Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 55 of 135
Found at i:22351294 original size:2 final size:2
Alignment explanation
Indices: 22351287--22351311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22351277 TGGTGTCATT
22351287 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22351312 TAATTAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22372002 original size:970 final size:970
Alignment explanation
Indices: 22370122--22372062 Score: 3882
Period size: 970 Copynumber: 2.0 Consensus size: 970
22370112 ATTACATCTA
22370122 ACAATATTACCTATTTACCCAATCTTAAAACTCAAGATTCACAACATCAAGCATAATCCAAGTAT
1 ACAATATTACCTATTTACCCAATCTTAAAACTCAAGATTCACAACATCAAGCATAATCCAAGTAT
22370187 CACATATACAAATAAATGCACATTACTATCGAAGCAAGCTTAAACCATGATCAAAATTATATACT
66 CACATATACAAATAAATGCACATTACTATCGAAGCAAGCTTAAACCATGATCAAAATTATATACT
22370252 TAATTATCATTTTTAGCCATTTTTGATTGGCTCATACGTTCAAGTTCAAACTTATAAAATACCGA
131 TAATTATCATTTTTAGCCATTTTTGATTGGCTCATACGTTCAAGTTCAAACTTATAAAATACCGA
22370317 AACAGCCAATAGTGTGATAGACTTCGCTGACGATCCCTGAGCCTGTAACTAACTTTCAAAATCTC
196 AACAGCCAATAGTGTGATAGACTTCGCTGACGATCCCTGAGCCTGTAACTAACTTTCAAAATCTC
22370382 GGATATCGACGGACGATATAAAACGACTATTCAACTATTTTTGTTTTCCCCCGATCCAAGTCTGA
261 GGATATCGACGGACGATATAAAACGACTATTCAACTATTTTTGTTTTCCCCCGATCCAAGTCTGA
22370447 TTTCTTTGGTTCTTGATCTTGAATTAAGCTTGATAGTTGCCGAAACCTAAAAAAAACATGAGAGA
326 TTTCTTTGGTTCTTGATCTTGAATTAAGCTTGATAGTTGCCGAAACCTAAAAAAAACATGAGAGA
22370512 TTTTCTTTCCTTGATGCAATCGGCCAACAAAGATGATAATGGCTTTATTTTATTTAATTATCATA
391 TTTTCTTTCCTTGATGCAATCGGCCAACAAAGATGATAATGGCTTTATTTTATTTAATTATCATA
22370577 TAATTATTCATTTCCATATATAACCTTTATAATTTTATTTTCTTTAATTATCATATAATTATTCA
456 TAATTATTCATTTCCATATATAACCTTTATAATTTTATTTTCTTTAATTATCATATAATTATTCA
22370642 TTTCCACTAACTCATGTCCATAAGTGCCCGTGCATGAATTAAATGGCCTAATTGCATCATAAATA
521 TTTCCACTAACTCATGTCCATAAGTGCCCGTGCATGAATTAAATGGCCTAATTGCATCATAAATA
22370707 CCTCATGCTATAAAGACATCAACAATTCAACCCTTACATATTTAGCTATCAACTTTTTCATCTTA
586 CCTCATGCTATAAAGACATCAACAATTCAACCCTTACATATTTAGCTATCAACTTTTTCATCTTA
22370772 CTCAATTAAGCCTTTTTATTAAATCGGCACTCAAATGAAAAAATTAAAACACGTAAATTTCATGG
651 CTCAATTAAGCCTTTTTATTAAATCGGCACTCAAATGAAAAAATTAAAACACGTAAATTTCATGG
22370837 ATATAAATTCACACAGTATAAACAAAGCTAATAATATTTAAATATTTTTTTGACTCGGATTTGTG
716 ATATAAATTCACACAGTATAAACAAAGCTAATAATATTTAAATATTTTTTTGACTCGGATTTGTG
22370902 GTCTCAAAACCACTGTTCCGATTAGGGTCGAAACCGGACTATTACACTCAACACTTACCATATAC
781 GTCTCAAAACCACTGTTCCGATTAGGGTCGAAACCGGACTATTACACTCAACACTTACCATATAC
22370967 ATTAAATAAAAATTATAACAATTAATAACTAGCTTCAGATTATAAAAATACAAACCAAAAATTTC
846 ATTAAATAAAAATTATAACAATTAATAACTAGCTTCAGATTATAAAAATACAAACCAAAAATTTC
22371032 GAGCTATTCCTCGTCGACTTTATCTTTCCCTTTTTTAGTCGAGGATTCCGGTACGACGTT
911 GAGCTATTCCTCGTCGACTTTATCTTTCCCTTTTTTAGTCGAGGATTCCGGTACGACGTT
22371092 ACAATATTACCTATTTACCCAATCTTAAAACTCAAGATTCACAACATCAAGCATAATCCAAGTAT
1 ACAATATTACCTATTTACCCAATCTTAAAACTCAAGATTCACAACATCAAGCATAATCCAAGTAT
22371157 CACATATACAAATAAATGCACATTACTATCGAAGCAAGCTTAAACCATGATCAAAATTATATACT
66 CACATATACAAATAAATGCACATTACTATCGAAGCAAGCTTAAACCATGATCAAAATTATATACT
22371222 TAATTATCATTTTTAGCCATTTTTGATTGGCTCATACGTTCAAGTTCAAACTTATAAAATACCGA
131 TAATTATCATTTTTAGCCATTTTTGATTGGCTCATACGTTCAAGTTCAAACTTATAAAATACCGA
22371287 AACAGCCAATAGTGTGATAGACTTCGCTGACGATCCCTGAGCCTGTAACTAACTTTCAAAATCTC
196 AACAGCCAATAGTGTGATAGACTTCGCTGACGATCCCTGAGCCTGTAACTAACTTTCAAAATCTC
22371352 GGATATCGACGGACGATATAAAACGACTATTCAACTATTTTTGTTTTCCCCCGATCCAAGTCTGA
261 GGATATCGACGGACGATATAAAACGACTATTCAACTATTTTTGTTTTCCCCCGATCCAAGTCTGA
22371417 TTTCTTTGGTTCTTGATCTTGAATTAAGCTTGATAGTTGCCGAAACCTAAAAAAAACATGAGAGA
326 TTTCTTTGGTTCTTGATCTTGAATTAAGCTTGATAGTTGCCGAAACCTAAAAAAAACATGAGAGA
22371482 TTTTCTTTCCTTGATGCAATCGGCCAACAAAGATGATAATGGCTTTATTTTATTTAATTATCATA
391 TTTTCTTTCCTTGATGCAATCGGCCAACAAAGATGATAATGGCTTTATTTTATTTAATTATCATA
22371547 TAATTATTCATTTCCATATATAACCTTTATAATTTTATTTTCTTTAATTATCATATAATTATTCA
456 TAATTATTCATTTCCATATATAACCTTTATAATTTTATTTTCTTTAATTATCATATAATTATTCA
22371612 TTTCCACTAACTCATGTCCATAAGTGCCCGTGCATGAATTAAATGGCCTAATTGCATCATAAATA
521 TTTCCACTAACTCATGTCCATAAGTGCCCGTGCATGAATTAAATGGCCTAATTGCATCATAAATA
22371677 CCTCATGCTATAAAGACATCAACAATTCAACCCTTACATATTTAGCTATCAACTTTTTCATCTTA
586 CCTCATGCTATAAAGACATCAACAATTCAACCCTTACATATTTAGCTATCAACTTTTTCATCTTA
22371742 CTCAATTAAGCCTTTTTATTAAATCGGCACTCAAATGAAAAAATTAAAACACGTAAATTTCATGG
651 CTCAATTAAGCCTTTTTATTAAATCGGCACTCAAATGAAAAAATTAAAACACGTAAATTTCATGG
22371807 ATATAAATTCACACAGTATAAACAAAGCTAATAATATTTAAATATTTTTTTGACTCGGATTTGTG
716 ATATAAATTCACACAGTATAAACAAAGCTAATAATATTTAAATATTTTTTTGACTCGGATTTGTG
22371872 GTCTCAAAACCACTGTTCCGATTAGGGTCGAAACCGGACTATTACACTCAACACTTACCATATAC
781 GTCTCAAAACCACTGTTCCGATTAGGGTCGAAACCGGACTATTACACTCAACACTTACCATATAC
22371937 ATTAAATAAAAATTATAACAATTAATAACTAGCTTCAGATTATAAAAATACAAACCAAAAATTTC
846 ATTAAATAAAAATTATAACAATTAATAACTAGCTTCAGATTATAAAAATACAAACCAAAAATTTC
22372002 GAGCTATTCCTCGTCGACTTTATCTTTCCCTTTTTTAGTCGAGGATTCCGGTACGACGTT
911 GAGCTATTCCTCGTCGACTTTATCTTTCCCTTTTTTAGTCGAGGATTCCGGTACGACGTT
22372062 A
1 A
22372063 GCTACGAAAT
Statistics
Matches: 971, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
970 971 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (970 bp):
ACAATATTACCTATTTACCCAATCTTAAAACTCAAGATTCACAACATCAAGCATAATCCAAGTAT
CACATATACAAATAAATGCACATTACTATCGAAGCAAGCTTAAACCATGATCAAAATTATATACT
TAATTATCATTTTTAGCCATTTTTGATTGGCTCATACGTTCAAGTTCAAACTTATAAAATACCGA
AACAGCCAATAGTGTGATAGACTTCGCTGACGATCCCTGAGCCTGTAACTAACTTTCAAAATCTC
GGATATCGACGGACGATATAAAACGACTATTCAACTATTTTTGTTTTCCCCCGATCCAAGTCTGA
TTTCTTTGGTTCTTGATCTTGAATTAAGCTTGATAGTTGCCGAAACCTAAAAAAAACATGAGAGA
TTTTCTTTCCTTGATGCAATCGGCCAACAAAGATGATAATGGCTTTATTTTATTTAATTATCATA
TAATTATTCATTTCCATATATAACCTTTATAATTTTATTTTCTTTAATTATCATATAATTATTCA
TTTCCACTAACTCATGTCCATAAGTGCCCGTGCATGAATTAAATGGCCTAATTGCATCATAAATA
CCTCATGCTATAAAGACATCAACAATTCAACCCTTACATATTTAGCTATCAACTTTTTCATCTTA
CTCAATTAAGCCTTTTTATTAAATCGGCACTCAAATGAAAAAATTAAAACACGTAAATTTCATGG
ATATAAATTCACACAGTATAAACAAAGCTAATAATATTTAAATATTTTTTTGACTCGGATTTGTG
GTCTCAAAACCACTGTTCCGATTAGGGTCGAAACCGGACTATTACACTCAACACTTACCATATAC
ATTAAATAAAAATTATAACAATTAATAACTAGCTTCAGATTATAAAAATACAAACCAAAAATTTC
GAGCTATTCCTCGTCGACTTTATCTTTCCCTTTTTTAGTCGAGGATTCCGGTACGACGTT
Found at i:22372148 original size:36 final size:36
Alignment explanation
Indices: 22372108--22372177 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
22372098 AACACAATTC
22372108 AATTTCATATTGAATATTTCAATATTTACTCAATAT
1 AATTTCATATTGAATATTTCAATATTTACTCAATAT
22372144 AATTTCATATTGAATATTTCAATATTTACTCAAT
1 AATTTCATATTGAATATTTCAATATTTACTCAAT
22372178 CTTTGTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (36 bp):
AATTTCATATTGAATATTTCAATATTTACTCAATAT
Found at i:22372611 original size:15 final size:14
Alignment explanation
Indices: 22372591--22372642 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
22372581 TCCTTTTTCC
22372591 TTCTTTCTTTCCTTT
1 TTCTTTCTTT-CTTT
22372606 TTCTTTCTGTTTCTTT
1 TTCTTTC--TTTCTTT
* *
22372622 TCACTTTGTTTCTTT
1 T-TCTTTCTTTCTTT
22372637 TTCTTT
1 TTCTTT
22372643 TTCTATTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.13
15 15 0.48
16 5 0.16
17 7 0.23
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (14 bp):
TTCTTTCTTTCTTT
Found at i:22372641 original size:6 final size:6
Alignment explanation
Indices: 22372583--22372673 Score: 53
Period size: 6 Copynumber: 14.8 Consensus size: 6
22372573 TGGCTTTCTC
* * *
22372583 CTTTTT CCTTCTTT C-TTTC CTTTTT C--TTT CTGTTT CTTTTCA CTTTGTTT
1 CTTTTT -CTT-TTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT-T C-TT-TTT
* * * *
22372633 CTTTTT CTTTTT CTATTT CTATTT CTATTT CTATTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
22372674 ATTTTGTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.06
5 3 0.04
6 48 0.69
7 7 0.10
8 6 0.09
9 2 0.03
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:22372651 original size:12 final size:12
Alignment explanation
Indices: 22372630--22372670 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
22372620 TTTCACTTTG
* *
22372630 TTTCTTTTTCTT
1 TTTCTATTTCTA
22372642 TTTCTATTTCTA
1 TTTCTATTTCTA
22372654 TTTCTATTTCTA
1 TTTCTATTTCTA
22372666 TTTCT
1 TTTCT
22372671 TTTATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTCTATTTCTA
Found at i:22372657 original size:18 final size:18
Alignment explanation
Indices: 22372630--22372673 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
22372620 TTTCACTTTG
*
22372630 TTTCTTTTTCTTTTTCTA
1 TTTCTTTTTCTATTTCTA
*
22372648 TTTCTATTTCTATTTCTA
1 TTTCTTTTTCTATTTCTA
22372666 TTTCTTTT
1 TTTCTTTT
22372674 ATTTTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTCTTTTTCTATTTCTA
Found at i:22373311 original size:75 final size:75
Alignment explanation
Indices: 22373182--22373325 Score: 175
Period size: 75 Copynumber: 1.9 Consensus size: 75
22373172 GCAATCACCA
* * *
22373182 TTGGTTGATCCAACTGGAGCTGGGCTCACAATTATTATCGTCGGTATACCCGACTAGCACTGGGT
1 TTGGTTGATCCAACTAGAGCTGGGCTCACAATTATTACCGTCGGTATACCCGACTAGCACTGGGC
22373247 GCAAATATTG
66 GCAAATATTG
* * * ** *
22373257 TTGGTTTATCCAACTAGAGCTGGGCTCAC-CTTCATTACCGTCAGT-TAATTCGACTAGCGCTGG
1 TTGGTTGATCCAACTAGAGCTGGGCTCACAATT-ATTACCGTCGGTAT-ACCCGACTAGCACTGG
22373320 GCGCAA
64 GCGCAA
22373326 CCTTTTCTGC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
74 3 0.05
75 55 0.95
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (75 bp):
TTGGTTGATCCAACTAGAGCTGGGCTCACAATTATTACCGTCGGTATACCCGACTAGCACTGGGC
GCAAATATTG
Found at i:22374076 original size:30 final size:30
Alignment explanation
Indices: 22374042--22374138 Score: 151
