Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 88 of 120
Found at i:25457109 original size:10 final size:10
Alignment explanation
Indices: 25457096--25457137 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
25457086 TTTTTTTTTG
25457096 TTTTTTATAT
1 TTTTTTATAT
25457106 TTTTTTGA-A-
1 TTTTTT-ATAT
25457115 TTTTTTATAT
1 TTTTTTATAT
*
25457125 TTTTTTGTAT
1 TTTTTTATAT
25457135 TTT
1 TTT
25457138 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
8 1 0.04
9 7 0.25
10 19 0.68
11 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:25457109 original size:19 final size:19
Alignment explanation
Indices: 25457088--25457137 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
25457078 GCTTTTCATT
25457088 TTTTTTTG--TTTTTTATA
1 TTTTTTTGAATTTTTTATA
25457105 TTTTTTTGAATTTTTTATA
1 TTTTTTTGAATTTTTTATA
*
25457124 TTTTTTTGTATTTT
1 TTTTTTTGAATTTT
25457138 AAAAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 8 0.27
19 22 0.73
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (19 bp):
TTTTTTTGAATTTTTTATA
Found at i:25457710 original size:57 final size:57
Alignment explanation
Indices: 25457647--25457767 Score: 206
Period size: 57 Copynumber: 2.1 Consensus size: 57
25457637 CTTATCGTAG
* *
25457647 CATGTTTTATGTAATTTATTACAGTGATTGAATTTAGAGAATATTTTATTTATTTAT
1 CATGTTTTATGTAATTTATTACAGTGATTGAATTTAGAAAATATTTTATTTACTTAT
*
25457704 CATGTTTTATGTAATTTATTATAGTGATTGAATTTAGAAAATATTTTATTTACTTAT
1 CATGTTTTATGTAATTTATTACAGTGATTGAATTTAGAAAATATTTTATTTACTTAT
*
25457761 CGTGTTT
1 CATGTTT
25457768 GCGTTTAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (57 bp):
CATGTTTTATGTAATTTATTACAGTGATTGAATTTAGAAAATATTTTATTTACTTAT
Found at i:25458413 original size:26 final size:26
Alignment explanation
Indices: 25458355--25458413 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
25458345 AAATCTAAAG
* *
25458355 GCCCAACACCCATACAAACCCAACAA
1 GCCCAATACACATACAAACCCAACAA
*
25458381 GCCCAATACACATACAAGCCCAACAA
1 GCCCAATACACATACAAACCCAACAA
25458407 GCCCAAT
1 GCCCAAT
25458414 GCACTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.44, C:0.42, G:0.07, T:0.07
Consensus pattern (26 bp):
GCCCAATACACATACAAACCCAACAA
Found at i:25475806 original size:97 final size:98
Alignment explanation
Indices: 25475661--25475883 Score: 270
Period size: 97 Copynumber: 2.3 Consensus size: 98
25475651 AGATATTGAG
* * * *
25475661 GGAAAGGTTGAGGCCGCAAAGACGAATCTGGTACCTTAAAAGACATGATGGAAAAGATCGAGACC
1 GGAAAGGTTGAGGTCGCAACGACGAACCTAGTACCTTAAAAGACATGATGGAAAAGATCGAGACC
*
25475726 GCAACGACGGATCTAATACCAT-AAGAATA-AAA
66 GCAACGACGAATCTAATACCATGAAG-ATACAAA
** * * * * *
25475758 GGAAAGGTTGAGGTCGCAACGGTGAACCTAGTATCTTAGAAGATATGATGGGAAAGATTGAGACC
1 GGAAAGGTTGAGGTCGCAACGACGAACCTAGTACCTTAAAAGACATGATGGAAAAGATCGAGACC
* **
25475823 GCAACGATGAATCTGGTACCATGAAGATACAAA
66 GCAACGACGAATCTAATACCATGAAGATACAAA
* *
25475856 AGAAAGGTTGAGGTCGCAACAACGAACC
1 GGAAAGGTTGAGGTCGCAACGACGAACC
25475884 CGATACCTTA
Statistics
Matches: 105, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
97 75 0.71
98 30 0.29
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (98 bp):
GGAAAGGTTGAGGTCGCAACGACGAACCTAGTACCTTAAAAGACATGATGGAAAAGATCGAGACC
GCAACGACGAATCTAATACCATGAAGATACAAA
Found at i:25475819 original size:50 final size:50
Alignment explanation
Indices: 25475615--25476017 Score: 162
Period size: 50 Copynumber: 8.2 Consensus size: 50
25475605 TTTGAAAGGG
* * * * *
25475615 AAGATTGAGGCTGGAACGGCGAAACT-GATACCTT-GGAGATATTGA-GGGA
1 AAGATTGAGGCCGCAACGGTGAACCTAG-TACCTTAGAAGATA-TGATGGGA
* * ** * * * * *
25475664 AAGGTTGAGGCCGCAAAGACGAATCTGGTACCTTAAAAGACATGATGGAA
1 AAGATTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATATGATGGGA
* * ** * * * * * **
25475714 AAGATCGAGACCGCAACGACGGATCTAATACC--ATAAGA-ATAAAAGGA
1 AAGATTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATATGATGGGA
* * *
25475761 AAGGTTGAGGTCGCAACGGTGAACCTAGTATCTTAGAAGATATGATGGGA
1 AAGATTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATATGATGGGA
* * * * * * ***
25475811 AAGATTGAGACCGCAACGATGAATCTGGTACCAT-GAAGATA-CAAAAGA
1 AAGATTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATATGATGGGA
* * *** * *
25475859 AAGGTTGAGGTCGCAACAACGAACC-CGATACCTTAGAAGATGTGATGGGA
1 AAGATTGAGGCCGCAACGGTGAACCTAG-TACCTTAGAAGATATGATGGGA
* * * * * *
25475909 ATGATTGAGGCCTCAACGGTGAATCTGGTACCAT-GAAGATATGAAGGGA
1 AAGATTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATATGATGGGA
* * * ** * * *
25475958 AAAATTGGGGCCGTAAC-GACAGACCTAGTACCTTAGACGGTGTGATGGGA
1 AAGATTGAGGCCGCAACGGTGA-ACCTAGTACCTTAGAAGATATGATGGGA
*
25476008 AAGATCGAGG
1 AAGATTGAGG
25476018 TCACAACGAT
Statistics
Matches: 252, Mismatches: 90, Indels: 23
0.69 0.25 0.06
Matches are distributed among these distances:
47 28 0.11
48 34 0.13
49 81 0.32
50 108 0.43
51 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (50 bp):
AAGATTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATATGATGGGA
Found at i:25475894 original size:98 final size:96
Alignment explanation
Indices: 25475662--25475949 Score: 310
Period size: 98 Copynumber: 3.0 Consensus size: 96
25475652 GATATTGAGG
* * * * * * *
25475662 GAAAGGTTGAGGCCGCAA-AGACGAATCTGGTACCTTAAAAGACATGATGGAAAAGATCGAGACC
1 GAAAGGTTGAGGTCGCAACA-ACGAA-CCGATACCTTAGAAGATATGATGGGAAAGATTGAGACC
* * ** *
25475726 GCAACGACGGATCTAATACCAT-AAGAATAAAAG
64 GCAACGATGAATCTGGTACCATGAAG-ATAAAAA
*** * *
25475759 GAAAGGTTGAGGTCGCAACGGTGAACCTAGTATCTTAGAAGATATGATGGGAAAGATTGAGACCG
1 GAAAGGTTGAGGTCGCAACAACGAACCGA-TACCTTAGAAGATATGATGGGAAAGATTGAGACCG
25475824 CAACGATGAATCTGGTACCATGAAGATACAAAA
65 CAACGATGAATCTGGTACCATGAAGATA-AAAA
* * * *
25475857 GAAAGGTTGAGGTCGCAACAACGAACCCGATACCTTAGAAGATGTGATGGGAATGATTGAGGCCT
1 GAAAGGTTGAGGTCGCAACAACGAA-CCGATACCTTAGAAGATATGATGGGAAAGATTGAGACCG
*
25475922 CAACGGTGAATCTGGTACCATGAAGATA
65 CAACGATGAATCTGGTACCATGAAGATA
25475950 TGAAGGGAAA
Statistics
Matches: 159, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
96 1 0.01
97 70 0.44
98 85 0.53
99 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (96 bp):
GAAAGGTTGAGGTCGCAACAACGAACCGATACCTTAGAAGATATGATGGGAAAGATTGAGACCGC
AACGATGAATCTGGTACCATGAAGATAAAAA
Found at i:25476025 original size:99 final size:100
Alignment explanation
Indices: 25475887--25476074 Score: 227
Period size: 99 Copynumber: 1.9 Consensus size: 100
25475877 ACGAACCCGA
* * * * * * *
25475887 TACCTTAGAAGATGTGATGGGAATGATTGAGGCCTCAACGGT-GAATCTGGTACCATGAAGATAT
1 TACCTTAGAAGATGTGATGGGAAAGATCGAGGCCACAACGATAG-ATCTAGTACCATAAAAATAT
* **
25475951 GAA-GGGAAAAATTGGGGCCGTAACGACAGACCTAG
65 AAAGGGGAAAAATTGAAGCCGTAACGACAGACCTAG
* * *
25475986 TACCTTAGACGGTGTGATGGGAAAGATCGAGGTCACAACGATAGATCTAGTACCATAAAAATATA
1 TACCTTAGAAGATGTGATGGGAAAGATCGAGGCCACAACGATAGATCTAGTACCATAAAAATATA
*
25476051 AAGGGGAAAAGTTGAAGCCGTAAC
66 AAGGGGAAAAATTGAAGCCGTAAC
25476075 AGCGAAACAT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
99 54 0.74
100 19 0.26
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (100 bp):
TACCTTAGAAGATGTGATGGGAAAGATCGAGGCCACAACGATAGATCTAGTACCATAAAAATATA
AAGGGGAAAAATTGAAGCCGTAACGACAGACCTAG
Found at i:25477124 original size:26 final size:26
Alignment explanation
Indices: 25477086--25477138 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
25477076 CTGAAGGCCT
* * *
25477086 AATACCGATACAAACCCAATAAGCCC
1 AATACCCAGACAAACCCAACAAGCCC
**
25477112 AATACCCAGACAATTCCAACAAGCCC
1 AATACCCAGACAAACCCAACAAGCCC
25477138 A
1 A
25477139 TACACTAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.36, G:0.08, T:0.11
Consensus pattern (26 bp):
AATACCCAGACAAACCCAACAAGCCC
Found at i:25477495 original size:6 final size:6
Alignment explanation
Indices: 25477486--25477542 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
25477476 TATACATGTA
*
25477486 TATTTT TA-TTT TATTTT TATCTTT TGTTATT TA-TTT TATTTT TATTGTT
1 TATTTT TATTTT TATTTT TAT-TTT TATT-TT TATTTT TATTTT TATT-TT
25477535 ATATTTT T
1 -TATTTT T
25477543 TTCTTTGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 9 0.21
6 18 0.42
7 12 0.28
8 4 0.09
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:25477515 original size:21 final size:21
Alignment explanation
Indices: 25477491--25477548 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 21
25477481 ATGTATATTT
*
25477491 TTATTTTATTTTTATCTTTTG
1 TTATTTTATTTTTATCTTTTA
25477512 TTA-TTTA-TTTTAT-TTTTA
1 TTATTTTATTTTTATCTTTTA
* * *
25477530 TTGTTATATTTTTTTCTTT
1 TTATTTTATTTTTATCTTT
25477549 GAAACTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 6 0.20
19 9 0.30
20 9 0.30
21 6 0.20
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (21 bp):
TTATTTTATTTTTATCTTTTA
Found at i:25480439 original size:19 final size:19
Alignment explanation
Indices: 25480415--25480498 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 19
25480405 GTTTGAATTG
25480415 AAAAATAACAAAATGTAGT
1 AAAAATAACAAAATGTAGT
* *
25480434 AAAAATAA-ATAAAAGT-TT
1 AAAAATAACA-AAATGTAGT
*
25480452 GAAATAA-AATAAAATTGTAG-
1 -AAA-AATAACAAAA-TGTAGT
*
25480472 CAAAATAACAAAATGTAGT
1 AAAAATAACAAAATGTAGT
25480491 AAAAATAA
1 AAAAATAA
25480499 ATAAAAGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
18 9 0.18
19 36 0.72
20 5 0.10
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.23
Consensus pattern (19 bp):
AAAAATAACAAAATGTAGT
Found at i:25480483 original size:57 final size:57
Alignment explanation
Indices: 25480416--25480534 Score: 229
Period size: 57 Copynumber: 2.1 Consensus size: 57
25480406 TTTGAATTGA
*
25480416 AAAATAACAAAATGTAGTAAAAATAAATAAAAGTTTGAAATAAAATAAAATTGTAGC
1 AAAATAACAAAATGTAGTAAAAATAAATAAAAGTTTAAAATAAAATAAAATTGTAGC
25480473 AAAATAACAAAATGTAGTAAAAATAAATAAAAGTTTAAAATAAAATAAAATTGTAGC
1 AAAATAACAAAATGTAGTAAAAATAAATAAAAGTTTAAAATAAAATAAAATTGTAGC
25480530 AAAAT
1 AAAAT
25480535 TGTAAAACAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.24
Consensus pattern (57 bp):
AAAATAACAAAATGTAGTAAAAATAAATAAAAGTTTAAAATAAAATAAAATTGTAGC
Found at i:25480494 original size:18 final size:18
Alignment explanation
Indices: 25480416--25480494 Score: 54
Period size: 18 Copynumber: 4.2 Consensus size: 18
25480406 TTTGAATTGA
25480416 AAAATAACAAAATGTAGT
1 AAAATAACAAAATGTAGT
* * *
25480434 AAAAATAAATAAAAGTTTGAAAT
1 -AAAAT-AACAAAA---TGTAGT
* *
25480457 AAAAT-A-AAATTGTAGC
1 AAAATAACAAAATGTAGT
25480473 AAAATAACAAAATGTAGT
1 AAAATAACAAAATGTAGT
25480491 AAAA
1 AAAA
25480495 ATAAATAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
16 8 0.18
17 1 0.02
18 12 0.27
19 8 0.18
20 7 0.16
22 5 0.11
23 4 0.09
