATTTAATAATTTTAATAATTCAATAATTTAAAT
1 TATCTTTTACTTTTAAAAATTATTTATATATTATTTAATAATTTTAATAATTCAATAATTTAAAT
3333555 ATGTAATTCGAATA
66 ATGTAATTCGAATA
3333569 TATCTTTTAC-TTTAAAAATTATTTATATATTATTTAATAATTTTAATAATTCAATAATTTAAAT
1 TATCTTTTACTTTTAAAAATTATTTATATATTATTTAATAATTTTAATAATTCAATAATTTAAAT
3333633 ATGTAATTCGAATA
66 ATGTAATTCGAATA
3333647 T
1 T
3333648 TTTGAATGGG
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 69 0.87
79 10 0.13
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.51
Consensus pattern (79 bp):
TATCTTTTACTTTTAAAAATTATTTATATATTATTTAATAATTTTAATAATTCAATAATTTAAAT
ATGTAATTCGAATA
Found at i:3334511 original size:33 final size:33
Alignment explanation
Indices: 3334469--3334535 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
3334459 CGTTTCTTTT
3334469 GTATCTTTT-CTTCTTGTGTGACCACCCCGTTGG
1 GTATCTTTTCCTT-TTGTGTGACCACCCCGTTGG
*
3334502 GTATCTTTTCCTTTTGTGTGACCACCCTGTTGG
1 GTATCTTTTCCTTTTGTGTGACCACCCCGTTGG
3334535 G
1 G
3334536 GCTTTCTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
GTATCTTTTCCTTTTGTGTGACCACCCCGTTGG
Found at i:3337787 original size:16 final size:17
Alignment explanation
Indices: 3337766--3337800 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3337756 AAAAATTGAC
3337766 ATTG-AAAATATTTTTT
1 ATTGAAAAATATTTTTT
3337782 ATTGAAAAATATTTTTT
1 ATTGAAAAATATTTTTT
3337799 AT
1 AT
3337801 AAATTCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
ATTGAAAAATATTTTTT
Found at i:3359049 original size:24 final size:24
Alignment explanation
Indices: 3358998--3359046 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
3358988 TAAGAAATAT
3358998 ATAATTTAATCTATTAATTTTAAA
1 ATAATTTAATCTATTAATTTTAAA
*
3359022 ATAATATTAATTTACTT-ATTTTAAA
1 ATAAT-TTAATCTA-TTAATTTTAAA
3359047 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 15 0.68
26 2 0.09
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAATTTAATCTATTAATTTTAAA
Found at i:3359120 original size:18 final size:19
Alignment explanation
Indices: 3359064--3359121 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
3359054 AAATTAATAC
*
3359064 ATTTATCTTCAATTTAAAAT
1 ATTTAT-TTAAATTTAAAAT
*
3359084 ATTT-TTTAAATATT-TAAT
1 ATTTATTTAAAT-TTAAAAT
3359102 ATTTATTT-AATTTAAAAT
1 ATTTATTTAAATTTAAAAT
3359120 AT
1 AT
3359122 AATTTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.06
18 20 0.62
19 6 0.19
20 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTATTTAAATTTAAAAT
Found at i:3365428 original size:19 final size:20
Alignment explanation
Indices: 3365383--3365420 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3365373 TCTTTTTACT
*
3365383 CAAAAGATAAAAAAAAGTTA
1 CAAAATATAAAAAAAAGTTA
3365403 CAAAATATAAAAAAAAGT
1 CAAAATATAAAAAAAAGT
3365421 ATAAAATAGT
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:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (20 bp):
CAAAATATAAAAAAAAGTTA
Found at i:3367487 original size:21 final size:23
Alignment explanation
Indices: 3367440--3367481 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3367430 AAAATAAATA
*
3367440 TAAATTTTATGGATGAATTTAAT
1 TAAATTTTATGGATCAATTTAAT
3367463 TAAATTTTAT-GA-CAATTTA
1 TAAATTTTATGGATCAATTTA
3367482 TCTAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (23 bp):
TAAATTTTATGGATCAATTTAAT
Found at i:3370575 original size:32 final size:33
Alignment explanation
Indices: 3370503--3370576 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 33
3370493 ACCCCGAATT
3370503 AAATTCATTTTCAATTTGATTTGATTTGATTCCAACC
1 AAATTCATTTTCAATTTGATTTGATTTGATT----CC
*
