Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 315 of 378
Found at i:95824884 original size:79 final size:79
Alignment explanation
Indices: 95824758--95824957 Score: 267
Period size: 79 Copynumber: 2.5 Consensus size: 79
95824748 AAGAGTATTC
* * * * *
95824758 AGGGGTACCAGAGTACAAAAAAGGGCACATACGTGCATTCAGGGGTACCGAAGAACAAACAAGGG
1 AGGGGTACCA-AGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCAAAGAACAAACAAGGG
95824823 CACACATGTGCATTT
65 CACACATGTGCATTT
* * *
95824838 AGGGGTACCGAAGTAC-AACAGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAATAGGGG
1 AGGGGTACC-AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCAAAGAACAAACAAGGG
*
95824902 CACACATGTGCCTTT
65 CACACATGTGCATTT
* *
95824917 AGGGGCACCAAAGTACAAACAGGGGCACGCATGTGCATTCA
1 AGGGGTACC-AAGTACAAACAGGGGCACGTATGTGCATTCA
95824958 TACAATAATT
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
79 68 0.64
80 37 0.35
81 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.29, T:0.16
Consensus pattern (79 bp):
AGGGGTACCAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCAAAGAACAAACAAGGGC
ACACATGTGCATTT
Found at i:95826112 original size:40 final size:40
Alignment explanation
Indices: 95826070--95826271 Score: 248
Period size: 40 Copynumber: 5.1 Consensus size: 40
95826060 ATATAAGAGT
** *
95826070 ATTTAGGGGTACCGAAGTACAAACAGGGGCACATATGTGT
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
* * *
95826110 ATTCAGGGGTACCGAAGTACAAATAAGGGCACGCATGTGC
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
* * *
95826150 ATTCT-GGGGTACCGAAGTAC-AACAAGGGCATGTATGTGC
1 ATT-TAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
* *
95826189 ATTCAGGGGTACCCAAGTACAAACAGGGGCACGCATGTGC
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
* *
95826229 CTTTAGGGGTACC-ACGGTACAAACAGGGGCACGCATGTGC
1 ATTTAGGGGTACCGA-AGTACAAACAGGGGCACGCATGTGC
95826269 ATT
1 ATT
95826272 CATACAATAA
Statistics
Matches: 139, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 34 0.24
40 105 0.76
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (40 bp):
ATTTAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
Found at i:95826186 original size:79 final size:80
Alignment explanation
Indices: 95826070--95826273 Score: 261
Period size: 79 Copynumber: 2.6 Consensus size: 80
95826060 ATATAAGAGT
* * * *
95826070 ATTTAGGGGTACCGAAGTACAAACAGGGGCACATATGTGTATTCAGGGGTACCGAAGTACAAATA
1 ATTTAGGGGTACCGAAGTACAAACAAGGGCACATATGTGCATTCAGGGGTACCCAAGTACAAACA
95826135 AGGGCACGCATGTGC
66 AGGGCACGCATGTGC
**
95826150 ATTCT-GGGGTACCGAAGTAC-AACAAGGGCATGTATGTGCATTCAGGGGTACCCAAGTACAAAC
1 ATT-TAGGGGTACCGAAGTACAAACAAGGGCACATATGTGCATTCAGGGGTACCCAAGTACAAAC
*
95826213 AGGGGCACGCATGTGC
65 AAGGGCACGCATGTGC
* * * **
95826229 CTTTAGGGGTACC-ACGGTACAAACAGGGGCACGCATGTGCATTCA
1 ATTTAGGGGTACCGA-AGTACAAACAAGGGCACATATGTGCATTCA
95826274 TACAATAATT
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
78 2 0.02
79 66 0.61
80 39 0.36
81 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.20
Consensus pattern (80 bp):
ATTTAGGGGTACCGAAGTACAAACAAGGGCACATATGTGCATTCAGGGGTACCCAAGTACAAACA
AGGGCACGCATGTGC
Found at i:95838981 original size:2 final size:2
Alignment explanation
Indices: 95838974--95839016 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
95838964 CGTGAAAAGG
95838974 AT AT AT AT 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 AT AT AT AT
95839016 A
1 A
95839017 CTTTGAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:95841983 original size:23 final size:23
Alignment explanation
Indices: 95841968--95842015 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
95841958 TAAAAGAAAG
*
95841968 AAAGAAACAAAATTAACATTGAA
1 AAAGAAACAAAATTAACATAGAA
*
95841991 AAAGAAACAAAATTAACATTGAA
1 AAAGAAACAAAATTAACATAGAA
95842014 AA
1 AA
95842016 TACCTTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.17
Consensus pattern (23 bp):
AAAGAAACAAAATTAACATAGAA
Found at i:95844821 original size:40 final size:38
Alignment explanation
Indices: 95844763--95844915 Score: 128
Period size: 40 Copynumber: 3.8 Consensus size: 38
95844753 GGATATAGCG
* * * *
95844763 ACTCGCTCAAAAGTCTTCGGGACATAGCCCGGTTATAAT
1 ACTCGCACAAATGCCTTCGGGACATAGCCCGGTT-TAGT
* * *
95844802 AGCTCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGT
1 A-CTCGCACAAATGCCTTCGGGACATAGCCCGG-TTTAGT
*
95844842 AACTCGCACAAATGCCTTCGGGA-ATTGACCCGGATTTAGT
1 -ACTCGCACAAATGCCTTCGGGACATAG-CCCGG-TTTAGT
* * *
95844882 CACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 -AC-TCGCACAAATGCCTTCGGGACATAGCCCGG
95844916 ACATCATTCG
Statistics
Matches: 91, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
39 2 0.02
40 61 0.67
41 26 0.29
42 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (38 bp):
ACTCGCACAAATGCCTTCGGGACATAGCCCGGTTTAGT
Found at i:95844904 original size:41 final size:40
Alignment explanation
Indices: 95844807--95844916 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
95844797 ATAATAGCTC
* * * *
95844807 GCACAAATGCCTTCGGGACTTAACCCGGTTTTGGTAACTC
1 GCACAAATGCCTTCGGGAATTAACCCGGATTTAGTAACTA
* *
95844847 GCACAAATGCCTTCGGGAATTGACCCGGATTTAGTCACTTA
1 GCACAAATGCCTTCGGGAATTAACCCGGATTTAGTAAC-TA
* * *
95844888 GCACAAAAGCCTTCGGGACTTAGCCCGGA
1 GCACAAATGCCTTCGGGAATTAACCCGGA
95844917 CATCATTCGA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
40 33 0.56
41 26 0.44
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGAATTAACCCGGATTTAGTAACTA
Found at i:95847988 original size:22 final size:22
Alignment explanation
Indices: 95847962--95848005 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
95847952 AAAGAAAATT
95847962 ATCCACTTATAAAATATCTTTA
1 ATCCACTTATAAAATATCTTTA
95847984 ATCCACTTATAAAATATCTTTA
1 ATCCACTTATAAAATATCTTTA
95848006 GTGTTTGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (22 bp):
ATCCACTTATAAAATATCTTTA
Found at i:95848606 original size:21 final size:21
Alignment explanation
Indices: 95848576--95848615 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
95848566 TTAACGGGAT
95848576 GCTGACGTGGCAAGTTAACCA
1 GCTGACGTGGCAAGTTAACCA
*
95848597 GCTGATGTGGCAAGTTAAC
1 GCTGACGTGGCAAGTTAAC
95848616 TTGCCACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACCA
Found at i:95849627 original size:3 final size:3
Alignment explanation
Indices: 95849610--95849680 Score: 76
Period size: 3 Copynumber: 24.3 Consensus size: 3
95849600 ATATCAATTT
* *
95849610 TTC TTC TT- TTCC TTC TTC TTC TTC TTC TTC TCC TTC TTC -TC CTC
1 TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
95849654 TTC TTC TTC TT- TTC TTT TTC TTT TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
95849681 CTAGCCCTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
2 6 0.11
3 49 0.86
4 2 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:95855265 original size:44 final size:44
Alignment explanation
Indices: 95855157--95855891 Score: 239
Period size: 44 Copynumber: 16.8 Consensus size: 44
95855147 ATTTGCTAAC
95855157 TTCGATCTGC-CCTCTGACAATACAGAGACGCCCAAATCTA-CTATT
1 TTCGATCTGCTCC-CTGACAATACAGAGACG-CCAAATCTATC-ATT
* * * *
95855202 TTTGATCCGCTTTCC-GACAATACAGAGACGCAAAATCTATCATT
1 TTCGATCTGC-TCCCTGACAATACAGAGACGCCAAATCTATCATT
* * *
95855246 TTCGATCTGCTCCCTGACAATACAGAGACTCCAAATCTATCGTC
1 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
* *
95855290 TTCGATTTGCTCTCTGACAATACAGAGACGCCAAATC-ATC---
1 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
** * * * * * *
95855330 TTCGATCTGCTTTCTGCCAATATAGAGATGCCAAATCTGTTATC
1 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
* * ** * * *
95855374 TTAGATTTGCTTTCTGCCAATACAGAGATGCTAAATC-ATC---
1 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
* * * * * * *
95855414 TTAGATTTGCTTCAAC-G-TAA-ACACGTGAAAGCCAAATC-AGCTATGT
1 TTCGATCTGC-TC-CCTGACAATACA-GAG-ACGCCAAATCTATC-AT-T
* * *
95855460 CTTCGAT-TGGCTCCCTGATAATACAGAGACGCCAAATCTGGT-ATC
1 -TTCGATCT-GCTCCCTGACAATACAGAGACGCCAAATCT-ATCATT
* * *
95855505 TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATC-ATC---
1 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
* * * * * * *
95855545 TTAGATTTGCTTCAAC-GTA-AACACATGA-AAGCCAAGTC-AACTATGT
1 TTCGATCTGC-TC-CCTG-ACAATACA-GAGACGCCAAATCTATC-AT-T
* * * * *
95855591 CTTCGATCTGCTCCCTGCCAATACAGAGATGCCAAATCTGTTATC
1 -TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
* * * * *
95855636 TTCGATCTACTCTCTGCCAATACAGAGATGCCAAATCT-GC-TGT
1 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCAT-T
* * *
95855679 CTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATC-ATC---
1 -TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
* * * * * * *
95855720 TTAGATTTGCTTCAAC-G-TAA-ACACGTGAAAGCCAAATC-AACTATGT
1 TTCGATCTGC-TC-CCTGACAATACA-GAG-ACGCCAAATCTATC-AT-T
* * * * *
95855766 CTTCGATCTGCTCCCTGCCAATACAGAGATGCCAAATCTGTTATC
1 -TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
* * * *
95855811 TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCT-GC-TGT
1 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCAT-T
* * * *
95855854 CTTCCATCTGCTCTCTGCCAATACAGAGATGCCAAATC
1 -TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATC
95855892 ATTTTAGATT
Statistics
Matches: 537, Mismatches: 94, Indels: 119
0.72 0.13 0.16
Matches are distributed among these distances:
39 6 0.01
40 66 0.12
41 45 0.08
42 8 0.01
43 7 0.01
44 288 0.54
45 30 0.06
46 48 0.09
47 33 0.06
48 6 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (44 bp):
TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTATCATT
Found at i:95855497 original size:131 final size:131
Alignment explanation
Indices: 95855328--95855672 Score: 530
Period size: 131 Copynumber: 2.6 Consensus size: 131
95855318 CGCCAAATCA
** * * * * *
95855328 TCTTCGATCTGCTTTCTGCCAATATAGAGATGCCAAATCTGTTATCTTAGATTTGCTTTCTGCCA
1 TCTTCGATCTGCTCCCTGACAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCA
* * *
95855393 ATACAGAGATGCTAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTAT
66 ATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAATCAACTAT
95855458 G
131 G
* * *
95855459 TCTTCGAT-TGGCTCCCTGATAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGCC
1 TCTTCGATCT-GCTCCCTGACAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
*
95855523 AATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAGTCAACTA
65 AATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAATCAACTA
95855588 TG
130 TG
* *
95855590 TCTTCGATCTGCTCCCTGCCAATACAGAGATGCCAAATCTGTTATCTTCGATCTACTCTCTGCCA
1 TCTTCGATCTGCTCCCTGACAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCA
95855655 ATACAGAGATGCCAAATC
66 ATACAGAGATGCCAAATC
95855673 TGCTGTCTTC
Statistics
Matches: 193, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
130 1 0.01
131 191 0.99
132 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (131 bp):
TCTTCGATCTGCTCCCTGACAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCA
ATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAATCAACTAT
G
Found at i:95855640 original size:175 final size:175
Alignment explanation
Indices: 95855479--95856022 Score: 980
Period size: 175 Copynumber: 3.1 Consensus size: 175
95855469 GCTCCCTGAT
* * *
95855479 AATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCAT
1 AATACAGAGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCAT
* *
95855544 CTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAGTCAACTATGTCTTCGATCTGCTCCCTGC
66 CTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTCCCTGC
*
95855609 CAATACAGAGATGCCAAATCTGTTATCTTCGATCTACTCTCTGCC
131 CAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
95855654 AATACAGAGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCAT
1 AATACAGAGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCAT
95855719 CTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTCCCTGC
66 CTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTCCCTGC
95855784 CAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
131 CAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
*
95855829 AATACAGAGATGCCAAATCTGCTGTCTTCCATCTGCTCTCTGCCAATACAGAGATGCCAAATCAT
1 AATACAGAGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCAT
* * * *
95855894 TTTAGATTTGCTTCAACATAAACACGTGAAAGTCAAATCAACTATGTCTTTGATCTGCTCCCTGC
66 CTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTCCCTGC
*
95855959 CAATACAGAGATACCAAATCTGTTATCTTCGATCTGCTCTCTGCC
131 CAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
95856004 AATACAGAGATGCCAAATC
1 AATACAGAGATGCCAAATC
95856023 ATCCTGGATC
Statistics
Matches: 357, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 357 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (175 bp):
AATACAGAGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCAT
CTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTCCCTGC
CAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
Found at i:95855698 original size:306 final size:303
Alignment explanation
Indices: 95855282--95855847 Score: 911
Period size: 306 Copynumber: 1.9 Consensus size: 303
95855272 GACTCCAAAT
* * * *
95855282 CTATCGTCTTCGATTTGCTCTCTGACAATACAGAGACGCCAAATCATCTTCGATCTGCTTTCTGC
1 CTATCGTCTTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCATCTTCGATCTACTCTCTGC
* * * * *
95855347 CAATATAGAGATGCCAAATCTGTTATCTTAGATTTGCTTTCTGCCAATACAGAGATGCTAAATCA
66 CAATACAGAGATGCCAAATCTGCTATCTTAGATCTGCTCTCTGCCAATACAGAGATGCCAAATCA
*
95855412 TCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGAT-TGGCTCCCT
131 TCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCT-GCTCCCT
*
95855476 GATAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAAT
195 GACAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAAT
95855541 CATCTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAGTCAA
260 CATCTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAGTCAA
* *
95855585 CTAT-GTCTTCGATCTGCTCCCTGCCAATACAGAGATGCCAAATCTGTTATCTTCGATCTACTCT
1 CTATCGTCTTCGATCTGCTCCCTGACAATACAGAGACGCCAAATC----ATCTTCGATCTACTCT
* *
95855649 CTGCCAATACAGAGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAA
62 CTGCCAATACAGAGATGCCAAATCTGCTATCTTAGATCTGCTCTCTGCCAATACAGAGATGCCAA
95855714 ATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTC
127 ATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTC
* * *
95855779 CCTGCCAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCA
192 CCTGACAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCA
95855844 AATC
257 AATC
95855848 TGCTGTCTTC
Statistics
Matches: 240, Mismatches: 18, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
302 36 0.15
303 4 0.02
306 199 0.83
307 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (303 bp):
CTATCGTCTTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCATCTTCGATCTACTCTCTGC
CAATACAGAGATGCCAAATCTGCTATCTTAGATCTGCTCTCTGCCAATACAGAGATGCCAAATCA
TCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATCTGCTCCCTG
ACAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATC
ATCTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAGTCAA
Found at i:95855961 original size:306 final size:304
Alignment explanation
Indices: 95855327--95856039 Score: 852
Period size: 306 Copynumber: 2.3 Consensus size: 304
95855317 ACGCCAAATC
* * * * *
95855327 ATCTTCGATCTGCTTTCTGCCAATATAGAGATGCCAAATCTGTTATCTTAGATTTGCTTTCTGCC
1 ATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
* *
95855392 AATACAGAGATGCTAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTA
66 AATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTA
*
95855457 TGTCTTCGATTGGCTCCCTGATAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGC
131 TGTCTTCGATTGGCTCCCTGACAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGC
* * *
95855522 CAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACATGAAAGCCAAGTCAACT
196 CAATACAGAGATGCCAAATCATCTTACATCTGCTTCAACGCAAACACATGAAAGCCAA--CAACT
* ** * * **
95855587 ATGTCTTCGATCTGCTCCCTGCCAATACAGAGATGCCAAATCTGTT
259 ATGTCTTAGATCTGCTCCCTAACAAAACAGAGAAGCCAAATCACTT
* * *
95855633 ATCTTCGATCTACTCTCTGCCAATACAGAGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGCC
1 ATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
95855698 AATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTA
66 AATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTA
* * *
95855763 TGTCTTCGATCT-GCTCCCTGCCAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTG
131 TGTCTTCGAT-TGGCTCCCTGACAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTG
* * * * * *
95855827 CCAATACAGAGATGCCAAATCTGCTGTCTTCCATCTGCTCTC--TGCCAATACA-GAGATGCCAA
195 CCAATACAGAGATGCCAAA--T-C-ATCTTACATCTGCT-TCAACGCAAACACATGA-AAGCCAA
* * * * *
95855889 -ATC-AT-T-TTAGATTTGCT-TC-AACATAAACACGTGAAAGTCAAATCAACTAT
254 CAACTATGTCTTAGATCTGCTCCCTAACA-AAACA-GAG-AAGCCAAATC-ACT-T
* * * *
95855939 GTCTTTGATCTGCTCCCTGCCAATACAGAGATACCAAATCTGTTATCTTCGATCTGCTCTCTGCC
1 ATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
* * *
95856004 AATACAGAGATGCCAAATCATCCTGGATCTGCTTCA
66 AATACAGAGATGCCAAATCATCTTAGATTTGCTTCA
95856040 GTGTAAATAC
Statistics
Matches: 350, Mismatches: 45, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
301 2 0.01
302 5 0.01
303 11 0.03
304 9 0.03
305 3 0.01
306 291 0.83
307 1 0.00
308 3 0.01
309 13 0.04
310 10 0.03
311 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (304 bp):
ATCTTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGCC
AATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAACTA
TGTCTTCGATTGGCTCCCTGACAATACAGAGACGCCAAATCTGGTATCTTCGATCTGCTCTCTGC
CAATACAGAGATGCCAAATCATCTTACATCTGCTTCAACGCAAACACATGAAAGCCAACAACTAT
GTCTTAGATCTGCTCCCTAACAAAACAGAGAAGCCAAATCACTT
Found at i:95860206 original size:40 final size:40
Alignment explanation
Indices: 95860129--95860349 Score: 320
Period size: 40 Copynumber: 5.5 Consensus size: 40
95860119 ACCCAAGTAT
*
95860129 CTTCGGGACTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* *
95860168 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
95860208 CTTCGGGATTTAGCCCGGATATAATCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
95860248 CTTCAGGATTTAGCCCGGATATAATCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
95860288 CTTCGGGACTTAGCCCGGGTATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
95860328 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
95860350 CATCTGAATA
Statistics
Matches: 165, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 12 0.07
40 152 0.92
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:95868355 original size:31 final size:31
Alignment explanation
Indices: 95868320--95868381 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
95868310 GTCTAGATCA
95868320 GATCTTTCAAAGCTCCCCACAGAATGCACTT
1 GATCTTTCAAAGCTCCCCACAGAATGCACTT
95868351 GATCTTTCAAAGCTCCCCACAGAATGCACTT
1 GATCTTTCAAAGCTCCCCACAGAATGCACTT
95868382 ACTCTCACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (31 bp):
GATCTTTCAAAGCTCCCCACAGAATGCACTT
Found at i:95873878 original size:45 final size:44
Alignment explanation
Indices: 95873795--95873929 Score: 135
Period size: 45 Copynumber: 3.0 Consensus size: 44
95873785 ATCTACATCG
* * *
95873795 TATTAGCAACTTTTATCTATACGATTAGTGGTTTATCCATACCA
1 TATTAGCAGCTTTTATCTACAAGATTAGTGGTTTATCCATACCA
* * * ***
95873839 TATTAGCAGTTTTTATCTACATTGATTAGTGGTTTATCCACATTG
1 TATTAGCAGCTTTTATCTACA-AGATTAGTGGTTTATCCATACCA
* * * *
95873884 TATTAGCAGGTTTTATCTGCAACATTTAGTGGTTCATCCATACCA
1 TATTAGCAGCTTTTATCTACAAGA-TTAGTGGTTTATCCATACCA
95873929 T
1 T
95873930 GGTGTAAAGG
Statistics
Matches: 72, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
44 19 0.26
45 53 0.74
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (44 bp):
TATTAGCAGCTTTTATCTACAAGATTAGTGGTTTATCCATACCA
Found at i:95873895 original size:23 final size:23
Alignment explanation
Indices: 95873839--95873896 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
95873829 ATCCATACCA
* *
95873839 TATTAGCAGTTTTTATCTACATTG
1 TATTAGCAG-GTTTATCCACATTG
*
95873863 -ATTAG-TGGTTTATCCACATTG
1 TATTAGCAGGTTTATCCACATTG
95873884 TATTAGCAGGTTT
1 TATTAGCAGGTTT
95873897 TATCTGCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 12 0.43
22 6 0.21
23 10 0.36
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (23 bp):
TATTAGCAGGTTTATCCACATTG
Found at i:95875484 original size:29 final size:29
Alignment explanation
Indices: 95875442--95875499 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
95875432 AAGATATGCA
* *
95875442 ATATGGTGGTTAATGCTATGAGTACTATG
1 ATATGGTGGTTAATGCTACGAATACTATG
95875471 ATATGGTGGTTAATGCTACGAATACTATG
1 ATATGGTGGTTAATGCTACGAATACTATG