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (18 bp):
AAAATAACAAAATGTAGT
Found at i:25480511 original size:18 final size:18
Alignment explanation
Indices: 25480433--25480522 Score: 62
Period size: 18 Copynumber: 4.8 Consensus size: 18
25480423 CAAAATGTAG
25480433 TAAAAATAAATAAAAGTT
1 TAAAAATAAATAAAAGTT
*
25480451 T-GAAATAAAATAAAA-TT
1 TAAAAAT-AAATAAAAGTT
* *
25480468 GTAGCAAAATAACA-AAATGTAG
1 -TA--AAAATAA-ATAAAAGT-T
25480490 TAAAAATAAATAAAAGTT
1 TAAAAATAAATAAAAGTT
25480508 T-AAAATAAAATAAAA
1 TAAAAAT-AAATAAAA
25480523 TTGTAGCAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
17 11 0.20
18 20 0.36
19 12 0.21
20 5 0.09
21 8 0.14
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (18 bp):
TAAAAATAAATAAAAGTT
Found at i:25480881 original size:29 final size:29
Alignment explanation
Indices: 25480849--25480963 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 29
25480839 ACAAAAAAAT
*
25480849 AGGGTTAAAATGAAATTTTGAAAAGTTTG
1 AGGGTCAAAATGAAATTTTGAAAAGTTTG
* * * * *
25480878 AGGG-CTAAATTCAAATTTTTAAGAGTTTA
1 AGGGTC-AAAATGAAATTTTGAAAAGTTTG
*
25480907 AGGGTCAAAATGTAAATTTTAAAAAGTTTG
1 AGGGTCAAAATG-AAATTTTGAAAAGTTTG
* * *
25480937 AGGATCAAAATG-TATTTTGGAAAGTTT
1 AGGGTCAAAATGAAATTTTGAAAAGTTT
25480964 AGGAACTACT
Statistics
Matches: 68, Mismatches: 15, Indels: 7
0.76 0.17 0.08
Matches are distributed among these distances:
28 12 0.18
29 30 0.44
30 26 0.38
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (29 bp):
AGGGTCAAAATGAAATTTTGAAAAGTTTG
Found at i:25480926 original size:30 final size:30
Alignment explanation
Indices: 25480849--25480950 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 30
25480839 ACAAAAAAAT
* *
25480849 AGGGTTAAAATG-AAATTTTGAAAAGTTTG
1 AGGGTCAAAATGTAAATTTTAAAAAGTTTG
* * * *
25480878 AGGG-CTAAAT-TCAAATTTTTAAGAGTTTA
1 AGGGTCAAAATGT-AAATTTTAAAAAGTTTG
25480907 AGGGTCAAAATGTAAATTTTAAAAAGTTTG
1 AGGGTCAAAATGTAAATTTTAAAAAGTTTG
*
25480937 AGGATCAAAATGTA
1 AGGGTCAAAATGTA
25480951 TTTTGGAAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
28 4 0.07
29 22 0.37
30 32 0.54
31 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (30 bp):
AGGGTCAAAATGTAAATTTTAAAAAGTTTG
Found at i:25480962 original size:28 final size:28
Alignment explanation
Indices: 25480891--25480967 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 28
25480881 GCTAAATTCA
* * *
25480891 AATTTTTAAGAGTTTAAGGGTCAAAATGT
1 AATTTTAAAAAGTTT-AGGATCAAAATGT
25480920 AAATTTTAAAAAGTTTGAGGATCAAAATGT
1 -AATTTTAAAAAGTTT-AGGATCAAAATGT
**
25480950 -ATTTTGGAAAGTTTAGGA
1 AATTTTAAAAAGTTTAGGA
25480968 ACTACTTGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.10
28 12 0.29
30 25 0.61
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (28 bp):
AATTTTAAAAAGTTTAGGATCAAAATGT
Found at i:25482257 original size:3 final size:3
Alignment explanation
Indices: 25482249--25482286 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
25482239 TGACCAGGCT
* *
25482249 TCA TCA TCA TCA TCT TCA TCA TCA TCT TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
25482287 CACCTTCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:25482269 original size:12 final size:12
Alignment explanation
Indices: 25482252--25482286 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
25482242 CCAGGCTTCA
25482252 TCATCATCATCT
1 TCATCATCATCT
25482264 TCATCATCATCT
1 TCATCATCATCT
25482276 TCATCATCATC
1 TCATCATCATC
25482287 CACCTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:25485406 original size:15 final size:15
Alignment explanation
Indices: 25485386--25485438 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
25485376 ATACTACAAA
25485386 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
25485401 ATATTTATAATTATAATT
1 ATATTTATTA-T-TAA-T
*
25485419 AATATTTATTATTAAA
1 -ATATTTATTATTAAT
25485435 ATAT
1 ATAT
25485439 CAATATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 13 0.42
16 1 0.03
17 6 0.19
18 2 0.06
19 9 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:25485490 original size:13 final size:13
Alignment explanation
Indices: 25485472--25485511 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
25485462 ATGTGAGGAA
25485472 TATTATTTAAAAT
1 TATTATTTAAAAT
25485485 TATTATTTTAAAATT
1 TATTA-TTTAAAA-T
25485500 TATTA-TTAAAAT
1 TATTATTTAAAAT
25485512 AATATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 11 0.44
14 7 0.28
15 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATTTAAAAT
Found at i:25485504 original size:15 final size:14
Alignment explanation
Indices: 25485472--25485506 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
25485462 ATGTGAGGAA
25485472 TATTA-TTTAAAAT
1 TATTATTTTAAAAT
25485485 TATTATTTTAAAATT
1 TATTATTTTAAAA-T
25485500 TATTATT
1 TATTATT
25485507 AAAATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 7 0.35
15 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATTTTAAAAT
Found at i:25485524 original size:7 final size:7
Alignment explanation
Indices: 25485512--25485551 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
25485502 TTATTAAAAT
25485512 AATATTA
1 AATATTA
25485519 AATATTA
1 AATATTA
25485526 AATATTA
1 AATATTA
25485533 AATA-TA
1 AATATTA
25485539 AATAATTA
1 AAT-ATTA
25485547 AATAT
1 AATAT
25485552 GCATGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.16
7 21 0.68
8 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATATTA
Found at i:25485585 original size:52 final size:53
Alignment explanation
Indices: 25485509--25485633 Score: 186
Period size: 52 Copynumber: 2.4 Consensus size: 53
25485499 TTATTATTAA
*
25485509 AATAATATT-AAATATTA-AAT-ATTAAATATAAATAATTAAATATGCATGTTT
1 AATAGTATTGAAA-ATTATAATAATTAAATATAAATAATTAAATATGCATGTTT
*
25485560 AATAGT-TTGAAAATTATAATAATTAAATATAAATAATTAAATATGTATGTTT
1 AATAGTATTGAAAATTATAATAATTAAATATAAATAATTAAATATGCATGTTT
*
25485612 AATAGTATTGAAAAATATAATA
1 AATAGTATTGAAAATTATAATA
25485634 TTTTATATTA
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
50 6 0.09
51 11 0.16
52 36 0.54
53 14 0.21
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (53 bp):
AATAGTATTGAAAATTATAATAATTAAATATAAATAATTAAATATGCATGTTT
Found at i:25485594 original size:14 final size:14
Alignment explanation
Indices: 25485577--25485603 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25485567 TGAAAATTAT
25485577 AATAATTAAATATA
1 AATAATTAAATATA
25485591 AATAATTAAATAT
1 AATAATTAAATAT
25485604 GTATGTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAATTAAATATA
Found at i:25486865 original size:3 final size:3
Alignment explanation
Indices: 25486851--25486890 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
25486841 TCATTAAACC
25486851 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
25486891 TGATAGCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25487943 original size:3 final size:3
Alignment explanation
Indices: 25487935--25487964 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25487925 AATATATCTA
25487935 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25487965 CTGAGAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25489953 original size:18 final size:18
Alignment explanation
Indices: 25489932--25489975 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
25489922 TTTTTAACTA
25489932 ATAATTATAAATTAAAT-T
1 ATAATTAT-AATTAAATGT
**
25489950 ATAATTATTTTTAAATGT
1 ATAATTATAATTAAATGT
25489968 ATAATTAT
1 ATAATTAT
25489976 CACAATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATAATTATAATTAAATGT
Found at i:25491170 original size:67 final size:67
Alignment explanation
Indices: 25491070--25491199 Score: 163
Period size: 67 Copynumber: 1.9 Consensus size: 67
25491060 TTTGTAATTA
* * * *
25491070 TGTGTGTGTCCCTAACTTTGTAACCAAAAACTAAAATTCCTATTGAAAAC-CTAACTTTGTAATT
1 TGTGAGTGTACCTAACTTTGTAACCAAAAACTAAAATTCCTATTAAAAACTC-AACCTTGTAATT
25491134 GCG
65 GCG
*** * *
25491137 TGTGAGTGTACCTAACTTTGTAATTGAATACTAAAATTCTTATTAAAAACTCAACCTTGTAAT
1 TGTGAGTGTACCTAACTTTGTAACCAAAAACTAAAATTCCTATTAAAAACTCAACCTTGTAAT
25491200 CAAATGCTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 52 0.98
68 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (67 bp):
TGTGAGTGTACCTAACTTTGTAACCAAAAACTAAAATTCCTATTAAAAACTCAACCTTGTAATTG
CG
Found at i:25491254 original size:80 final size:80
Alignment explanation
Indices: 25491123--25491348 Score: 188
Period size: 80 Copynumber: 2.8 Consensus size: 80
25491113 TGAAAACCTA
* * ** *
25491123 ACTTTGTAATTGCGTGTGAGTGTACCTAACTTTGTAATTGAATACTAAAA-TTCTTATTAAAAAC
1 ACTTTGTAATT--GTGTGAGTGTACCCAACTTCGTAATCAAAAACTAAAATTTC-TATTAAAAAC
25491187 TCAACCTTGTAATCAAA-T
63 TCAACCTTGTAA-CAAAGT
* * * * ** *
25491205 GCTTTGTAATTGTGTGAGTGTGCCCAACTTCGTAATCAAAAATTCAAATTTCTATTGGAAACTTA
1 ACTTTGTAATTGTGTGAGTGTACCCAACTTCGTAATCAAAAACTAAAATTTCTATTAAAAACTCA
*
25491270 ACTTTGTAACAAAGT
66 ACCTTGTAACAAAGT
* * * * * * *
25491285 ACTTTGTAAATGTGTGTGGGTGTACCCAATTTTC-TAACCGAATACTAACATTTCTATTGAAAAC
1 ACTTTGT-AAT-TGTGTGAGTGTACCCAA-CTTCGTAATCAAAAACTAAAATTTCTATTAAAAAC
25491349 CCAATTTTAT
Statistics
Matches: 115, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
79 4 0.03
80 54 0.47
81 6 0.05
82 48 0.42
83 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (80 bp):
ACTTTGTAATTGTGTGAGTGTACCCAACTTCGTAATCAAAAACTAAAATTTCTATTAAAAACTCA
ACCTTGTAACAAAGT
Found at i:25492202 original size:58 final size:58
Alignment explanation
Indices: 25492114--25492267 Score: 177
Period size: 58 Copynumber: 2.6 Consensus size: 58
25492104 TTTAATAAAA
* ** * *
25492114 ATAGATTTTGATATCCCT-TAAAAGAGTTGTTATATAAATAGATATGTTGATATATATT
1 ATAGATTTTGGTATCAGTATAAAATA-TTGTTATATAAATAGATATGTTGATATACATT
* *
25492172 ATAGATTTTGGTATCAGTATAAAATATTGTTATACAAATAGATATGTTGTTATACATT
1 ATAGATTTTGGTATCAGTATAAAATATTGTTATATAAATAGATATGTTGATATACATT
* *
25492230 ATAAATTTTGGTAGT-TGTCATAAAAATATTGTTATATA
1 ATAGATTTTGGTA-TCAGT-AT-AAAATATTGTTATATA
25492268 TTATATATAT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 58 0.71
59 9 0.11
60 15 0.18
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.44
Consensus pattern (58 bp):
ATAGATTTTGGTATCAGTATAAAATATTGTTATATAAATAGATATGTTGATATACATT
Found at i:25492588 original size:661 final size:661
Alignment explanation
Indices: 25491326--25492647 Score: 2468
Period size: 661 Copynumber: 2.0 Consensus size: 661
25491316 TTCTAACCGA
*
25491326 ATACTAACATTTCTATTGAAAACCCAATTTTATAATTAAATACTATGTAAAAATTCTTAAAAATT
1 ATACTAACATTTCTATTGAAAACCCAATTTTATAATTAAATACTACGTAAAAATTCTTAAAAATT
*
25491391 GTAAAAATTATAATGCCAAAAAATTAATTTTATAATTTTTATGATTTTTATTTTTAATAAAAATA