3370540 AAATTCATTTTCAATTTGATTTGATTTTATT-C
1 AAATTCATTTTCAATTTGATTTGATTTGATTCC
3370572 AAATT
1 AAATT
3370577 AGTTTAAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
32 6 0.17
37 30 0.83
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (33 bp):
AAATTCATTTTCAATTTGATTTGATTTGATTCC
Found at i:3371245 original size:33 final size:31
Alignment explanation
Indices: 3371173--3371245 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
3371163 GACCCCTCAA
3371173 AAGTTTATGTACCAAATTAAGAAAAAAATGTC
1 AAGTTTA-GTACCAAATTAAGAAAAAAATGTC
* *
3371205 AAATTTAGATACCAAATTAGGAAAAAAAGTGTC
1 AAGTTTAG-TACCAAATTAAGAAAAAAA-TGTC
*
3371238 TAGTTTAG
1 AAGTTTAG
3371246 GAATCAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.03
32 24 0.69
33 10 0.29
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (31 bp):
AAGTTTAGTACCAAATTAAGAAAAAAATGTC
Found at i:3371564 original size:15 final size:15
Alignment explanation
Indices: 3371544--3371574 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3371534 TTGAGACTAA
*
3371544 TGTCTAATCAATATT
1 TGTCTAATAAATATT
3371559 TGTCTAATAAATATT
1 TGTCTAATAAATATT
3371574 T
1 T
3371575 TAGAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (15 bp):
TGTCTAATAAATATT
Found at i:3374715 original size:13 final size:13
Alignment explanation
Indices: 3374699--3374734 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
3374689 CATTACTTTT
3374699 GAAAAGTACTGTG
1 GAAAAGTACTGTG
*
3374712 GAAAAGTGCTGTG
1 GAAAAGTACTGTG
3374725 GAAAAGTACT
1 GAAAAGTACT
3374735 TTTGAGAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22
Consensus pattern (13 bp):
GAAAAGTACTGTG
Found at i:3379077 original size:27 final size:27
Alignment explanation
Indices: 3379047--3379106 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
3379037 CAAAGAAAAG
* * * *
3379047 AAAATTTAAAATGTAAAAATTAAATTA
1 AAAATTAAAAATATAAAAATAAAAATA
* *
3379074 AAAATAAAAAATATTAAAATAAAAATA
1 AAAATTAAAAATATAAAAATAAAAATA
3379101 AAAATT
1 AAAATT
3379107 GGCGAAATTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAATTAAAAATATAAAAATAAAAATA
Found at i:3379091 original size:21 final size:20
Alignment explanation
Indices: 3379061--3379104 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
3379051 TTTAAAATGT
*
3379061 AAAAATTAAATTAAAAATAA
1 AAAAATTAAAATAAAAATAA
3379081 AAAATATTAAAATAAAAATAA
1 AAAA-ATTAAAATAAAAATAA
3379102 AAA
1 AAA
3379105 TTGGCGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATTAAAATAAAAATAA
Found at i:3379583 original size:14 final size:14
Alignment explanation
Indices: 3379564--3379595 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3379554 ATTTAAAAGG
3379564 GCATGTAAAGAAAA
1 GCATGTAAAGAAAA
*
3379578 GCATGTAAAGTAAA
1 GCATGTAAAGAAAA
3379592 GCAT
1 GCAT
3379596 TCAACAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19
Consensus pattern (14 bp):
GCATGTAAAGAAAA
Found at i:3380107 original size:21 final size:20
Alignment explanation
Indices: 3380079--3380119 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
3380069 TGCTTCTTGG
*
3380079 CAAATGGATATTGCGATACC
1 CAAATGGATATCGCGATACC
3380099 CAAAGTGGATATCGCGATACC
1 CAAA-TGGATATCGCGATACC
3380120 ATTGAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
CAAATGGATATCGCGATACC
Found at i:3382418 original size:21 final size:20
Alignment explanation
Indices: 3382371--3382420 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
3382361 AAAATTATCC
* *
3382371 TTATTTTTATATTTGACAAT
1 TTATTTTTAAATTTAACAAT
*
3382391 TTAATTTTTAAATGTTAATAAT
1 TT-ATTTTTAAAT-TTAACAAT
3382413 TTATTTTT