Period size: 30 Copynumber: 3.2 Consensus size: 30
22374032 GTATCTCAGC
*
22374042 CGTGTGTGACACACAGCCAGGTAACACGGT
1 CGTGTGTGACACACGGCCAGGTAACACGGT
22374072 CGTGTGTGACACACGGCCAGGTAACACGGT
1 CGTGTGTGACACACGGCCAGGTAACACGGT
* *
22374102 CGTGTGTGACACATGGTCAGGTAACACGG-
1 CGTGTGTGACACACGGCCAGGTAACACGGT
22374131 CTGTGTGT
1 C-GTGTGT
22374139 CCCCTGTAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
29 1 0.02
30 62 0.98
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.21
Consensus pattern (30 bp):
CGTGTGTGACACACGGCCAGGTAACACGGT
Found at i:22374087 original size:17 final size:17
Alignment explanation
Indices: 22374065--22374119 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
22374055 CAGCCAGGTA
22374065 ACACGGTCGTGTGTGAC
1 ACACGGTCGTGTGTGAC
**
22374082 ACACGG-CCAG-GT-A-
1 ACACGGTCGTGTGTGAC
22374095 ACACGGTCGTGTGTGAC
1 ACACGGTCGTGTGTGAC
*
22374112 ACATGGTC
1 ACACGGTC
22374120 AGGTAACACG
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
13 6 0.21
14 3 0.10
15 4 0.14
16 3 0.10
17 13 0.45
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (17 bp):
ACACGGTCGTGTGTGAC
Found at i:22375063 original size:15 final size:15
Alignment explanation
Indices: 22375026--22375071 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
22375016 TTATTGTATA
*
22375026 TTATTTTTAAATAT-
1 TTATTTTTAAATTTG
22375040 TTATATTTTAAATTTG
1 TTAT-TTTTAAATTTG
*
22375056 TTATTTTTATATTTG
1 TTATTTTTAAATTTG
22375071 T
1 T
22375072 ACATGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
TTATTTTTAAATTTG
Found at i:22376086 original size:15 final size:17
Alignment explanation
Indices: 22376061--22376092 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22376051 TAATTCATCT
22376061 TTTTAATTAAT-ATATC
1 TTTTAATTAATAATATC
22376077 TTTT-ATTAATAATATC
1 TTTTAATTAATAATATC
22376093 AAATTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATTAATAATATC
Found at i:22386626 original size:2 final size:2
Alignment explanation
Indices: 22386619--22386652 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22386609 ATTGTAGAAC
22386619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22386653 GTGCATGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22394023 original size:6 final size:6
Alignment explanation
Indices: 22394012--22394055 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
22394002 GGGTACTGGA
22394012 TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TT
1 TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TT
22394056 TGAAAGGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (6 bp):
TTGGGG
Found at i:22403525 original size:19 final size:18
Alignment explanation
Indices: 22403491--22403526 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22403481 AAATTTAAAT
*
22403491 TTTGAGTTATTTGAATTG
1 TTTGAGTTAGTTGAATTG
22403509 TTTGAGTTGAGTTGAATT
1 TTTGAGTT-AGTTGAATT
22403527 TTATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (18 bp):
TTTGAGTTAGTTGAATTG
Found at i:22403671 original size:19 final size:18
Alignment explanation
Indices: 22403647--22403693 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
22403637 TAAAAATATT
*
22403647 TTTTTAAAAATTGAAATAA
1 TTTTTAAAAATTAAAAT-A
*
22403666 TTTTTAAAATTTAAAATA
1 TTTTTAAAAATTAAAATA
*
22403684 TTTATAAAAA
1 TTTTTAAAAA
22403694 AATCAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTTTAAAAATTAAAATA
Found at i:22403686 original size:18 final size:18
Alignment explanation
Indices: 22403633--22403692 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
22403623 TTATAAATGG
22403633 AATTTAAAAATATTTTTTTAA
1 AATTT-AAAATA--TTTTTAA
* *
22403654 AAATTGAAATAATTTTTAA
1 AATTTAAAAT-ATTTTTAA
*
22403673 AATTTAAAATATTTATAA
1 AATTTAAAATATTTTTAA
22403691 AA
1 AA
22403693 AAATCAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 4 0.12
21 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTTAAAATATTTTTAA
Found at i:22403989 original size:22 final size:21
Alignment explanation
Indices: 22403960--22404008 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
22403950 TTCATTCAAT
22403960 TTAAAAAAAAACTAAATTAAA
1 TTAAAAAAAAACTAAATTAAA
* *
22403981 TTAATAAAATAACTAAATTAAT
1 TTAA-AAAAAAACTAAATTAAA
22404003 TTAAAA
1 TTAAAA
22404009 TTTTTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAAAAAAAACTAAATTAAA
Found at i:22425158 original size:2 final size:2
Alignment explanation
Indices: 22425151--22425175 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22425141 TGGTATTTTC
22425151 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 A
22425176 ATTTATCGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22425223 original size:95 final size:95
Alignment explanation
Indices: 22425110--22425299 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 95
22425100 ACTAAGGCGT
22425110 TTATTTTATAAATATATTTGTTAAATAAGTGTGGTATTTTCATATATATATATATATATATATAT
1 TTATTTTATAAATATATTTGTTAAATAAGTGTGGTATTTTCATATATATATATATATATATATAT
22425175 AATTTATCGTCAAAAATACACTGCATTCAC
66 AATTTATCGTCAAAAATACACTGCATTCAC
22425205 TTATTTTATAAATATATTTGTTAAATAAGTGTGGTATTTTCATATATATATATATATATATATAT
1 TTATTTTATAAATATATTTGTTAAATAAGTGTGGTATTTTCATATATATATATATATATATATAT
*
22425270 AATTTATCGTTAAAAATACACTGCATTCAC
66 AATTTATCGTCAAAAATACACTGCATTCAC
22425300 CGATGTAAAT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (95 bp):
TTATTTTATAAATATATTTGTTAAATAAGTGTGGTATTTTCATATATATATATATATATATATAT
AATTTATCGTCAAAAATACACTGCATTCAC
Found at i:22425253 original size:2 final size:2
Alignment explanation
Indices: 22425246--22425270 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22425236 TGGTATTTTC
22425246 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 A
22425271 ATTTATCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22433218 original size:322 final size:322
Alignment explanation
Indices: 22432633--22433279 Score: 1285
Period size: 322 Copynumber: 2.0 Consensus size: 322
22432623 CAGTTTACAG
22432633 TACCGTCATAATTCCCTTTTTGGACAAATATCTTTACTATTTCACAGTTTCTCCATCAGACCCAC
1 TACCGTCATAATTCCCTTTTTGGACAAATATCTTTACTATTTCACAGTTTCTCCATCAGACCCAC
22432698 TTAAATAGTACGATCAATCGTTTTAACTCCGATAACGTTAACGATGAAGTCATCCAATGAGGACG
66 TTAAATAGTACGATCAATCGTTTTAACTCCGATAACGTTAACGATGAAGTCATCCAATGAGGACG
22432763 TCAGTTTTGACTCGCAGTCCTGAAGAGCTGACAGAGCATTAAAAAGTAAAACTCTGAAAACAAAT
131 TCAGTTTTGACTCGCAGTCCTGAAGAGCTGACAGAGCATTAAAAAGTAAAACTCTGAAAACAAAT
22432828 CAATGTTTTTTTTCCATTAAAGCAAAATCATTTTTTCCGGTCATAAAACAAAGTCAATGGTTTTT
196 CAATGTTTTTTTTCCATTAAAGCAAAATCATTTTTTCCGGTCATAAAACAAAGTCAATGGTTTTT
*
22432893 TTTTTGGGTAAAAAATGTCCTCGGTGCTTGTCTTTTTTTTTTTTTTTTAGATAGTCTTTTTT
261 TTTTTGGGTAAAAAATGTCCTCGGTGCTTGTCTTTTTTTTTTTTTTTGAGATAGTCTTTTTT
22432955 TACCGTCATAATTCCCTTTTTGGACAAATATCTTTACTATTTCACAGTTTCTCCATCAGACCCAC
1 TACCGTCATAATTCCCTTTTTGGACAAATATCTTTACTATTTCACAGTTTCTCCATCAGACCCAC
22433020 TTAAATAGTACGATCAATCGTTTTAACTCCGATAACGTTAACGATGAAGTCATCCAATGAGGACG
66 TTAAATAGTACGATCAATCGTTTTAACTCCGATAACGTTAACGATGAAGTCATCCAATGAGGACG
22433085 TCAGTTTTGACTCGCAGTCCTGAAGAGCTGACAGAGCATTAAAAAGTAAAACTCTGAAAACAAAT
131 TCAGTTTTGACTCGCAGTCCTGAAGAGCTGACAGAGCATTAAAAAGTAAAACTCTGAAAACAAAT
22433150 CAATGTTTTTTTTCCATTAAAGCAAAATCATTTTTTCCGGTCATAAAACAAAGTCAATGGTTTTT
196 CAATGTTTTTTTTCCATTAAAGCAAAATCATTTTTTCCGGTCATAAAACAAAGTCAATGGTTTTT
22433215 TTTTTGGGTAAAAAATGTCCTCGGTGCTTGTCTTTTTTTTTTTTTTTGAGATAGTCTTTTTT
261 TTTTTGGGTAAAAAATGTCCTCGGTGCTTGTCTTTTTTTTTTTTTTTGAGATAGTCTTTTTT
22433277 TAC
1 TAC
22433280 TTTTAATTAT
Statistics
Matches: 324, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
322 324 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (322 bp):
TACCGTCATAATTCCCTTTTTGGACAAATATCTTTACTATTTCACAGTTTCTCCATCAGACCCAC
TTAAATAGTACGATCAATCGTTTTAACTCCGATAACGTTAACGATGAAGTCATCCAATGAGGACG
TCAGTTTTGACTCGCAGTCCTGAAGAGCTGACAGAGCATTAAAAAGTAAAACTCTGAAAACAAAT
CAATGTTTTTTTTCCATTAAAGCAAAATCATTTTTTCCGGTCATAAAACAAAGTCAATGGTTTTT
TTTTTGGGTAAAAAATGTCCTCGGTGCTTGTCTTTTTTTTTTTTTTTGAGATAGTCTTTTTT
Found at i:22453304 original size:13 final size:14
Alignment explanation
Indices: 22453286--22453315 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22453276 ACTGTAATAA
22453286 TTTTTTAGATTA-T
1 TTTTTTAGATTACT
22453299 TTTTTTAGATTACT
1 TTTTTTAGATTACT
22453313 TTT
1 TTT
22453316 AACTTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTTTTAGATTACT
Found at i:22454858 original size:16 final size:19
Alignment explanation
Indices: 22454827--22454866 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
22454817 TTACGAGTAG
22454827 GTTTTTGTATGTTATTT-T
1 GTTTTTGTATGTTATTTCT
22454845 GTTTTTG-A-GTTATTTCT
1 GTTTTTGTATGTTATTTCT
22454862 GTTTT
1 GTTTT
22454867 AGAAATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 7 0.33
18 7 0.33
ACGTcount: A:0.10, C:0.03, G:0.17, T:0.70
Consensus pattern (19 bp):
GTTTTTGTATGTTATTTCT
Found at i:22458159 original size:51 final size:51
Alignment explanation
Indices: 22457984--22458136 Score: 306
Period size: 51 Copynumber: 3.0 Consensus size: 51
22457974 GATTCAGGTG
22457984 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
1 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
22458035 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
1 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
22458086 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
1 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
22458137 ACTCTCAGGC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 102 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (51 bp):
CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
Found at i:22465413 original size:68 final size:69