95875500 CGATTGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36
Consensus pattern (29 bp):
ATATGGTGGTTAATGCTACGAATACTATG
Found at i:95878880 original size:22 final size:22
Alignment explanation
Indices: 95878840--95878884 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
95878830 TACACTTTTT
* *
95878840 AAAAATATTTAATACATATACAA
1 AAAAATAATTAATAAATAT-CAA
95878863 AAAAATAATT-ATAAATATCAA
1 AAAAATAATTAATAAATATCAA
95878884 A
1 A
95878885 TGAATAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATAATTAATAAATATCAA
Found at i:95880076 original size:2 final size:2
Alignment explanation
Indices: 95880069--95880093 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
95880059 TGAAGTTTTA
95880069 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
95880094 ACATGTTTAA
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:95885465 original size:204 final size:207
Alignment explanation
Indices: 95885094--95885507 Score: 620
Period size: 204 Copynumber: 2.0 Consensus size: 207
95885084 AATTTTATAA
*
95885094 ATTTTTAAAAATATATATAACTTGACATTTTGTAAATGTTGGAGGTTAACTTTATTGAATTTTTT
1 ATTTTTAAAAATATATATAACTTGACATTTTGTAAACGTTGGAGGTTAACTTTATTGAATTTTTT
* * * *
95885159 GGAGTTTGAATTAAAATCACAAATTTTATACAAAATAATGAGGTGTAGTGCGGTGGTTGTTTATT
66 AGAGTTTGAATCAAAATCACAAATTTTATACAAAACAATGAGGTGTAGTGCGGTGGTTGTTTACT
** *
95885224 TCATCTTATAATTACAAGATTAGAGGTTTAAGGTTTGATCCTTACTCATGAGAATGAAGTATATT
131 TCATCCCATAATCACAAGATTAGAGGTTTAAGGTTTGATCCTTACTCATGAGAATGAAGTATATT
*
95885289 TTATGACCAACC
196 TTATGACAAACC
* *
95885301 ATTTTT-AAAA-AT-TATAATTTGACATTTTGTAAACGTTGGAGGTTAACTTTATTGATTTTTTT
1 ATTTTTAAAAATATATATAACTTGACATTTTGTAAACGTTGGAGGTTAACTTTATTGAATTTTTT
* * * * *
95885363 AGAGTTTGAATCAAAATCACCAATTTTATACATAACGATGAGGTGTGGTGTGGTGGTTGTTTACT
66 AGAGTTTGAATCAAAATCACAAATTTTATACAAAACAATGAGGTGTAGTGCGGTGGTTGTTTACT
* * *
95885428 TCATCCCATAATCACAAGCTTGGA-GTTTCAAGGTTTGATCCTTACTCATGGGAATGAAGTATAT
131 TCATCCCATAATCACAAGATTAGAGGTTT-AAGGTTTGATCCTTACTCATGAGAATGAAGTATAT
95885492 TTTATGACAAACC
195 TTTATGACAAACC
95885505 ATT
1 ATT
95885508 AACCTTTAGT
Statistics
Matches: 187, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
203 4 0.02
204 171 0.91
205 2 0.01
206 4 0.02
207 6 0.03
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (207 bp):
ATTTTTAAAAATATATATAACTTGACATTTTGTAAACGTTGGAGGTTAACTTTATTGAATTTTTT
AGAGTTTGAATCAAAATCACAAATTTTATACAAAACAATGAGGTGTAGTGCGGTGGTTGTTTACT
TCATCCCATAATCACAAGATTAGAGGTTTAAGGTTTGATCCTTACTCATGAGAATGAAGTATATT
TTATGACAAACC
Found at i:95885913 original size:165 final size:165
Alignment explanation
Indices: 95885641--95885969 Score: 525
Period size: 165 Copynumber: 2.0 Consensus size: 165
95885631 TTAATAGATA
* * * *
95885641 ATCTAAATATATTCTTAGTCTAATCAAAATTGAACAAATCAATTGAAAGATTAATATGTTGCCTG
1 ATCTAAATACATTCTTAGTCTAATCAAAATTGAACAAATCAATTAAAAGACTAATATGTTGCCTA
* * *
95885706 TCAAGTCCAATTGGGAGATATCTTATCTTAGGTATCGAAGCAGATGTCTCTTGAAAAATAGAGAC
66 TCAAGTCCAATTGGAAGATATCTTAACTTAGGTATAGAAGCAGATGTCTCTTGAAAAATAGAGAC
* *
95885771 ATATATATGACTGACTGGAATAAAGTACATTATAT
131 ATAGATATGACTGACTAGAATAAAGTACATTATAT
* *
95885806 ATCTAAATACATTCTTAGTCTAATCAAAATTGAGCAAATCGAA-TAAAAGACTAATATGTTGTCT
1 ATCTAAATACATTCTTAGTCTAATCAAAATTGAACAAATC-AATTAAAAGACTAATATGTTGCCT
*
95885870 ATCAAGTCCAATTGGAAGATATCTTAACTTAGGTATAGAAGCAGATTTCTCTTGAAAAATAGAGA
65 ATCAAGTCCAATTGGAAGATATCTTAACTTAGGTATAGAAGCAGATGTCTCTTGAAAAATAGAGA
*
95885935 CATAGATATGACTGACTATAATAAAGTACATTATA
130 CATAGATATGACTGACTAGAATAAAGTACATTATA
95885970 CATGACTCAA
Statistics
Matches: 150, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
165 148 0.99
166 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (165 bp):
ATCTAAATACATTCTTAGTCTAATCAAAATTGAACAAATCAATTAAAAGACTAATATGTTGCCTA
TCAAGTCCAATTGGAAGATATCTTAACTTAGGTATAGAAGCAGATGTCTCTTGAAAAATAGAGAC
ATAGATATGACTGACTAGAATAAAGTACATTATAT
Found at i:95887581 original size:29 final size:29
Alignment explanation
Indices: 95887517--95887581 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
95887507 TGGGATGAAC
* *
95887517 AAAATGTGATAAAAGTTCAAATTATGTTT
1 AAAATGTCATAAAAGTTCAAATTATGTAT
*
95887546 AACATGTCATAAAAGTT-AAATTGAT-TAT
1 AAAATGTCATAAAAGTTCAAATT-ATGTAT
95887574 AGAAATGT
1 A-AAATGT
95887582 TCTAATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (29 bp):
AAAATGTCATAAAAGTTCAAATTATGTAT
Found at i:95890848 original size:24 final size:23
Alignment explanation
Indices: 95890821--95890898 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
95890811 TCATAAGTGT
**
95890821 TTACTGTTTTCAGCTCGTTGGAGC
1 TTACTGTTTT-AGCTCGTAAGAGC
* * *
95890845 TTACTGTTTTAACTCATAAAAGC
1 TTACTGTTTTAGCTCGTAAGAGC
*
95890868 TTACTGTTTTTAGCTCGTCAGAGC
1 TTACTG-TTTTAGCTCGTAAGAGC
95890892 TTACTGT
1 TTACTGT
95890899 CCATCAGCTT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 15 0.34
24 29 0.66
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (23 bp):
TTACTGTTTTAGCTCGTAAGAGC
Found at i:95891078 original size:20 final size:20
Alignment explanation
Indices: 95891032--95891072 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
95891022 CAACGGGCAT
95891032 AAATACTATTTATATGGATG
1 AAATACTATTTATATGGATG
95891052 AAATACTATTTATATGGATG
1 AAATACTATTTATATGGATG
95891072 A
1 A
95891073 GCTACTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (20 bp):
AAATACTATTTATATGGATG
Found at i:95897180 original size:27 final size:27
Alignment explanation
Indices: 95897150--95897204 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
95897140 ATATATTTAC
95897150 TCAGATTCTAATAAGATAAAATCATTA
1 TCAGATTCTAATAAGATAAAATCATTA
95897177 TCAGATTCTAATAAGATAAAATCATTA
1 TCAGATTCTAATAAGATAAAATCATTA
95897204 T
1 T
95897205 AACTTTTACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (27 bp):
TCAGATTCTAATAAGATAAAATCATTA
Found at i:95899956 original size:41 final size:41
Alignment explanation
Indices: 95899906--95900213 Score: 311
Period size: 41 Copynumber: 7.6 Consensus size: 41
95899896 CTTAATTATT
* * *
95899906 CCCTGAATTGTACATACGTGCCCTTATTTGTACTTCAGTAC
1 CCCTAAATTGCACATACGTGCCCTTATTTGTACTTCGGTAC
* * * *
95899947 CCCTAAATTGCACATACGTGCCCCTATTTGCATTTCAGTAC
1 CCCTAAATTGCACATACGTGCCCTTATTTGTACTTCGGTAC
** * * * *
95899988 CCCTAAATTTTACATACATGCCCATGTTTGTACTTTGGTAC
1 CCCTAAATTGCACATACGTGCCCTTATTTGTACTTCGGTAC
* * * * * * *
95900029 CCTTAAATTGCACATATGCGCCC-TGTTTGTCCATCAGTAC
1 CCCTAAATTGCACATACGTGCCCTTATTTGTACTTCGGTAC
* **
95900069 CCCT-GATTGCACATACGTGCCCTTATTCATACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCTTATTTGTACTTCGGTAC
* * *
95900109 CCCTAAATTGCACATACATGCCCTTATTTCTACTACGGTAC
1 CCCTAAATTGCACATACGTGCCCTTATTTGTACTTCGGTAC
* *
95900150 CCCTGAATTGCACATACGTG-CC-TATGTTGTACTTTGGTAC
1 CCCTAAATTGCACATACGTGCCCTTAT-TTGTACTTCGGTAC
95900190 CCCTGAAA-TGCACATACGTGCCCT
1 CCCT-AAATTGCACATACGTGCCCT
95900214 GTTTACACTC
Statistics
Matches: 216, Mismatches: 45, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
39 18 0.08
40 60 0.28
41 138 0.64
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (41 bp):
CCCTAAATTGCACATACGTGCCCTTATTTGTACTTCGGTAC
Found at i:95900190 original size:121 final size:121
Alignment explanation
Indices: 95899906--95900213 Score: 336
Period size: 121 Copynumber: 2.5 Consensus size: 121
95899896 CTTAATTATT
* *
95899906 CCCTGAATTGTACATACGTGCCCTTAT-TTGTACTTCAGTACCCCTAAATTGCACATACGTGCCC
1 CCCTGAATTGCACATACGTG-CC-TATGTTGTACTTCAGTACCCCT-GATTGCACATACGTGCCC
* ** * * **
95899970 CTATTTGCATTTCAGTACCCCTAAATTTTACATACATGCCCATGTTTGTACTTTGGTAC
63 TTATTTGCATTTCAGTACCCCTAAATTGCACATACATGCCCATATTTCTACTACGGTAC
* * * * * * *
95900029 CCTTAAATTGCACATATGCGCC-CTGTTTGTCCATCAGTACCCCTGATTGCACATACGTGCCCTT
1 CCCTGAATTGCACATACGTGCCTATG-TTGTACTTCAGTACCCCTGATTGCACATACGTGCCCTT
* *
95900093 A-TT-CATACTTCGGTACCCCTAAATTGCACATACATGCCCTTATTTCTACTACGGTAC
65 ATTTGCAT--TTCAGTACCCCTAAATTGCACATACATGCCCATATTTCTACTACGGTAC
** *
95900150 CCCTGAATTGCACATACGTGCCTATGTTGTACTTTGGTACCCCTGAAATGCACATACGTGCCCT
1 CCCTGAATTGCACATACGTGCCTATGTTGTACTTCAGTACCCCTG-ATTGCACATACGTGCCCT
95900214 GTTTACACTC
Statistics
Matches: 151, Mismatches: 28, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
119 3 0.02
120 3 0.02
121 93 0.62
122 37 0.25
123 15 0.10
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (121 bp):
CCCTGAATTGCACATACGTGCCTATGTTGTACTTCAGTACCCCTGATTGCACATACGTGCCCTTA
TTTGCATTTCAGTACCCCTAAATTGCACATACATGCCCATATTTCTACTACGGTAC
Found at i:95903034 original size:23 final size:23
Alignment explanation
Indices: 95903008--95903052 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
95902998 TATTAGTTAA
*
95903008 AAGGCTTATA-TGGTAAATTAACC
1 AAGGCTTAAATTGG-AAATTAACC
*
95903031 AAGGTTTAAATTGGAAATTAAC
1 AAGGCTTAAATTGGAAATTAAC
95903053 TACTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (23 bp):
AAGGCTTAAATTGGAAATTAACC
Found at i:95904251 original size:22 final size:22
Alignment explanation
Indices: 95904221--95904344 Score: 85
Period size: 22 Copynumber: 5.7 Consensus size: 22
95904211 TAGCACTTCA
*
95904221 GTGCCCTCTATTTAGTACTTTT
1 GTGCTCTCTATTTAGTACTTTT
* *
95904243 ATGCTCTCTAATTA-TCACTTTT
1 GTGCTCTCTATTTAGT-ACTTTT
* *
95904265 GGGCTCTCTAATTT-GCACTTTT
1 GTGCTCTCT-ATTTAGTACTTTT
* * * *
95904287 GTGCTCTCTGTATAGCACTTAT
1 GTGCTCTCTATTTAGTACTTTT
* * *
95904309 GTACTCTCTGA-TT-GCACTTTG
1 GTGCTCTCT-ATTTAGTACTTTT
95904330 GTGCTCTCTATTTAG
1 GTGCTCTCTATTTAG
95904345 CATTTATGTA
Statistics
Matches: 78, Mismatches: 17, Indels: 14
0.72 0.16 0.13
Matches are distributed among these distances:
20 1 0.01
21 19 0.24
22 55 0.71
23 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.15, T:0.46
Consensus pattern (22 bp):
GTGCTCTCTATTTAGTACTTTT
Found at i:95904338 original size:43 final size:43
Alignment explanation
Indices: 95904268--95904376 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
95904258 CACTTTTGGG
* * *
95904268 CTCTCTAATTTGCACTTTTGTGCTCTCTGTATAGCACTTATGTA
1 CTCTCTGA-TTGCACTTTGGTGCTCTCTATATAGCACTTATGTA
* *
95904312 CTCTCTGATTGCACTTTGGTGCTCTCTATTTAGCATTTATGTA
1 CTCTCTGATTGCACTTTGGTGCTCTCTATATAGCACTTATGTA
95904355 CTCTCTGATTGCACTTTGGTGC
1 CTCTCTGATTGCACTTTGGTGC
95904377 CTTTGATTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
43 53 0.88
44 7 0.12
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.45
Consensus pattern (43 bp):
CTCTCTGATTGCACTTTGGTGCTCTCTATATAGCACTTATGTA