66 GTAAAAATTATAATGCCAAAAAAATAATTTTATAATTTTTATGATTTTTATTTTTAATAAAAATA
*
25491456 GATTTTGATATCCCTTAAAAGAGTTGTTACATAAATAGGCATGTTGATATATATTATAGATTTTG
131 GATTTTGATATCCCTTAAAAGAGTTGTTACATAAATAGACATGTTGATATATATTATAGATTTTG
*
25491521 GTATCAGTATAAAATATTATTATATAAATAGATATGTTATTATACATTATAAATTTTGGTAGTTG
196 GTATCAGTATAAAATATTATTATACAAATAGATATGTTATTATACATTATAAATTTTGGTAGTTG
25491586 TCATAAAAATATTGTTATATATTATATAAATAAATTTCAGAACTGATGACGTGATATGTTGACCC
261 TCATAAAAATATTGTTATATATTATATAAATAAATTTCAGAACTGATGACGTGATATGTTGACCC
* *
25491651 TAAATGTTAATCGGTGTTGACCAACGTTATCGGCTAATGTCCGAAGTCAACGTGCCACATCGATT
326 TAAATGTTAATCGGTGCTGACCAACGTTAACGGCTAATGTCCGAAGTCAACGTGCCACATCGATT
25491716 TCAAAATCTATTATATAATATATAACAACATATCTATTTATTCAACAATTTTTTTAAGAGATACA
391 TCAAAATCTATTATATAATATATAACAACATATCTATTTATTCAACAATTTTTTTAAGAGATACA
25491781 AGATCTATTTATATAAAAATAAAAAAAGCATAAAAATTATAAAATTATTTTTTGGCATTATAATT
456 AGATCTATTTATATAAAAATAAAAAAAGCATAAAAATTATAAAATTATTTTTTGGCATTATAATT
*
25491846 TTTATAATTTTTAATTAACAATTTTTTAAAGGATTTTAACAAAGTCCTTAATTACAAAGTTGGGT
521 TTTATAATTTTTAATTAACAATTTTTTAAAGGATTTTAACAAAGTCCTTAATTACAAAGTTGGAT
*
25491911 TTTCAATAAGAATTTTAATATTTGGTTACAAAGTCAAGTTTCGAGTAAAAATTTTAGTATTTAGT
586 TTTCAATAAAAATTTTAATATTTGGTTACAAAGTCAAGTTTCGAGTAAAAATTTTAGTATTTAGT
25491976 TACAAAGTTGG
651 TACAAAGTTGG
25491987 ATACTAACATTTCTATTGAAAACCCAATTTTATAATTAAATACTACGTAAAAATTCTTAAAAATT
1 ATACTAACATTTCTATTGAAAACCCAATTTTATAATTAAATACTACGTAAAAATTCTTAAAAATT
25492052 GTAAAAATTATAATGCCAAAAAAATAATTTTATAATTTTTATGATTTTTATTTTTAATAAAAATA
66 GTAAAAATTATAATGCCAAAAAAATAATTTTATAATTTTTATGATTTTTATTTTTAATAAAAATA
* *
25492117 GATTTTGATATCCCTTAAAAGAGTTGTTATATAAATAGATATGTTGATATATATTATAGATTTTG
131 GATTTTGATATCCCTTAAAAGAGTTGTTACATAAATAGACATGTTGATATATATTATAGATTTTG
* *
25492182 GTATCAGTATAAAATATTGTTATACAAATAGATATGTTGTTATACATTATAAATTTTGGTAGTTG
196 GTATCAGTATAAAATATTATTATACAAATAGATATGTTATTATACATTATAAATTTTGGTAGTTG
* * *
25492247 TCATAAAAATATTGTTATATATTATATATATAAATTTCAGAATTGATGACGTGGTATGTTGACCC
261 TCATAAAAATATTGTTATATATTATATAAATAAATTTCAGAACTGATGACGTGATATGTTGACCC
*
25492312 TAAATGTTAATCGGTGCTGACCAATGTTAACGG-TCAATGTCCGAAGTCAACGTGCCACATCGAT
326 TAAATGTTAATCGGTGCTGACCAACGTTAACGGCT-AATGTCCGAAGTCAACGTGCCACATCGAT
25492376 TTCAAAATCTATTATATAATATATAACAACATATCTATTTATTCAACAA-TTTTTTAAGAGATAC
390 TTCAAAATCTATTATATAATATATAACAACATATCTATTTATTCAACAATTTTTTTAAGAGATAC
25492440 AAGATCTATTTATATAAAAATAAAAAAAAGCATAAAAATTATAAAATTATTTTTTGGCATTATAA
455 AAGATCTATTTATATAAAAAT-AAAAAAAGCATAAAAATTATAAAATTATTTTTTGGCATTATAA
25492505 TTTTTATAATTTTTAATTAACAATTTTTTAAAGGATTTTAACAAAGTCCTTAATTACAAAGTTGG
519 TTTTTATAATTTTTAATTAACAATTTTTTAAAGGATTTTAACAAAGTCCTTAATTACAAAGTTGG
25492570 ATTTTCAATAAAAATTTTAATATTTGGTTACAAAGTCAAGTTTCGAGTAAAAATTTTAGTATTTA
584 ATTTTCAATAAAAATTTTAATATTTGGTTACAAAGTCAAGTTTCGAGTAAAAATTTTAGTATTTA
25492635 GTTACAAAGTTGG
649 GTTACAAAGTTGG
25492648 GTACACGCAC
Statistics
Matches: 643, Mismatches: 16, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
660 37 0.06
661 606 0.94
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (661 bp):
ATACTAACATTTCTATTGAAAACCCAATTTTATAATTAAATACTACGTAAAAATTCTTAAAAATT
GTAAAAATTATAATGCCAAAAAAATAATTTTATAATTTTTATGATTTTTATTTTTAATAAAAATA
GATTTTGATATCCCTTAAAAGAGTTGTTACATAAATAGACATGTTGATATATATTATAGATTTTG
GTATCAGTATAAAATATTATTATACAAATAGATATGTTATTATACATTATAAATTTTGGTAGTTG
TCATAAAAATATTGTTATATATTATATAAATAAATTTCAGAACTGATGACGTGATATGTTGACCC
TAAATGTTAATCGGTGCTGACCAACGTTAACGGCTAATGTCCGAAGTCAACGTGCCACATCGATT
TCAAAATCTATTATATAATATATAACAACATATCTATTTATTCAACAATTTTTTTAAGAGATACA
AGATCTATTTATATAAAAATAAAAAAAGCATAAAAATTATAAAATTATTTTTTGGCATTATAATT
TTTATAATTTTTAATTAACAATTTTTTAAAGGATTTTAACAAAGTCCTTAATTACAAAGTTGGAT
TTTCAATAAAAATTTTAATATTTGGTTACAAAGTCAAGTTTCGAGTAAAAATTTTAGTATTTAGT
TACAAAGTTGG
Found at i:25492601 original size:39 final size:40
Alignment explanation
Indices: 25492558--25492647 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 40
25492548 AAGTCCTTAA
* *
25492558 TTACAAAGTTGGATTTTC-AATAAAAATTTTAATATTTGG
1 TTACAAAGTTGGAGTTTCGAATAAAAATTTTAATATTTAG
** * *
25492597 TTACAAAG-TCAAGTTTCGAGTAAAAATTTTAGTATTTAG
1 TTACAAAGTTGGAGTTTCGAATAAAAATTTTAATATTTAG
25492636 TTACAAAGTTGG
1 TTACAAAGTTGG
25492648 GTACACGCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
38 6 0.15
39 34 0.83
40 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (40 bp):
TTACAAAGTTGGAGTTTCGAATAAAAATTTTAATATTTAG
Found at i:25492935 original size:58 final size:58
Alignment explanation
Indices: 25492826--25492937 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
25492816 ATCTACTTAC
* * *
25492826 TTATATGACAACATTTTATACAGATACCAAAATCTATAATATATTCAAACATATCGAT
1 TTATATAACAACATTTTATACAGATAACAAAATCTATAATATATGCAAACATATCGAT
* * * *
25492884 TTATATAATAACATTTTATACGGATAATAAAATTTATAATATATAGC-AACATAT
1 TTATATAACAACATTTTATACAGATAACAAAATCTATAATATAT-GCAAACATAT
25492938 TTAACATCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 45 0.98
59 1 0.02
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (58 bp):
TTATATAACAACATTTTATACAGATAACAAAATCTATAATATATGCAAACATATCGAT
Found at i:25494085 original size:6 final size:5
Alignment explanation
Indices: 25494063--25494175 Score: 68
Period size: 5 Copynumber: 20.6 Consensus size: 5
25494053 ATCCTGGGGC
*
25494063 AAATGA AAATA AAATA AATATA AAATTA AAATTA AAATA ACTTATTA AAATAA
1 AAAT-A AAATA AAATA AA-ATA AAA-TA AAA-TA AAATA A---AATA AAAT-A
* * *
25494116 AAATTA AAATA AAATA AAATG ACATGA AAAT- AAATA AAGATG AAATA
1 AAA-TA AAATA AAATA AAATA AAAT-A AAATA AAATA AA-ATA AAATA
25494163 AGAA-A AAATA AAA
1 A-AATA AAATA AAA
25494176 ATTATACAGG
Statistics
Matches: 87, Mismatches: 8, Indels: 25
0.73 0.07 0.21
Matches are distributed among these distances:
4 6 0.07
5 39 0.45
6 37 0.43
7 1 0.01
8 4 0.05
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:25494147 original size:21 final size:20
Alignment explanation
Indices: 25494063--25494175 Score: 68
Period size: 21 Copynumber: 5.2 Consensus size: 20
25494053 ATCCTGGGGC
25494063 AAATGAAAATAAAATAAATATA
1 AAATG-AAATAAAATAAA-ATA
* *
25494085 AAATTAAAATTAAAATAACTTATTA
1 AAA-TGAAA-TAAAATAA---AATA
*
25494110 AAATAAAAATTAAAATAAAATA
1 AAAT-GAAA-TAAAATAAAATA
*
25494132 AAATGACATGAAAAT-AAATA
1 AAATGAAAT-AAAATAAAATA
25494152 AAGATGAAATAAGAA-AAAATA
1 AA-ATGAAATAA-AATAAAATA
25494173 AAA
1 AAA
25494176 ATTATACAGG
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
20 11 0.15
21 22 0.29
22 13 0.17
23 9 0.12
24 1 0.01
25 18 0.24
26 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (20 bp):
AAATGAAATAAAATAAAATA
Found at i:25498101 original size:21 final size:19
Alignment explanation
Indices: 25498072--25498139 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
25498062 GAACCTCGAA
25498072 GTTTAGGGTTTGAGTTTGAG
1 GTTTAGGGTTTGAGTTT-AG
*
25498092 GTTTAAGGGTTTAGAATTTAG
1 GTTT-AGGGTTT-GAGTTTAG
*
25498113 AGTTTAGAGTTTGAGATTTAAG
1 -GTTTAGGGTTTGAG-TTT-AG
25498135 GTTTA
1 GTTTA
25498140 TGTTTAAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 6 0.15
21 23 0.57
22 11 0.28
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (19 bp):
GTTTAGGGTTTGAGTTTAG
Found at i:25503862 original size:27 final size:27
Alignment explanation
Indices: 25503789--25503863 Score: 100
Period size: 26 Copynumber: 2.7 Consensus size: 27
25503779 CAAATAATTT
25503789 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATT-AAA-TATTTTTTAAAATA
25503818 TAAAATCT-TTAAATATTTTTT-AAATA
1 TAAAAT-TATTAAATATTTTTTAAAATA
*
25503844 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATATTTTT
25503864 AATTTTCAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 1 0.02
26 22 0.51
27 8 0.19
28 3 0.07
29 8 0.19
30 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (27 bp):
TAAAATTATTAAATATTTTTTAAAATA
Found at i:25504755 original size:28 final size:28
Alignment explanation
Indices: 25504724--25504813 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 28
25504714 AATTATTTAA
25504724 TAATTTTATTATTTTAAAAAATTAATTT
1 TAATTTTATTATTTTAAAAAATTAATTT
* * **
25504752 TAATAATTT-TATATTTTTAAAAATAAACTAA
1 TAAT--TTTAT-TATTTTAAAAAATTAA-TTT
* * *
25504783 AAAATTTA-TATTTTAAAAAATTATTTT
1 TAATTTTATTATTTTAAAAAATTAATTT
25504810 TAAT
1 TAAT
25504814 AATTTTAAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 11
0.65 0.19 0.16
Matches are distributed among these distances:
27 3 0.07
28 17 0.39
29 4 0.09
30 17 0.39
31 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
TAATTTTATTATTTTAAAAAATTAATTT
Found at i:25504771 original size:17 final size:17
Alignment explanation
Indices: 25504719--25504771 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
25504709 ATTAAAATTA
25504719 TTTAATAATTTTAT-TAT
1 TTTAATAATTTTATAT-T
**
25504736 TTTAA-AAAATTA-A-T
1 TTTAATAATTTTATATT
25504750 TTTAATAATTTTATATT
1 TTTAATAATTTTATATT
25504767 TTTAA
1 TTTAA
25504772 AAATAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 6 0.21
17 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATAATTTTATATT
Found at i:25507769 original size:26 final size:26
Alignment explanation
Indices: 25507709--25507769 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
25507699 TATGATGATT
*
25507709 ATATAAAAATTTCAATAAATAAAAAA
1 ATATAAAATTTTCAATAAATAAAAAA
*
25507735 ATATAAAATTATTCAAT-ATTAAAATAA
1 ATATAAAATT-TTCAATAAATAAAA-AA
25507762 A-ATAAAAT
1 ATATAAAAT
25507770 AAATATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (26 bp):
ATATAAAATTTTCAATAAATAAAAAA
Found at i:25507785 original size:22 final size:22
Alignment explanation
Indices: 25507753--25507803 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
25507743 TTATTCAATA
* *
25507753 TTAAAATAAAATAAAATAAATATT
1 TTAAAA-AAATTAAAA-AAATAAT
*
25507777 TTAAAAAAATTCAAAAAATAAT
1 TTAAAAAAATTAAAAAAATAAT
25507799 TTAAA
1 TTAAA
25507804 CGAACTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 7 0.29
24 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TTAAAAAAATTAAAAAAATAAT
Found at i:25511672 original size:26 final size:26
Alignment explanation
Indices: 25511632--25511685 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
25511622 TAATTTGAAC
25511632 AATTTCATTCGATTCGACTCGATCCG
1 AATTTCATTCGATTCGACTCGATCCG
*
25511658 AATTTCATTTC-ATTCGACTCGATTCG
1 AATTTCA-TTCGATTCGACTCGATCCG
25511684 AA
1 AA
25511686 AAAGTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (26 bp):
AATTTCATTCGATTCGACTCGATCCG
Found at i:25514317 original size:14 final size:15
Alignment explanation
