Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 39 of 356
Found at i:12817128 original size:27 final size:27
Alignment explanation
Indices: 12817055--12817161 Score: 126
Period size: 27 Copynumber: 4.0 Consensus size: 27
12817045 GTAATTCTGT
**
12817055 AAATCGAGGGTATTTTGGTAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTAC
* *
12817082 AAGTCGAAGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTAC
* *
12817109 AAATCGAGGGTATTTTAGTATTTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTAC
* *
12817136 AAA-CTAAGCGTATTTCAGTAATTTTA
1 AAATC-GAGGGTATTTCAGTAATTTTA
12817162 GTAAACTAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 66 0.99
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
AAATCGAGGGTATTTCAGTAATTTTAC
Found at i:12817159 original size:54 final size:54
Alignment explanation
Indices: 12817055--12817161 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
12817045 GTAATTCTGT
* *
12817055 AAATCGAGGGTATTTTGGTAATTTTACAAGTCGAAGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTATTTTAGTAATTTTACAAGACGAAGGTATTTCAGTAATTTTAC
* *
12817109 AAATCGAGGGTATTTTAGTATTTTTACAA-ACTAAGCGTATTTCAGTAATTTTA
1 AAATCGAGGGTATTTTAGTAATTTTACAAGACGAAG-GTATTTCAGTAATTTTA
12817162 GTAAACTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 4 0.08
54 44 0.92
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (54 bp):
AAATCGAGGGTATTTTAGTAATTTTACAAGACGAAGGTATTTCAGTAATTTTAC
Found at i:12817175 original size:27 final size:26
Alignment explanation
Indices: 12817072--12817176 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 26
12817062 GGGTATTTTG
* * *
12817072 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAA-ACTAAAGTATTTCA
* ** *
12817099 GTAATTTTACAAATCGAGGGTATTTTA
1 GTAATTTTACAAA-CTAAAGTATTTCA
* *
12817126 GTATTTTTACAAACTAAGCGTATTTCA
1 GTAATTTTACAAACTAA-AGTATTTCA
*
12817153 GTAATTTTAGTAAACTAAAGTATT
1 GTAATTTTA-CAAACTAAAGTATT
12817177 CTAAACAGGC
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
26 2 0.03
27 55 0.86
28 7 0.11
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (26 bp):
GTAATTTTACAAACTAAAGTATTTCA
Found at i:12819675 original size:79 final size:79
Alignment explanation
Indices: 12819530--12819750 Score: 327
Period size: 79 Copynumber: 2.8 Consensus size: 79
12819520 GAGTCACATC
* * * *
12819530 TCATGTAACTGTAGTGAATCAAGATTACCC-TTTCAGGTCAAATCCTACCCACCTTAAGTTATCA
1 TCATGTAACCGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
*
12819594 TAAGGAATCATGTA
66 TAAGGAATCATATA
* * *
12819608 TCATGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAGGTTGCCA
1 TCATGTAACCGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
*
12819673 TAATGAATCATATA
66 TAAGGAATCATATA
* * *
12819687 TCATGTAACCGTAGTGACTCAGGATTACCCTTTTTAGGTCAAATCCTATCCGCCTTAAGTTACC
1 TCATGTAACCGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACC
12819751 CTAGTGAATC
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 27 0.21
79 100 0.79
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (79 bp):
TCATGTAACCGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
TAAGGAATCATATA
Found at i:12819790 original size:40 final size:40
Alignment explanation
Indices: 12819726--12819823 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 40
12819716 CTTTTTAGGT
* * * *
12819726 CAAATCCTATCCGCCTTAAGTTACCCTAGTGAATCAAGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
* *
12819766 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAAGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
12819806 CAAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
12819824 TATTCTCGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
Found at i:12821414 original size:40 final size:40
Alignment explanation
Indices: 12821370--12821449 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12821360 AGGACCAAAT