Alignment explanation
Indices: 22465321--22465457 Score: 231
Period size: 68 Copynumber: 2.0 Consensus size: 69
22465311 TTAAACAGTG
*
22465321 TATAAATTTTCGTTTTCATCCTTTAGTTAAAAATTCATAAATTTCATTTAAATCACTGAATTATT
1 TATAAATTTTCGTTTTCATCCTTTAATTAAAAATTCATAAATTTCATTTAAATCACTGAATTATT
22465386 CAAA
66 CAAA
* * *
22465390 TATAAATTTT-GTTTTCATTCTTTAATTAAAAATTCATAATTTTCATTTAAATTACTGAATTATT
1 TATAAATTTTCGTTTTCATCCTTTAATTAAAAATTCATAAATTTCATTTAAATCACTGAATTATT
22465454 CAAA
66 CAAA
22465458 AGTTTTTATT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 54 0.84
69 10 0.16
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (69 bp):
TATAAATTTTCGTTTTCATCCTTTAATTAAAAATTCATAAATTTCATTTAAATCACTGAATTATT
CAAA
Found at i:22465487 original size:68 final size:66
Alignment explanation
Indices: 22465347--22465479 Score: 153
Period size: 68 Copynumber: 2.0 Consensus size: 66
22465337 CATCCTTTAG
* ** *
22465347 TTAAAAATTCATAAATTTCATTTAAATCACTGAATTATTCAAATATAAATTTTGTTTTCATTCTT
1 TTAAAAATTCATAAATTTCATTTAAATCACTGAATTATTCAAATAT--ATTTTATTTAAATTCTA
*
22465412 TAA
64 GAA
* *
22465415 TTAAAAATTCATAATTTTCATTTAAATTACTGAATTATTCAAA-AGT-TTTTATTTAAATTACTA
1 TTAAAAATTCATAAATTTCATTTAAATCACTGAATTATTCAAATA-TATTTTATTTAAATT-CTA
22465478 GA
64 GA
22465480 CTCTTAAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
65 10 0.18
66 3 0.05
67 1 0.02
68 42 0.75
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.47
Consensus pattern (66 bp):
TTAAAAATTCATAAATTTCATTTAAATCACTGAATTATTCAAATATATTTTATTTAAATTCTAGA
A
Found at i:22467441 original size:15 final size:15
Alignment explanation
Indices: 22467412--22467449 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
22467402 CTGTAGCAGC
*
22467412 TTTTGT-TGTTTCTG
1 TTTTGTATGGTTCTG
22467426 TTTTGTATGGTTCTG
1 TTTTGTATGGTTCTG
22467441 TTTTGTATG
1 TTTTGTATG
22467450 TTTGTATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.05, C:0.05, G:0.24, T:0.66
Consensus pattern (15 bp):
TTTTGTATGGTTCTG
Found at i:22493184 original size:15 final size:15
Alignment explanation
Indices: 22493164--22493193 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22493154 ATCATATCGT
22493164 TTATAAAATTCATAA
1 TTATAAAATTCATAA
22493179 TTATAAAATTCATAA
1 TTATAAAATTCATAA
22493194 AATTCATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
TTATAAAATTCATAA
Found at i:22493474 original size:27 final size:27
Alignment explanation
Indices: 22493444--22493503 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
22493434 GTAACACAAT
** *
22493444 AGATGGTCGAGTCGACGGTGATGCAGC
1 AGATGGTCGAGTCGACGGCAATGCAAC
* * *
22493471 AGATAGTCGGGTTGACGGCAATGCAAC
1 AGATGGTCGAGTCGACGGCAATGCAAC
22493498 AGATGG
1 AGATGG
22493504 GTTGGGATTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.38, T:0.18
Consensus pattern (27 bp):
AGATGGTCGAGTCGACGGCAATGCAAC
Found at i:22494453 original size:28 final size:27
Alignment explanation
Indices: 22494416--22494550 Score: 94
Period size: 28 Copynumber: 4.8 Consensus size: 27
22494406 TATCAAAATC
*
22494416 CCTAAACCCTAAAACATAAACAATGAAT
1 CCTAAACCCTAAAACATAAACAAT-AAA
*
22494444 CCTAAACCCTAAAATCCTAAA-ACATAAA
1 CCTAAACCCTAAAA-CATAAACA-ATAAA
* **
22494472 CCTTAAACCAT-AAACATTAAACACCAAA
1 CC-TAAACCCTAAAACA-TAAACAATAAA
* * * *
22494500 CACCAAACACTAAAACATAAACACTAATC
1 C-CTAAACCCTAAAACATAAACAATAA-A
*
22494529 CCTAAACCCAAAAACACTAAAC
1 CCTAAACCCTAAAACA-TAAAC
22494551 CATGAACATT
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 56 0.67
29 27 0.32
ACGTcount: A:0.54, C:0.30, G:0.01, T:0.16
Consensus pattern (27 bp):
CCTAAACCCTAAAACATAAACAATAAA
Found at i:22494817 original size:7 final size:7
Alignment explanation
Indices: 22494801--22494845 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
22494791 TAACACATTA
*
22494801 AAACCCT
1 AAACCTT
22494808 AAACCTT
1 AAACCTT
*
22494815 AAACATT
1 AAACCTT
*
22494822 AAATCTT
1 AAACCTT
22494829 AAACCTT
1 AAACCTT
*
22494836 AAACCCT
1 AAACCTT
22494843 AAA
1 AAA
22494846 ATAAAATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (7 bp):
AAACCTT
Found at i:22494833 original size:21 final size:22
Alignment explanation
Indices: 22494789--22494839 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
22494779 GAGTCAGTTG
22494789 CTTAACACATTAAAACCCTAAAC
1 CTTAA-ACATTAAAACCCTAAAC
* *
22494812 CTTAAACATT-AAATCTTAAAC
1 CTTAAACATTAAAACCCTAAAC
22494833 CTTAAAC
1 CTTAAAC
22494840 CCTAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 16 0.62
22 5 0.19
23 5 0.19
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
CTTAAACATTAAAACCCTAAAC
Found at i:22495445 original size:41 final size:41
Alignment explanation
Indices: 22495380--22495484 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
22495370 TTTTTTACGA
* *
22495380 CGTTTTTCTCATAAATGCCTCTACTGCTTGACCTTTTGCGG
1 CGTTTTTCTCATAAACGCCGCTACTGCTTGACCTTTTGCGG
* * * *
22495421 TGTTTTTCTCACAAACACCGCTACTGCTTGACCTTTTGGGG
1 CGTTTTTCTCATAAACGCCGCTACTGCTTGACCTTTTGCGG
*
22495462 CGTTTTTCTAATAAACGCCGCTA
1 CGTTTTTCTCATAAACGCCGCTA
22495485 TAGCTCTAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (41 bp):
CGTTTTTCTCATAAACGCCGCTACTGCTTGACCTTTTGCGG
Found at i:22505513 original size:19 final size:19
Alignment explanation
Indices: 22505485--22505523 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
22505475 TAACAAGATA
* *
22505485 GTAAAGATACCATTGTGAT
1 GTAAACATACCATTATGAT
22505504 GTAAACATACCATTATGAT
1 GTAAACATACCATTATGAT
22505523 G
1 G
22505524 GTGGCATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (19 bp):
GTAAACATACCATTATGAT
Found at i:22510829 original size:7 final size:8
Alignment explanation
Indices: 22510804--22510833 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
22510794 TAGTATTTAA
22510804 TTAATATTT
1 TTAA-ATTT
22510813 TTAAATTT
1 TTAAATTT
22510821 TTAAATTT
1 TTAAATTT
22510829 TTAAA
1 TTAAA
22510834 AAAATTATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTAAATTT
Found at i:22511001 original size:89 final size:90
Alignment explanation
Indices: 22510893--22511071 Score: 351
Period size: 89 Copynumber: 2.0 Consensus size: 90
22510883 AGAAATATTT
22510893 TTTAATATTTCTAAATTTTAAAATTTTAATTAAATCTTAACATATTATCTATGCGTATGTCACAT
1 TTTAATATTTCTAAATTTTAAAATTTTAATTAAATCTTAACATATTATCTATGCGTATGTCACAT
22510958 CAATAAAGTTAACAAATTATTTTAG
66 CAATAAAGTTAACAAATTATTTTAG
22510983 TTTAATATTT-TAAATTTTAAAATTTTAATTAAATCTTAACATATTATCTATGCGTATGTCACAT
1 TTTAATATTTCTAAATTTTAAAATTTTAATTAAATCTTAACATATTATCTATGCGTATGTCACAT
22511047 CAATAAAGTTAACAAATTATTTTAG
66 CAATAAAGTTAACAAATTATTTTAG
22511072 ACATCCATTT
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 79 0.89
90 10 0.11
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (90 bp):
TTTAATATTTCTAAATTTTAAAATTTTAATTAAATCTTAACATATTATCTATGCGTATGTCACAT
CAATAAAGTTAACAAATTATTTTAG
Found at i:22517729 original size:78 final size:79
Alignment explanation
Indices: 22517625--22517786 Score: 310
Period size: 78 Copynumber: 2.1 Consensus size: 79
22517615 TAAAATTTTT
22517625 ATTT-TAATTTTATTGTAAATAATTAAAGTTTCATTTATGTTCGTTTTACCATCTACGAAGATTA
1 ATTTGTAATTTTATTGTAAATAATTAAAGTTTCATTTATGTTCGTTTTACCATCTACGAAGATTA
22517689 TCTTTTTTTCCAGA
66 TCTTTTTTTCCAGA
22517703 ATTTGTAATTTTATTG-AAATAATTAAAGTTTCATTTATGTTCGTTTTACCATCTACGAAGATTA
1 ATTTGTAATTTTATTGTAAATAATTAAAGTTTCATTTATGTTCGTTTTACCATCTACGAAGATTA
22517767 TCTTTTTTTCCAGA
66 TCTTTTTTTCCAGA
22517781 ATTTGT
1 ATTTGT
22517787 GATTGTCCTC
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
78 72 0.87
79 11 0.13
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (79 bp):
ATTTGTAATTTTATTGTAAATAATTAAAGTTTCATTTATGTTCGTTTTACCATCTACGAAGATTA
TCTTTTTTTCCAGA
Found at i:22518769 original size:20 final size:20
Alignment explanation
Indices: 22518744--22518785 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
22518734 TTAACAAGCA
22518744 AATGCCTCTAAAATAATAAC
1 AATGCCTCTAAAATAATAAC
*
22518764 AATGCCTTTAAAATAATAAC
1 AATGCCTCTAAAATAATAAC
22518784 AA
1 AA
22518786 AATTAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (20 bp):
AATGCCTCTAAAATAATAAC
Found at i:22520152 original size:19 final size:18
Alignment explanation
Indices: 22520149--22520191 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
22520139 TTTAAAATAC
*
22520149 TTTTAAAATAATTTTTTAT
1 TTTTAAAAT-ATTTTTTAA
22520168 TTTTAAAATATTTTTTAA
1 TTTTAAAATATTTTTTAA
22520186 TGTTTA
1 T-TTTA
22520192 TTAAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTAAAATATTTTTTAA
Found at i:22520170 original size:18 final size:18
Alignment explanation
Indices: 22520149--22520184 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
22520139 TTTAAAATAC
22520149 TTTTAAAATAATTTTTTAT
1 TTTTAAAAT-ATTTTTTAT
22520168 TTTTAAAATATTTTTTA
1 TTTTAAAATATTTTTTA
22520185 ATGTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAAAATATTTTTTAT
Found at i:22526998 original size:2 final size:2
Alignment explanation
Indices: 22526991--22527027 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22526981 ATTTAACGTA
22526991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22527028 CTTTTTGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22527367 original size:39 final size:39
Alignment explanation
Indices: 22527313--22527391 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
22527303 TTATACTGGT
22527313 AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
1 AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
22527352 AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
1 AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
22527391 A
1 A
22527392 CCTTAGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (39 bp):
AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
Found at i:22527776 original size:21 final size:21
Alignment explanation
Indices: 22527750--22527798 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
22527740 GCTGTTTTTG
22527750 TTGTTTTTCCA-TGTTTTG-CTA
1 TTGTTTTTCCACT-TTTTGTC-A
22527771 TTGTTTTTCCACTTTTTGTCA
1 TTGTTTTTCCACTTTTTGTCA
22527792 TTGTTTT
1 TTGTTTT
22527799 GCTACCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.08, C:0.14, G:0.12, T:0.65
Consensus pattern (21 bp):
TTGTTTTTCCACTTTTTGTCA
Found at i:22529405 original size:9 final size:9
Alignment explanation
Indices: 22529391--22529422 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
22529381 GTTTAAAAAT
22529391 AATTTTTTA
1 AATTTTTTA
22529400 AATTTTTTA
1 AATTTTTTA
22529409 AATTTTTTA
1 AATTTTTTA
22529418 AATTT
1 AATTT
22529423 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
AATTTTTTA
Found at i:22530017 original size:7 final size:7
Alignment explanation
Indices: 22530005--22530047 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
22529995 TGCTGTAATT
22530005 ATTTTTA
1 ATTTTTA
22530012 ATTTTTA
1 ATTTTTA
22530019 TATGTTTTA
1 -AT-TTTTA
22530028 TATTTTTA
1 -ATTTTTA
*
22530036 AATTTTA
1 ATTTTTA
22530043 ATTTT
1 ATTTT
22530048 CACGAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 17 0.53
8 7 0.22
9 8 0.25
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:22530028 original size:9 final size:8
Alignment explanation
Indices: 22530004--22530041 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
22529994 TTGCTGTAAT
22530004 TATTTTTA
1 TATTTTTA
22530012 -ATTTTTA
1 TATTTTTA
22530019 TATGTTTTA
1 TAT-TTTTA
22530028 TATTTTTA
1 TATTTTTA
*
22530036 AATTTT
1 TATTTT
22530042 AATTTTCACG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 7 0.26
8 12 0.44
9 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (8 bp):
TATTTTTA
Found at i:22532022 original size:16 final size:15
Alignment explanation
Indices: 22532001--22532030 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
22531991 AGTTAACTCC
22532001 TCTTTTTTTATTTTTT
1 TCTTTTTTT-TTTTTT
22532017 TCTTTTTTTTTTTT
1 TCTTTTTTTTTTTT
22532031 AACTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (15 bp):
TCTTTTTTTTTTTTT
Found at i:22541751 original size:20 final size:18
Alignment explanation
Indices: 22541720--22541776 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 18
22541710 TCATTTTTCA
22541720 ATAAATTCAATTTCAATAATT
1 ATAAA-TCAATTT-AAT-ATT
22541741 -TAATATCAATTTAATATT
1 ATAA-ATCAATTTAATATT
22541759 ATAAATCAATTATAATAT
1 ATAAATCAATT-TAATAT
22541777 AGTCTGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 10 0.30
19 12 0.36
20 10 0.30
21 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATCAATTTAATATT
Found at i:22575315 original size:17 final size:16
Alignment explanation
Indices: 22575288--22575335 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
22575278 TGATAGTATA
22575288 ATTAT-ATTATTTAAT
1 ATTATAATTATTTAAT
22575303 ATTATGAATTATTT--T
1 ATTAT-AATTATTTAAT
*
22575318 ATTATAATT-GTTAAT
1 ATTATAATTATTTAAT
22575333 ATT
1 ATT
22575336 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 2 0.07
14 4 0.14
15 15 0.54
17 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTATAATTATTTAAT
Found at i:22582419 original size:2 final size:2
Alignment explanation
Indices: 22582414--22582441 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22582404 TCAAACTGTT
22582414 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22582442 GTAGGTATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22586918 original size:18 final size:18
Alignment explanation
Indices: 22586895--22586933 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
22586885 ATAACTGCCA
22586895 CTTAAATTTGCCTGGTAC
1 CTTAAATTTGCCTGGTAC
22586913 CTTAAATTTGCCTGGTAC
1 CTTAAATTTGCCTGGTAC
22586931 CTT
1 CTT
22586934 GTATTATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (18 bp):
CTTAAATTTGCCTGGTAC
Found at i:22597207 original size:9 final size:9
Alignment explanation
Indices: 22597193--22597217 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
22597183 CCTCCACCAC
22597193 CAACGACAA
1 CAACGACAA
22597202 CAACGACAA
1 CAACGACAA
22597211 CAACGAC
1 CAACGAC
22597218 GAAGATGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.36, G:0.12, T:0.00
Consensus pattern (9 bp):
CAACGACAA
Found at i:22606009 original size:29 final size:29
Alignment explanation
Indices: 22605955--22606010 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
22605945 CAACGGTGCC
* *
22605955 TTCGAACCAATAACTCAGATATCACTTGG
1 TTCGAACCAACAACTCAGATACCACTTGG
*
22605984 TTCGAACCAACAGCTCTA-ATACCACTT
1 TTCGAACCAACAACTC-AGATACCACTT
22606011 ATCATGGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.96
30 1 0.04
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.27
Consensus pattern (29 bp):
TTCGAACCAACAACTCAGATACCACTTGG
Found at i:22616762 original size:21 final size:21
Alignment explanation
Indices: 22616736--22616776 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22616726 AAATGAAACT
22616736 TGTTCTAATGGTCTCGAGACA
1 TGTTCTAATGGTCTCGAGACA
** *
22616757 TGTTCTTTTTGTCTCGAGAC
1 TGTTCTAATGGTCTCGAGAC
22616777 TAAATGGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (21 bp):
TGTTCTAATGGTCTCGAGACA
Found at i:22624915 original size:12 final size:12
Alignment explanation
Indices: 22624898--22624922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22624888 GGTGTTCATT
22624898 CGGTTAACCGAC
1 CGGTTAACCGAC
22624910 CGGTTAACCGAC
1 CGGTTAACCGAC
22624922 C
1 C
22624923 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:22625097 original size:9 final size:9
Alignment explanation
Indices: 22625083--22625344 Score: 384
Period size: 9 Copynumber: 29.1 Consensus size: 9
22625073 TTTGGTTAAA
22625083 AATTACCCG
1 AATTACCCG
22625092 AATTACCCG
1 AATTACCCG
22625101 AATTACCCG
1 AATTACCCG
22625110 AATTACCCG
1 AATTACCCG
22625119 AATTACCCG
1 AATTACCCG
22625128 AATTACCCG
1 AATTACCCG
*
22625137 AATTAACCG
1 AATTACCCG
22625146 AATTACCCG
1 AATTACCCG
*
22625155 AATTAACCG
1 AATTACCCG
22625164 AATTA-CCG
1 AATTACCCG
*
22625172 AAAAATA-CCG
1 --AATTACCCG
22625182 AATTACCCG
1 AATTACCCG
*
22625191 AATTAACCG
1 AATTACCCG
22625200 AATTACCCG
1 AATTACCCG
*
22625209 AATTAACCG
1 AATTACCCG
22625218 AATTACCCG
1 AATTACCCG
*
22625227 AATTAACCG
1 AATTACCCG
22625236 AATTACCCG
1 AATTACCCG
*
22625245 AATTAACCG
1 AATTACCCG
22625254 AATTACCCG
1 AATTACCCG
*
22625263 AATTAACCG
1 AATTACCCG
22625272 AATTACCCG
1 AATTACCCG
*
22625281 AATTAACCG
1 AATTACCCG
22625290 AATTACCCG
1 AATTACCCG
*
22625299 AATTAACCG
1 AATTACCCG
22625308 AATTACCCG
1 AATTACCCG
*
22625317 AATTAACCG
1 AATTACCCG
22625326 AATTACCCG
1 AATTACCCG
*
22625335 AATTAACCG
1 AATTACCCG
22625344 A
1 A
22625345 CCGATTAACT
Statistics
Matches: 228, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
8 7 0.03
9 214 0.94
10 7 0.03
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:22625106 original size:18 final size:18
Alignment explanation
Indices: 22625083--22625344 Score: 463
Period size: 18 Copynumber: 14.6 Consensus size: 18
22625073 TTTGGTTAAA
*
22625083 AATTACCCGAATTACCCG
1 AATTAACCGAATTACCCG
*
22625101 AATTACCCGAATTACCCG
1 AATTAACCGAATTACCCG
*
22625119 AATTACCCGAATTACCCG
1 AATTAACCGAATTACCCG
22625137 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625155 AATTAACCGAATTA-CCG
1 AATTAACCGAATTACCCG
**
22625172 AAAAATACCGAATTACCCG
1 AATTA-ACCGAATTACCCG
22625191 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625209 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625227 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625245 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625263 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625281 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625299 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625317 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
22625335 AATTAACCGA
1 AATTAACCGA
22625345 CCGATTAACT
Statistics
Matches: 237, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
17 6 0.03
18 225 0.95
19 6 0.03
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:22627733 original size:18 final size:17
Alignment explanation
Indices: 22627710--22627743 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22627700 TAAATTTGAT
*
22627710 TGAAAATATATAAAAAAA
1 TGAAAACAT-TAAAAAAA
22627728 TGAAAACATTAAAAAA
1 TGAAAACATTAAAAAA
22627744 TCTAAGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (17 bp):
TGAAAACATTAAAAAAA
Found at i:22640743 original size:33 final size:33
Alignment explanation
Indices: 22640706--22640772 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
22640696 TCGTCAAAAG
*
22640706 TAAAGAAAATACATCTAAATTTCTCGAGAATAA
1 TAAAGAAAATACATCTAAATTGCTCGAGAATAA
22640739 TAAAGAAAATACATCTAAATTGCTCGAGAATAA
1 TAAAGAAAATACATCTAAATTGCTCGAGAATAA
22640772 T
1 T
22640773 CTCCATAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (33 bp):
TAAAGAAAATACATCTAAATTGCTCGAGAATAA
Found at i:22646288 original size:22 final size:21
Alignment explanation
Indices: 22646255--22646298 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
22646245 CCAATATATA
* *
22646255 TATTTTAAATTTTTTTTAATT
1 TATTTTAAATTTGTTTGAATT
*
22646276 TATTATTATATTTGTTTGAATT
1 TATT-TTAAATTTGTTTGAATT
22646298 T
1 T
22646299 TTAGAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TATTTTAAATTTGTTTGAATT
Found at i:22673640 original size:126 final size:127
Alignment explanation
Indices: 22673404--22673746 Score: 526