Indices: 25514298--25514326 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25514288 TTAAATTAAA
25514298 CTCTAATA-TAAATT
1 CTCTAATATTAAATT
25514312 CTCTAATATTAAATT
1 CTCTAATATTAAATT
25514327 AATTTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
CTCTAATATTAAATT
Found at i:25514827 original size:88 final size:89
Alignment explanation
Indices: 25514670--25514925 Score: 304
Period size: 88 Copynumber: 2.8 Consensus size: 89
25514660 TTAAGGGTGT
* * * *
25514670 AAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGTCCTTGCTTTTATTTTACACTCACTTG
1 AAAAAGACCCTCAAACTTTTTC-AAAAAAGCAATTAAGCCCCTGCTTTTAATTTACACTCAATTG
* *
25514734 GATACTTGAACTTTTAAAATGCATC
65 AATACTTGAACTTTCAAAATGCATC
* * *
25514759 AAAAA-ATCCTCAAATTTTTTCAAAAAAGCAATTAAGCCCCTGCTTTTAATTTGCACTCAATTGA
1 AAAAAGACCCTCAAACTTTTTCAAAAAAGCAATTAAGCCCCTGCTTTTAATTTACACTCAATTGA
25514823 ATACTTGAACTTTCAAAATGCATC
66 ATACTTGAACTTTCAAAATGCATC
* * *
25514847 AAAAAGGCCCTCAAACTTTTTCAAAAAAAAAAAACAATTAAGCCCCTGATTGTT--TTTACACTC
1 AAAAAGACCCTCAAACTTTTTC-----AAAAAAGCAATTAAGCCCCTGCTT-TTAATTTACACTC
*
25514910 AATTGAGTACTTGAAC
60 AATTGAATACTTGAAC
25514926 CGTCCCTAAT
Statistics
Matches: 143, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
88 65 0.45
89 31 0.22
93 23 0.16
94 22 0.15
95 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (89 bp):
AAAAAGACCCTCAAACTTTTTCAAAAAAGCAATTAAGCCCCTGCTTTTAATTTACACTCAATTGA
ATACTTGAACTTTCAAAATGCATC
Found at i:25515047 original size:28 final size:28
Alignment explanation
Indices: 25515026--25515080 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
25515016 TTTATAATTT
25515026 TTTTTAAT-TTTAATAAAATTTATTTTA
1 TTTTTAATCTTTAATAAAATTTATTTTA
* *
25515053 TTTTTATTCTTTATTAAAATTTAATTTT
1 TTTTTAATCTTTAATAAAATTT-ATTTT
25515081 TATAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 12 0.50
29 5 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTTAATCTTTAATAAAATTTATTTTA
Found at i:25515106 original size:16 final size:16
Alignment explanation
Indices: 25515072--25515105 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
25515062 TTTATTAAAA
25515072 TTTAATTTTTATAATT
1 TTTAATTTTTATAATT
*
25515088 TTTACTTTTTAT-ATT
1 TTTAATTTTTATAATT
25515103 TTT
1 TTT
25515106 TGCCACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAATTTTTATAATT
Found at i:25515381 original size:93 final size:92
Alignment explanation
Indices: 25515191--25515425 Score: 217
Period size: 92 Copynumber: 2.5 Consensus size: 92
25515181 GTCAAAAGGC
* * ** ***
25515191 TTTTTTGATGTA-TTTGATAGTTCAAGTATCCAATTTAGTGCGAAAAAAATTGGTGGCTTAATTG
1 TTTTTTGATGTATTTTGAAAGTTCAAGTATCCAATTGAGTGAAAAAAAAACAAGTGGCTTAATTG
**** *
25515255 CTTTTTTTTTTTTTTTAAGTTTGAGGGT
66 C-TTTTTTTTTTGAAAAAGTTTGAGGAT
* *
25515283 CTTTTTGATGTATTTTGAAAGTTCAAATATCCAATTGAGTGTAAAATAAAAACAAG-GGCTTAAT
1 TTTTTTGATGTATTTTGAAAGTTCAAGTATCCAATTGAGTG-AAAA-AAAAACAAGTGGCTTAAT
25515347 TG-TTTTTTTTTTGAAAAAGTTTGAGGAT
64 TGCTTTTTTTTTTGAAAAAGTTTGAGGAT
** * * * *
25515375 ATTTTTTG-TACATTTTAAAAATTTAAGTATCCAAATGAGTGCAAAAAAAAA
1 -TTTTTTGATGTATTTTGAAAGTTCAAGTATCCAATTGAGTG-AAAAAAAAA
25515426 AGACTTAATT
Statistics
Matches: 116, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
91 5 0.04
92 62 0.53
93 31 0.27
94 12 0.10
95 6 0.05
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (92 bp):
TTTTTTGATGTATTTTGAAAGTTCAAGTATCCAATTGAGTGAAAAAAAAACAAGTGGCTTAATTG
CTTTTTTTTTTGAAAAAGTTTGAGGAT
Found at i:25515647 original size:2 final size:2
Alignment explanation
Indices: 25515640--25515666 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25515630 TTGTCATTTA
25515640 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
25515667 AGTCAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25517775 original size:4 final size:4
Alignment explanation
Indices: 25517766--25517793 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
25517756 CCATGTTCAA
25517766 CCAG CCAG CCAG CCAG CCAG CCAG CCAG
1 CCAG CCAG CCAG CCAG CCAG CCAG CCAG
25517794 GTAGTGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.50, G:0.25, T:0.00
Consensus pattern (4 bp):
CCAG
Found at i:25525509 original size:21 final size:21
Alignment explanation
Indices: 25525467--25525510 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25525457 TGATTATTAA
**
25525467 TTAATTAGGTGTTTCATGACT
1 TTAATTAGGTGCATCATGACT
25525488 TTAATTAGGTGCAT-ATGAACT
1 TTAATTAGGTGCATCATG-ACT
25525509 TT
1 TT
25525511 CGATGTTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (21 bp):
TTAATTAGGTGCATCATGACT
Found at i:25537850 original size:19 final size:20
Alignment explanation
Indices: 25537826--25537863 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25537816 GACTAAAAAT
*
25537826 GACTAAAT-TAAAATATAAA
1 GACTAAATGCAAAATATAAA
25537845 GACTAAATGCAAAATATAA
1 GACTAAATGCAAAATATAA
25537864 TTATTTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (20 bp):
GACTAAATGCAAAATATAAA
Found at i:25539149 original size:20 final size:20
Alignment explanation
Indices: 25539121--25539177 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
25539111 CCATGTTAGT
*
25539121 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
25539141 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
25539161 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
25539178 TTTTGAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:25539162 original size:29 final size:30
Alignment explanation
Indices: 25539130--25539201 Score: 128
Period size: 29 Copynumber: 2.4 Consensus size: 30
25539120 TAAATGATTT
25539130 TAAAATTATTAAAATTATTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTAAAATAA
*
25539159 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAATAA
25539189 TAAAATTATTAAA
1 TAAAATTATTAAA
25539202 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 27 0.66
30 14 0.34
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAATAA
Found at i:25539721 original size:24 final size:24
Alignment explanation
Indices: 25539694--25539744 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
25539684 AGTTGGACTC
*
25539694 AAACAAATAAAAAGAGTTTAATTG
1 AAACAAATAAAAAGAGTTTAACTG
* *
25539718 AAACAATTAAATAGAGTTTAACTG
1 AAACAAATAAAAAGAGTTTAACTG
25539742 AAA
1 AAA
25539745 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.06, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAAATAAAAAGAGTTTAACTG
Found at i:25540799 original size:21 final size:21
Alignment explanation
Indices: 25540775--25540844 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
25540765 AAAATTATAT
25540775 AATAATTTTATTATTTAAAAA
1 AATAATTTTATTATTTAAAAA
*
25540796 AATAATTTT-TATATTT--TAA
1 AATAATTTTAT-TATTTAAAAA
25540815 AAT-ATTTTA-TATTTAAAAAA
1 AATAATTTTATTATTT-AAAAA
25540835 AATAATTTTA
1 AATAATTTTA
25540845 ATAAGTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 5 0.12
20 6 0.15
21 20 0.49
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATTTTATTATTTAAAAA
Found at i:25540823 original size:39 final size:41
Alignment explanation
Indices: 25540779--25540862 Score: 120
Period size: 39 Copynumber: 2.1 Consensus size: 41
25540769 TTATATAATA
* *
25540779 ATTTTATTATTT-AAAAAAATAATTTTTAT-ATTTTAAAAT-
1 ATTTTA-TATTTAAAAAAAATAATTTTAATAAGTTTAAAATC
25540818 ATTTTATATTTAAAAAAAATAATTTTAATAAGTTTAAAATC
1 ATTTTATATTTAAAAAAAATAATTTTAATAAGTTTAAAATC
25540859 ATTT
1 ATTT
25540863 GCTAACGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
38 5 0.12
39 22 0.55
40 9 0.22
41 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (41 bp):
ATTTTATATTTAAAAAAAATAATTTTAATAAGTTTAAAATC
Found at i:25541288 original size:38 final size:38
Alignment explanation
Indices: 25541244--25541329 Score: 172
Period size: 38 Copynumber: 2.3 Consensus size: 38
25541234 ATCAGAGAAA
25541244 AAAGTTGTTTGAATTTTGATTCAAAAATCCTGACGTCT
1 AAAGTTGTTTGAATTTTGATTCAAAAATCCTGACGTCT
25541282 AAAGTTGTTTGAATTTTGATTCAAAAATCCTGACGTCT
1 AAAGTTGTTTGAATTTTGATTCAAAAATCCTGACGTCT
25541320 AAAGTTGTTT
1 AAAGTTGTTT
25541330 CATAGAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (38 bp):
AAAGTTGTTTGAATTTTGATTCAAAAATCCTGACGTCT
Found at i:25551525 original size:24 final size:24
Alignment explanation
Indices: 25551491--25551540 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
25551481 TGATGTGAAA
25551491 CCAGTACAAAATGAAGATCCAACT
1 CCAGTACAAAATGAAGATCCAACT
*
25551515 CCAGTAGAAAATGAAGATCCAACT
1 CCAGTACAAAATGAAGATCCAACT
25551539 CC
1 CC
25551541 GTGTATGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (24 bp):
CCAGTACAAAATGAAGATCCAACT
Found at i:25556224 original size:12 final size:12
Alignment explanation
Indices: 25556189--25556227 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
25556179 GAACTAGATA
*
25556189 AAAAATTTAAATA
1 AAAAA-TTAAATT
25556202 AAAAATT-AATT
1 AAAAATTAAATT
25556213 AAAAATTAAATT
1 AAAAATTAAATT
25556225 AAA
1 AAA
25556228 CAAAACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 10 0.42
12 9 0.38
13 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:25558303 original size:4 final size:4
Alignment explanation
Indices: 25558280--25558355 Score: 57
Period size: 4 Copynumber: 18.5 Consensus size: 4
25558270 CAAACGGGTG
* * *
25558280 AGAA GAGAA GAGAGA AGAA AGAA AGAA AGAA AGAA AGAA A-TA AGAA TGAG
1 AGAA -AGAA -AGA-A AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
* *
25558330 AGAAA AGAA AG-A AGAA GGAG AGAA AG
1 AG-AA AGAA AGAA AGAA AGAA AGAA AG
25558356 GTTTTTTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
3 5 0.09
4 37 0.65
5 14 0.25
6 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (4 bp):
AGAA
Found at i:25558317 original size:20 final size:19
Alignment explanation
Indices: 25558280--25558355 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 19
25558270 CAAACGGGTG
*
25558280 AGAAGAGAAGAGAG-AAGAA
1 AGAAGA-AAGAAAGAAAGAA
25558299 AGAAAGAAAGAAAGAAAGAA
1 AG-AAGAAAGAAAGAAAGAA
* * *
25558319 ATAAGAATGAGAGAAAAGAA
1 AGAAGAAAGAAAG-AAAGAA
* *
25558339 AGAAGAAGGAGAGAAAG
1 AGAAGAAAGAAAGAAAG
25558356 GTTTTTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 21 0.44
20 27 0.56
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (19 bp):
AGAAGAAAGAAAGAAAGAA
Found at i:25560193 original size:43 final size:44
Alignment explanation
Indices: 25560099--25560195 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 44
25560089 ATGTTATTTA
** * * * * *
25560099 TTGACATGTTAGTAAATTATATTACTTTATTCGTGTTAATTTGG
1 TTGACATGTTACAAAATTATATTACTTGACTCGTATTAATATGC
*
25560143 TTG-CATGTTACAAAATTATATTACTTGACTCTTATTAATAT-C