12821370 TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
1 TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
12821410 TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
1 TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
12821450 ACATGAATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (40 bp):
TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
Found at i:12821530 original size:8 final size:8
Alignment explanation
Indices: 12821519--12821544 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12821509 TAAATAAATT
12821519 AATAATAA
1 AATAATAA
12821527 AATAATAA
1 AATAATAA
12821535 AATAATAA
1 AATAATAA
12821543 AA
1 AA
12821545 AATCTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAATAA
Found at i:12825429 original size:21 final size:21
Alignment explanation
Indices: 12825416--12825453 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 21
12825406 TTAATTATAA
12825416 AATATAT-ATATTT-ATTAGT
1 AATATATGATATTTAATTAGT
*
12825435 AATATATGATATTAAATTA
1 AATATATGATATTTAATTA
12825454 ATTTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 5 0.31
21 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
AATATATGATATTTAATTAGT
Found at i:12826035 original size:20 final size:21
Alignment explanation
Indices: 12825998--12826045 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
12825988 ATATATGTAT
*
12825998 TTAATTATTAATAGATATTTA
1 TTAATTATTAAAAGATATTTA
12826019 TTAATTA-TAAAAGATATTTA
1 TTAATTATTAAAAGATATTTA
12826039 TTAATTA
1 TTAATTA
12826046 AATAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
TTAATTATTAAAAGATATTTA
Found at i:12827401 original size:41 final size:41
Alignment explanation
Indices: 12827355--12827489 Score: 104
Period size: 40 Copynumber: 3.4 Consensus size: 41
12827345 GACCTCGAGT
**
12827355 CGATGAGACACTGGGTGTCACTATATTT-CTTCGGATAGATT
1 CGATGAGACACTGGGTGTCACTATATTTACTTCGGATAG-GC
* ** * *
12827396 TGATGAGGTACT-GG-GT-ACCAT-TTTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCACTATATTTACTTCGGATAGGC
* * *
12827433 CGATGAGACACTGGGTGTCACTATA-TTACTTTGAACTA-TC
1 CGATGAGACACTGGGTGTCACTATATTTACTTCGGA-TAGGC
*
12827473 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
12827490 CCATTCTGGT
Statistics
Matches: 72, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
37 12 0.17
38 15 0.21
39 4 0.06
40 30 0.42
41 11 0.15
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (41 bp):
CGATGAGACACTGGGTGTCACTATATTTACTTCGGATAGGC
Found at i:12830183 original size:20 final size:20
Alignment explanation
Indices: 12830127--12830183 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
12830117 TTAACAGACT
12830127 TTTATTTATTTTTGTTTTGGA
1 TTTATTTATTTTTG-TTTGGA
* *
12830148 TTT-TGTTTTTTTTGTTTGGG
1 TTTAT-TTATTTTTGTTTGGA
*
12830168 TTTATTTATTTGTGTT
1 TTTATTTATTTTTGTT
12830184 GGGCAGGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.09, C:0.00, G:0.18, T:0.74
Consensus pattern (20 bp):
TTTATTTATTTTTGTTTGGA
Found at i:12831783 original size:22 final size:21
Alignment explanation
Indices: 12831758--12831822 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
12831748 TGCGCATGGG
12831758 TTGGATAAAAGAAGTAAAAAGT
1 TTGGATAAAAGAA-TAAAAAGT
** *
12831780 TTGGATATCCA-AA-AACAAGT
1 TTGGATA-AAAGAATAAAAAGT
12831800 TTGGATAAAAGAAATAAAAAGT
1 TTGGATAAAAG-AATAAAAAGT
12831822 T
1 T
12831823 GTACTGATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 1 0.03
20 13 0.39
21 2 0.06
22 16 0.48
23 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.25
Consensus pattern (21 bp):
TTGGATAAAAGAATAAAAAGT
Found at i:12832247 original size:30 final size:30
Alignment explanation
Indices: 12832213--12832283 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
12832203 TAGCAAAATG
12832213 GGACCTGGTGGACCGGGAGGA-GGGCCG-GGA