1 TTATTTTT
3382421 TCCTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.60
22 8 0.32
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
TTATTTTTAAATTTAACAAT
Found at i:3383296 original size:13 final size:13
Alignment explanation
Indices: 3383280--3383321 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3383270 ATATTCCCTA
*
3383280 AATTAAATGTAAT
1 AATTAAATATAAT
3383293 AATT-AATAATAA-
1 AATTAAAT-ATAAT
3383305 AATTAAATATAAT
1 AATTAAATATAAT
3383318 AATT
1 AATT
3383322 TTATTAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
AATTAAATATAAT
Found at i:3384560 original size:125 final size:125
Alignment explanation
Indices: 3384420--3384670 Score: 502
Period size: 125 Copynumber: 2.0 Consensus size: 125
3384410 ATAAATTTTA
3384420 TTTAAAATTAATTTTTTTGTTTGATTTTATATTATTTTGCGGATCCGAATTCGGATTTTTGCAGA
1 TTTAAAATTAATTTTTTTGTTTGATTTTATATTATTTTGCGGATCCGAATTCGGATTTTTGCAGA
3384485 TTTGGATATCCGACATTTGATTGAAAATGTAAAATTTGAATTTTTTGTTGATTTAGATAT
66 TTTGGATATCCGACATTTGATTGAAAATGTAAAATTTGAATTTTTTGTTGATTTAGATAT
3384545 TTTAAAATTAATTTTTTTGTTTGATTTTATATTATTTTGCGGATCCGAATTCGGATTTTTGCAGA
1 TTTAAAATTAATTTTTTTGTTTGATTTTATATTATTTTGCGGATCCGAATTCGGATTTTTGCAGA
3384610 TTTGGATATCCGACATTTGATTGAAAATGTAAAATTTGAATTTTTTGTTGATTTAGATAT
66 TTTGGATATCCGACATTTGATTGAAAATGTAAAATTTGAATTTTTTGTTGATTTAGATAT
3384670 T
1 T
3384671 CGACGAATAA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (125 bp):
TTTAAAATTAATTTTTTTGTTTGATTTTATATTATTTTGCGGATCCGAATTCGGATTTTTGCAGA
TTTGGATATCCGACATTTGATTGAAAATGTAAAATTTGAATTTTTTGTTGATTTAGATAT
Found at i:3385498 original size:20 final size:21
Alignment explanation
Indices: 3385475--3385515 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3385465 ATTTTTATGC
3385475 TTCACT-AAAAAAAAAAAGAA
1 TTCACTCAAAAAAAAAAAGAA
* *
3385495 TTCACTCAAAATAATAAAGAA
1 TTCACTCAAAAAAAAAAAGAA
3385516 GAAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.20
Consensus pattern (21 bp):
TTCACTCAAAAAAAAAAAGAA
Found at i:3386420 original size:3 final size:3
Alignment explanation
Indices: 3386412--3386447 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3386402 TTTAGCTCAT
3386412 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3386448 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3388215 original size:17 final size:17
Alignment explanation
Indices: 3388170--3388209 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3388160 AATTGTTGAC
*
3388170 AAAAATTAATAATATAT
1 AAAAATTAAAAATATAT
3388187 AAAAATTAAAAATATAT
1 AAAAATTAAAAATATAT
3388204 AAAAAT
1 AAAAAT
3388210 ACAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATTAAAAATATAT
Found at i:3388537 original size:11 final size:11
Alignment explanation
Indices: 3388517--3388553 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3388507 GGCCCAACCC
*
3388517 ATATTAAATAT
1 ATATTTAATAT
3388528 ATATTTAATAT
1 ATATTTAATAT
3388539 ATA--TAATAT
1 ATATTTAATAT
3388548 ATATTT
1 ATATTT
3388554 GATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATTTAATAT
Found at i:3394982 original size:23 final size:23
Alignment explanation
Indices: 3394956--3394999 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3394946 TTTCTTACTA
* *
3394956 TAGTAATTTTTGGGGTATTACAG
1 TAGTAATTTTCGGGATATTACAG
3394979 TAGTAATTTTCGGGATATTAC
1 TAGTAATTTTCGGGATATTAC
3395000 GAAAATAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (23 bp):
TAGTAATTTTCGGGATATTACAG
Found at i:3397255 original size:29 final size:31
Alignment explanation
Indices: 3397220--3397287 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