1 TTGACATGTTACAAAATTATATTACTTGACTCGTATTAATATGC
25560185 TTGACATGTTA
1 TTGACATGTTA
25560196 TTAATTGTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 3 0.07
43 38 0.86
44 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (44 bp):
TTGACATGTTACAAAATTATATTACTTGACTCGTATTAATATGC
Found at i:25565423 original size:28 final size:27
Alignment explanation
Indices: 25565387--25565439 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
25565377 ATTTTAATTG
* *
25565387 ATATGTTTTAAGGTTTTGTTTTTTATGA
1 ATATGTTTTAAGATTTT-TTATTTATGA
*
25565415 ATATTTTTTAAGATTTTTTATTTAT
1 ATATGTTTTAAGATTTTTTATTTAT
25565440 AATGTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (27 bp):
ATATGTTTTAAGATTTTTTATTTATGA
Found at i:25570446 original size:24 final size:23
Alignment explanation
Indices: 25570419--25570463 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
25570409 AAACTAGAAG
*
25570419 AAAATCAAAATATAAAAGAAAAAC
1 AAAAACAAAATATAAAA-AAAAAC
*
25570443 AAAAACTAAATATAAAAAAAA
1 AAAAACAAAATATAAAAAAAA
25570464 TTAAGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (23 bp):
AAAAACAAAATATAAAAAAAAAC
Found at i:25570452 original size:18 final size:18
Alignment explanation
Indices: 25570407--25570452 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
25570397 AAAGGCAGAT
* *
25570407 AAAAACTAGAAGAAAATC
1 AAAAACTAAAAGAAAAAC
25570425 AAAATA-TAAAAGAAAAAC
1 AAAA-ACTAAAAGAAAAAC
25570443 AAAAACTAAA
1 AAAAACTAAA
25570453 TATAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.11
Consensus pattern (18 bp):
AAAAACTAAAAGAAAAAC
Found at i:25578773 original size:26 final size:27
Alignment explanation
Indices: 25578737--25578798 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
25578727 GTATAAATGG
25578737 GTGGTGCCTACCTGACA-GCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
* *
25578763 GTGGCGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
25578790 GTGGTGCCT
1 GTGGTGCCT
25578799 TCTATCAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 15 0.47
27 17 0.53
ACGTcount: A:0.15, C:0.34, G:0.34, T:0.18
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:25579204 original size:27 final size:27
Alignment explanation
Indices: 25579164--25579224 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
25579154 TTTTACAAGA
25579164 GGTGCCTACAAGGTAGGCGGCACTAGT
1 GGTGCCTACAAGGTAGGCGGCACTAGT
*
25579191 GGTGCCTACCAGGTAGGCGGCACTAGT
1 GGTGCCTACAAGGTAGGCGGCACTAGT
25579218 GGTGCCT
1 GGTGCCT
25579225 TTGTCAATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.38, T:0.20
Consensus pattern (27 bp):
GGTGCCTACAAGGTAGGCGGCACTAGT
Found at i:25579293 original size:25 final size:25
Alignment explanation
Indices: 25579258--25579307 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
25579248 CAGATCTGTT
25579258 TAACAGCAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
*
25579283 TAACAGTAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
25579308 AGGAAACAAA
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:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (25 bp):
TAACAGCAAATTTTTGAAGAAGGAA
Found at i:25582070 original size:28 final size:28
Alignment explanation
Indices: 25582017--25582074 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
25582007 CATTTTTCTG
*
25582017 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
25582045 TTGGAATTAATTCTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
25582073 TT
1 TT
25582075 ATTTAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:25582115 original size:26 final size:26
Alignment explanation
Indices: 25582066--25582115 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
25582056 TCTATTTAAA
* *
25582066 TTTGAATTTATTTAATAGTTTTTATG
1 TTTGAATTAATTTAATAGTGTTTATG
25582092 TTTGAATTAATTTAATTAG-GTTTA
1 TTTGAATTAATTTAA-TAGTGTTTA
25582116 GCAAATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTAATTTAATAGTGTTTATG
Found at i:25582192 original size:6 final size:6
Alignment explanation
Indices: 25582181--25582239 Score: 93
Period size: 6 Copynumber: 9.8 Consensus size: 6
25582171 ATATTTGCAT
*
25582181 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATAA ACATAA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATAA
25582229 ACATAA ACATA
1 ACATAA ACATA
25582240 TTTAATGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
5 1 0.02
6 47 0.96
7 1 0.02
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:25582684 original size:6 final size:6
Alignment explanation
Indices: 25582675--25582716 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
25582665 CTGCGACTGC
25582675 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA -GCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
25582717 CCGGCTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
GGCTCA
Found at i:25584630 original size:13 final size:12
Alignment explanation
Indices: 25584606--25584647 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
25584596 ATTACTAATG
25584606 TTTTTT-ATTTT
1 TTTTTTAATTTT
25584617 TTTCTTTAATTTT
1 TTT-TTTAATTTT
*
25584630 TCGTTTTAATTTT
1 T-TTTTTAATTTT
25584643 TTTTT
1 TTTTT
25584648 AAAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.12
12 6 0.23
13 16 0.62
14 1 0.04
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTAATTTT
Found at i:25584682 original size:17 final size:16
Alignment explanation
Indices: 25584650--25584681 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25584640 TTTTTTTTAA
25584650 AAAATATTTAATATAT
1 AAAATATTTAATATAT
25584666 AAAATATTTAA-ATAT
1 AAAATATTTAATATAT
25584681 A
1 A
25584682 TCAATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:25585680 original size:27 final size:27
Alignment explanation
Indices: 25585650--25585711 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
25585640 CTGGTAGGTT
25585650 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
*
25585677 GGCACCACTGGTGCCGCCTATCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
25585704 GGCACCAC
1 GGCACCAC
25585712 CCAAAAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.23, C:0.40, G:0.26, T:0.11
Consensus pattern (27 bp):
GGCACCACTGGTGCCGCCTACCAGACA
Found at i:25590634 original size:17 final size:18
Alignment explanation
Indices: 25590577--25590634 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 18
25590567 ATCTTCTTTC
* *
25590577 CCATTTTTCCATTTAACA
1 CCATTTTTCTATCTAACA
25590595 CCACTTTTTCT-TCT--CA
1 CCA-TTTTTCTATCTAACA
*
25590611 TCATTTTTCTATCTAACA
1 CCATTTTTCTATCTAACA
25590629 -CATTTT
1 CCATTTT
25590635 AAGTTCCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
15 7 0.21
16 7 0.21
17 6 0.18
18 7 0.21
19 6 0.18
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (18 bp):
CCATTTTTCTATCTAACA
Found at i:25590965 original size:15 final size:17
Alignment explanation
Indices: 25590944--25590984 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
25590934 TAACCCTTTA
25590944 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
25590960 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
25590976 AAAATTATA
1 AAAATTATA
25590985 TTTTTACTAT
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:25596393 original size:59 final size:58
Alignment explanation
Indices: 25596318--25596492 Score: 165
Period size: 59 Copynumber: 3.0 Consensus size: 58
25596308 AGGTTCGAGG
* * *
25596318 TCAAAAATGGAATTTTTGGACA-TCTGGGGATAAAATGGTCATTTTTGGAAAGTTTAAGA
1 TCAAAAATGAAATTTTT-GAAAGTCTGGGG-TAAAATGGTAATTTTTGGAAAGTTTAAGA
* * * * * * *
25596377 TCAAAAATGAAATTTTTAGATATTCAGGGGTAAAATGGTAATTTTTGAAAATTTTAGGG
1 TCAAAAATGAAATTTTT-GAAAGTCTGGGGTAAAATGGTAATTTTTGGAAAGTTTAAGA
* * * * *
25596436 TTAAAAATGTAATTTTTGAAAGTTTAGGGGTAAAAT-GTGATTTTTGGAAAGATTAAG
1 TCAAAAATGAAATTTTTGAAAGTCT-GGGGTAAAATGGTAATTTTTGGAAAGTTTAAG
25596493 GGTTAAAATG
Statistics
Matches: 94, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
58 20 0.21
59 68 0.72
60 6 0.06
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (58 bp):
TCAAAAATGAAATTTTTGAAAGTCTGGGGTAAAATGGTAATTTTTGGAAAGTTTAAGA
Found at i:25596495 original size:59 final size:60
Alignment explanation
Indices: 25596343--25596525 Score: 198
Period size: 59 Copynumber: 3.1 Consensus size: 60
25596333 TTGGACATCT
* * * * * * *
25596343 GGGGATAAAATGGTCATTTTTGGAAAGTTTAA-GATCAAAAATGAAATTTTTAGATA-TTCA
1 GGGG-TAAAATGGTAATTTTTGGAAAGATTAAGGGTTAAAAATGTAATTTTT-GAAAGTTTA
*
25596403 GGGGTAAAATGGTAATTTTT-GAAA-ATTTTAGGGTTAAAAATGTAATTTTTGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAGA-TTAAGGGTTAAAAATGTAATTTTTGAAAGTTTA
* *
25596462 GGGGTAAAAT-GTGATTTTTGGAAAGATTAAGGGTT-AAAATGTAATTTTTGTGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAGATTAAGGGTTAAAAATGTAATTTTTG-AAAGTTTA
25596521 GGGGT
1 GGGGT
25596526 CAATATATAA
Statistics
Matches: 106, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
58 33 0.31
59 68 0.64
60 5 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.38
Consensus pattern (60 bp):
GGGGTAAAATGGTAATTTTTGGAAAGATTAAGGGTTAAAAATGTAATTTTTGAAAGTTTA
Found at i:25596561 original size:60 final size:58
Alignment explanation
Indices: 25596358--25596578 Score: 175
Period size: 59 Copynumber: 3.7 Consensus size: 58
25596348 TAAAATGGTC
* * * * * *
25596358 ATTTTTGGAAAGTTTAA-GATCAAAAATGAAATTTTTAGATA-TTCAGGGGTAAAATGGTA
1 ATTTTTGGAAAGATTAAGGGTC-AAAATGTAATTTTT-GAAAGTTTAGGGGTAAAAT-ATA
* * * *
25596417 ATTTTT-GAAA-ATTTTAGGGTTAAAAATGTAATTTTTGAAAGTTTAGGGGTAAAATGTG
1 ATTTTTGGAAAGA-TTAAGGG-TCAAAATGTAATTTTTGAAAGTTTAGGGGTAAAATATA
* * *
25596475 ATTTTTGGAAAGATTAAGGGTTAAAATGTAATTTTTGTGAAGTTTAGGGGTCAATATATA
1 ATTTTTGGAAAGATTAAGGGTCAAAATGTAATTTTTG-AAAGTTTAGGGGT-AAAATATA
* *
25596535 ATTTTTAGG-AAG-TTCGAGGGTCAAAATGTGATTTTTGAATAGTT
1 ATTTTT-GGAAAGATT-AAGGGTCAAAATGTAATTTTTGAA-AGTT
25596579 CATGGATCTT
Statistics
Matches: 133, Mismatches: 18, Indels: 21
0.77 0.10 0.12
Matches are distributed among these distances:
58 34 0.26
59 58 0.44
60 39 0.29
61 2 0.02
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (58 bp):
ATTTTTGGAAAGATTAAGGGTCAAAATGTAATTTTTGAAAGTTTAGGGGTAAAATATA
Found at i:25596579 original size:30 final size:29
Alignment explanation
Indices: 25596254--25596578 Score: 168
Period size: 30 Copynumber: 11.0 Consensus size: 29
25596244 TTTTGGATAC
* * *
25596254 TTAGGGGT-AAAACGATAATTTTTGATACT
1 TTAGGGGTCAAAATG-TAATTTTTGAAAGT
* *
25596283 TT-GGGGGCAAAATAGTAATTTTT-AAAGG
1 TTAGGGGTCAAAAT-GTAATTTTTGAAAGT
* * * *
25596311 TTCGAGGTCAAAAATGGAATTTTTGGACA-T
1 TTAGGGGTC-AAAATGTAATTTTT-GAAAGT
* *