Period size: 126 Copynumber: 2.7 Consensus size: 127
22673394 GAGAGGTCTG
* * *
22673404 TTTTAGGTCAGATGCACTGTTGTCAATCGGAGGTTGCTCCAAATCATCCATTAATGAAGAGGAAG
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATT-A-GAAGAGGAAG
* * *
22673469 TTGGCTGGCATGCCTCAAACTTAAAGTCGGCTGCATCGTAGGTAATCAGATTCTCCTCACCCTC
64 TTGGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATAGTAGGTAATCAGATTCTCCTCACCCTC
* * *
22673533 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTTCTCCAAATGATCCATTA-AAGAGGATGTT
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAGAAGAGGAAGTT
* *
22673597 GGCTGGCATGCCTCGAACTTAAAGTCAGTTGCATAGTAGGTAATCAGATTCTCTTCACCCTC
66 GGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATAGTAGGTAATCAGATTCTCCTCACCCTC
*
22673659 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTACTGTAGAGGAAG
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTA--GAAGAGGAAG
*
22673724 TTGTCTGGCATGCCTCGAACTTA
64 TTGGCTGGCATGCCTCGAACTTA
22673747 GAGTTGGCTG
Statistics
Matches: 195, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
126 118 0.61
128 1 0.01
129 76 0.39
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (127 bp):
TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAGAAGAGGAAGTT
GGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATAGTAGGTAATCAGATTCTCCTCACCCTC
Found at i:22675934 original size:15 final size:14
Alignment explanation
Indices: 22675911--22675945 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
22675901 TGCATATGTG
22675911 AAAAAAGAACAGTT
1 AAAAAAGAACAGTT
*
22675925 AAAAAGAGAATAGTT
1 AAAAA-AGAACAGTT
22675940 AAAAAA
1 AAAAAA
22675946 AAAAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAAAGAACAGTT
Found at i:22679952 original size:31 final size:30
Alignment explanation
Indices: 22679880--22679952 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
22679870 AATTAAATTA
*
22679880 AAATTAAAATTTTATATATTTATATCAACC
1 AAATTAAAATTTTATATATTTATAGCAACC
* *
22679910 ACAATTTAAATTTTATATGTATTAGT-GCAACC
1 A-AATTAAAATTTTATATAT-TTA-TAGCAACC
22679942 AAATTAAAATT
1 AAATTAAAATT
22679953 CATTCATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 1 0.03
31 25 0.69
32 9 0.25
33 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (30 bp):
AAATTAAAATTTTATATATTTATAGCAACC
Found at i:22680595 original size:18 final size:18
Alignment explanation
Indices: 22680574--22680627 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
22680564 TTTTTGTTCA
*
22680574 AAAATACTTTTTAACCCG
1 AAAATACTTTTTAGCCCG
* *
22680592 AAAATA--TTTT-GCTCA
1 AAAATACTTTTTAGCCCG
22680607 AAAATACTTTTTAGCCCG
1 AAAATACTTTTTAGCCCG
22680625 AAA
1 AAA
22680628 GCATTTTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 4 0.14
18 12 0.43
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAATACTTTTTAGCCCG
Found at i:22680602 original size:33 final size:33
Alignment explanation
Indices: 22680565--22680627 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
22680555 AAATTTTAAT
*
22680565 TTTTGTTCAAAAATACTTTTTAACCCGAAAATA
1 TTTTGCTCAAAAATACTTTTTAACCCGAAAATA
*
22680598 TTTTGCTCAAAAATACTTTTTAGCCCGAAA
1 TTTTGCTCAAAAATACTTTTTAACCCGAAA
22680628 GCATTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (33 bp):
TTTTGCTCAAAAATACTTTTTAACCCGAAAATA
Found at i:22680618 original size:17 final size:17
Alignment explanation
Indices: 22680564--22680618 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
22680554 AAAATTTTAA
*
22680564 TTTTTGTTCAAAAATAC
1 TTTTTGCTCAAAAATAC
* * *
22680581 TTTTTAACCCGAAAATA-
1 TTTTT-GCTCAAAAATAC
22680598 -TTTTGCTCAAAAATAC
1 TTTTTGCTCAAAAATAC
22680614 TTTTT
1 TTTTT
22680619 AGCCCGAAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 9 0.32
18 7 0.25
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (17 bp):
TTTTTGCTCAAAAATAC
Found at i:22685268 original size:43 final size:43
Alignment explanation
Indices: 22685202--22685348 Score: 174
Period size: 43 Copynumber: 3.4 Consensus size: 43
22685192 TCCCAAACGT
* *
22685202 GGTCTTACATGTAATCAAATAACGATGCCACTGTCCTAGACAG
1 GGTCTTACACGTAATCAAATAACGATGCCACTGTCCCAGACAG
* *
22685245 GGTCTTACACGTAATTAAGTAACGATGCCACTGTCCCAGACAG
1 GGTCTTACACGTAATCAAATAACGATGCCACTGTCCCAGACAG
* *
22685288 GGTCTTACACGTAAATCTCAAAT--TGATGCCAAC-GTCCCAGACAT
1 GGTCTTACACGT-AA--TCAAATAACGATGCC-ACTGTCCCAGACAG
*
22685332 GGTCTTACACGAAATCA
1 GGTCTTACACGTAATCA
22685349 CATTTCAGCA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
41 3 0.03
43 53 0.58
44 29 0.32
45 2 0.02
46 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
GGTCTTACACGTAATCAAATAACGATGCCACTGTCCCAGACAG
Found at i:22708708 original size:18 final size:19
Alignment explanation
Indices: 22708663--22708710 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
22708653 TTTTATGTTC
*
22708663 AAAATTTTAA-TATATTTT
1 AAAATTTTAAGTATATTTA
* *
22708681 AATATATTAAGTATA-TTA
1 AAAATTTTAAGTATATTTA
22708699 AAAATTTTAAGT
1 AAAATTTTAAGT
22708711 TAGTTATACT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
AAAATTTTAAGTATATTTA
Found at i:22709072 original size:18 final size:17
Alignment explanation
Indices: 22709026--22709064 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
22709016 AAAATATATA
* *
22709026 TTAAGTATATTAAAATT
1 TTAAATATATTAAACTT
22709043 TTAAATATATTAAACTT
1 TTAAATATATTAAACTT
22709060 TTAAA
1 TTAAA
22709065 ATTAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATATATTAAACTT
Found at i:22715160 original size:21 final size:20
Alignment explanation
Indices: 22715130--22715169 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
22715120 CCGCCACTCT
22715130 TTCTCCCCCTTAC-CCTCCCC
1 TTCTCCCCCTT-CTCCTCCCC
22715150 TTCTCGCCCCTTCTCCTCCC
1 TTCTC-CCCCTTCTCCTCCC
22715170 GAACGCCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.03, C:0.62, G:0.03, T:0.33
Consensus pattern (20 bp):
TTCTCCCCCTTCTCCTCCCC
Found at i:22727802 original size:26 final size:26
Alignment explanation
Indices: 22727766--22727818 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
22727756 ATCGAGGTTC
22727766 AACATTTGTTGCGAACTTTCGTGTTT
1 AACATTTGTTGCGAACTTTCGTGTTT
22727792 AACATTTGTTGCGAACTTTCGTGTTT
1 AACATTTGTTGCGAACTTTCGTGTTT
22727818 A
1 A
22727819 CTTTCCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (26 bp):
AACATTTGTTGCGAACTTTCGTGTTT
Found at i:22727880 original size:21 final size:21
Alignment explanation
Indices: 22727856--22727932 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
22727846 GTTGAACTCA
*
22727856 TATGAGTTTCTGTTTAACCCT
1 TATGAGTTTCTGTTCAACCCT
* * *
22727877 TATGGGTTTCCGTTCAGCTCC-
1 TATGAGTTTCTGTTCAAC-CCT
* *
22727898 TATGAGCTTCCGTTCAACCCT
1 TATGAGTTTCTGTTCAACCCT
22727919 TAT-AGGTTTCTGTT
1 TATGA-GTTTCTGTT
22727933 TAGCACTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.07
21 39 0.89
22 2 0.05
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (21 bp):
TATGAGTTTCTGTTCAACCCT
Found at i:22730500 original size:44 final size:44
Alignment explanation
Indices: 22730452--22730817 Score: 516
Period size: 44 Copynumber: 8.0 Consensus size: 44
22730442 TGAGTACTTC
* * * *
22730452 TGATCAATGACAAGTGATAATTAGTAGCTTCAGCTACACTTATCT
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTAT-T
* * * * *
22730497 GATCAATGACAAGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATC
1 --T-GAT--C-AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
*
22730547 TGATAAGTGAAAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
1 TGATCA--G-----TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
22730598 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
22730642 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
22730686 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
22730730 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
22730774 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
22730818 GGGCCCAAAA
Statistics
Matches: 294, Mismatches: 14, Indels: 25
0.88 0.04 0.08
Matches are distributed among these distances:
44 214 0.73
46 1 0.00
47 3 0.01
48 3 0.01
49 1 0.00
50 1 0.00
51 71 0.24
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (44 bp):
TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATT
Found at i:22732191 original size:17 final size:17
Alignment explanation
Indices: 22732169--22732202 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22732159 GACTAACCCC
*
22732169 TATACATCACTTAGGTA
1 TATACATCACCTAGGTA
*
22732186 TATACATTACCTAGGTA
1 TATACATCACCTAGGTA
22732203 CATGCCACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
TATACATCACCTAGGTA
Found at i:22735357 original size:2 final size:2
Alignment explanation
Indices: 22735350--22735402 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
22735340 NNNNNNNNAG
22735350 AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22735387 AT A- AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
22735403 AAAACATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
1 8 0.19
2 35 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:22735374 original size:5 final size:5
Alignment explanation
Indices: 22735352--22735430 Score: 67
Period size: 5 Copynumber: 15.6 Consensus size: 5
22735342 NNNNNNAGAT
22735352 ATATA TATATA TATATA ATATA ATATA ATAT- AT-TA ATAATA ATATA
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
* *
22735398 ATATA A-A-A ACATA ATCATTA CTATA ATATA ATA
1 ATATA ATATA ATATA AT-A-TA ATATA ATATA ATA
22735431 ATATTTTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
3 3 0.05
4 6 0.10
5 34 0.54
6 17 0.27
7 3 0.05
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:22735382 original size:19 final size:18