3397210 AAGTTATAGA
*
3397220 TTTAGTCCTTGTA-TTTTTAA-TTGATCACT
1 TTTAGTCCTTGTACTTTTCAAGTTGATCACT
* *
3397249 TTTAGTCTTTGTACTTTTCAAGTTGGTCACT
1 TTTAGTCCTTGTACTTTTCAAGTTGATCACT
3397280 TTTAGTCC
1 TTTAGTCC
3397288 CAATACTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 12 0.36
30 6 0.18
31 15 0.45
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (31 bp):
TTTAGTCCTTGTACTTTTCAAGTTGATCACT
Found at i:3401831 original size:54 final size:55
Alignment explanation
Indices: 3401748--3401856 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 55
3401738 ATCACTCGAA
3401748 TTTTTAATGTTAATAATTGAACAACTCAAAAGCTGGTTTTTGGTTTGCAGAGCTG
1 TTTTTAATGTTAATAATTGAACAACTCAAAAGCTGGTTTTTGGTTTGCAGAGCTG
3401803 TTTTTAATG-TAATAATTGAACAACTCAAAAGCTGGTTTTTGGTTTGCAGAGCTG
1 TTTTTAATGTTAATAATTGAACAACTCAAAAGCTGGTTTTTGGTTTGCAGAGCTG
3401857 CCTAAGGTTG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 45 0.83
55 9 0.17
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.39
Consensus pattern (55 bp):
TTTTTAATGTTAATAATTGAACAACTCAAAAGCTGGTTTTTGGTTTGCAGAGCTG
Found at i:3412801 original size:5 final size:5
Alignment explanation
Indices: 3412791--3412819 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3412781 TCTCTTTGGG
3412791 TCTTT TCTTT TCTTT TCTTT T-TTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
3412820 AATCGGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:3425267 original size:14 final size:13
Alignment explanation
Indices: 3425239--3425264 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3425229 TTATATAAAT
3425239 TATTAATTAAAAA
1 TATTAATTAAAAA
3425252 TATTAATTAAAAA
1 TATTAATTAAAAA
3425265 ATAAAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:3428436 original size:28 final size:29
Alignment explanation
Indices: 3428405--3428474 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
3428395 TAATTAATTA
*
3428405 ATTTTTTAAAATTAAAAATAT-TAAAAAT
1 ATTTTTAAAAATTAAAAATATATAAAAAT
* * *
3428433 ATTTTTAAAAAAT-AAAATGTATAAAATT
1 ATTTTTAAAAATTAAAAATATATAAAAAT
3428461 A-TTTTAAAAATTAA
1 ATTTTTAAAAATTAA
3428475 TTAATTGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (29 bp):
ATTTTTAAAAATTAAAAATATATAAAAAT
Found at i:3443053 original size:3 final size:3
Alignment explanation
Indices: 3443045--3443108 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
3443035 AAGCTATTAT
* * *
3443045 ATA ATA ATA AT- ATG ATA AGTA ACA ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
3443090 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
3443109 AATTACTGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3444529 original size:3 final size:3
Alignment explanation
Indices: 3444521--3444561 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
3444511 AAGTTAGTAC
* *
3444521 TAT TAT TAT TAT TAT TAT TAT T-T TAA TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3444562 CATCATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3444569 original size:20 final size:20
Alignment explanation
Indices: 3444527--3444570 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3444517 GTACTATTAT
**
3444527 TATTATTATTATTATTTTAA
1 TATTATTATTATTATCATAA
* *
3444547 TATTATTGTTATTATCATCA
1 TATTATTATTATTATCATAA
3444567 TATT
1 TATT
3444571 TCCATTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTATTATTATTATCATAA
Found at i:3445692 original size:13 final size:13
Alignment explanation
Indices: 3445658--3445684 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3445648 TTCATTGACA
3445658 AAGAAAATGAAAT
1 AAGAAAATGAAAT