Found at i:95904359 original size:22 final size:22
Alignment explanation
Indices: 95904237--95904371 Score: 84
Period size: 22 Copynumber: 6.2 Consensus size: 22
95904227 TCTATTTAGT
* *
95904237 ACTTTTATGCTCTCTAATTAT-C
1 ACTTTTGTACTCTCTAATT-TGC
**
95904259 ACTTTTGGGCTCTCTAATTTGC
1 ACTTTTGTACTCTCTAATTTGC
* * *
95904281 ACTTTTGTGCTCTCT-GTATAGC
1 ACTTTTGTACTCTCTAAT-TTGC
* *
95904303 ACTTATGTACTCTCTGA-TTGC
1 ACTTTTGTACTCTCTAATTTGC
* *
95904324 ACTTTGGTGCTCTCT-ATTTAGC
1 ACTTTTGTACTCTCTAATTT-GC
*
95904346 A-TTTATGTACTCTCTGA-TTGC
1 ACTTT-TGTACTCTCTAATTTGC
95904367 ACTTT
1 ACTTT
95904372 GGTGCCTTTG
Statistics
Matches: 91, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
20 1 0.01
21 25 0.27
22 64 0.70
23 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.47
Consensus pattern (22 bp):
ACTTTTGTACTCTCTAATTTGC
Found at i:95904397 original size:20 final size:20
Alignment explanation
Indices: 95904360--95904398 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
95904350 ATGTACTCTC
* *
95904360 TGATTGCACTTTGGTGCCTT
1 TGATTGCACTTCGATGCCTT
*
95904380 TGATTGTACTTCGATGCCT
1 TGATTGCACTTCGATGCCT
95904399 CTGTTCAGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.44
Consensus pattern (20 bp):
TGATTGCACTTCGATGCCTT
Found at i:95906228 original size:24 final size:24
Alignment explanation
Indices: 95906199--95906245 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
95906189 TAATTGATTG
95906199 TTGTGAAGGGATTTTTTAAGCGGA
1 TTGTGAAGGGATTTTTTAAGCGGA
95906223 TTGTGAAGGGATTTTTTAAGCGG
1 TTGTGAAGGGATTTTTTAAGCGG
95906246 GTGAGCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.34, T:0.38
Consensus pattern (24 bp):
TTGTGAAGGGATTTTTTAAGCGGA
Found at i:95910122 original size:28 final size:27
Alignment explanation
Indices: 95910059--95910128 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
95910049 ATAGTGAGTC
95910059 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
95910086 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
95910114 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
95910129 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:95917875 original size:28 final size:27
Alignment explanation
Indices: 95917812--95917881 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
95917802 ATAGTGAGTC
95917812 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
95917839 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
95917867 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
95917882 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:95923702 original size:36 final size:36
Alignment explanation
Indices: 95923662--95923733 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
95923652 TTATTTGGAT
*
95923662 CAATTCATCGTGGTCTTCATCAATGACATTTTGGCA
1 CAATTCATCGTGGTCTTCATCAACGACATTTTGGCA
95923698 CAATTCATCGTGGTCTTCATCAACGACATTTTGGCA
1 CAATTCATCGTGGTCTTCATCAACGACATTTTGGCA
95923734 TACTCTAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (36 bp):
CAATTCATCGTGGTCTTCATCAACGACATTTTGGCA
Found at i:95940203 original size:15 final size:15
Alignment explanation
Indices: 95940169--95940217 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
95940159 AAAGATAACA
* *
95940169 AGAAAACCAAG-TAA
1 AGAAATCCAAGATAG
95940183 AGAAATCCAAGATAG
1 AGAAATCCAAGATAG
95940198 AGAAATCCCAAGATACG
1 AGAAAT-CCAAGATA-G
95940215 AGA
1 AGA
95940218 GTATATCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 10 0.33
15 8 0.27
16 8 0.27
17 4 0.13
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.10
Consensus pattern (15 bp):
AGAAATCCAAGATAG
Found at i:95940210 original size:16 final size:16
Alignment explanation
Indices: 95940183--95940217 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
95940173 AACCAAGTAA
95940183 AGAAATCCAAGATA-G
1 AGAAATCCAAGATACG
95940198 AGAAATCCCAAGATACG
1 AGAAAT-CCAAGATACG
95940215 AGA
1 AGA
95940218 GTATATCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.51, C:0.17, G:0.20, T:0.11
Consensus pattern (16 bp):
AGAAATCCAAGATACG
Found at i:95944669 original size:43 final size:43
Alignment explanation
Indices: 95944621--95944718 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
95944611 TAAGCCACGG
*
95944621 CTTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTGAAAGTCACAA
1 CTTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAAGTCACAA
* ***
95944664 CTTTTAGCAGCGTTTGTGGGTAAAGCGCCGCTAAAAGTCATGG
1 CTTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAAGTCACAA
95944707 CTTTTAGCGGCG
1 CTTTTAGCGGCG
95944719 CTTTTTCTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (43 bp):
CTTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAAGTCACAA
Found at i:95949189 original size:14 final size:15
Alignment explanation
Indices: 95949165--95949194 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
95949155 CACAAACTTC
95949165 AGAATTTATGTATTT
1 AGAATTTATGTATTT
95949180 AGAA-TTATGTATTT
1 AGAATTTATGTATTT
95949194 A
1 A
95949195 TATAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
AGAATTTATGTATTT
Found at i:95950448 original size:16 final size:16
Alignment explanation
Indices: 95950427--95950480 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
95950417 AGAATTAGAT
95950427 AAAATTTGAAATCTTG
1 AAAATTTGAAATCTTG
95950443 AAAA-TT---A--TTG
1 AAAATTTGAAATCTTG
*
95950453 AAAATTTGAAATCTTT
1 AAAATTTGAAATCTTG
95950469 AAAATTTGAAAT
1 AAAATTTGAAAT
95950481 TATTTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
10 7 0.23
11 2 0.06
12 1 0.03
14 1 0.03
15 2 0.06
16 18 0.58
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (16 bp):
AAAATTTGAAATCTTG
Found at i:95950727 original size:15 final size:15
Alignment explanation
Indices: 95950709--95950739 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
95950699 TGTACCCTTA
95950709 ACCCTTAACCCCTAG
1 ACCCTTAACCCCTAG
*
95950724 ACCCTTAACTCCTAG
1 ACCCTTAACCCCTAG
95950739 A
1 A
95950740 AACTTACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.42, G:0.06, T:0.23
Consensus pattern (15 bp):
ACCCTTAACCCCTAG
Found at i:95950838 original size:14 final size:15
Alignment explanation
Indices: 95950809--95950846 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
95950799 CATAAATCAC
*
95950809 AATCCCTAAGTCCAT
1 AATCCATAAGTCCAT
95950824 AATCCATAA-TCCAT
1 AATCCATAAGTCCAT
*
95950838 AAACCATAA
1 AATCCATAA
95950847 ACCTTGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.24
Consensus pattern (15 bp):
AATCCATAAGTCCAT
Found at i:95950847 original size:7 final size:7
Alignment explanation
Indices: 95950820--95950975 Score: 53
Period size: 7 Copynumber: 21.3 Consensus size: 7
95950810 ATCCCTAAGT
*
95950820 CCATAAT
1 CCATAAA
*
95950827 CCATAAT
1 CCATAAA
95950834 CCATAAA
1 CCATAAA
95950841 CCATAAA
1 CCATAAA
* *
95950848 CCTTGAGA
1 CCAT-AAA
* *
95950856 -TATTAA
1 CCATAAA
95950862 CTCATAAA
1 C-CATAAA
*
95950870 CCCTAAA
1 CCATAAA
*
95950877 CCCCTAAA
1 -CCATAAA
*
95950885 CCTTAAA
1 CCATAAA
*
95950892 CCCTAAA
1 CCATAAA
*
95950899 CCCATAAT
1 -CCATAAA
*
95950907 TCATAAA
1 CCATAAA
*
95950914 CCTTAAA
1 CCATAAA
**
95950921 ATATTAACTCA
1 CCA-TAA---A
*
95950932 TCATAAA
1 CCATAAA
95950939 CCATAAA
1 CCATAAA
*
95950946 CCTTAAA
1 CCATAAA
* *
95950953 CTATATA
1 CCATAAA
*
95950960 CCCTAAA
1 CCATAAA
95950967 CCATAAA
1 CCATAAA
95950974 CC
1 CC
95950976 TTGAACTATA
Statistics
Matches: 108, Mismatches: 32, Indels: 18
0.68 0.20 0.11
Matches are distributed among these distances:
6 1 0.01
7 80 0.74
8 22 0.20
10 3 0.03
11 2 0.02
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (7 bp):
CCATAAA
Found at i:95950886 original size:15 final size:14
Alignment explanation
Indices: 95950866--95950901 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
95950856 TATTAACTCA
95950866 TAAACCCTAAACCCC
1 TAAACCCTAAA-CCC
*
95950881 TAAACCTTAAACCC
1 TAAACCCTAAACCC
95950895 TAAACCC
1 TAAACCC
95950902 ATAATTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAACCCTAAACCC
Found at i:95950913 original size:22 final size:22
Alignment explanation
Indices: 95950863--95950920 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
95950853 AGATATTAAC
*
95950863 TCATAAACCCTAAACCCCTAAA
1 TCATAAACCCTAAACCCATAAA
* * *
95950885 CCTTAAACCCTAAACCCATAAT
1 TCATAAACCCTAAACCCATAAA
*
95950907 TCATAAACCTTAAA
1 TCATAAACCCTAAA
95950921 ATATTAACTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (22 bp):
TCATAAACCCTAAACCCATAAA
Found at i:95950966 original size:14 final size:14
Alignment explanation
Indices: 95950864--95950975 Score: 62
Period size: 14 Copynumber: 7.6 Consensus size: 14
95950854 GATATTAACT
95950864 CATAAACCCTAAACC
1 CATAAACCCTAAA-C
* *
95950879 CCTAAACCTTAAAC
1 CATAAACCCTAAAC
* **
95950893 CCTAAACCCATAATT
1 CATAAACCC-TAAAC
* *
95950908 CATAAACCTTAAAA
1 CATAAACCCTAAAC
* *
95950922 TATTAACTCATCATAAAC
1 CATAAAC-C--C-TAAAC
*
95950940 CATAAACCTTAAAC
1 CATAAACCCTAAAC
* *
95950954 TATATACCCTAAAC
1 CATAAACCCTAAAC
95950968 CATAAACC
1 CATAAACC
95950976 TTGAACTATA
Statistics
Matches: 71, Mismatches: 21, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
14 39 0.55
15 22 0.31
17 1 0.01
18 9 0.13
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
CATAAACCCTAAAC
Found at i:95950986 original size:14 final size:14
Alignment explanation
Indices: 95950935--95950986 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
95950925 TAACTCATCA
*
95950935 TAAACCATAAACCT
1 TAAACTATAAACCT
* *
95950949 TAAACTATATACCC
1 TAAACTATAAACCT
*
95950963 TAAACCATAAACCT
1 TAAACTATAAACCT
*
95950977 TGAACTATAA
1 TAAACTATAA
95950987 TGATAAGTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (14 bp):
TAAACTATAAACCT
Found at i:95951121 original size:29 final size:30
Alignment explanation
Indices: 95951088--95951155 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
95951078 CTTTAAAATT
*
95951088 ATTTTAAATGATAGTATTTTTAT-T-TTTTC
1 ATTTTAAATCATA-TATTTTTATATGTTTTC
* *
95951117 ATTTTTAA-CATATATTTTTATATGTTTTT
1 ATTTTAAATCATATATTTTTATATGTTTTC
95951146 ATTTTCAAAT
1 ATTTT-AAAT
95951156 TTTTTCTACG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
27 9 0.29
28 4 0.13
29 16 0.52
30 2 0.06
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (30 bp):
ATTTTAAATCATATATTTTTATATGTTTTC
Found at i:95951399 original size:81 final size:81