Alignment explanation
Indices: 22735350--22735402 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
22735340 NNNNNNNNAG
22735350 ATAT-ATATATATATATATA
1 ATATAATATA-ATATAT-TA
22735369 ATATAATATAATATATTA
1 ATATAATATAATATATTA
22735387 ATAATAATATAATATA
1 AT-ATAATATAATATA
22735403 AAAACATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.12
19 23 0.72
20 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATATAATATATTA
Found at i:22735412 original size:24 final size:25
Alignment explanation
Indices: 22735366--22735431 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
22735356 ATATATATAT
* *
22735366 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
22735390 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
22735415 TTACTATAATATAATAA
1 ATAATATAATATAATAA
22735432 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 18 0.51
25 13 0.37
26 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:22737086 original size:25 final size:26
Alignment explanation
Indices: 22737031--22737166 Score: 82
Period size: 24 Copynumber: 5.7 Consensus size: 26
22737021 GTCGTAATCA
*
22737031 GGAAGCTCAT-GCA-AGCCAA-TATTG
1 GGAAGCTCATAG-AGAGCCAATTATCG
22737055 GGAAGCTC-TAGAGAGCCAATTATCG
1 GGAAGCTCATAGAGAGCCAATTATCG
* * *
22737080 GGAAGCTCATA-TGAGCC-ATAAACG
1 GGAAGCTCATAGAGAGCCAATTATCG
* * *
22737104 GAAAGCTCA-ATAGAGTC-ATTAATCG
1 GGAAGCTCATAGAGAGCCAATT-ATCG
*
22737129 GGAAGCTCGT-GAGAGCC-A-TA-CG
1 GGAAGCTCATAGAGAGCCAATTATCG
*
22737151 GGATGCTCATA-AGAGC
1 GGAAGCTCATAGAGAGC
22737167 TAAATAATGG
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
22 15 0.17
23 4 0.04
24 35 0.39
25 33 0.37
26 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (26 bp):
GGAAGCTCATAGAGAGCCAATTATCG
Found at i:22739489 original size:22 final size:21
Alignment explanation
Indices: 22739456--22739498 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
22739446 TTACATGTAG
*
22739456 TTATTAAGTAAATTATATTAT
1 TTATTAAGTAAATAATATTAT
*
22739477 TTATGTAATTAAATAATATTAT
1 TTAT-TAAGTAAATAATATTAT
22739499 ACTTCGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATTAAGTAAATAATATTAT
Found at i:22755372 original size:17 final size:17
Alignment explanation
Indices: 22755341--22755379 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
22755331 TTTTATATTG
22755341 AATTGAATGTATGTGA-
1 AATTGAATGTATGTGAT
*
22755357 AATTGAGATTTATGTGAT
1 AATTGA-ATGTATGTGAT
22755375 AATTG
1 AATTG
22755380 TGGCATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (17 bp):
AATTGAATGTATGTGAT
Found at i:22757815 original size:74 final size:75
Alignment explanation
Indices: 22757583--22757850 Score: 242
Period size: 74 Copynumber: 3.6 Consensus size: 75
22757573 AGCATGTAAA
* * * * *
22757583 CAGGAAGCTCTTCCAAGCCATATAATGGGAAGCTCATGTGAGCCATGTAA-CGGGAAGCTCATAA
1 CAGGAAGCTCATACGAGCCATATAATGGGAAGCTCATGAGAGCCAT-TAATCGGGAAGCTCATGA
* *
22757647 GAGTCGTA-AT
65 GAGCCATATAT
* * * ** * *
22757657 CAAGAAGCTCATGCAAGCCA-AT-ATCGGGAAGCTCCGGAGAGCCATTAATCAGAAAGCTCATGA
1 CAGGAAGCTCATACGAGCCATATAAT-GGGAAGCTCATGAGAGCCATTAATCGGGAAGCTCATGA
22757720 GAGCCA-ATTAT
65 GAGCCATA-TAT
* * *
22757731 CAGGAGGCTCATACGAGCCATA-AATGGGAAGCTCAAGAGAGCCATTAATCGGGAAGCTCGTGAG
1 CAGGAAGCTCATACGAGCCATATAATGGGAAGCTCATGAGAGCCATTAATCGGGAAGCTCATGAG
*
22757795 AGCCATATAA
66 AGCCATATAT
* * * * * * *
22757805 CGGGATGCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAT
1 CAGGAAGCTCATACGAGCCATATAATGGGAAGCTCATGAGAGCCAT
22757851 ATAACATGAT
Statistics
Matches: 157, Mismatches: 29, Indels: 15
0.78 0.14 0.07
Matches are distributed among these distances:
72 6 0.04
73 34 0.22
74 93 0.59
75 24 0.15
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (75 bp):
CAGGAAGCTCATACGAGCCATATAATGGGAAGCTCATGAGAGCCATTAATCGGGAAGCTCATGAG
AGCCATATAT
Found at i:22757834 original size:50 final size:50
Alignment explanation
Indices: 22757780--22757884 Score: 183
Period size: 50 Copynumber: 2.1 Consensus size: 50
22757770 AGCCATTAAT
*
22757780 CGGGAAGCTCGTGAGAGCCATATAACGGGATGCTCATAAGAGCTAAATAA
1 CGGGAAGCTCGTGAGAGCCATATAACAGGATGCTCATAAGAGCTAAATAA
*
22757830 CGGGAAGCTCGTGAGAGCCATATAACATGATGCTCATAAGAGCTAAATAA
1 CGGGAAGCTCGTGAGAGCCATATAACAGGATGCTCATAAGAGCTAAATAA
*
22757880 TGGGA
1 CGGGA
22757885 CGCTTTTGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (50 bp):
CGGGAAGCTCGTGAGAGCCATATAACAGGATGCTCATAAGAGCTAAATAA
Found at i:22757855 original size:25 final size:25
Alignment explanation
Indices: 22757598--22757855 Score: 190
Period size: 25 Copynumber: 10.4 Consensus size: 25
22757588 AGCTCTTCCA
* *
22757598 AGCCATATAATGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGAG
* *
22757623 AGCCATGTAACGGGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
* * * **
22757648 AGTCGTA-ATCAAGAAGCTCATGCA-
1 AGCCATATAACGGGAAGCTCATG-AG
* **
22757672 AGCCA-ATATCGGGAAGCTCCGGAG
1 AGCCATATAACGGGAAGCTCATGAG
* *
22757696 AGCCAT-TAATCAGAAAGCTCATGAG
1 AGCCATATAA-CGGGAAGCTCATGAG
* * *
22757721 AGCCA-ATTATCAGGAGGCTCAT-ACG
1 AGCCATA-TAACGGGAAGCTCATGA-G
* *
22757746 AGCCATA-AATGGGAAGCTCAAGAG
1 AGCCATATAACGGGAAGCTCATGAG
*
22757770 AGCCAT-TAATCGGGAAGCTCGTGAG
1 AGCCATATAA-CGGGAAGCTCATGAG
* *
22757795 AGCCATATAACGGGATGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
* * *
22757820 AGCTAAATAACGGGAAGCTCGTGAG
1 AGCCATATAACGGGAAGCTCATGAG
22757845 AGCCATATAAC
1 AGCCATATAAC
22757856 ATGATGCTCA
Statistics
Matches: 177, Mismatches: 43, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
23 2 0.01
24 51 0.29
25 118 0.67
26 6 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.18
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGAG
Found at i:22757871 original size:25 final size:25
Alignment explanation
Indices: 22757737--22757872 Score: 116
Period size: 25 Copynumber: 5.5 Consensus size: 25
22757727 TTATCAGGAG
* * *
22757737 GCTCATACGAGCCATA-AATGGGAA
1 GCTCATAAGAGCCATATAACGGGAT
*
22757761 GCTCA-AGAGAGCCAT-TAATCGGGAA
1 GCTCATA-AGAGCCATATAA-CGGGAT
* *
22757786 GCTCGTGAGAGCCATATAACGGGAT
1 GCTCATAAGAGCCATATAACGGGAT
* * *
22757811 GCTCATAAGAGCTAAATAACGGGAA
1 GCTCATAAGAGCCATATAACGGGAT
* * **
22757836 GCTCGTGAGAGCCATATAACATGAT
1 GCTCATAAGAGCCATATAACGGGAT
22757861 GCTCATAAGAGC
1 GCTCATAAGAGC
22757873 TAAATAATGG
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
23 1 0.01
24 14 0.16
25 70 0.80
26 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.18
Consensus pattern (25 bp):
GCTCATAAGAGCCATATAACGGGAT
Found at i:22769116 original size:29 final size:31
Alignment explanation
Indices: 22769065--22769126 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
22769055 TCATTTCAAC
22769065 TTTATAATTTTTAAAGGATTAAA-TAAAATT
1 TTTATAATTTTTAAAGGATTAAAGTAAAATT
* *
22769095 TTTATCATTTTT-AA-GAGTTAAAGTACAATT
1 TTTATAATTTTTAAAGGA-TTAAAGTAAAATT
22769125 TT
1 TT
22769127 ACTTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 7 0.25
30 19 0.68
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGATTAAAGTAAAATT
Found at i:22778832 original size:12 final size:12
Alignment explanation
Indices: 22778815--22778850 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
22778805 AGGCATTCTT
*
22778815 CTGCTACTGCTA
1 CTGCTACTACTA
22778827 CTGCTACTACTA
1 CTGCTACTACTA
*
22778839 CTACTACTACTA
1 CTGCTACTACTA
22778851 TCTTTTATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.08, T:0.33
Consensus pattern (12 bp):
CTGCTACTACTA
Found at i:22792095 original size:22 final size:23
Alignment explanation
Indices: 22792067--22792120 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
22792057 ATTAATGAAT
*
22792067 AGAGAGCACTA-AAGTGCTATAC
1 AGAGAGCACTAGAAGTGCTAAAC
*
22792089 AGAGAGCAC-AGATGTGCTAAAC
1 AGAGAGCACTAGAAGTGCTAAAC
*
22792111 GGAGAGCACT
1 AGAGAGCACT
22792121 GTCGTGCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.15
Consensus pattern (23 bp):
AGAGAGCACTAGAAGTGCTAAAC
Found at i:22800115 original size:22 final size:22
Alignment explanation
Indices: 22800090--22800152 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
22800080 TGGTTATAAT
22800090 TAATTAAATAGTTAGTGAATTC
1 TAATTAAATAGTTAGTGAATTC
22800112 TAATCT-AAT-G--A-TG-A-T-
1 TAAT-TAAATAGTTAGTGAATTC
22800127 TAATTAAATAGTTAGTGAATTC
1 TAATTAAATAGTTAGTGAATTC
22800149 TAAT
1 TAAT
22800153 CTAATGGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 18
0.64 0.00 0.36
Matches are distributed among these distances:
14 1 0.03
15 7 0.22
16 2 0.06
17 1 0.03
18 3 0.09
19 3 0.09
20 1 0.03
21 2 0.06
22 11 0.34
23 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (22 bp):
TAATTAAATAGTTAGTGAATTC
Found at i:22800129 original size:37 final size:37
Alignment explanation
Indices: 22800088--22800158 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
22800078 GCTGGTTATA
22800088 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGATG
1 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGATG
22800125 ATTAATTAAATAGTTAGTGAATTCTAATCTAATG
1 ATTAATTAAATAGTTAGTGAATTCTAATCTAATG
22800159 GAAAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (37 bp):
ATTAATTAAATAGTTAGTGAATTCTAATCTAATGATG
Found at i:22801746 original size:35 final size:36
Alignment explanation
Indices: 22801702--22801778 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 36
22801692 ATTTGTTAGA
*
22801702 TATTGATTATGTTTTAACCTTA-TTGGATATTGAATT
1 TATTGATTATGTTTTAACC-TAGTTGGATATTGAAAT
*
22801738 TATT-ATTATGTTTTAAGCTAGTTGGATATTGAAAT
1 TATTGATTATGTTTTAACCTAGTTGGATATTGAAAT
22801773 TATTGA
1 TATTGA
22801779 CAATGATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 2 0.05
35 30 0.81
36 5 0.14
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.51