3445671 AAGAAAATGAAAT
1 AAGAAAATGAAAT
3445684 A
1 A
3445685 GAACAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAGAAAATGAAAT
Found at i:3454548 original size:16 final size:17
Alignment explanation
Indices: 3454523--3454562 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3454513 GCCCAAATGC
3454523 CAAA-CCCAAAT-AAAA
1 CAAAGCCCAAATCAAAA
*
3454538 CAAAGCCCAAATCCAAA
1 CAAAGCCCAAATCAAAA
3454555 C-AAGCCCA
1 CAAAGCCCA
3454563 TTACAGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.55, C:0.35, G:0.05, T:0.05
Consensus pattern (17 bp):
CAAAGCCCAAATCAAAA
Found at i:3455778 original size:17 final size:17
Alignment explanation
Indices: 3455756--3455801 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3455746 CTATTACAAC
3455756 TATTATTATTATTATTA
1 TATTATTATTATTATTA
* *
3455773 TATTATTATTTTTTTTA
1 TATTATTATTATTATTA
3455790 TATATATT-TTAT
1 TAT-TATTATTAT
3455802 AATTTATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:3458263 original size:34 final size:32
Alignment explanation
Indices: 3458203--3458268 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
3458193 ACTTTTTTTA
**
3458203 ATAAATTTATTGATTTTTAATTTTTAAAAATT
1 ATAAATTTATTGATTTTTAAAATTTAAAAATT
*
3458235 ATAAATGTTCTTGATTTTTTAAAATTTAAAAATT
1 ATAAAT-TTATTGA-TTTTTAAAATTTAAAAATT
3458269 TAATTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 6 0.21
33 6 0.21
34 17 0.59
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (32 bp):
ATAAATTTATTGATTTTTAAAATTTAAAAATT
Found at i:3458787 original size:3 final size:3
Alignment explanation
Indices: 3458779--3458810 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3458769 GCCGCTGTTG
*
3458779 CTT CTT CTT CTT CTT CTT CTT CCT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
3458811 CACTTTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:3473544 original size:78 final size:78
Alignment explanation
Indices: 3473415--3473573 Score: 282
Period size: 78 Copynumber: 2.0 Consensus size: 78
3473405 CTATTGACAA
*
3473415 TAACTGTAGCTTGTAGGTGATAATGCTAAATACTAAAACTCACCCTAAACAATGTTTACTTTCAT
1 TAACTGTAGCTTGTAGGTGATAATGCTAAATACGAAAACTCACCCTAAACAATGTTTACTTTCAT
*
3473480 CTACATTCGGAAC
66 CTACATTCAGAAC
**
3473493 TAACTGTAGCTTGTAGGTGATAATGCTAAATACGAAAGTTCACCCTAAACAATGTTTACTTTCAT
1 TAACTGTAGCTTGTAGGTGATAATGCTAAATACGAAAACTCACCCTAAACAATGTTTACTTTCAT
3473558 CTACATTCAGAAC
66 CTACATTCAGAAC
3473571 TAA
1 TAA
3473574 GTCCAATAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (78 bp):
TAACTGTAGCTTGTAGGTGATAATGCTAAATACGAAAACTCACCCTAAACAATGTTTACTTTCAT
CTACATTCAGAAC
Found at i:3482458 original size:2 final size:2
Alignment explanation
Indices: 3482445--3482530 Score: 75
Period size: 2 Copynumber: 43.0 Consensus size: 2
3482435 ATCTTCATAC
* * * * *
3482445 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT GGT A- AT TT TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
* * * *
3482487 TT AT GT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3482529 AT
1 AT
3482531 GGTAATTGCT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.01
2 68 0.97
3 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3482559 original size:56 final size:56
Alignment explanation
Indices: 3482441--3482550 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 56
3482431 TGTGATCTTC
** *
3482441 ATACATATAC--ATATATATATATATATATATATATGGTAATTTTTTTTTATGTAT
1 ATACATATACATATATATATATATATATATATATATGGTAATTGCTTTTTATGAAT
3482495 ATACATATACATATATATATATATATATATATATATGGTAATTGCTTTTTATGAAT
1 ATACATATACATATATATATATATATATATATATATGGTAATTGCTTTTTATGAAT