25596341 CT-GGGGAT-AAAATGGTCATTTTTGGAAAGT
1 TTAGGGG-TCAAAAT-GTAATTTTT-GAAAGT
* * * *
25596371 TTA-AGATCAAAAATGAAATTTTTAGATA-T
1 TTAGGGGTC-AAAATGTAATTTTT-GAAAGT
* *
25596400 TCAGGGGT-AAAATGGTAATTTTTGAAAATT
1 TTAGGGGTCAAAAT-GTAATTTTTG-AAAGT
* *
25596430 TTAGGGTTAAAAATGTAATTTTTGAAAGT
1 TTAGGGGTCAAAATGTAATTTTTGAAAGT
* *
25596459 TTAGGGGT-AAAATGTGATTTTTGGAAAGA
1 TTAGGGGTCAAAATGTAATTTTT-GAAAGT
* * *
25596488 TTAAGGGTTAAAATGTAATTTTTGTGAAGT
1 TTAGGGGTCAAAATGTAATTTTTG-AAAGT
* * *
25596518 TTAGGGGTCAATATATAATTTTTAGGAAG-
1 TTAGGGGTCAAAATGTAATTTTT-GAAAGT
* *
25596547 TTCGAGGGTCAAAATGTGATTTTTGAATAGT
1 TTAG-GGGTCAAAATGTAATTTTTGAA-AGT
25596578 T
1 T
25596579 CATGGATCTT
Statistics
Matches: 226, Mismatches: 46, Indels: 46
0.71 0.14 0.14
Matches are distributed among these distances:
28 32 0.14
29 83 0.37
30 97 0.43
31 14 0.06
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (29 bp):
TTAGGGGTCAAAATGTAATTTTTGAAAGT
Found at i:25597634 original size:3 final size:3
Alignment explanation
Indices: 25597626--25597665 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
25597616 TTTCGCTTTC
25597626 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25597666 ATTTATGACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:25600798 original size:6 final size:6
Alignment explanation
Indices: 25600787--25600877 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
25600777 AATGGGACTT
* * * ** *
25600787 TTTAAA TTTAAA -ATAAT TTTAAT TTTAAA AGTAAA TTTAAA CTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
25600833 TTTAAA TTTAAA TTTAAA -ACAAA TTTAAA TTTATAA --TAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAA
25600878 TCTTATAATA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
4 2 0.03
5 12 0.18
6 49 0.75
7 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:25600808 original size:17 final size:17
Alignment explanation
Indices: 25600787--25600895 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
25600777 AATGGGACTT
*
25600787 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
25600804 TTTAATTTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
* **
25600822 TTTAAACTTAATTTAAA
1 TTTAAATTTAAAATAAA
*
25600839 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
*
25600856 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
*
25600873 TTT-AATCTTATAATAAA
1 TTTAAAT-TTAAAATAAA
25600890 TTTAAA
1 TTTAAA
25600896 AAAGGGTTCA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
16 3 0.04
17 60 0.78
18 14 0.18
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:25600836 original size:11 final size:12
Alignment explanation
Indices: 25600818--25600850 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
25600808 ATTTTAAAAG
25600818 TAAATTTAAACT
1 TAAATTTAAACT
*
25600830 T-AATTTAAATT
1 TAAATTTAAACT
25600841 TAAATTTAAA
1 TAAATTTAAA
25600851 ACAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATTTAAACT
Found at i:25600836 original size:23 final size:24
Alignment explanation
Indices: 25600805--25600850 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
25600795 TAAAATAATT
25600805 TTAATTTTAAAAGTAAATTTAAAC
1 TTAATTTTAAAAGTAAATTTAAAC
**
25600829 TTAA-TTTAAATTTAAATTTAAA
1 TTAATTTTAAAAGTAAATTTAAA
25600851 ACAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTAATTTTAAAAGTAAATTTAAAC
Found at i:25600836 original size:29 final size:29
Alignment explanation
Indices: 25600789--25600844 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
25600779 TGGGACTTTT
*
25600789 TAAATTTAAAATAATTTTAATTTTAAAAG
1 TAAATTTAAAATAATTTTAAATTTAAAAG
*
25600818 TAAATTTAAACTTAA-TTTAAATTTAAA
1 TAAATTTAAA-ATAATTTTAAATTTAAA
25600845 TTTAAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATTTAAAATAATTTTAAATTTAAAAG
Found at i:25600850 original size:29 final size:29
Alignment explanation
Indices: 25600787--25600850 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
25600777 AATGGGACTT
*
25600787 TTTAAATTTAAAATAATTTTAATTTTAAA
1 TTTAAATTTAAAATAATTTTAAATTTAAA
** *
25600816 AGTAAATTTAAACTTAA-TTTAAATTTAAA
1 TTTAAATTTAAA-ATAATTTTAAATTTAAA
25600845 TTTAAA
1 TTTAAA
25600851 ACAAATTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTAAATTTAAAATAATTTTAAATTTAAA
Found at i:25600857 original size:23 final size:23
Alignment explanation
Indices: 25600818--25600865 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25600808 ATTTTAAAAG
*
25600818 TAAATTTAAACTTAATTTAAATT
1 TAAATTTAAACTAAATTTAAATT
25600841 TAAATTTAAAAC-AAATTTAAATT
1 TAAATTT-AAACTAAATTTAAATT
25600864 TA
1 TA
25600866 TAATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATTTAAACTAAATTTAAATT
Found at i:25601925 original size:206 final size:206
Alignment explanation
Indices: 25601199--25602065 Score: 1111
Period size: 206 Copynumber: 4.2 Consensus size: 206
25601189 GGTGTCATTA
* * * **
25601199 ATTTGGTCTACTTCTCAGTATCTCATTAGGAAAATGACCACATCACTTATTTTGATCCACTTCTC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTC
* * * * * * *
25601264 TGTGTCTTATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCACTTT
66 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTT
* * *
25601329 ATTTCTTCGAC-TGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTT-GCTCAC-TTG
131 ATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAG-TTTCGCTCACATTG
**
25601391 -GTTTCA---TTG
195 AGCCT-AGGTTTG
* *
25601400 ATTTGGTCCT-CTTCTCAGTATCTCATTAGGAAGATGACCACATCACTTGTTTCAATCCGCTTCT
1 ATTTGGT-CTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCT
* * *
25601464 CTGTATCTCATTAGGAAGACGAATTTGGTCCACTTTTCAATATCTCATGACTCATGAGGAAGCTA
65 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTC---A-TC---AGGAAGCTA
* *
25601529 ACCACTTTATTGCTTCGACTTGCTTCTCAGTATCTCATTAGGAAGCTGGAGTTTGAAGTTTCGCT
123 ACCACTTTATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGTTTCGCT
* * *
25601594 CACATTGAGCTTTGTTTTATTG
188 CACATTGAGCCTAG--GT-TTG
* * * ** * *
25601616 ATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGTTGACCGTATCAGTTGTTTCAATCCGCTTCTC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTC
25601681 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTT
66 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTT
25601746 ATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGTTTCGCTCACATTGA
131 ATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGTTTCGCTCACATTGA
25601811 GCCTAGGTTTG
196 GCCTAGGTTTG
*
25601822 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTC
* * * *
25601887 TGTATCTCATCAGGAAAACAAATTTGGTCCACTTCTCAGTATCTCATCGGGAAGCTAACCATTTT
66 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTT
* * * * *
25601952 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTCGCTCACTTTGA
131 ATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGTTTCGCTCACATTGA
* *
25602017 GACTGGGTTTG
196 GCCTAGGTTTG
* * *
25602028 ATTTGGTCTACTTCTCTGTTATTTAATCAGGAAGATGA
1 ATTTGGTCTACTTCTCAG-TATCTCATCAGGAAGATGA
25602066 TTGCTTCATT
Statistics
Matches: 590, Mismatches: 56, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
201 93 0.16
202 2 0.00
204 1 0.00
205 2 0.00
206 209 0.35
207 18 0.03
208 29 0.05
209 124 0.21
210 3 0.01
211 3 0.01
212 2 0.00
213 1 0.00
215 2 0.00
216 101 0.17
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (206 bp):
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTC
TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTT
ATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGTTTCGCTCACATTGA
GCCTAGGTTTG
Found at i:25605041 original size:30 final size:30
Alignment explanation
Indices: 25605007--25605382 Score: 603
Period size: 30 Copynumber: 12.5 Consensus size: 30
25604997 TTCGGGGAGT
*
25605007 AAAATGGTAATTTTTG-AAAGTTTTGGGGTC
1 AAAAT-GTAATTTTGGAAAAGTTTTGGGGTC
25605037 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
25605067 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
25605097 AAAATATAATTTTGGAAAAGTTTCGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
25605127 AAAATGTAATTTTGGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
25605157 AAAATATAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
25605187 AAAACGTAATTTTGGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
25605217 AAAACGTAATTTTGGAAGAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
25605247 AAAACGTAATTTTGG-AAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
25605276 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
25605306 AAAATATAATTTTGGAAAAGTTTTGAGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
25605336 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
25605366 AAAATGTAATTTCTGGA
1 AAAATGTAATTT-TGGA
25605383 TAATTTAGGG
Statistics
Matches: 322, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
29 35 0.11
30 283 0.88
31 4 0.01
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTC
Found at i:25605051 original size:19 final size:19
Alignment explanation
Indices: 25605027--25605081 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
25605017 TTTTTGAAAG
25605027 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
25605046 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
25605057 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
25605076 TTTTGG
1 TTTTGG
25605082 AAAAGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:25607247 original size:6 final size:6
Alignment explanation
Indices: 25607204--25607323 Score: 79
Period size: 6 Copynumber: 20.2 Consensus size: 6
25607194 CTTTGGACTC
* * ** * *
25607204 TTAAATT TTTAAT TTAATAT TTTAAT TTTTAT TAAAAT TTAAAT TCAAA-
1 TTAAA-T TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
25607253 TTAAAT TTAAATAT TTAAAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA-
1 TTAAAT TT-AA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
25607301 -TAAAT TTAAA- ATCAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT T
25607324 CAAAAGTCCA
Statistics
Matches: 88, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
4 4 0.05
5 11 0.12
6 56 0.64
7 13 0.15
8 4 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:25607258 original size:17 final size:17
Alignment explanation
Indices: 25607238--25607323 Score: 81
Period size: 17 Copynumber: 5.3 Consensus size: 17
25607228 ATTTTTATTA
25607238 AAATTTAAATTCAAATT
1 AAATTTAAATTCAAATT
*
25607255 AAATTTAAA-T--ATTT
1 AAATTTAAATTCAAATT
* *
25607269 AAATTTAAATTTAAAAT
1 AAATTTAAATTCAAATT
* *
25607286 AAATCTAAATTTAAA-T
1 AAATTTAAATTCAAATT
* *
25607302 AAATTTAAAATCAATTT
1 AAATTTAAATTCAAATT