1 GGACCTGGTGGACCGGGAGGATGGG--GAGGA
*
12832243 GGACCAGGTGGACCGGGAGGATGGGGAGGA
1 GGACCTGGTGGACCGGGAGGATGGGGAGGA
12832273 GGACCTGGTGG
1 GGACCTGGTGG
12832284 TTGGGGTCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 1 0.03
30 33 0.89
31 3 0.08
ACGTcount: A:0.18, C:0.17, G:0.56, T:0.08
Consensus pattern (30 bp):
GGACCTGGTGGACCGGGAGGATGGGGAGGA
Found at i:12837246 original size:2 final size:2
Alignment explanation
Indices: 12837239--12837271 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12837229 AAACCTTTAA
12837239 AG 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 AG A
12837272 TCAAAGCAGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12841795 original size:14 final size:14
Alignment explanation
Indices: 12841776--12841805 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12841766 ATGTTAGCAC
12841776 TACTAAGTTTCCAT
1 TACTAAGTTTCCAT
12841790 TACTAAGTTTCCAT
1 TACTAAGTTTCCAT
12841804 TA
1 TA
12841806 AGTCTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (14 bp):
TACTAAGTTTCCAT
Found at i:12842318 original size:5 final size:5
Alignment explanation
Indices: 12842308--12842358 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
12842298 CACGTTAGTG
*
12842308 AATAA AATAA AAT-A AATATA AAT-A AATACA TATAA AATAA AGATAA
1 AATAA AATAA AATAA AATA-A AATAA AATA-A AATAA AATAA A-ATAA
12842354 AATAA
1 AATAA
12842359 TTTATATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 8 0.21
5 18 0.46
6 13 0.33
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:12853500 original size:27 final size:27
Alignment explanation
Indices: 12853470--12853535 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
12853460 TAGTCCGACA
** * *
12853470 GGACGTTAAACATTGGATTTTTCAATG
1 GGACGTTAAACAGGGGATTGTCCAATG
*
12853497 GGACGTTCAACAGGGGATTGTCCAATG
1 GGACGTTAAACAGGGGATTGTCCAATG
*
12853524 GGACATTAAACA
1 GGACGTTAAACA
12853536 CTTGATAGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (27 bp):
GGACGTTAAACAGGGGATTGTCCAATG
Found at i:12853614 original size:81 final size:81
Alignment explanation
Indices: 12853458--12853626 Score: 178
Period size: 81 Copynumber: 2.1 Consensus size: 81
12853448 TGACATCAAA
* * * * * * * *
12853458 GATAGTCCGACAGGACGTTAAACATTGGATTTTTCAATGGGACGTTCAACAGGGGATTGTCCAAT
1 GATAGTCCGACAGGACGTTAAACATTGAATTGTCCAATAGAACGTTAAACACGGAATTGTCCAAT
* **
12853523 GGGACATTAAACACTT
66 GAGACATTAAACACAG
* * *
12853539 GATAGTCCGACAGGACGTTAAGCA-TGTAATTGTCCAATAGAAGGTTAAACACGGAATTGTCCGA
1 GATAGTCCGACAGGACGTTAAACATTG-AATTGTCCAATAGAACGTTAAACACGGAATTGTCCAA
**
12853603 TGAGATGTTAAACACAG
65 TGAGACATTAAACACAG
12853620 GATAGTC
1 GATAGTC
12853627 AGATGGGATG
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
80 2 0.03
81 69 0.97
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (81 bp):
GATAGTCCGACAGGACGTTAAACATTGAATTGTCCAATAGAACGTTAAACACGGAATTGTCCAAT
GAGACATTAAACACAG
Found at i:12853652 original size:27 final size:27
Alignment explanation
Indices: 12853582--12853641 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
12853572 CCAATAGAAG
* *
12853582 GTTAAACAC-GGAATTGTCCGATGAGAT
1 GTTAAACACAGG-ATAGTCAGATGAGAT
*
12853609 GTTAAACACAGGATAGTCAGATGGGAT
1 GTTAAACACAGGATAGTCAGATGAGAT
12853636 GTTAAA
1 GTTAAA
12853642 TATGGGATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (27 bp):
GTTAAACACAGGATAGTCAGATGAGAT
Found at i:12857085 original size:45 final size:45
Alignment explanation
Indices: 12856989--12857095 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
12856979 GTAACGGTAG
* *
12856989 CAGTAACAGTAACAATATTTAACACACAAAGTGCTGAATCAATAA
1 CAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCAATAA
* * * * *
12857034 CGGTAACAGTAATAGTATTCGACACACAAAGTG-TCGAATTAGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAGTGCT-GAATCAATAA
*