Alignment explanation
Indices: 95951272--95951476 Score: 252
Period size: 81 Copynumber: 2.5 Consensus size: 81
95951262 AAAACGTTGA
* * * *
95951272 TATAAATC-GAGCATTAGCGACG-TTTTTCAAAAAGCACCGTTATAGATCTAAGCATTGGCGACG
1 TATAGATCTGAGCATTAGCGACGCTTTTTGAAAAAG--CCGCTATAGATCTAAGCATTAGCGACG
95951335 TTTTCCAAAAAGCGCCGC
64 TTTTCCAAAAAGCGCCGC
* * *
95951353 TATAGATCTGAGCATTAGCGGCGCTTTTTGAAAAAGCCGCTATAGATCTGAGCATTAGCGGCGTT
1 TATAGATCTGAGCATTAGCGACGCTTTTTGAAAAAGCCGCTATAGATCTAAGCATTAGCGACGTT
* * *
95951418 TTTCAATAAGCGTCGC
66 TTCCAAAAAGCGCCGC
* * *
95951434 TATAGATATGAGCATTAGCGACGCTTTTGGAATAACGCCGCTA
1 TATAGATCTGAGCATTAGCGACGCTTTTTGAA-AAAGCCGCTA
95951477 ATAACACTAA
Statistics
Matches: 107, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
81 74 0.69
82 22 0.21
83 11 0.10
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (81 bp):
TATAGATCTGAGCATTAGCGACGCTTTTTGAAAAAGCCGCTATAGATCTAAGCATTAGCGACGTT
TTCCAAAAAGCGCCGC
Found at i:95951476 original size:41 final size:41
Alignment explanation
Indices: 95951272--95951461 Score: 233
Period size: 41 Copynumber: 4.7 Consensus size: 41
95951262 AAAACGTTGA
* * *
95951272 TATAAATC-GAGCATTAGCGACGTTTTTCAAAAAGCACCGT
1 TATAGATCTGAGCATTAGCGACGTTTTTCAAAAAGCGCCGC
* * *
95951312 TATAGATCTAAGCATTGGCGACGTTTTCCAAAAAGCGCCGC
1 TATAGATCTGAGCATTAGCGACGTTTTTCAAAAAGCGCCGC
* *
95951353 TATAGATCTGAGCATTAGCGGCGCTTTTTGAAAAA--GCCGC
1 TATAGATCTGAGCATTAGCGACG-TTTTTCAAAAAGCGCCGC
* * *
95951393 TATAGATCTGAGCATTAGCGGCGTTTTTCAATAAGCGTCGC
1 TATAGATCTGAGCATTAGCGACGTTTTTCAAAAAGCGCCGC
* *
95951434 TATAGATATGAGCATTAGCGACGCTTTT
1 TATAGATCTGAGCATTAGCGACGTTTTT
95951462 GGAATAACGC
Statistics
Matches: 129, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
39 9 0.07
40 35 0.27
41 76 0.59
42 9 0.07
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (41 bp):
TATAGATCTGAGCATTAGCGACGTTTTTCAAAAAGCGCCGC
Found at i:95951571 original size:39 final size:38
Alignment explanation
Indices: 95951519--95951593 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
95951509 TCCTGCTTTA
*
95951519 ATTTTTGCGGCGTTTTTTTAAAACACCGCTAATGCTCG
1 ATTTTTGAGGCGTTTTTTTAAAACACCGCTAATGCTCG
* *
95951557 ATTTTTAGAGGCGTTTTTTTAAAGCGCCGCTAATGCT
1 ATTTTT-GAGGCGTTTTTTTAAAACACCGCTAATGCT
95951594 AGATCGTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.18
39 27 0.82
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (38 bp):
ATTTTTGAGGCGTTTTTTTAAAACACCGCTAATGCTCG
Found at i:95951609 original size:39 final size:38
Alignment explanation
Indices: 95951527--95951630 Score: 111
Period size: 39 Copynumber: 2.6 Consensus size: 38
95951517 TAATTTTTGC
* * **
95951527 GGCGTTTTTTTAAAACACCGCTAATGCTCGATTTTTAGA
1 GGCGTTTTTTT-AAACGCCGCTAATGCTAGATCGTTAGA
95951566 GGCGTTTTTTTAAAGCGCCGCTAATGCTAGATCGTTA-A
1 GGCGTTTTTTTAAA-CGCCGCTAATGCTAGATCGTTAGA
95951604 TGGCGTTTTTCATTCAAACGCCGCTAA
1 -GGCGTTTTT--TT-AAACGCCGCTAA
95951631 AAACGCCACG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 4 0.07
39 38 0.68
41 11 0.20
42 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (38 bp):
GGCGTTTTTTTAAACGCCGCTAATGCTAGATCGTTAGA
Found at i:95953887 original size:2 final size:2
Alignment explanation
Indices: 95953882--95953908 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95953872 ATATATATAT
95953882 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
95953909 AAAGTATACT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:95956083 original size:8 final size:8
Alignment explanation
Indices: 95956072--95956127 Score: 53
Period size: 7 Copynumber: 6.8 Consensus size: 8
95956062 TAAAATTATA
95956072 TAAAAATT
1 TAAAAATT
95956080 TAAAAA-T
1 TAAAAATT
95956087 TAAAAATAT
1 TAAAAAT-T
*
95956096 TGAAATTATT
1 T-AAA-AATT
95956106 TAAAAATT
1 TAAAAATT
95956114 ATAAAAA-T
1 -TAAAAATT
95956122 TAAAAA
1 TAAAAA
95956128 AACATTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
7 13 0.32
8 10 0.24
9 11 0.27
10 5 0.12
11 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (8 bp):
TAAAAATT
Found at i:95956083 original size:26 final size:27
Alignment explanation
Indices: 95956055--95956147 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 27
95956045 GTTTTAAAAT
95956055 AAAATTATAAAATTATATAAAAATTTA
1 AAAATTATAAAATTATATAAAAATTTA
*
95956082 AAAATTA-AAAA-TAT-TGAAATTATTTA
1 AAAATTATAAAATTATAT-AAA-AATTTA
*
95956108 AAAATTATAAAAATTA-AAAAAACATTTTA
1 AAAATTAT-AAAATTATATAAAA-A-TTTA
95956137 AAAA-TATAAAA
1 AAAATTATAAAA
95956148 AAACTAAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
24 1 0.02
25 6 0.11
26 16 0.29
27 11 0.20
28 11 0.20
29 10 0.18
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAATTATAAAATTATATAAAAATTTA
Found at i:95956118 original size:9 final size:9
Alignment explanation
Indices: 95956055--95956148 Score: 63
Period size: 8 Copynumber: 10.4 Consensus size: 9
95956045 GTTTTAAAAT
95956055 AAAATTATA
1 AAAATTATA
*
95956064 AAATTATATA
1 AAAAT-TATA
95956074 AAAATT-TA
1 AAAATTATA
95956082 AAAA-T-TA
1 AAAATTATA
*
95956089 AAAA-TATT
1 AAAATTATA
*
95956097 GAAATTATTTA
1 AAAATTA--TA
95956108 AAAATTATA
1 AAAATTATA
*
95956117 AAAATTAAAA
1 AAAATT-ATA
*
95956127 AAACATTTTA
1 AAA-ATTATA
95956137 AAAA-TATA
1 AAAATTATA
95956145 AAAA
1 AAAA
95956149 AACTAAAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
7 8 0.12
8 17 0.25
9 16 0.24
10 17 0.25
11 10 0.15
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:95956395 original size:13 final size:13
Alignment explanation
Indices: 95956377--95956401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95956367 TAATTTTAAT
95956377 ATTTTTTAAAATA
1 ATTTTTTAAAATA
95956390 ATTTTTTAAAAT
1 ATTTTTTAAAAT
95956402 TTCTTTGTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTTAAAATA
Found at i:95956543 original size:31 final size:31
Alignment explanation
Indices: 95956505--95956569 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
95956495 AACGTCCAAA
* *
95956505 GGACTAAATTGAAAATGTCTGATAATGTTAG
1 GGACTAAATTGAAAATATCTGATAACGTTAG
* *
95956536 GGACTAAATTGAAAATATCTTATACCGTTAG
1 GGACTAAATTGAAAATATCTGATAACGTTAG
95956567 GGA
1 GGA
95956570 TTAGTAGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (31 bp):
GGACTAAATTGAAAATATCTGATAACGTTAG
Found at i:95956825 original size:2 final size:2
Alignment explanation
Indices: 95956818--95956850 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
95956808 CCTAATTTAA
95956818 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 A
95956851 AATACATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95958464 original size:29 final size:27
Alignment explanation
Indices: 95958410--95958475 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 27
95958400 GATGTATTTC
* *
95958410 TTTAAAATTTTTAGAATTAGATTTAAA
1 TTTAAAATTTTTAAAATTAGAATTAAA
* *
95958437 TTTAAAATATTTGTAAAATTATAATTAAG
1 TTTAAAAT-TTT-TAAAATTAGAATTAAA
*
95958466 TTTGAAATTT
1 TTTAAAATTT
95958476 GAGTTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 8 0.25
28 5 0.16
29 19 0.59
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (27 bp):
TTTAAAATTTTTAAAATTAGAATTAAA
Found at i:95969883 original size:96 final size:96
Alignment explanation
Indices: 95969718--95969905 Score: 315
Period size: 96 Copynumber: 2.0 Consensus size: 96
95969708 CTCACTTCTT
* *
95969718 CTTGCTCCTCTTAGCCCTCTTGGCTTCGGCTTTTCTCTTGCTCGAACCAAGCTTCTTGGGCTCCT
1 CTTGCTCCTCTTAGCCCTCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGCTTCTTGGGCTCCG
* * *
95969783 TGTCTGCTCTATCGTTCCCTTCGATGATAAA
66 TGTCTACTCCATCGTTCCCATCGATGATAAA
95969814 CTTGCTCCTCTTTA-CCCTCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGCTTCTTGGGCTCC
1 CTTGCTCCTC-TTAGCCCTCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGCTTCTTGGGCTCC
95969878 GTGTCTACTCCATCGTTCCCATCGATGA
65 GTGTCTACTCCATCGTTCCCATCGATGA
95969906 CAGACTTCCT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
96 83 0.97
97 3 0.03
ACGTcount: A:0.11, C:0.34, G:0.18, T:0.37
Consensus pattern (96 bp):
CTTGCTCCTCTTAGCCCTCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGCTTCTTGGGCTCCG
TGTCTACTCCATCGTTCCCATCGATGATAAA
Found at i:95974158 original size:4 final size:4
Alignment explanation
Indices: 95974144--95974207 Score: 74
Period size: 4 Copynumber: 16.0 Consensus size: 4
95974134 TATGTTTTGT
* * * * *
95974144 TTTA ATTA TTTA TTTA TATA TTTA TTCA TTTA TTTA TATA TTTA TTCA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
95974192 TTTA TTTA TTTC TTTA
1 TTTA TTTA TTTA TTTA
95974208 CTTTTTTTTT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:95974207 original size:20 final size:20
Alignment explanation
Indices: 95974151--95974200 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
95974141 TGTTTTAATT
95974151 ATTTATTTATATATTTATTC
1 ATTTATTTATATATTTATTC
95974171 ATTTATTTATATATTTATTC
1 ATTTATTTATATATTTATTC
95974191 ATTTATTTAT
1 ATTTATTTAT
95974201 TTCTTTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTATTTATATATTTATTC
Found at i:95974268 original size:3 final size:3
Alignment explanation
Indices: 95974260--95974323 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
95974250 TATCTGCACA
95974260 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
95974308 TAT TAT TAT TAC TAT T
1 TAT TAT TAT TAT TAT T
95974324 GTTTATCTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:95975412 original size:2 final size:2
Alignment explanation
Indices: 95975407--95975479 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
95975397 AACCAAAACA
95975407 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
95975449 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
95975480 AGAACTTGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:95975972 original size:14 final size:14
Alignment explanation
Indices: 95975953--95975979 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
95975943 AGAAGAGTTG
95975953 GATTTATTCATTTA
1 GATTTATTCATTTA
95975967 GATTTATTCATTT
1 GATTTATTCATTT
95975980 TGATCTAAGG
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:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
GATTTATTCATTTA
Found at i:95982031 original size:2 final size:2
Alignment explanation
Indices: 95982024--95982068 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
95982014 AAATTACCAA
* *