25607319 AAATT
1 AAATT
25607324 CAAAAGTCCA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.21
15 1 0.02
16 13 0.23
17 31 0.54
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTAAATTCAAATT
Found at i:25607735 original size:68 final size:68
Alignment explanation
Indices: 25607585--25608237 Score: 1080
Period size: 68 Copynumber: 9.5 Consensus size: 68
25607575 GCTCTTCAGG
* * *
25607585 GAGATAAAGACTTTGCTATCCAACTCTACTT-ATATTTC-AGGAGGATGTCGTTGCTTCTTACTT
1 GAGATAAAGAC-ATGTTATCC-ACTCTACTTCA-ATTTCAAGG-GGATGACGTTGC-TCTTACTT
25607648 CAATTTCA
61 CAATTTCA
*
25607656 GAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
25607721 TCA
66 TCA
25607724 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
25607789 TCA
66 TCA
* *
25607792 GAGATGAAGACATGTTATCCACTCTACTTCAATCTCAAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
25607857 TCA
66 TCA
* * *
25607860 GAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGACGACGTTGCTTTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
25607925 TCA
66 TCA
* *
25607928 GAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGACGACGTTTTGCTCTTACTTCAA
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACG--TTGCTCTTACTTCAA
25607993 TTTCA
64 TTTCA
25607998 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
25608063 TCA
66 TCA
* * *
25608066 GAGATGAAGACATGTTATCCACTCTACTTCAATTTCGAGGGGACGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
25608131 TCA
66 TCA
25608134 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
25608199 TCA
66 TCA
25608202 GAGATGAAA-ACATGTTATCCACTCTACTTC-ATTTCA
1 GAGAT-AAAGACATGTTATCCACTCTACTTCAATTTCA
25608238 TCAAGGGACG
Statistics
Matches: 558, Mismatches: 19, Indels: 14
0.94 0.03 0.02
Matches are distributed among these distances:
67 6 0.01
68 438 0.78
69 28 0.05
70 76 0.14
71 10 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (68 bp):
GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
TCA
Found at i:25608129 original size:274 final size:274
Alignment explanation
Indices: 25607585--25608252 Score: 1130
Period size: 274 Copynumber: 2.4 Consensus size: 274
25607575 GCTCTTCAGG
* * *
25607585 GAGATAAAGACTTTGCTATCCAACTCTACTT-ATATTTC-AGGAGGATGTCGTTGCTTCTTACTT
1 GAGATAAAGAC-ATGTTATCC-ACTCTACTTCA-ATTTCAAGG-GGATGACGTTGCTT-TTACTT
*
25607648 CAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACG--TTGCTCT
61 CAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGACGACGTTTTGCTCT
25607711 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGC
126 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGC
*
25607776 TCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATCTCAAGGGGATGACGT
191 TCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATCTCAAGGGGACGACGT
25607841 TGCTCTTACTTCAATTTCA
256 TGCTCTTACTTCAATTTCA
* *
25607860 GAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGACGACGTTGCTTTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTTTTACTTCAATT
25607925 TCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGACGACGTTTTGCTCTTACTT
66 TCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGACGACGTTTTGCTCTTACTT
25607990 CAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
131 CAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
* *
25608055 CTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCGAGGGGACGACGTTGCTC
196 CTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATCTCAAGGGGACGACGTTGCTC
25608120 TTACTTCAATTTCA
261 TTACTTCAATTTCA
*
25608134 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTTTTACTTCAATT
* *
25608199 TCAGAGATGAAAACATGTTATCCACTCTACTTC-ATTTCATCAAGGGACGACGTT
66 TCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCA--AGGGGACGACGTT
25608253 GAGATCTGCA
Statistics
Matches: 373, Mismatches: 14, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
272 61 0.16
273 32 0.09
274 258 0.69
275 22 0.06
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (274 bp):
GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTTTTACTTCAATT
TCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGACGACGTTTTGCTCTTACTT
CAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
CTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATCTCAAGGGGACGACGTTGCTC
TTACTTCAATTTCA
Found at i:25608937 original size:1 final size:1
Alignment explanation
Indices: 25608931--25608981 Score: 84
Period size: 1 Copynumber: 51.0 Consensus size: 1
25608921 GACCTCTCCG
* *
25608931 TTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25608982 AGTGTAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (1 bp):
T
Found at i:25608960 original size:27 final size:27
Alignment explanation
Indices: 25608930--25608981 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
25608920 TGACCTCTCC
*
25608930 GTTTTTTTTTTTTTTTTTTTTTTTTTT
1 GTTTTTTTTTTTTGTTTTTTTTTTTTT
25608957 GTTTTTTTTTTTTGTTTTTTTTTTT
1 GTTTTTTTTTTTTGTTTTTTTTTTT
25608982 AGTGTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (27 bp):
GTTTTTTTTTTTTGTTTTTTTTTTTTT
Found at i:25620334 original size:30 final size:30
Alignment explanation
Indices: 25620300--25620672 Score: 604
Period size: 30 Copynumber: 12.4 Consensus size: 30
25620290 TTCGGGGAGT
*
25620300 AAAATGGTAATTTTTG-AAAGTTTTGGGGTC
1 AAAAT-GTAATTTTGGAAAAGTTTTGGGGTC
25620330 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
25620360 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* ***
25620390 AAAATATAATTTTGGAAAAGTTTCAAGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
25620420 AAAATGTAATTTTGGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
25620450 AAAATATAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
** *
25620480 AAAACATAATTTTGGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
25620510 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
25620540 AAAACGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
25620570 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
25620600 AAAATATAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
25620630 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
25620660 AAAATGTAATTTT
1 AAAATGTAATTTT
25620673 TGGATAATTT
Statistics
Matches: 321, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
29 9 0.03
30 312 0.97
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTC
Found at i:25620344 original size:19 final size:19
Alignment explanation
Indices: 25620320--25620374 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
25620310 TTTTTGAAAG
25620320 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
25620339 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
25620350 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
25620369 TTTTGG
1 TTTTGG
25620375 AAAAGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:25622561 original size:17 final size:17
Alignment explanation
Indices: 25622539--25622630 Score: 59
Period size: 17 Copynumber: 5.6 Consensus size: 17
25622529 TAATTTTTAT
25622539 TTAAATTCAAATTCAAA
1 TTAAATTCAAATTCAAA
* *
25622556 TTAAATTTAAA-T--AT
1 TTAAATTCAAATTCAAA
* *
25622570 TTAAATTTAAATTTAAA
1 TTAAATTCAAATTCAAA
* *
25622587 ATAAA-TCTAAATTTAAA
1 TTAAATTC-AAATTCAAA
* * *
25622604 -TAAATTTAAAATCAAT
1 TTAAATTCAAATTCAAA
25622620 TTAAATTCAAA
1 TTAAATTCAAA
25622631 AGTCCAAGCC
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
14 12 0.20
15 1 0.02
16 12 0.20
17 34 0.58
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATTCAAATTCAAA
Found at i:25622573 original size:31 final size:31
Alignment explanation
Indices: 25622536--25622598 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
25622526 TTTTAATTTT
* *
25622536 TATTTAAATTCAAATTCAAATTAAATTTAAA
1 TATTTAAATTCAAATTCAAAATAAATCTAAA
* *
25622567 TATTTAAATTTAAATTTAAAATAAATCTAAA
1 TATTTAAATTCAAATTCAAAATAAATCTAAA
25622598 T
1 T
25622599 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (31 bp):
TATTTAAATTCAAATTCAAAATAAATCTAAA
Found at i:25622577 original size:6 final size:6
Alignment explanation
Indices: 25622507--25622626 Score: 79
Period size: 6 Copynumber: 20.2 Consensus size: 6
25622497 CTTTGGACTC
* * ** * *
25622507 TTAAATT TTTAAT TTAATAT TTTAAT TTTTAT TTAAAT TCAAAT TCAAA-
1 TTAAA-T TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
25622556 TTAAAT TTAAATAT TTAAAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA-
1 TTAAAT TT-AA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
25622604 -TAAAT TTAAA- ATCAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT T
25622627 CAAAAGTCCA
Statistics
Matches: 90, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
4 4 0.04
5 11 0.12
6 58 0.64
7 13 0.14
8 4 0.04
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:25622606 original size:16 final size:17
Alignment explanation
Indices: 25622537--25622613 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
25622527 TTTAATTTTT
* *
25622537 ATTTAAATTCAAATTCAA
1 ATTTAAATTTAAAAT-AA
25622555 A-TTAAATTTAAATATTTAA
1 ATTTAAATTTAAA-A--TAA
25622574 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
25622591 ATCTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
25622607 ATTTAAA
1 ATTTAAA
25622614 ATCAATTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
16 12 0.24
17 22 0.43
18 1 0.02
19 4 0.08
20 12 0.24
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:25628897 original size:23 final size:24
Alignment explanation
Indices: 25628852--25628897 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
25628842 CTTTATCGAC
* *
25628852 CATGCAATGCGAATAAAATGCATG
1 CATGCAATGCGAAGAAAAGGCATG
*
25628876 CATGTAATGC-AAGAAAAGGCAT
1 CATGCAATGCGAAGAAAAGGCAT
25628898 TGATTTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (24 bp):
CATGCAATGCGAAGAAAAGGCATG
Found at i:25632955 original size:59 final size:59
Alignment explanation
Indices: 25632881--25633020 Score: 158
Period size: 60 Copynumber: 2.4 Consensus size: 59
25632871 AAGGTTCAAG
* **
25632881 GTCAAAAATGGAATTTTTGGACATCCCA-GGGTAAAATGGTCATTTTTGGAAAGTTCGG-
1 GTCAAAAATGGAATTTTTGGACAT-CCAGGGGTAAAATGGTAATTTTTAAAAAGTTCGGT
* ** * * *
25632939 GATCAAAAATGAAATTTTTTATACATCTAGGGGTAAAATGGTAATTTTTAAAAATTTTGGT
1 G-TCAAAAATGGAA-TTTTTGGACATCCAGGGGTAAAATGGTAATTTTTAAAAAGTTCGGT
25633000 GTCAAAAATGGAATTTTTGGA
1 GTCAAAAATGGAATTTTTGGA
25633021 AGTTTAGGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
58 1 0.02
59 19 0.29
60 45 0.68
61 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (59 bp):
GTCAAAAATGGAATTTTTGGACATCCAGGGGTAAAATGGTAATTTTTAAAAAGTTCGGT