12857079 CAGTAACGGTAACAGTA
1 CAGTAACAGTAACAGTA
12857096 ACAGTAGTCG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.02
45 50 0.98
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCAATAA
Found at i:12858401 original size:24 final size:23
Alignment explanation
Indices: 12858374--12858431 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
12858364 TTTAAGTAAA
*
12858374 TTATTTATTAATTTACATTTGTAT
1 TTATTTATTAA-TTACAGTTGTAT
12858398 TTATTTTCATT-ATTACAGTTGTAT
1 TTA-TTT-ATTAATTACAGTTGTAT
*
12858422 TTAATTATTA
1 TTATTTATTA
12858432 CCTTACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
22 3 0.10
23 2 0.07
24 17 0.59
25 4 0.14
26 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (23 bp):
TTATTTATTAATTACAGTTGTAT
Found at i:12864465 original size:45 final size:45
Alignment explanation
Indices: 12864414--12864517 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
12864404 GTAACGGTAG
*
12864414 CAGTAACAGTAACAATATTCAACACACAAAGTG-CTGAATCGGTAA
1 CAGTAACAGTAACAATATTCAACACACAAAGTGTC-GAATCAGTAA
* * * * *
12864459 CGGTAACAGTAATAATATTCGACATACAAAGTGTCGAATTAGTAA
1 CAGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCAGTAA
*
12864504 CAGTAACGGTAACA
1 CAGTAACAGTAACA
12864518 GTAACAGTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (45 bp):
CAGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCAGTAA
Found at i:12865186 original size:22 final size:22
Alignment explanation
Indices: 12865144--12865189 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12865134 CTAATTAAAC
*
12865144 TCATATATTTTTCTTCTTCAAT
1 TCATATATTTTTATTCTTCAAT
*
12865166 TCATATCTTTTTATTAC-TCAAT
1 TCATATATTTTTATT-CTTCAAT
12865188 TC
1 TC
12865190 CCTACCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.57
Consensus pattern (22 bp):
TCATATATTTTTATTCTTCAAT
Found at i:12874032 original size:43 final size:42
Alignment explanation
Indices: 12873927--12874068 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 42
12873917 AACATTCCAG
* *
12873927 ACGTGGTCTTACATGT-AATCAAATATCGATGCCACTGTCCCAA
1 ACGTGGTCTTACAAGTAAATCAAATA-CGATGCTAC-GTCCCAA
* * * *
12873970 ATAG-GGTCTTACACG-AAATCAAATACGATGCTATCATCCTAA
1 A-CGTGGTCTTACAAGTAAATCAAATACGATGCTA-CGTCCCAA
*
12874012 ACGTGGTCTTACAAGTAAATCATAAGT-CGATGCTAACGTCCCAG
1 ACGTGGTCTTACAAGTAAATCA-AA-TACGATGCT-ACGTCCCAA
12874056 ACGTGGTCTTACA
1 ACGTGGTCTTACA
12874069 CGATAACACA
Statistics
Matches: 81, Mismatches: 10, Indels: 15
0.76 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 23 0.28
43 27 0.33
44 28 0.35
45 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (42 bp):
ACGTGGTCTTACAAGTAAATCAAATACGATGCTACGTCCCAA
Found at i:12875098 original size:33 final size:33
Alignment explanation
Indices: 12875056--12875121 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
12875046 ATACAAATTT
12875056 TAATATCTCATAATATGAAATTCTTATGCTTAC
1 TAATATCTCATAATATGAAATTCTTATGCTTAC
12875089 TAATATCTCATAATATGAAATTCTTATGCTTAC
1 TAATATCTCATAATATGAAATTCTTATGCTTAC
12875122 ACCGTTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (33 bp):
TAATATCTCATAATATGAAATTCTTATGCTTAC
Found at i:12876234 original size:40 final size:39
Alignment explanation
Indices: 12876185--12876313 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 39
12876175 ATTTTAAGGA
* *
12876185 AAATCCTATCCACCTTAAGTTACCATAGTGAATCAGGAAC
1 AAATCCTATCCACCTTAA-TTACTATAGTGAATCAGGAAT
* *
12876225 AAATCCTATCCA-CTTTATATATTTATAGTGAATCAGGAAT
1 AAATCCTATCCACCTTAAT-TA-CTATAGTGAATCAGGAAT
* * * * *
12876265 AAATCCAATTCACTTTAATTTCTTTTAGTGAATCAGGAAT
1 AAATCCTATCCACCTTAATTAC-TATAGTGAATCAGGAAT
12876305 AAATCCTAT
1 AAATCCTAT
12876314 TCACTTTTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 1 0.01
39 6 0.08
40 62 0.85
41 4 0.05
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (39 bp):
AAATCCTATCCACCTTAATTACTATAGTGAATCAGGAAT