Consensus pattern (36 bp):
TATTGATTATGTTTTAACCTAGTTGGATATTGAAAT
Found at i:22802926 original size:14 final size:15
Alignment explanation
Indices: 22802904--22802980 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
22802894 CAATCAAACA
22802904 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
22802918 CCAGGAAATCATTTT
1 CCAGAAAATCATTTT
*
22802933 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
22802953 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
22802967 CCGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
22802981 ACTGCCAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 22 0.43
15 15 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:22807441 original size:23 final size:24
Alignment explanation
Indices: 22807421--22807466 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
22807411 AAATAGGATG
22807421 TGATAGGTG-AAATTTTTAGGAAT
1 TGATAGGTGAAAATTTTTAGGAAT
* *
22807444 TGATGGGTGAAAATTTTTTGGAA
1 TGATAGGTGAAAATTTTTAGGAA
22807467 GAGTGGACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (24 bp):
TGATAGGTGAAAATTTTTAGGAAT
Found at i:22807851 original size:6 final size:6
Alignment explanation
Indices: 22807836--22807880 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
22807826 GTTTCCCTGC
22807836 AAAAAT -AAAAT AAAAAT AAAAAT -AAAAT AAAATAGT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA
22807881 TAAATAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 10 0.29
6 18 0.51
7 2 0.06
8 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:22807852 original size:11 final size:11
Alignment explanation
Indices: 22807836--22807869 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
22807826 GTTTCCCTGC
22807836 AAAAATAAAAT
1 AAAAATAAAAT
22807847 AAAAATAAAA-
1 AAAAATAAAAT
22807857 ATAAAATAAAAT
1 A-AAAATAAAAT
22807869 A
1 A
22807870 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 19 0.90
12 1 0.05
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:22807858 original size:17 final size:17
Alignment explanation
Indices: 22807836--22807890 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 17
22807826 GTTTCCCTGC
22807836 AAAAATAAAATAAAAAT
1 AAAAATAAAATAAAAAT
22807853 AAAAATAAAATAAAATAGT
1 AAAAATAAAATAAAA-A-T
22807872 AAAAAT-AAATAAATAAT
1 AAAAATAAAATAAA-AAT
22807889 AA
1 AA
22807891 TTATAATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 18 0.51
18 9 0.26
19 8 0.23
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:22811542 original size:18 final size:18
Alignment explanation
Indices: 22811521--22811563 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
22811511 ATGATATCGA
*
22811521 TATTGATGATAGTGACGC
1 TATTGATGATAATGACGC
*
22811539 TATTGATGATAATGACTC
1 TATTGATGATAATGACGC
22811557 TATTGAT
1 TATTGAT
22811564 CGTGACCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (18 bp):
TATTGATGATAATGACGC
Found at i:22812232 original size:249 final size:250
Alignment explanation
Indices: 22811787--22812285 Score: 964
Period size: 249 Copynumber: 2.0 Consensus size: 250
22811777 GATTGTGAAA
22811787 GATGTTCCATTAGAAATATTCTTGTTATTGCTTCGACTCATATTCCCCAAAAAGTGGATCCCACT
1 GATGTTCCATTAGAAATATTCTTGTTATTGCTTCGACTCATATTCCCCAAAAAGTGGATCCCACT
*
22811852 CTAATAGCCCCGAATAAATTAAATACATGTATTAAGATACGAAGGCTTCTTATTCCACAACAACG
66 CTAATAGCCCCGAATAAATTAAATACATGTATTAAGATACCAAGGCTTCTTATTCCACAACAACG
22811917 AAAGCACTTTTTCACTCTTTCATATACTAGGGGATTTCACTTGAAAAAGAAAATGTTCCATACTA
131 AAAGCACTTTTTCACTCTTTCATATACTAGGGGATTTCACTTGAAAAAGAAAATGTTCCATACTA
22811982 ATAGATTCGGGTCCATAACCGTGGGTTTCATAGTATTACCGGTAATGTGTCTTTC
196 ATAGATTCGGGTCCATAACCGTGGGTTTCATAGTATTACCGGTAATGTGTCTTTC
* *
22812037 GATGTT-CATTAGAAATATTCTTGTTATTGCTTCGACTCATATTCCCCAAAATGTGGATCTCACT
1 GATGTTCCATTAGAAATATTCTTGTTATTGCTTCGACTCATATTCCCCAAAAAGTGGATCCCACT
22812101 CTAATAGCCCCGAATAAATTAAATACATGTATTAAGATACCAAGGCTTCTTATTCCACAACAACG
66 CTAATAGCCCCGAATAAATTAAATACATGTATTAAGATACCAAGGCTTCTTATTCCACAACAACG
22812166 AAAGCACTTTTTCACTCTTTCATATACTAGGGGATTTCACTTGAAAAAGAAAATGTTCCATACTA
131 AAAGCACTTTTTCACTCTTTCATATACTAGGGGATTTCACTTGAAAAAGAAAATGTTCCATACTA
22812231 ATAGATTCGGGTCCATAACCGTGGGTTTCATAGTATTACCGGTAATGTGTCTTTC
196 ATAGATTCGGGTCCATAACCGTGGGTTTCATAGTATTACCGGTAATGTGTCTTTC
22812286 TCTCCCAAAA
Statistics
Matches: 246, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
249 240 0.98
250 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (250 bp):
GATGTTCCATTAGAAATATTCTTGTTATTGCTTCGACTCATATTCCCCAAAAAGTGGATCCCACT
CTAATAGCCCCGAATAAATTAAATACATGTATTAAGATACCAAGGCTTCTTATTCCACAACAACG
AAAGCACTTTTTCACTCTTTCATATACTAGGGGATTTCACTTGAAAAAGAAAATGTTCCATACTA
ATAGATTCGGGTCCATAACCGTGGGTTTCATAGTATTACCGGTAATGTGTCTTTC
Found at i:22814748 original size:43 final size:43
Alignment explanation
Indices: 22814679--22814902 Score: 292
Period size: 43 Copynumber: 5.3 Consensus size: 43
22814669 GATATGATTT
* *
22814679 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
*
22814722 CGTGTAAGACCACATCTGCGACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
** * * * *
22814765 CGTGTAAGACCATGTTTGAGACGTTGGCACCAACTTGTGTTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
* *
22814808 CGTGTAAGACCACATCTGGAACATTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
* * *
22814851 CGTGTAAGACCATATCTGGGACATTGGCATCGTA-TT-TGATT-
1 CGTGTAAGACCACATCTGGGACGTTGGCATCG-ACTTGTGTTTA
22814892 CGTGTAAGACC
1 CGTGTAAGACC
22814903 CTGTCTAGGA
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
41 11 0.07
42 4 0.03
43 144 0.90
44 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
Found at i:22819065 original size:13 final size:13
Alignment explanation
Indices: 22819013--22819089 Score: 100
Period size: 13 Copynumber: 5.9 Consensus size: 13
22819003 AGTTCTTCAT
22819013 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
22819026 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
22819039 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
22819052 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
22819065 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
22819078 TGCTTTTGAAAA
1 TGCTTTTGAAAA
22819090 ATTTGAGTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 58 1.00
ACGTcount: A:0.29, C:0.08, G:0.30, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:22823276 original size:1 final size:1
Alignment explanation
Indices: 22823270--22823295 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
22823260 AGCCATGCCC
22823270 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
22823296 ACGCTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22828710 original size:46 final size:46
Alignment explanation
Indices: 22828574--22828712 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 46
22828564 ACAATGCTAT
* * *
22828574 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCAC
* * *
22828620 AACTTAGTATGGTTTTCGTTACTGAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCAC
* * * *
22828666 AACTCAGTATGATTTTCTTTACTGAATTACCATACTTGCATTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCAC
22828712 A
1 A
22828713 CTTTGCCATG
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCAC
Found at i:22832805 original size:109 final size:110
Alignment explanation
Indices: 22832650--22832870 Score: 435
Period size: 109 Copynumber: 2.0 Consensus size: 110
22832640 ATAAGAAAAT
22832650 AATTAAAAGAAATTTATTTAAATATATATAAATTCTATAAAATAATTTAAATCCAAAATAAATAA
1 AATTAAAAGAAATTTATTTAAATATATATAAATTCTATAAAATAATTTAAATCCAAAATAAATAA
22832715 CTCAATTTTGTAATTTCAAACAAATTCTCATTTATTTCTTACTTA
66 CTCAATTTTGTAATTTCAAACAAATTCTCATTTATTTCTTACTTA
22832760 AATTAAAAG-AATTTATTTAAATATATATAAATTCTATAAAATAATTTAAATCCAAAATAAATAA
1 AATTAAAAGAAATTTATTTAAATATATATAAATTCTATAAAATAATTTAAATCCAAAATAAATAA
22832824 CTCAATTTTGTAATTTCAAACAAATTCTCATTTATTTCTTACTTA
66 CTCAATTTTGTAATTTCAAACAAATTCTCATTTATTTCTTACTTA
22832869 AA
1 AA
22832871 GTTTTTATAA
Statistics
Matches: 111, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
109 102 0.92
110 9 0.08
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.41
Consensus pattern (110 bp):
AATTAAAAGAAATTTATTTAAATATATATAAATTCTATAAAATAATTTAAATCCAAAATAAATAA
CTCAATTTTGTAATTTCAAACAAATTCTCATTTATTTCTTACTTA
Found at i:22845978 original size:1 final size:1
Alignment explanation
Indices: 22845974--22846019 Score: 83
Period size: 1 Copynumber: 46.0 Consensus size: 1
22845964 ACAAAAACGT
*
22845974 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22846020 CAAACCCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.98, C:0.02, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22853920 original size:16 final size:18
Alignment explanation
Indices: 22853881--22853914 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22853871 TAAGTTTATA
22853881 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
22853898 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
22853915 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:22866358 original size:41 final size:41
Alignment explanation
Indices: 22866301--22866444 Score: 234
Period size: 41 Copynumber: 3.5 Consensus size: 41
22866291 AATTGAAATT
*
22866301 TTCAGACTTAAAGTCTAGCAGGTTTAATGCCGGTGATATAA
1 TTCAGACTTAAAGTCTAGCAGGTTTAAGGCCGGTGATATAA
*
22866342 TTCAGACTTAAAGTCTAGCAGGCTTAAGGCCGGTGATATAA
1 TTCAGACTTAAAGTCTAGCAGGTTTAAGGCCGGTGATATAA
* *
22866383 TTCAGACTTAAAGTCTAGCAGGTTTAAGGCCAGTGAAATAA
1 TTCAGACTTAAAGTCTAGCAGGTTTAAGGCCGGTGATATAA
* *
22866424 TTCGGACTTTAAGTCTAGCAG
1 TTCAGACTTAAAGTCTAGCAG
22866445 ACTAATTGCT
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (41 bp):