Found at i:25633036 original size:29 final size:29
Alignment explanation
Indices: 25632966--25633195 Score: 170
Period size: 30 Copynumber: 7.8 Consensus size: 29
25632956 TTTATACATC
** *
25632966 TAGGGGT-AAAATGGTAATTTTTAAAAATT
1 TAGGGGTAAAAATGG-AATTTTTGGAAGTT
* *
25632995 TTGGTGTCAAAAATGGAATTTTTGGAAGTT
1 TAGGGGT-AAAAATGGAATTTTTGGAAGTT
* *
25633025 TAGGTGTAAAAATATG-ATTTTTGGAAAGTT
1 TAGGGGTAAAAAT-GGAATTTTTGG-AAGTT
*
25633055 TA-GGGTCAAAAATGTAATTTTTGTGAAGTT
1 TAGGGGT-AAAAATGGAATTTTTG-GAAGTT
* **
25633085 T-GAGGGTAAAAAT-GATTTTTTTTAAAGTT
1 TAG-GGGTAAAAATGGA-ATTTTTGGAAGTT
**
25633114 TAGGGGTAAAAATATAATTTTTGTGAAGTT
1 TAGGGGTAAAAATGGAATTTTTG-GAAGTT
25633144 TAGGGGTTAAAAAT--AATTTTTGGAAAGTT
1 TAGGGG-TAAAAATGGAATTTTTGG-AAGTT
*
25633173 TAGGGGTCAAAATGTG-ATTTTTG
1 TAGGGGTAAAAATG-GAATTTTTG
25633196 AATAGTTCAG
Statistics
Matches: 164, Mismatches: 19, Indels: 35
0.75 0.09 0.16
Matches are distributed among these distances:
28 7 0.04
29 63 0.38
30 75 0.46
31 19 0.12
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.40
Consensus pattern (29 bp):
TAGGGGTAAAAATGGAATTTTTGGAAGTT
Found at i:25633059 original size:89 final size:88
Alignment explanation
Indices: 25632966--25633207 Score: 210
Period size: 89 Copynumber: 2.7 Consensus size: 88
25632956 TTTATACATC
* * *
25632966 TAGGGGTAAAATGGTAATTTTTAAAAATTTTG-GTGTCAAAAATGGA-ATTTTTGGAAGTTTAGG
1 TAGGGGTAAAAT-GTAATTTTTAAAAAGTTTGAGGGT-AAAAAT-GATATTTTTGAAAGTTTAGG
* *
25633029 TGTAAAAATATGATTTTTG-GAAAGTT
63 GGTAAAAATATAATTTTTGTG-AAGTT
*** * *
25633055 TA-GGGTCAAAAATGTAATTTTTGTGAAGTTTGAGGGTAAAAATGATTTTTTTTAAAGTTTAGGG
1 TAGGGGT--AAAATGTAATTTTTAAAAAGTTTGAGGGTAAAAATGATATTTTTGAAAGTTTAGGG
25633119 GTAAAAATATAATTTTTGTGAAGTT
64 GTAAAAATATAATTTTTGTGAAGTT
* ** * *
25633144 TAGGGGTTAAAA-ATAATTTTTGGAAAGTTT-AGGGGTCAAAATG-TGATTTTTGAATAGTTCAG
1 TAGGGG-TAAAATGTAATTTTTAAAAAGTTTGA-GGGTAAAAATGAT-ATTTTTGAA-AGTTTAG
25633206 GG
62 GG
25633208 ACCTTTTGGG
Statistics
Matches: 126, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
87 2 0.02
88 38 0.30
89 73 0.58
90 12 0.10
91 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (88 bp):
TAGGGGTAAAATGTAATTTTTAAAAAGTTTGAGGGTAAAAATGATATTTTTGAAAGTTTAGGGGT
AAAAATATAATTTTTGTGAAGTT
Found at i:25633063 original size:59 final size:60
Alignment explanation
Indices: 25633000--25633195 Score: 246
Period size: 59 Copynumber: 3.3 Consensus size: 60
25632990 AAATTTTGGT
*
25633000 GTCAAAAATGGAATTTTTG-GAAGTTTAGGTGTAAAAATATGATTTTTGGAAAGTTTA-GG
1 GTCAAAAATGTAATTTTTGTGAAGTTTAGG-GTAAAAATATGATTTTTGGAAAGTTTAGGG
**
25633059 GTCAAAAATGTAATTTTTGTGAAGTTTGAGGGT-AAAA-ATGATTTTTTTTAAAGTTTAGGG
1 GTCAAAAATGTAATTTTTGTGAAGTTT-AGGGTAAAAATATGA-TTTTTGGAAAGTTTAGGG
*
25633119 GT-AAAAATATAATTTTTGTGAAGTTTAGGGGTTAAAAATA--ATTTTTGGAAAGTTTAGGG
1 GTCAAAAATGTAATTTTTGTGAAGTTTA-GGG-TAAAAATATGATTTTTGGAAAGTTTAGGG
*
25633178 GTC-AAAATGTGATTTTTG
1 GTCAAAAATGTAATTTTTG
25633196 AATAGTTCAG
Statistics
Matches: 120, Mismatches: 8, Indels: 18
0.82 0.05 0.12
Matches are distributed among these distances:
58 5 0.04
59 92 0.77
60 15 0.12
61 7 0.06
62 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.40
Consensus pattern (60 bp):
GTCAAAAATGTAATTTTTGTGAAGTTTAGGGTAAAAATATGATTTTTGGAAAGTTTAGGG
Found at i:25634975 original size:6 final size:6
Alignment explanation
Indices: 25634964--25635053 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
25634954 AATGGGACTT
* * **
25634964 TTTAAA TTTAAA -TTAAT TTTAAT TTTAAA AGTAAA -TT-AA TCTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
** *
25635009 TTTAAA TTTAAA TTTAAA -ACAAA TTTAAA TTTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
25635054 TCTTATAATA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
4 2 0.03
5 14 0.21
6 51 0.76
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:25634985 original size:17 final size:17
Alignment explanation
Indices: 25634964--25635071 Score: 105
Period size: 17 Copynumber: 6.4 Consensus size: 17
25634954 AATGGGACTT
* *
25634964 TTTAAATTTAAATTAAT
1 TTTAAATTTAAAATAAA
*
25634981 TTTAATTTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
**
25634999 -TT-AATCTTAATTTAAA
1 TTTAAAT-TTAAAATAAA
*
25635015 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
25635032 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
25635049 TTT-AATCTTATAATAAA
1 TTTAAAT-TTAAAATAAA
25635066 TTTAAA
1 TTTAAA
25635072 AAGGGGTTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
16 9 0.12
17 57 0.77
18 8 0.11
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:25634989 original size:23 final size:23
Alignment explanation
Indices: 25634963--25635022 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
25634953 TAATGGGACT
*
25634963 TTTTAAATTTAAATTAATTTTAA
1 TTTTAAATTTAAATTAATCTTAA
**
25634986 TTTTAAAAGTAAATTAATCTTAA
1 TTTTAAATTTAAATTAATCTTAA
25635009 -TTTAAATTTAAATT
1 TTTTAAATTTAAATT
25635023 TAAAACAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTAAATTTAAATTAATCTTAA
Found at i:25651907 original size:21 final size:19
Alignment explanation
Indices: 25651852--25651907 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 19
25651842 CCTAAATCAA
*
25651852 AAATGAAAATC-TAAATCT
1 AAATAAAAATCATAAATCT
*
25651870 AAATCAAAATCGAATAAATCCT
1 AAATAAAAATC--ATAAAT-CT
25651892 AAATAAAAAATCATAA
1 AAAT-AAAAATCATAA
25651908 TCAATATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 10 0.32
21 9 0.29
22 6 0.19
23 6 0.19
ACGTcount: A:0.61, C:0.12, G:0.04, T:0.23
Consensus pattern (19 bp):
AAATAAAAATCATAAATCT
Found at i:25651923 original size:47 final size:48
Alignment explanation
Indices: 25651824--25651931 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 48
25651814 AAACAGTAGC
* *
25651824 AATCAAAATCGAA-ATAACCCTAAATCAAAAATGAAAATCTAAATCTA
1 AATCAAAATCGAATATAACCCTAAATAAAAAATCAAAATCTAAATCTA
* *
25651871 AATCAAAATCGAATA-AATCCTAAATAAAAAATCATAATC-AATATC-A
1 AATCAAAATCGAATATAACCCTAAATAAAAAATCAAAATCTAA-ATCTA
*
25651917 ACATCAAATTCGAAT
1 A-ATCAAAATCGAAT
25651932 TAATTACTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
46 4 0.08
47 48 0.91
48 1 0.02
ACGTcount: A:0.56, C:0.17, G:0.04, T:0.23
Consensus pattern (48 bp):
AATCAAAATCGAATATAACCCTAAATAAAAAATCAAAATCTAAATCTA
Found at i:25652158 original size:61 final size:62
Alignment explanation
Indices: 25652080--25652196 Score: 175
Period size: 61 Copynumber: 1.9 Consensus size: 62
25652070 TTCAATTTTT
* *
25652080 AATTTTCAAAATTAAGATTAAATT-GACAGAATAATTAAATATTGAAGGTTAAATTTGTTGAA
1 AATTTTCAAAATCAAGATTAAATTAG-CAAAATAATTAAATATTGAAGGTTAAATTTGTTGAA
* *
25652142 AATTTT-AAAATCAAGATTAAATTAGCAAAATAGTTATATATTGAAGGTTAAATTT
1 AATTTTCAAAATCAAGATTAAATTAGCAAAATAATTAAATATTGAAGGTTAAATTT
25652197 ATTATTATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 43 0.86
62 7 0.14
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (62 bp):
AATTTTCAAAATCAAGATTAAATTAGCAAAATAATTAAATATTGAAGGTTAAATTTGTTGAA
Found at i:25653976 original size:101 final size:100
Alignment explanation
Indices: 25653801--25654050 Score: 356
Period size: 101 Copynumber: 2.5 Consensus size: 100
25653791 GCATGCACAC
* * *
25653801 GTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGCCAGCTTATTTATGCGTTTACGCTCACCAA
1 GTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATGCGTTTACGCTCACCAA
* *
25653866 CTTGCACACGTTTACGCTCGTTAGCTTATTTATCGA
66 CTTGCACACGTTTACACTCGTCAGCTTATTTAT-GA
* * ** *
25653902 GTTTACGCTCTCCAGCTTGCACACGTTTACTCTCGTTAGCTTATTTATGCGTTTACGCTTGCCAG
1 GTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATGCGTTTACGCTCACCAA
*
25653967 CTTGCACACGTTTACACTCGTCAGCTTATTTATGT
66 CTTGCACACGTTTACACTCGTCAGCTTATTTATGA
* ** *
25654002 GGTTACGCTCTCCAGCTTGCACAAATTTACGCTCGTCAGCTTATATATG
1 GTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATG
25654051 TACATATAAA
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 44 0.33
101 88 0.67
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.36
Consensus pattern (100 bp):
GTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATGCGTTTACGCTCACCAA
CTTGCACACGTTTACACTCGTCAGCTTATTTATGA
Found at i:25653991 original size:24 final size:24
Alignment explanation
Indices: 25653777--25654043 Score: 149
Period size: 24 Copynumber: 10.8 Consensus size: 24
25653767 TATTTATTGA
*
25653777 GTTTACGCTCGCCAGCATGCACAC
1 GTTTACGCTCGCCAGCTTGCACAC
*
25653801 GTTTATGCTCGCCAGCTTGCACAC
1 GTTTACGCTCGCCAGCTTGCACAC
** **
25653825 GTTTACGCTCGCCAGCTTATTTATGC
1 GTTTACGCTCGCCAGC-T-TGCACAC
* *
25653851 GTTTACGCTCACCAACTTGCACAC
1 GTTTACGCTCGCCAGCTTGCACAC
** **
25653875 GTTTACGCTCGTTAGCTTATTTATCGA-
1 GTTTACGCTCGCCAGC-T-TGCA-C-AC
*
25653902 GTTTACGCTCTCCAGCTTGCACAC
1 GTTTACGCTCGCCAGCTTGCACAC
* ** ** **
25653926 GTTTACTCTCGTTAGCTTATTTATGC
1 GTTTACGCTCGCCAGC-T-TGCACAC
*
25653952 GTTTACGCTTGCCAGCTTGCACAC
1 GTTTACGCTCGCCAGCTTGCACAC
* * **** *
25653976 GTTTACACTCGTCAGCTTATTTAT
1 GTTTACGCTCGCCAGCTTGCACAC
* *
25654000 GTGGTTACGCTCTCCAGCTTGCACAA
1 GT--TTACGCTCGCCAGCTTGCACAC
* *
25654026 ATTTACGCTCGTCAGCTT
1 GTTTACGCTCGCCAGCTT
25654044 ATATATGTAC
Statistics
Matches: 173, Mismatches: 59, Indels: 22
0.68 0.23 0.09
Matches are distributed among these distances:
23 1 0.01
24 100 0.58
25 7 0.04
26 50 0.29
27 14 0.08
28 1 0.01
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.34
Consensus pattern (24 bp):
GTTTACGCTCGCCAGCTTGCACAC
Found at i:25654051 original size:50 final size:50
Alignment explanation
Indices: 25653800--25654050 Score: 342
Period size: 50 Copynumber: 5.0 Consensus size: 50
25653790 AGCATGCACA
* * *
25653800 CGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGCCAGCTTATTTATG
1 CGTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATG
* * *
25653850 CGTTTACGCTCACCAACTTGCACACGTTTACGCTCGTTAGCTTATTTATCG
1 CGTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTAT-G
* * *
25653901 AGTTTACGCTCTCCAGCTTGCACACGTTTACTCTCGTTAGCTTATTTATG
1 CGTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATG
*
25653951 CGTTTACGCT-TGCCAGCTTGCACACGTTTACACTCGTCAGCTTATTTATG
1 CGTTTACGCTCT-CCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATG
* * ** *
25654001 TGGTTACGCTCTCCAGCTTGCACAAATTTACGCTCGTCAGCTTATATATG
1 CGTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATG
25654051 TACATATAAA
Statistics
Matches: 180, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 132 0.73
51 47 0.26
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.36
Consensus pattern (50 bp):
CGTTTACGCTCTCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATG
Done.