Found at i:12876316 original size:40 final size:40
Alignment explanation
Indices: 12876209--12876327 Score: 168
Period size: 40 Copynumber: 3.0 Consensus size: 40
12876199 TTAAGTTACC
* * *
12876209 ATAGTGAATCAGGAACAAATCCTATCCACTTTATATAT-TT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTA-ATTTCTT
*
12876249 ATAGTGAATCAGGAATAAATCCAATTCACTTTAATTTCTT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCTT
* *
12876289 TTAGTGAATCAGGAATAAATCCTATTCACTTTTATTTCT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCT
12876328 CGAGAAGGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
39 3 0.04
40 68 0.96
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (40 bp):
ATAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCTT
Found at i:12877217 original size:13 final size:13
Alignment explanation
Indices: 12877187--12877220 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
12877177 CTAATTCTTC
*
12877187 CTTTTTCTTTTTT
1 CTTTTTCTCTTTT
12877200 C-TTTTCTCTTTT
1 CTTTTTCTCTTTT
12877212 CTTTTTCTC
1 CTTTTTCTC
12877221 CCTTTCTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTTCTCTTTT
Found at i:12877476 original size:3 final size:3
Alignment explanation
Indices: 12877468--12877501 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12877458 TTATTTTATT
12877468 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12877502 CTAGTAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12885519 original size:27 final size:27
Alignment explanation
Indices: 12885485--12885556 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
12885475 TATAATAAAT
*
12885485 AATTAATAT-AACTTATTATTTTAAAAA
1 AATTAATATAAAATT-TTATTTTAAAAA
*
12885512 AATTAATATCAAAATTTTATTTTAATAA
1 AATTAATAT-AAAATTTTATTTTAAAAA
* *
12885540 CATTAATA-ATAATTTTA
1 AATTAATATAAAATTTTA
12885557 AAATTTAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 8 0.21
27 9 0.23
28 18 0.46
29 4 0.10
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
AATTAATATAAAATTTTATTTTAAAAA
Found at i:12886869 original size:22 final size:21
Alignment explanation
Indices: 12886843--12886889 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12886833 AATGTAAATA
12886843 AGACAAAAGAAAAACTATATGG
1 AGACAAAAG-AAAACTATATGG
** *
12886865 AGACATCAGGAAACTATATGG
1 AGACAAAAGAAAACTATATGG
12886886 AGAC
1 AGAC
12886890 GTCATCCCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (21 bp):
AGACAAAAGAAAACTATATGG
Found at i:12887084 original size:20 final size:20
Alignment explanation
Indices: 12887061--12887110 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12887051 AAATCCAAAT
*
12887061 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAAGA
*
12887081 TAAAAT-CTTGAAATTCAAGA
1 TAAAATAC-TAAAATTCAAGA
12887101 TAAGAATACT
1 TAA-AATACT
12887111 GATGTGGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 4 0.16
22 1 0.04
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (20 bp):
TAAAATACTAAAATTCAAGA
Found at i:12888682 original size:9 final size:9
Alignment explanation
Indices: 12888668--12888700 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
12888658 AAAATGCATG
12888668 TATATATAT
1 TATATATAT
*
12888677 TATATATGT
1 TATATATAT
12888686 TATATATA-
1 TATATATAT
12888694 TATATAT
1 TATATAT
12888701 GTTAACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:12890149 original size:16 final size:16
Alignment explanation
Indices: 12890123--12890155 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12890113 AATATCCATT
12890123 TCATGTATTTCATTAAA
1 TCATGTATTTCA-TAAA
12890140 TCAT-TATTTCATAAA
1 TCATGTATTTCATAAA
12890155 T
1 T
12890156 TTCATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (16 bp):
TCATGTATTTCATAAA
Found at i:12892391 original size:23 final size:24
Alignment explanation