3482551 TTTAATATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 10 0.20
56 41 0.80
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (56 bp):
ATACATATACATATATATATATATATATATATATATGGTAATTGCTTTTTATGAAT
Found at i:3482639 original size:47 final size:47
Alignment explanation
Indices: 3482553--3482711 Score: 248
Period size: 47 Copynumber: 3.3 Consensus size: 47
3482543 TTATGAATTT
* * *
3482553 TAATATATATGGTAAT-TACTCTTTTTTATTACCTTTAATATATATGGCAA
1 TAATAT-TATGGTAATGT--TC-TTTTCATTGCCTTTAATATATATGGTAA
3482603 TAATATTATGGTAATGTTCTTTTCATTGCCTTTAATATATATGGTAA
1 TAATATTATGGTAATGTTCTTTTCATTGCCTTTAATATATATGGTAA
3482650 TAATATTATGGTAATGTTCTTTTCATTGCCTTTAATATATATGGTAA
1 TAATATTATGGTAATGTTCTTTTCATTGCCTTTAATATATATGGTAA
3482697 TAATATTATGGTAAT
1 TAATATTATGGTAAT
3482712 TGCAATTTTA
Statistics
Matches: 105, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
47 87 0.83
48 2 0.02
49 9 0.09
50 7 0.07
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.48
Consensus pattern (47 bp):
TAATATTATGGTAATGTTCTTTTCATTGCCTTTAATATATATGGTAA
Found at i:3482661 original size:14 final size:15
Alignment explanation
Indices: 3482635--3482664 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3482625 TCATTGCCTT
3482635 TAATATATATGGTAA
1 TAATATATATGGTAA
3482650 TAATAT-TATGGTAA
1 TAATATATATGGTAA
3482664 T
1 T
3482665 GTTCTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TAATATATATGGTAA
Found at i:3482708 original size:14 final size:15
Alignment explanation
Indices: 3482682--3482711 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3482672 TCATTGCCTT
3482682 TAATATATATGGTAA
1 TAATATATATGGTAA
3482697 TAATAT-TATGGTAA
1 TAATATATATGGTAA
3482711 T
1 T
3482712 TGCAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TAATATATATGGTAA
Found at i:3483228 original size:15 final size:16
Alignment explanation
Indices: 3483208--3483245 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3483198 TATTATATTT
**
3483208 TAAAAAAATTTAA-TA
1 TAAAAAAATAAAATTA
3483223 TAAAAAAATAAAATTA
1 TAAAAAAATAAAATTA
3483239 TAAAAAA
1 TAAAAAA
3483246 TTAATATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAAAATAAAATTA
Found at i:3485972 original size:18 final size:19
Alignment explanation
Indices: 3485951--3485991 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3485941 ATTTTGAAAT
*
3485951 TTTTATAAA-TATTCTGAA
1 TTTTAAAAATTATTCTGAA
*
3485969 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTCTGAA
3485988 TTTT
1 TTTT
3485992 TTTTTTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTCTGAA
Found at i:3485972 original size:19 final size:18
Alignment explanation
Indices: 3485936--3485992 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
3485926 TAAAAAAAAA
3485936 TATAAAT-TTTGAAATTTT
1 TATAAATATTTG-AATTTT
3485954 TATAAATATTCTGAA-TTT
1 TATAAATATT-TGAATTTT
*
3485972 TAAAAATTATTTTGAATTTT
1 TATAAA-TA-TTTGAATTTT
3485992 T
1 T
3485993 TTTTTGTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 15 0.45
19 10 0.30
20 8 0.24
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (18 bp):
TATAAATATTTGAATTTT
Found at i:3494828 original size:31 final size:31
Alignment explanation
Indices: 3494791--3494854 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3494781 TGGGTAGGAG
3494791 AAAAAGGCGGGCAATAGCTAACCTGGAGACT
1 AAAAAGGCGGGCAATAGCTAACCTGGAGACT
3494822 AAAAAGGCGGGCAATAGCTAACCTGGAGACT
1 AAAAAGGCGGGCAATAGCTAACCTGGAGACT
3494853 AA
1 AA
3494855 CACCACGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (31 bp):
AAAAAGGCGGGCAATAGCTAACCTGGAGACT
Done.