95982024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AA AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
95982065 AT AT
1 AT AT
95982069 TAAAACTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:95983917 original size:2 final size:2
Alignment explanation
Indices: 95983910--95983937 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
95983900 TTAAATCACA
95983910 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
95983938 TAATGGTGTT
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):
AT
Found at i:95984329 original size:13 final size:14
Alignment explanation
Indices: 95984311--95984340 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
95984301 CATTCGTCTC
95984311 TTTTTTTTTTAA-A
1 TTTTTTTTTTAATA
95984324 TTTTTTTTTTAATA
1 TTTTTTTTTTAATA
95984338 TTT
1 TTT
95984341 CATTATATCC
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:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTTAATA
Found at i:95986973 original size:70 final size:69
Alignment explanation
Indices: 95986899--95987046 Score: 183
Period size: 70 Copynumber: 2.1 Consensus size: 69
95986889 ATTATATAAG
* * * *
95986899 TAAGAACATAT-AGCAAACCAACACTTACCCAAAACAACAGTTTACAAACAGTAGCCAAAA-AGT
1 TAAGAACATATGA-CAAACCAACACTTAACCAAAACAACA-CTTAAAAACAATAG-CAAAATAGT
95986962 AGATATT
63 AGATATT
* * * *
95986969 TAAGAACATATGACAAACTAACACTTAATCAAAACAAGACTTAAAAACAATAGCAAAATATTAGA
1 TAAGAACATATGACAAACCAACACTTAACCAAAACAACACTTAAAAACAATAGCAAAATAGTAGA
95987034 TATT
66 TATT
95987038 TAAGAACAT
1 TAAGAACAT
95987047 GTGAAAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
68 5 0.07
69 29 0.43
70 33 0.49
71 1 0.01
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.21
Consensus pattern (69 bp):
TAAGAACATATGACAAACCAACACTTAACCAAAACAACACTTAAAAACAATAGCAAAATAGTAGA
TATT
Found at i:95987098 original size:213 final size:212
Alignment explanation
Indices: 95986723--95987198 Score: 663
Period size: 213 Copynumber: 2.2 Consensus size: 212
95986713 AAAGTATGTT
* *
95986723 ACACCTAAAAACAGTAGCAAAATC-TTAGATATTTAAGAACATATGGCAAACCAACACTTAACTA
1 ACACTTAAAAACAGTAGCAAAA-CATTAGATATTTAAGAACATATGACAAACCAACACTTAACTA
* *
95986787 AAACAAGACTTAAAAACAGTAGCAAAACATTAGATATTTGAGAACATAAGAAAATTTTGACATAT
65 AAACAAGACTTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACATAT
*
95986852 GTTACACTTTAAAACATATTAAAAACAGTAGCAAATCATTATATAAGTAAGAACATATAGCAAAC
130 GTTACACTTTAAAACATATTAAAAACAGTAGCAAATCATTATATAAGTAAGAACATATAGAAAAC
*
95986917 CAACACT-TACCCAAAACA
195 CAACA-TATAACCAAAACA
* * * *
95986935 ACAGTTTACAAACAGTAGCCAAAA-AGTAGATATTTAAGAACATATGACAAACTAACACTTAA-T
1 ACA-CTTAAAAACAGTAG-CAAAACATTAGATATTTAAGAACATATGACAAACCAACACTTAACT
* ** *
95986998 CAAAACAAGACTTAAAAACAATAGCAAAATATTAGATATTTAAGAACATGTGAAAATTTTGGCAT
64 -AAAACAAGACTTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACAT
* ** ** *
95987063 ATGTTACACTTTAAAACATATTTAAAATGGTAGCAAATCATTATATAAGTAAGGGCATATGGAAA
128 ATGTTACACTTTAAAACATATTAAAAACAGTAGCAAATCATTATATAAGTAAGAACATATAGAAA
*
95987128 ACCAACATATAACCAAAACT
193 ACCAACATATAACCAAAACA
* * *
95987148 ACACTTAAAAATAGTAGTAAAACATTAGATATTTAAGAACATATGAAAAAC
1 ACACTTAAAAACAGTAGCAAAACATTAGATATTTAAGAACATATGACAAAC
95987199 AGTAGCAAAT
Statistics
Matches: 231, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
211 4 0.02
212 42 0.18
213 180 0.78
214 5 0.02
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.25
Consensus pattern (212 bp):
ACACTTAAAAACAGTAGCAAAACATTAGATATTTAAGAACATATGACAAACCAACACTTAACTAA
AACAAGACTTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACATATG
TTACACTTTAAAACATATTAAAAACAGTAGCAAATCATTATATAAGTAAGAACATATAGAAAACC
AACATATAACCAAAACA
Found at i:95987197 original size:39 final size:39
Alignment explanation
Indices: 95987154--95987230 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
95987144 AACTACACTT
* * **
95987154 AAAAATAGTAGTAAAACATTAGATATTTAAGAACATATG
1 AAAAACAGTAGCAAAACATTAGATAAGTAAGAACATATG
* *
95987193 AAAAACAGTAGCAAATCATTATATAAGTAAGAACATAT
1 AAAAACAGTAGCAAAACATTAGATAAGTAAGAACATAT
95987231 CGCAAACCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.26
Consensus pattern (39 bp):
AAAAACAGTAGCAAAACATTAGATAAGTAAGAACATATG
Found at i:95991749 original size:33 final size:33
Alignment explanation
Indices: 95991664--95991761 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
95991654 GATTGAGTGG
* *
95991664 GAGTGTTTGGTTGCTGGACAAGAGCTGGAAT-T
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
* *
95991696 GAGTGTTTTGCTGCTAGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
* *
95991729 GGGTGTTTTGTTGCTGGACAGGAGCTGAAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
95991762 CAAGAAGAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 27 0.47
33 30 0.53
ACGTcount: A:0.20, C:0.10, G:0.38, T:0.32
Consensus pattern (33 bp):
GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
Found at i:95998477 original size:20 final size:21
Alignment explanation
Indices: 95998438--95998477 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
95998428 TTTCTTCCCT
*
95998438 CAAAAACACCACTTTCTCCTA
1 CAAAAACACCACTTTATCCTA
*
95998459 CAAAAACA-CATTTTATCCT
1 CAAAAACACCACTTTATCCT
95998478 GAAACTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.28
Consensus pattern (21 bp):
CAAAAACACCACTTTATCCTA
Found at i:96013787 original size:27 final size:28
Alignment explanation
Indices: 96013757--96013809 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
96013747 CTAAATTCAT
*
96013757 ACTTTAATTA-TAAAATAATTAATTTGC
1 ACTTAAATTATTAAAATAATTAATTTGC
* *
96013784 ACTTAAATTATTAACATATTTAATTT
1 ACTTAAATTATTAAAATAATTAATTT
96013810 TAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATTAATTTGC
Found at i:96025875 original size:15 final size:15
Alignment explanation
Indices: 96025857--96025920 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
96025847 GACAAGAAGA
*
96025857 CCAAAATAAAGAAAT
1 CCAAGATAAAGAAAT
*
96025872 CCAAGACAGAA-AAAT
1 CCAAGATA-AAGAAAT
*
96025887 CCAAGATGAAGAAAT
1 CCAAGATAAAGAAAT
*
96025902 CCAAGATATAGAAAT
1 CCAAGATAAAGAAAT
96025917 CCAA
1 CCAA
96025921 TATGCAATAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 2 0.05
15 37 0.90
16 2 0.05
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.12
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:96029993 original size:45 final size:45
Alignment explanation
Indices: 96029921--96030009 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
96029911 ACTCGATGCT
* ** * *
96029921 TCACATATATCATGAACTTGGATCAACTCAACAAGTTCGGATTTC
1 TCACATATATCACGAACTCAGACCAACTCAACAAGCTCGGATTTC
* *
96029966 TCACATATATCACGAACTCAGACCAACTCGACGAGCTCGGATTT
1 TCACATATATCACGAACTCAGACCAACTCAACAAGCTCGGATTT
96030010 TCTAAATTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.27
Consensus pattern (45 bp):
TCACATATATCACGAACTCAGACCAACTCAACAAGCTCGGATTTC
Found at i:96035438 original size:78 final size:78
Alignment explanation
Indices: 96035309--96035464 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
96035299 ATTGTTCCCA
96035309 TGAGGATAGGATCAAGGCACAAAGTGGTCAAGTTATTATAATAAAATACGATTAATGCTATGCCA
1 TGAGGATAGGATCAAGGCACAAAGTGGTCAAGTTATTATAATAAAATACGATTAATGCTATGCCA
96035374 AAGTCAATGATAC
66 AAGTCAATGATAC
*
96035387 TGAGGATAGGATCAAGGCACAAAGTGGTCAAGTTATTATAATAAAATACGATTAATGCTATGCTA
1 TGAGGATAGGATCAAGGCACAAAGTGGTCAAGTTATTATAATAAAATACGATTAATGCTATGCCA
96035452 AAGTCAATGATAC
66 AAGTCAATGATAC
96035465 ATTTGTAGTG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (78 bp):
TGAGGATAGGATCAAGGCACAAAGTGGTCAAGTTATTATAATAAAATACGATTAATGCTATGCCA
AAGTCAATGATAC
Found at i:96043525 original size:5 final size:5
Alignment explanation
Indices: 96043515--96043539 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
96043505 TTTAACTAAG
96043515 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
96043540 ATTTCAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:96054535 original size:43 final size:42
Alignment explanation
Indices: 96054456--96054609 Score: 191
Period size: 43 Copynumber: 3.6 Consensus size: 42
96054446 CATACCAACA
* * * * *
96054456 CCATATCCTAGATATGGTCTTACATGTAATTTCGTATCGATT
1 CCATATCCCAGATATGGTCTTACACGAAATCTCGTATCGATG
* *
96054498 CCAATAGCCCAGATATGGTCTTACACGAAATCACGTATCGATG
1 CC-ATATCCCAGATATGGTCTTACACGAAATCTCGTATCGATG
* ** *
96054541 CCATATCCCAGATATGGTCTTACATGTAAATCTCACATTGATG
1 CCATATCCCAGATATGGTCTTACACG-AAATCTCGTATCGATG
96054584 CCATATCCCAGATATGGTCTTACACG
1 CCATATCCCAGATATGGTCTTACACG
96054610 TAGTCTTAGT
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 24 0.25
43 72 0.75
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
CCATATCCCAGATATGGTCTTACACGAAATCTCGTATCGATG
Found at i:96061035 original size:13 final size:13
Alignment explanation
Indices: 96061017--96061051 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
96061007 TTTCAAAAGA
96061017 AAGATGGAATCCC
1 AAGATGGAATCCC
96061030 AAGATGGAATCCC
1 AAGATGGAATCCC
96061043 AAGATGGAA
1 AAGATGGAA
96061052 AGTTGATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (13 bp):
AAGATGGAATCCC
Found at i:96068788 original size:21 final size:21
Alignment explanation
Indices: 96068764--96068841 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 21
96068754 ATATAAATTG
96068764 CCTAAAATGCTCATTTTATTA
1 CCTAAAATGCTCATTTTATTA
* * ** *
96068785 CCTAACCCATAAGGTCATATAAATTG
1 CCTAA---A-ATGCTCAT-TTTATTA
96068811 CCTAAAATGCTCATTTTATTA
1 CCTAAAATGCTCATTTTATTA
96068832 CCT-AAATGCT
1 CCTAAAATGCT
96068842 GAAAGCAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 11
0.67 0.16 0.17
Matches are distributed among these distances:
20 7 0.17
21 12 0.29
22 6 0.14
23 1 0.02
24 1 0.02
25 6 0.14
26 9 0.21
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.36
Consensus pattern (21 bp):
CCTAAAATGCTCATTTTATTA
Found at i:96068812 original size:47 final size:47
Alignment explanation
Indices: 96068743--96068836 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
96068733 CCTAACTTGG
96068743 CCCATAAGGTCATATAAATTGCCTAAAATGCTCATTTTATTACCTAA
1 CCCATAAGGTCATATAAATTGCCTAAAATGCTCATTTTATTACCTAA
96068790 CCCATAAGGTCATATAAATTGCCTAAAATGCTCATTTTATTACCTAA
1 CCCATAAGGTCATATAAATTGCCTAAAATGCTCATTTTATTACCTAA
96068837 ATGCTGAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (47 bp):
CCCATAAGGTCATATAAATTGCCTAAAATGCTCATTTTATTACCTAA