Indices: 12892335--12892393 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
12892325 AAATAAATTA
* *
12892335 TTTTATAACAAGTGTACATATATC
1 TTTTATTACAAATGTACATATATC
12892359 TATTTATTACAAATGTACCA-ATAT-
1 T-TTTATTACAAATGTA-CATATATC
12892383 TTTTATTACAA
1 TTTTATTACAA
12892394 TTGTTAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 10 0.32
24 2 0.06
25 17 0.55
26 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (24 bp):
TTTTATTACAAATGTACATATATC
Found at i:12899496 original size:53 final size:52
Alignment explanation
Indices: 12899343--12899508 Score: 145
Period size: 52 Copynumber: 3.1 Consensus size: 52
12899333 GACGGAAGAG
* ** * * * * **
12899343 ATGTGATATGTGCGCCCGCATAATACCATAGCTGGGCTATGACATTGGTACA
1 ATGTGATACGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTA
* * * *
12899395 ATGTGATACGTGTTCCCGTATAAGACTATAGATGGGCTATAGCGTCGGTGTA
1 ATGTGATACGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTA
* * *
12899447 ATGTGATAATGTGATT-CCGTATAAGACCATACCTGGGATATGGCATCGGTAGTA
1 ATGTGAT-ACGTG-TTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGT-GTA
12899501 TATGTGAT
1 -ATGTGAT
12899509 CCATGTAATA
Statistics
Matches: 90, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
52 46 0.51
53 32 0.36
54 5 0.06
55 7 0.08
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (52 bp):
ATGTGATACGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTA
Found at i:12904882 original size:26 final size:26
Alignment explanation
Indices: 12904836--12904902 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
12904826 CTCAAATTGT
*
12904836 ATTTCTCATTTCA-TCTTATAATATCA
1 ATTTCTCATTTCATTCTAATAAT-TCA
*
12904862 CTTTCTCATTTCATTC-AATAATTCA
1 ATTTCTCATTTCATTCTAATAATTCA
*
12904887 ATTTATCAATTTCATT
1 ATTTCTC-ATTTCATT
12904903 TTATTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 8 0.23
26 25 0.71
27 2 0.06
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTCTCATTTCATTCTAATAATTCA
Found at i:12905862 original size:21 final size:22
Alignment explanation
Indices: 12905816--12905862 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12905806 CAATCCTTTA
12905816 ATCAATTTAAATCAAAATTTCT
1 ATCAATTTAAATCAAAATTTCT
*
12905838 ATCAA-TTAAACTCATAATTTC-
1 ATCAATTTAAA-TCAAAATTTCT
12905859 ATCA
1 ATCA
12905863 TTAGTTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (22 bp):
ATCAATTTAAATCAAAATTTCT
Found at i:12909747 original size:52 final size:52
Alignment explanation
Indices: 12909673--12909827 Score: 161
Period size: 52 Copynumber: 3.0 Consensus size: 52
12909663 GACGGAAGAG
** * *
12909673 ATGTGATATGTGCGCCCATATAAGACCATAGCTGGGCTATGACATCGGTACA
1 ATGTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGACATCGGTACA
* * * **
12909725 ATGTGATACGTGTTCCCGTATAAGACCATAAATGGGCTAT-AGCGTCGGTGTA
1 ATGTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGA-CATCGGTACA
* * *
12909777 ATGTGATAATGTGATT-CCGTATAAGACCATATCTGGGATATGGCATCGGTA
1 ATGTGAT-ATGTG-TTCCCGTATAAGACCATAACTGGGCTATGACATCGGTA
12909828 GTTTATGTGA
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
51 1 0.01
52 48 0.58
53 32 0.39
54 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (52 bp):
ATGTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGACATCGGTACA
Found at i:12920134 original size:22 final size:22
Alignment explanation
Indices: 12920093--12920151 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
12920083 ATAATAAATC
* *
12920093 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
12920113 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
12920135 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
12920152 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:12928959 original size:28 final size:27
Alignment explanation
Indices: 12928928--12928991 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