TTCAGACTTAAAGTCTAGCAGGTTTAAGGCCGGTGATATAA
Found at i:22866966 original size:41 final size:41
Alignment explanation
Indices: 22866909--22867292 Score: 768
Period size: 41 Copynumber: 9.4 Consensus size: 41
22866899 ATTGAAATTT
22866909 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22866950 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22866991 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22867032 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22867073 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22867114 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22867155 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22867196 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22867237 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
22867278 GTGATCTGAATCAGG
1 GTGATCTGAATCAGG
22867293 GGAACTTAAA
Statistics
Matches: 343, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 343 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (41 bp):
GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
Found at i:22867591 original size:2 final size:2
Alignment explanation
Indices: 22867546--22867575 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22867536 TTTGTTAAGC
22867546 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22867576 GCATTTCGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22873488 original size:15 final size:15
Alignment explanation
Indices: 22873468--22873498 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
22873458 CAGCTAGTGA
22873468 ACCTCGAATCCATTC
1 ACCTCGAATCCATTC
22873483 ACCTCGAATCCATTC
1 ACCTCGAATCCATTC
22873498 A
1 A
22873499 ACAGACGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.39, G:0.06, T:0.26
Consensus pattern (15 bp):
ACCTCGAATCCATTC
Found at i:22881792 original size:17 final size:18
Alignment explanation
Indices: 22881762--22881800 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
22881752 GTTGAACTGA
*
22881762 AATTTTTAAAAA-TTTTT
1 AATTTGTAAAAATTTTTT
*
22881779 AATTTGTAATAATTTTTT
1 AATTTGTAAAAATTTTTT
22881797 AATT
1 AATT
22881801 AGATTGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTTGTAAAAATTTTTT
Found at i:22883708 original size:16 final size:16
Alignment explanation
Indices: 22883686--22883724 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
22883676 TACACCATAA
22883686 AAAATTAAAT-TAATT
1 AAAATTAAATATAATT
22883701 ATAAATTAAATAATAATT
1 A-AAATTAAAT-ATAATT
22883719 AAAATT
1 AAAATT
22883725 CGATTGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 9 0.43
17 5 0.24
18 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTAAATATAATT
Found at i:22888003 original size:13 final size:13
Alignment explanation
Indices: 22887982--22888015 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
22887972 TCTTTGATTT
22887982 ATTATTTTATTTTA
1 ATTA-TTTATTTTA
*
22887996 GTTATTTATTTTA
1 ATTATTTATTTTA
22888009 ATTATTT
1 ATTATTT
22888016 TATCTGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
ATTATTTATTTTA
Found at i:22889677 original size:22 final size:22
Alignment explanation
Indices: 22889650--22889705 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
22889640 TGGGCACGGT
22889650 AAAGAAAAAAAAAAGAGAGAAAG
1 AAAGAAAAAAAAAAGA-AGAAAG
* * *
22889673 -GAGAAAAGAAGAAGAAGAAAG
1 AAAGAAAAAAAAAAGAAGAAAG
22889694 AAAGAAAAAAAA
1 AAAGAAAAAAAA
22889706 GGTAATGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAAAAAGAAGAAAG
Found at i:22889786 original size:12 final size:12
Alignment explanation
Indices: 22889769--22889794 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22889759 TTTGTGAATT
22889769 TTTTAGAAGATA
1 TTTTAGAAGATA
22889781 TTTTAGAAGATA
1 TTTTAGAAGATA
22889793 TT
1 TT
22889795 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:22889911 original size:19 final size:19
Alignment explanation
Indices: 22889887--22890049 Score: 100
Period size: 19 Copynumber: 8.1 Consensus size: 19
22889877 TTTAACTTTT
22889887 TTGTATGAATATTGTAATA
1 TTGTATGAATATTGTAATA
22889906 TTGTATGAATATTGTAATTAA
1 TTGTATGAATATTGTAA-T-A
*
22889927 TT-TAT-AATTAAATTTGTATTTA
1 TTGTATGAA-T--A-TTGTA-ATA
* * * *
22889949 TAGTTTTGGAT-TAGTAAT-
1 TTG-TATGAATATTGTAATA
*
22889967 TTGTATGAATATTGTAATTTT
1 TTGTATGAATATTGTAA--TA
*
22889988 TTGTATGAATATTGTAATT
1 TTGTATGAATATTGTAATA
* *
22890007 TTGTATGAATGTTGTAATTTTT
1 TTGTATGAATATTGTAA---TA
22890029 TTGTATGAATATTGTAATA
1 TTGTATGAATATTGTAATA
22890048 TT
1 TT
22890050 ATAGTTTTGT
Statistics
Matches: 114, Mismatches: 13, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
17 5 0.04
18 7 0.06
19 41 0.36
20 10 0.09
21 20 0.18
22 21 0.18
23 6 0.05
24 3 0.03
25 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATA
Found at i:22890004 original size:101 final size:101
Alignment explanation
Indices: 22889844--22890199 Score: 313
Period size: 101 Copynumber: 3.7 Consensus size: 101
22889834 ATATTTAGTG
*
22889844 TTTATAGTTTAGATTAGAATTTTGTATGAATATTTTAACTTTTTTGTATGAATATTGTAATATTG
1 TTTATAGTTTAGATTAGAATTTTGTATGAATATTGTAACTTTTTTGTATGAATATTGTAATATTG
22889909 TATGAATATTGTAATTAATTTATAATTAAATTTGTA
66 TATGAATATTGTAATTAATTTATAATTAAATTTGTA
* *
22889945 TTTATAGTTTTGGATTAGTAA-TTTGTATGAATATTGTAA-TTTTTTGTATGAATATTGTAATTT
1 TTTATAG-TTTAGATTAG-AATTTTGTATGAATATTGTAACTTTTTTGTATGAATATTGTAATAT
* ** * *
22890008 TGTATGAATGTTGTAATTTTTTTGT-A-TGAATATTGTA
64 TGTATGAATATTGTAATTAATTTATAATTAAAT-TTGTA
*
22890045 ---ATA--TT--A-TAG--TTTTGTATGAATATTG-AATTTTTTTTGTATGAATATTGTAAT-TT
1 TTTATAGTTTAGATTAGAATTTTGTATGAATATTGTAA-CTTTTTTGTATGAATATTGTAATATT
* * * * **
22890098 -TGT-AATTTTGT-ATGAATATTGTAATT-TTTTTGTA
65 GTATGAATATTGTAATTAAT-TTATAATTAAATTTGTA
** * * * *
22890132 TAAATA-TTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATAT
1 TTTATAGTT-T-AGATTAGAATTTTGTATGAATATTGTAACTTTTTTGTATGAATATTGTAATAT
22890196 TGTA
64 TGTA
22890200 ATTTTTTGTA
Statistics
Matches: 215, Mismatches: 17, Indels: 47
0.77 0.06 0.17
Matches are distributed among these distances:
86 3 0.01
87 16 0.07
88 6 0.03
89 18 0.08
90 25 0.12
91 4 0.02
92 2 0.01
94 2 0.01
95 1 0.00
96 2 0.01
97 3 0.01
98 39 0.18
99 8 0.04
100 7 0.03
101 51 0.24
102 26 0.12
103 2 0.01
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (101 bp):
TTTATAGTTTAGATTAGAATTTTGTATGAATATTGTAACTTTTTTGTATGAATATTGTAATATTG
TATGAATATTGTAATTAATTTATAATTAAATTTGTA
Found at i:22890011 original size:90 final size:90
Alignment explanation
Indices: 22889917--22890202 Score: 253
Period size: 98 Copynumber: 3.1 Consensus size: 90
22889907 TGTATGAATA
** **
22889917 TTGTAATTAAT-TTATAATTAAATTTGTATTTATAGTT-TTGGATTAGTA-ATTTGTATGAATAT
1 TTGTAATTAATGTTATAATT-AATTTGTATGAATA-TTGTAAGATTA-TAGATTTGTATGAATAT
22889979 TGTAA-TTTTTTGTATGAATATTGTAATT
63 TG-AATTTTTTTGTATGAATATTGTAATT
* * ** * *
22890007 TTGT-ATGAATGTTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGA
1 TTGTAATTAATGTTATAATTAATTTGTATGAATATTGTAAGATTATAGATTTGTATGAATATTGA
22890071 ATTTTTTTTGTATGAATATTGTAATT
66 A-TTTTTTTGTATGAATATTGTAATT
* * * *
22890097 TTGTAATT-TTGTATGAATATTGTAATTTTTTTGTATAAATATTGTAATATTATA-ATTTTGTAT
1 TTGTAATTAATGT-T--ATAAT-TAA----TTTGTATGAATATTGTAAGATTATAGA-TTTGTAT
*
22890160 GAATATTGCAATTTTTTTGTATGAATATTGTAATA
57 GAATATTG-AATTTTTTTGTATGAATATTGTAATT
22890195 TTGTAATT
1 TTGTAATT
22890203 TTTTGTATGA
Statistics
Matches: 161, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
88 6 0.04
89 35 0.22
90 41 0.25
91 3 0.02
93 3 0.02
94 1 0.01
98 70 0.43
99 2 0.01
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (90 bp):
TTGTAATTAATGTTATAATTAATTTGTATGAATATTGTAAGATTATAGATTTGTATGAATATTGA
ATTTTTTTGTATGAATATTGTAATT
Found at i:22890031 original size:22 final size:22
Alignment explanation
Indices: 22889966--22890193 Score: 250
Period size: 22 Copynumber: 9.9 Consensus size: 22
22889956 GGATTAGTAA
22889966 TTTGTATGAATATTGTAA-TTT
1 TTTGTATGAATATTGTAATTTT
22889987 TTTGTATGAATATTGTAA---T
1 TTTGTATGAATATTGTAATTTT
*
22890006 TTTGTATGAATGTTGTAATTTT
1 TTTGTATGAATATTGTAATTTT
22890028 TTTGTATGAATATTGTAATATTATAGT
1 TTTGTATGAATATTGT-A-ATT-T--T
22890055 TTTGTATGAATATTG-AATTTTT
1 TTTGTATGAATATTGTAA-TTTT
22890077 TTTGTATGAATATTGTAATTTTGTAAT
1 TTTGTATGAATATTGTAA--TT-T--T
22890104 TTTGTATGAATATTGTAATTTT
1 TTTGTATGAATATTGTAATTTT
*
22890126 TTTGTATAAATATTGTAATATTATAAT
1 TTTGTATGAATATTGT-A-ATT-T--T
*
22890153 TTTGTATGAATATTGCAATTTT
1 TTTGTATGAATATTGTAATTTT
22890175 TTTGTATGAATATTGTAAT
1 TTTGTATGAATATTGTAAT
22890194 ATTGTAATTT
Statistics
Matches: 182, Mismatches: 6, Indels: 37
0.81 0.03 0.16
Matches are distributed among these distances:
19 18 0.10
21 18 0.10
22 67 0.37
23 4 0.02
24 13 0.07
25 11 0.06
26 1 0.01
27 50 0.27
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (22 bp):
TTTGTATGAATATTGTAATTTT
Found at i:22890058 original size:49 final size:49
Alignment explanation
Indices: 22889995--22890221 Score: 357
Period size: 49 Copynumber: 4.6 Consensus size: 49
22889985 TTTTTGTATG
*
22889995 AATATTGTAATTTTGTATGAATGTTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* *
22890044 AATATTATAGTTTTGTATGAATATTG-AATTTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAA-TTTTTTTGTATGAATATTGT
* *
22890093 AATTTTGTAATTTTGTATGAATATTGTAATTTTTTTGTATAAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* *
22890142 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
22890191 AATATTGTAATTTTTTGTATGAATATTGTAA
1 AATATTGTAA--TTTTGTATGAATATTGTAA
22890222 CGTTTTATAA
Statistics
Matches: 161, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
48 2 0.01
49 139 0.86
50 2 0.01
51 18 0.11
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
Done.