Found at i:96068814 original size:26 final size:26
Alignment explanation
Indices: 96068743--96068815 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 26
96068733 CCTAACTTGG
96068743 CCCATAAGGTCATATAAATTGCCTAA
1 CCCATAAGGTCATATAAATTGCCTAA
* * ** *
96068769 ---A-ATGCTCAT-TTTATTACCTAA
1 CCCATAAGGTCATATAAATTGCCTAA
96068790 CCCATAAGGTCATATAAATTGCCTAA
1 CCCATAAGGTCATATAAATTGCCTAA
96068816 AATGCTCATT
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
21 9 0.28
22 6 0.19
23 1 0.03
24 1 0.03
25 6 0.19
26 9 0.28
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (26 bp):
CCCATAAGGTCATATAAATTGCCTAA
Found at i:96072988 original size:48 final size:48
Alignment explanation
Indices: 96072867--96073096 Score: 142
Period size: 48 Copynumber: 4.9 Consensus size: 48
96072857 ACACATGAAA
* * * *
96072867 GATGCCAATGCCATGTCCCAGACGTGGTCTTACATGGGATCTCTCAT--C
1 GATGCCAATGCCATATCCCAGACATGGTCTTACACGAGA-C-CTCATAAC
*
96072915 GATGCCAA-G--A-AT-CCAG-CTATGGTCTTACACGA-AGTCTCATAAC
1 GATGCCAATGCCATATCCCAGAC-ATGGTCTTACACGAGA-CCTCATAAC
* * * * * * *
96072958 GGTGTCAATGCCATGTCCCAGACATGGTCTTATATGGGACCTCATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACACGAGACCTCATAAC
* ** *
96073006 GATGCCAATGCCATATCCCAGATATGGTCTTACATAAGATCTCAT-AC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACACGAGACCTCATAAC
* * * *
96073053 TGATGCCGATGTCATATCCC--ACTATGGCCTTACACGAGATCTCA
1 -GATGCCAATGCCATATCCCAGAC-ATGGTCTTACACGAGACCTCA
96073097 ATACTCACAT
Statistics
Matches: 141, Mismatches: 29, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
41 5 0.04
42 2 0.01
43 22 0.16
44 2 0.01
45 1 0.01
46 2 0.01
47 21 0.15
48 84 0.60
49 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGACATGGTCTTACACGAGACCTCATAAC
Found at i:96073227 original size:6 final size:6
Alignment explanation
Indices: 96073216--96073377 Score: 324
Period size: 6 Copynumber: 27.0 Consensus size: 6
96073206 AGAAAGTCAA
96073216 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
96073264 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
96073312 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
96073360 ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT
96073378 TTCATGCAAT
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 156 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:96077284 original size:22 final size:23
Alignment explanation
Indices: 96077244--96077291 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
96077234 TACATCATTG
*
96077244 CATACACATCATAAACCTTTATT
1 CATACACATCATAAACCTTAATT
* *
96077267 CATAC-CATTATAAGCCTTAATT
1 CATACACATCATAAACCTTAATT
96077289 CAT
1 CAT
96077292 CATAAGTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (23 bp):
CATACACATCATAAACCTTAATT
Found at i:96079153 original size:48 final size:48
Alignment explanation
Indices: 96078919--96079153 Score: 211
Period size: 48 Copynumber: 5.0 Consensus size: 48
96078909 ACACATGAAA
* ** *
96078919 GATGCCAATGCCATGTCCCAGACGTGGTCTTACATGGGATCTC-T-CAT
1 GATGCCAATGCCATATCCCAGATATGGTCTTACACGGGATCTCATAC-T
* * * *
96078966 CGATGCCAA----A-AACCCAGCTATGGTCTTACAC-GAAGTCTCATAAT
1 -GATGCCAATGCCATATCCCAGATATGGTCTTACACGGGA-TCTCATACT
* * * * * *
96079010 GGTGCCGATGCCATGTCCCAGACATGGTCTTATACGGGACCTCATA-T
1 GATGCCAATGCCATATCCCAGATATGGTCTTACACGGGATCTCATACT
**
96079057 CGATGCCAATGCCATATCCCAGATATGGTCTTACATAGGATCTCATACT
1 -GATGCCAATGCCATATCCCAGATATGGTCTTACACGGGATCTCATACT
96079106 GATGCCAATGCCATATCCCA-ATATGGTCTTACACGGGATCTCAATACT
1 GATGCCAATGCCATATCCCAGATATGGTCTTACACGGGATCTC-ATACT
96079154 CACATGTCGT
Statistics
Matches: 148, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
42 2 0.01
43 25 0.17
44 3 0.02
47 22 0.15
48 93 0.63
49 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGATATGGTCTTACACGGGATCTCATACT
Found at i:96079279 original size:6 final size:6
Alignment explanation
Indices: 96079268--96079363 Score: 183
Period size: 6 Copynumber: 16.0 Consensus size: 6
96079258 AAAAAGTCAA
*
96079268 ATACAT ATACAT ATACAT ATATAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
96079316 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
96079364 TTCATGCAAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 88 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATACAT
Found at i:96081620 original size:23 final size:23
Alignment explanation
Indices: 96081601--96081649 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
96081591 ACTAAACTAT
96081601 AATTACAACTAAAAAGAAACCTA
1 AATTACAACTAAAAAGAAACCTA
* * * *
96081624 AATTTCAAGTAAAAATAAAACTA
1 AATTACAACTAAAAAGAAACCTA
96081647 AAT
1 AAT
96081650 AGGAAACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.61, C:0.12, G:0.04, T:0.22
Consensus pattern (23 bp):
AATTACAACTAAAAAGAAACCTA
Found at i:96096046 original size:40 final size:40
Alignment explanation
Indices: 96095991--96096158 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
96095981 TGAATGATAC
* * *
96095991 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGCTATAT
* * *
96096031 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGCTATAT
*
96096071 CCGGGCTAAGACCCGAAGGCATTTGTG-TGAGTTGCTATA-
1 CCGGGCTAAGACCCGAAGGCATTTGTGCT-AGTGGCTATAT
* * * *
96096110 CTCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 C-CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGCTATAT
96096151 CC-GGCTAA
1 CCGGGCTAA
96096159 ATTCCGAAGA
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
39 6 0.06
40 100 0.93
41 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGCTATAT
Found at i:96096124 original size:80 final size:80
Alignment explanation
Indices: 96095991--96096158 Score: 236
Period size: 80 Copynumber: 2.1 Consensus size: 80
96095981 TGAATGATAC
* *
96095991 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCCGGGTTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACTATATCCGGGTTAAGACCCGAAGGCAATTG
96096056 TGCGAGTGGTTATAT
66 TGCGAGTGGTTATAT
*
96096071 CCGGGCTAAGACCCGAAGGCATTTGTG-TGAGTTG-CTATA-CTCGGGTTAAGACCCGAAGGCAA
1 CCGGGCTAAGACCCGAAGGCATTTATGCT-AG-TGACTATATC-CGGGTTAAGACCCGAAGGCAA
**
96096133 TTGTGCTTGTGGTTATAT
63 TTGTGCGAGTGGTTATAT
96096151 CC-GGCTAA
1 CCGGGCTAA
96096159 ATTCCGAAGA
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
79 8 0.10
80 70 0.88
81 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACTATATCCGGGTTAAGACCCGAAGGCAATTG
TGCGAGTGGTTATAT
Found at i:96098452 original size:27 final size:27
Alignment explanation
Indices: 96098422--96098473 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
96098412 AATATCTATC
* *
96098422 CTGGTGGCTCTACCACAATATCTGTAT
1 CTGGTGACTCCACCACAATATCTGTAT
**
96098449 CTGGTGACTCCGTCACAATATCTGT
1 CTGGTGACTCCACCACAATATCTGT
96098474 TTTGGCAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (27 bp):
CTGGTGACTCCACCACAATATCTGTAT
Found at i:96104739 original size:44 final size:44
Alignment explanation
Indices: 96104671--96104760 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
96104661 TGTGACGCCA
* *
96104671 CATAGGTGCTTGGGGAGTGCCGTGGGAGGTGCTTGGGTTCGAGG
1 CATAGGTGCTTGGGGAGTGCCGTGGAAGGTGCTTGGGTTCAAGG
*
96104715 CATAGGTGCTTGGGGAGTGGCGTGGAAGGTGCTTGGGTTCAAGG
1 CATAGGTGCTTGGGGAGTGCCGTGGAAGGTGCTTGGGTTCAAGG
96104759 CA
1 CA
96104761 CGGCGCACGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.14, C:0.13, G:0.48, T:0.24
Consensus pattern (44 bp):
CATAGGTGCTTGGGGAGTGCCGTGGAAGGTGCTTGGGTTCAAGG
Found at i:96104748 original size:23 final size:23
Alignment explanation
Indices: 96104674--96104751 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
96104664 GACGCCACAT
*
96104674 AGGTGCTTGGGGAGTGCCGTGGG
1 AGGTGCTTGGGGAGTGCCGTGGA
* *
96104697 AGGTGCTT--GG-GT-TCGAGGCA
1 AGGTGCTTGGGGAGTGCCGTGG-A
*
96104717 TAGGTGCTTGGGGAGTGGCGTGGA
1 -AGGTGCTTGGGGAGTGCCGTGGA
96104741 AGGTGCTTGGG
1 AGGTGCTTGGG
96104752 TTCAAGGCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 4 0.09
20 2 0.05
21 10 0.23
23 21 0.48
24 3 0.07
25 4 0.09
ACGTcount: A:0.12, C:0.12, G:0.53, T:0.24
Consensus pattern (23 bp):
AGGTGCTTGGGGAGTGCCGTGGA
Found at i:96106643 original size:28 final size:27
Alignment explanation
Indices: 96106598--96106664 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 27
96106588 TAGAGGAAGC
*
96106598 GTTCTGGTGGCTATGCCACAAACATCT
1 GTTCTGGTGGCTACGCCACAAACATCT
*
96106625 GTTTCTGGTGGCTACGCCACAAATATCT
1 G-TTCTGGTGGCTACGCCACAAACATCT
96106653 GTTCTGGTGGCT
1 GTTCTGGTGGCT
96106665 CTACCACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 12 0.32
28 25 0.68
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (27 bp):
GTTCTGGTGGCTACGCCACAAACATCT
Found at i:96106671 original size:27 final size:26
Alignment explanation
Indices: 96106598--96106712 Score: 124
Period size: 27 Copynumber: 4.3 Consensus size: 26
96106588 TAGAGGAAGC
* *
96106598 GTTCTGGTGGCTATGCCACAAACATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
96106625 GTTTCTGGTGGCTAC-GCCACAAATATCT
1 G-TTCTGGTGGCT-CTGCCAC-AATATCT
*
96106653 GTTCTGGTGGCTCTACCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
96106679 GTATCTAGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
96106706 GTTCTGG
1 GTTCTGG
96106713 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
26 14 0.18
27 38 0.50
28 24 0.32
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:96116285 original size:21 final size:21
Alignment explanation
Indices: 96116259--96116301 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
96116249 ATAAATTCGG
96116259 TCAAAATAATGAAGAAAAAGA
1 TCAAAATAATGAAGAAAAAGA
96116280 TCAAAATAATGAAGAAAAAGA
1 TCAAAATAATGAAGAAAAAGA
96116301 T
1 T
96116302 GATACATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.65, C:0.05, G:0.14, T:0.16
Consensus pattern (21 bp):
TCAAAATAATGAAGAAAAAGA
Found at i:96116348 original size:26 final size:25
Alignment explanation
Indices: 96116319--96116370 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
96116309 ATTTTGTATC
*
96116319 TTTTA-ATTTTAAGCTATTAATTATTA
1 TTTTACATTTTAACCT-TT-ATTATTA
96116345 TTTTACCATTTTAACCTTTATTATTA
1 TTTTA-CATTTTAACCTTTATTATTA
96116371 AACATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 12 0.52
27 2 0.09
28 9 0.39
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTACATTTTAACCTTTATTATTA
Found at i:96117078 original size:21 final size:21