12928918 TATAAAAAAA
*
12928928 TTATTTTAATC-TT-AATTTAAATTTTCGT
1 TTATTTTAATCATTAAATTT--ATGTT-GT
12928956 TTATTTTAATCATTAAATTTATGTTGT
1 TTATTTTAATCATTAAATTTATGTTGT
12928983 TTATTTTAA
1 TTATTTTAA
12928992 ATTTTTACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 11 0.33
28 15 0.45
29 2 0.06
30 5 0.15
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (27 bp):
TTATTTTAATCATTAAATTTATGTTGT
Found at i:12938297 original size:6 final size:6
Alignment explanation
Indices: 12938288--12938321 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
12938278 CGATTTCATA
12938288 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCT
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCT
12938322 GCACTACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTTC
Found at i:12942378 original size:21 final size:21
Alignment explanation
Indices: 12942354--12942395 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12942344 AAATCTGAAT
* *
12942354 AAAATTAACATTTATTGTTTA
1 AAAAATAACATTTAATGTTTA
*
12942375 AAAAATATCATTTAATGTTTA
1 AAAAATAACATTTAATGTTTA
12942396 TCGTATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
AAAAATAACATTTAATGTTTA
Found at i:12948473 original size:42 final size:42
Alignment explanation
Indices: 12948411--12948532 Score: 118
Period size: 43 Copynumber: 2.9 Consensus size: 42
12948401 TAAGGTTAGT
* * *
12948411 TGAGATTACGTATAATACCATATCTGGGATATGACATCGATA
1 TGAGATTACGTGTAAAACCATACCTGGGATATGACATCGATA
* * * * * *
12948453 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATTGATA
1 TGAGATTACGTGTAAAACCATACCTGGGATA-TGACATCGATA
* ** *
12948496 TAAGATCCCATGTAAAACCATACCTGGGATATGACAT
1 TGAGATTACGTGTAAAACCATACCTGGGATATGACAT
12948533 TGGTATGATT
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 31 0.48
43 33 0.52
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (42 bp):
TGAGATTACGTGTAAAACCATACCTGGGATATGACATCGATA
Found at i:12952866 original size:22 final size:23
Alignment explanation
Indices: 12952840--12952886 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
12952830 TAAAAGAAAT
12952840 AGAATAAAGAAAAGA-AACAAAA
1 AGAATAAAGAAAAGAGAACAAAA
* *
12952862 AGAATAGAGAAAAGAGAACAGAA
1 AGAATAAAGAAAAGAGAACAAAA
12952885 AG
1 AG
12952887 CATTCGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.70, C:0.04, G:0.21, T:0.04
Consensus pattern (23 bp):
AGAATAAAGAAAAGAGAACAAAA
Found at i:12952875 original size:27 final size:30
Alignment explanation
Indices: 12952831--12952885 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 30
12952821 TAAAGTAAAT
12952831 AAAAGAAATAGAATAAAGA-AA-AGAAACA
1 AAAAGAAATAGAATAAAGAGAACAGAAACA
12952859 AAAAG-AATAGAGA-AAAGAGAACAGAAA
1 AAAAGAAATAGA-ATAAAGAGAACAGAAA
12952886 GCATTCGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (30 bp):
AAAAGAAATAGAATAAAGAGAACAGAAACA
Found at i:12953495 original size:23 final size:23
Alignment explanation
Indices: 12953469--12953543 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 23
12953459 AGGCACTTTA
12953469 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
12953492 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
12953513 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
12953534 TGTGTCGTAT
1 TGTGTCGTAT
12953544 ACTGATTAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 35 0.76
22 2 0.04
23 9 0.20
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:12963539 original size:114 final size:114
Alignment explanation
Indices: 12963404--12963638 Score: 364
Period size: 114 Copynumber: 2.1 Consensus size: 114
12963394 CTAGAAACTT
* * *
12963404 TTTTTAGGGGGGCCGGAATTAAATTGTATATTTTTACGATAGTAAAAATGCATTTTCACCATTTT
1 TTTTTAGGGGGGCCGAAATTAAATTGTATATTCTTACGATAGTAAAAATGCAATTTCACCATTTT
* * *
12963469 AATATCTATATTTTTATAATTTTTAAAGGTTTAAATCAAAATTTTATCA
66 AATATCTATATCTTTATAATTTTTAAAAGATTAAATCAAAATTTTATCA