Alignment explanation
Indices: 96117052--96117107 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
96117042 ACCCATAAAG
96117052 GTTGAACGGAAGCTCGTAAGA
1 GTTGAACGGAAGCTCGTAAGA
* * *
96117073 GTTGAACGGAAACCCGTAAGG
1 GTTGAACGGAAGCTCGTAAGA
* *
96117094 GTTAAACAGAAGCT
1 GTTGAACGGAAGCT
96117108 TAATAGAGCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (21 bp):
GTTGAACGGAAGCTCGTAAGA
Found at i:96117158 original size:42 final size:41
Alignment explanation
Indices: 96117014--96117168 Score: 114
Period size: 42 Copynumber: 3.7 Consensus size: 41
96117004 CCGGAGGATG
* * ** *
96117014 AACAGAAGCTCATGAGAGCTAAATAGAAACCCATAA-AGGTTG
1 AACAGAAGCTCGT-AGAGCTGAACGGAAACCCATAAGA-GTTA
* * * *
96117056 AACGGAAGCTCGTAAGAGTTGAACGGAAACCCGTAAGGGTTA
1 AACAGAAGCTCGT-AGAGCTGAACGGAAACCCATAAGAGTTA
** * *
96117098 AACAGAAGCTTAATAGAGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGC-TCGTAGAGCTGAACGGAAACCCATAAGAGTTA
* * *
96117140 AATAGAAGCTCGTGAGAGCTAAATGGAAA
1 AACAGAAGCTCGT-AGAGCTGAACGGAAA
96117169 GTAAACCTGA
Statistics
Matches: 87, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
41 2 0.02
42 83 0.95
43 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (41 bp):
AACAGAAGCTCGTAGAGCTGAACGGAAACCCATAAGAGTTA
Found at i:96120128 original size:19 final size:19
Alignment explanation
Indices: 96120104--96120140 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
96120094 GTAATTTTTA
96120104 TATT-AAAATTTATCATATT
1 TATTAAAAATTTAT-ATATT
96120123 TATTAAAAATTTATATAT
1 TATTAAAAATTTATATAT
96120141 AAAAAGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAAAAATTTATATATT
Found at i:96127894 original size:3 final size:3
Alignment explanation
Indices: 96127886--96127939 Score: 83
Period size: 3 Copynumber: 17.7 Consensus size: 3
96127876 TCTTATTTAA
96127886 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT AT-T ATT
96127933 -TT ATT AT
1 ATT ATT AT
96127940 ATGCATATAC
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:96132313 original size:17 final size:18
Alignment explanation
Indices: 96132291--96132330 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
96132281 ATTTGTATAT
96132291 ATTAAATTTT-A-ATTTTC
1 ATTAAATTTTCACA-TTTC
96132308 ATTAAATTTTCACATTTC
1 ATTAAATTTTCACATTTC
96132326 ATTAA
1 ATTAA
96132331 TTCCATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 10 0.48
19 1 0.05
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAAATTTTCACATTTC
Found at i:96134467 original size:3 final size:3
Alignment explanation
Indices: 96134456--96134487 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
96134446 GTATAAAAAA
96134456 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
96134488 GGGTCTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:96136860 original size:29 final size:29
Alignment explanation
Indices: 96136822--96136877 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
96136812 AGTTTTAGAC
96136822 AAAAAAGATTAAGTATAAATGGAGATACA
1 AAAAAAGATTAAGTATAAATGGAGATACA
96136851 AAAAAAGATTAAGTATAAATGGAGATA
1 AAAAAAGATTAAGTATAAATGGAGATA
96136878 ATTGAGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.59, C:0.02, G:0.18, T:0.21
Consensus pattern (29 bp):
AAAAAAGATTAAGTATAAATGGAGATACA
Found at i:96140213 original size:43 final size:41
Alignment explanation
Indices: 96140044--96140211 Score: 135
Period size: 43 Copynumber: 4.0 Consensus size: 41
96140034 ACATAAGCTC
* * ** *
96140044 ATACAATGCCA-GATCCTAGATATGGTCTTACACTTAATCAT
1 ATACAATGCCACG-TCCCAGACATGGTCTTACAAGTAATCAA
* * * *
96140085 ATATCAATGCCACTATCCCAAACAGGGTCTTACACG-AATCAA
1 ATA-CAATGCCAC-GTCCCAGACATGGTCTTACAAGTAATCAA
* * *
96140127 TATACGATGCCAATGTCCCAGACATGGTCTTACACA-CAATCACA
1 -ATACAATGCC-ACGTCCCAGACATGGTCTTACA-AGTAATCA-A
96140171 ATACAATGCCAACGTCCCAGACATGGTCTTACAAGTAATCA
1 ATACAATGCC-ACGTCCCAGACATGGTCTTACAAGTAATCA
96140212 CATCTCGATA
Statistics
Matches: 102, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
41 3 0.03
42 37 0.36
43 61 0.60
44 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (41 bp):
ATACAATGCCACGTCCCAGACATGGTCTTACAAGTAATCAA
Found at i:96142513 original size:22 final size:24
Alignment explanation
Indices: 96142483--96142526 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
96142473 CTATCTAGAT
96142483 ATCAAATC-TCT-AAGATTACAAA
1 ATCAAATCTTCTAAAGATTACAAA
*
96142505 ATCATATCTTCTAAAGATTACA
1 ATCAAATCTTCTAAAGATTACA
96142527 TTTAATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (24 bp):
ATCAAATCTTCTAAAGATTACAAA
Found at i:96145920 original size:390 final size:390
Alignment explanation
Indices: 96145201--96145984 Score: 1460
Period size: 390 Copynumber: 2.0 Consensus size: 390
96145191 ACCAACTTAA
* *
96145201 TCAAAAAAATTCACAATAAGAGGAATAGAGTACCTGTTCTTCACAACGATCTTGTTTAGAGCCCG
1 TCAAAAAAAATCACAATAAAAGGAATAGAGTACCTGTTCTTCACAACGATCTTGTTTAGAGCCCG
96145266 ATAATCGATCCACATTCTCAACAACCCATCATGTTTTTCTGAAACAACACTGGCGCACCATATGG
66 ATAATCGATCCACATTCTCAACAACCCATCATGTTTTTCTGAAACAACACTGGCGCACCATATGG
*
96145331 AAATTTAGATGGCCTAATGAATCCCACATCTAAAAACTCCTCCAATTGTTTCCGGAACTCGTCTA
131 AAATTTAGATGGCCTAATGAATCCCACATCTAAAAACTCCTCCAATTGTTTCCGCAACTCGTCTA
96145396 ATTTTGGCGGAGACTTACAATATGGGGCCCTTGCTGGCGGCACCATATTAGACACTAACTCGATC
196 ATTTTGGCGGAGACTTACAATATGGGGCCCTTGCTGGCGGCACCATATTAGACACTAACTCGATC
* *
96145461 TTATGGTCCACCTCTCTCTTCGGTGGCAAAATTTTGGGCAACAAGGTAGGTATCACATCCCGAAA
261 TTATGGTCCACCTCCCTCTTCGGTGGCAAAATTTTGGGCAACAAGGCAGGTATCACATCCCGAAA
*
96145526 AGGCTGCAACAATTGGCACACTTCTTTCGGGATCTCACCAACGGACTTAACGATTTCCTCAATCT
326 AGGCTACAACAATTGGCACACTTCTTTCGGGATCTCACCAACGGACTTAACGATTTCCTCAATCT
*
96145591 TCAAAAAAAATCACAATAAAAGGAATAGAGTACCTGTTCTTTACAACGATCTTGTTTAGAGCCCG
1 TCAAAAAAAATCACAATAAAAGGAATAGAGTACCTGTTCTTCACAACGATCTTGTTTAGAGCCCG
96145656 ATAATCGATCCACATTCTCAACAACCCATCATGTTTTTCTGAAACAACACTGGCGCACCATATGG
66 ATAATCGATCCACATTCTCAACAACCCATCATGTTTTTCTGAAACAACACTGGCGCACCATATGG
* * *
96145721 AAATTTAGATGGCCTAATGTATCCCACATCTAAAAACTCCTCCAATTGTTTTCGCAACTCTTCTA
131 AAATTTAGATGGCCTAATGAATCCCACATCTAAAAACTCCTCCAATTGTTTCCGCAACTCGTCTA
* *
96145786 ATTTTGGCGGAGACTTACAATATGGGGCCCTTGCTGGCGGCACCATATTGGACACTAACTTGATC
196 ATTTTGGCGGAGACTTACAATATGGGGCCCTTGCTGGCGGCACCATATTAGACACTAACTCGATC
96145851 TTATGGTCCACCTCCCTCTTCGGTGGCAAAATTTTGGGCAACAAGGCAGGTATCACATCCCGAAA
261 TTATGGTCCACCTCCCTCTTCGGTGGCAAAATTTTGGGCAACAAGGCAGGTATCACATCCCGAAA
96145916 AGGCTACAACAATTGGCACACTTCTTTCGGGATCTCACCAACGGACTTAACGATTTCCTCAATCT
326 AGGCTACAACAATTGGCACACTTCTTTCGGGATCTCACCAACGGACTTAACGATTTCCTCAATCT
96145981 TCAA
1 TCAA
96145985 GGTGGCTAAA
Statistics
Matches: 382, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
390 382 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (390 bp):
TCAAAAAAAATCACAATAAAAGGAATAGAGTACCTGTTCTTCACAACGATCTTGTTTAGAGCCCG
ATAATCGATCCACATTCTCAACAACCCATCATGTTTTTCTGAAACAACACTGGCGCACCATATGG
AAATTTAGATGGCCTAATGAATCCCACATCTAAAAACTCCTCCAATTGTTTCCGCAACTCGTCTA
ATTTTGGCGGAGACTTACAATATGGGGCCCTTGCTGGCGGCACCATATTAGACACTAACTCGATC
TTATGGTCCACCTCCCTCTTCGGTGGCAAAATTTTGGGCAACAAGGCAGGTATCACATCCCGAAA
AGGCTACAACAATTGGCACACTTCTTTCGGGATCTCACCAACGGACTTAACGATTTCCTCAATCT
Found at i:96148637 original size:23 final size:23
Alignment explanation
Indices: 96148607--96148652 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
96148597 CTATAATTTT
96148607 CATGTTTCTGCGAGATTAAGTTA
1 CATGTTTCTGCGAGATTAAGTTA
96148630 CATGTTTCTGCGAGATTAAGTTA
1 CATGTTTCTGCGAGATTAAGTTA
96148653 AATATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (23 bp):
CATGTTTCTGCGAGATTAAGTTA
Found at i:96152501 original size:51 final size:53
Alignment explanation
Indices: 96152441--96152550 Score: 143
Period size: 51 Copynumber: 2.1 Consensus size: 53
96152431 AGTCATTGGG
* *
96152441 TATGTTAATGCTGATTTTACCGAAGATCTTGAT-AAAGAAGA-TCTCACAAGT
1 TATGTTAATGCTGATTTTACCGAAGACCTTAATAAAAGAAGACTCTCACAAGT
* ** *
96152492 TATGTTAATGTTGATTTTGTCGAAGACCTTAATAAAATAAGATCTCTCACAAGT
1 TATGTTAATGCTGATTTTACCGAAGACCTTAATAAAAGAAGA-CTCTCACAAGT
96152546 TATGT
1 TATGT
96152551 CTTTATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
51 28 0.56
52 7 0.14
54 15 0.30
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (53 bp):
TATGTTAATGCTGATTTTACCGAAGACCTTAATAAAAGAAGACTCTCACAAGT
Found at i:96160804 original size:4 final size:4
Alignment explanation
Indices: 96160795--96160835 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
96160785 TGCAAAATTT
*
96160795 AGAA AGAA AGAA AG-A A-AA AGAA AGAA AAAA AGAAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG-AA AGAA AG
96160836 GGAGAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 4 0.12
4 24 0.75
5 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:96160816 original size:10 final size:9
Alignment explanation
Indices: 96160795--96160835 Score: 59
Period size: 8 Copynumber: 4.7 Consensus size: 9
96160785 TGCAAAATTT
96160795 AGAAAG-AA
1 AGAAAGAAA
96160803 AGAAAGAAAA
1 AGAAAG-AAA
96160813 AGAAAGAAA
1 AGAAAGAAA
96160822 A-AAAGAAA
1 AGAAAGAAA
96160830 AGAAAG
1 AGAAAG
96160836 GGAGAAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 14 0.47
9 8 0.27
10 8 0.27
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AGAAAGAAA
Found at i:96160843 original size:17 final size:18
Alignment explanation
Indices: 96160795--96160835 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
96160785 TGCAAAATTT
96160795 AGAAAGAAAGAAAGAAAA
1 AGAAAGAAAGAAAGAAAA
*
96160813 AGAAAGAAAAAAAG-AAA
1 AGAAAGAAAGAAAGAAAA
96160830 AGAAAG
1 AGAAAG
96160836 GGAGAAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAGAAAGAAAA
Found at i:96161294 original size:19 final size:18
Alignment explanation
Indices: 96161272--96161307 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
96161262 CAAAATATAG
96161272 TGTGAAATTTGAAATGTAA
1 TGTGAAA-TTGAAATGTAA
*
96161291 TGTGGAATTGAAATGTA
1 TGTGAAATTGAAATGTA
96161308 TAATATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (18 bp):
TGTGAAATTGAAATGTAA
Found at i:96176257 original size:13 final size:13
Alignment explanation
Indices: 96176239--96176267 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
96176229 GGTTGTTTAT
96176239 TAAACTAATTAAC
1 TAAACTAATTAAC
96176252 TAAACTAATTAAC
1 TAAACTAATTAAC
96176265 TAA
1 TAA
96176268 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Done.