12963518 TTTTTAGGGGGGCC-AATATTAAATTGTATATTCTTACGATAGTAAAAATGCAATTTCACCATTT
1 TTTTTAGGGGGGCCGAA-ATTAAATTGTATATTCTTACGATAGTAAAAATGCAATTTCACCATTT
* * * *
12963582 TAATATCTATCTCTTTATGATTTTTAAAAGATTAAATTAAATTTTTATCA
65 TAATATCTATATCTTTATAATTTTTAAAAGATTAAATCAAAATTTTATCA
12963632 TTTTTAG
1 TTTTTAG
12963639 CGGGCGGGGG
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 1 0.01
114 109 0.99
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (114 bp):
TTTTTAGGGGGGCCGAAATTAAATTGTATATTCTTACGATAGTAAAAATGCAATTTCACCATTTT
AATATCTATATCTTTATAATTTTTAAAAGATTAAATCAAAATTTTATCA
Found at i:12968704 original size:3 final size:3
Alignment explanation
Indices: 12968690--12968728 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
12968680 ACGAGGTTGT
* *
12968690 TCA TCT TCA TCA TCA TCA TCA TCA TCA CCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
12968729 ACCCATTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:12974182 original size:17 final size:17
Alignment explanation
Indices: 12974162--12974209 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
12974152 AAAAACCATT
12974162 AAAAAATAAAAAATGAG
1 AAAAAATAAAAAATGAG
* * *
12974179 AAAAATTATAAAAT-AT
1 AAAAAATAAAAAATGAG
*
12974195 AAAAAATAATAAATG
1 AAAAAATAAAAAATG
12974210 TTAAATATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAAATAAAAAATGAG
Found at i:12974191 original size:9 final size:9
Alignment explanation
Indices: 12974161--12974399 Score: 52
Period size: 10 Copynumber: 25.7 Consensus size: 9
12974151 AAAAAACCAT
*
12974161 TAAAAAATA
1 TAAAAATTA
*
12974170 -AAAAATGA
1 TAAAAATTA
*
12974178 GAAAAATTA
1 TAAAAATTA
12974187 T-AAAA-TA
1 TAAAAATTA
12974194 TAAAAA--A
1 TAAAAATTA
12974201 TAATAAATGT-
1 TAA-AAAT-TA
* *
12974211 TAAATATTT
1 TAAAAATTA
12974220 TAAAATATT-
1 TAAAA-ATTA
12974229 TGAAAAA-TA
1 T-AAAAATTA
*
12974238 TGAAAATTGA
1 TAAAAATT-A
* *
12974248 TATGAATTTA
1 TA-AAAATTA
12974258 TAAAAATGATA
1 TAAAAAT--TA
*
12974269 AAAAAATATA
1 TAAAAAT-TA
* *
12974279 AAAAAACTA
1 TAAAAATTA
12974288 TAAAAAATTA
1 T-AAAAATTA
12974298 T-AAAATTAA
1 TAAAAATT-A
*
12974307 TAAAACATATT
1 TAAAA-AT-TA
**
12974318 TAAATTTTTA
1 TAAA-AATTA
12974328 TAAAAAAATT-
1 T--AAAAATTA
12974338 T-AAAATCCTA
1 TAAAAAT--TA
*
12974348 TAAAAATCA
1 TAAAAATTA
12974357 T-AAAATTA
1 TAAAAATTA
*
12974365 TAAAAAGTA
1 TAAAAATTA
*
12974374 TTAAAATTGA
1 TAAAAATT-A
*
12974384 TATAAACTTA
1 TA-AAAATTA
12974394 TAAAAA
1 TAAAAA
12974400 AATCATAAAA
Statistics
Matches: 170, Mismatches: 30, Indels: 60
0.65 0.12 0.23
Matches are distributed among these distances:
7 12 0.07
8 36 0.21
9 43 0.25
10 44 0.26
11 31 0.18
12 4 0.02
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:12974198 original size:33 final size:33
Alignment explanation
Indices: 12974161--12974227 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
12974151 AAAAAACCAT
12974161 TAAAAAATAAAAAATGAGAAAAATTATAAAATA
1 TAAAAAATAAAAAATGAGAAAAATTATAAAATA
* ** * *
12974194 TAAAAAATAATAAATGTTAAATATTTTAAAATA
1 TAAAAAATAAAAAATGAGAAAAATTATAAAATA
12974227 T
1 T
12974228 TTGAAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (33 bp):
TAAAAAATAAAAAATGAGAAAAATTATAAAATA
Found at i:12974275 original size:11 final size:10
Alignment explanation
Indices: 12974259--12974302 Score: 61
Period size: 10 Copynumber: 4.2 Consensus size: 10
12974249 ATGAATTTAT
12974259 AAAAATGATAA
1 AAAAAT-ATAA
12974270 AAAAATATAA
1 AAAAATATAA
12974280 AAAAACTATAA
1 AAAAA-TATAA
*
12974291 AAAATTATAA
1 AAAAATATAA
12974301 AA
1 AA
12974303 TTAATAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
10 16 0.52
11 15 0.48
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (10 bp):
AAAAATATAA
Found at i:12974309 original size:19 final size:18
Alignment explanation
Indices: 12974179--12974398 Score: 71
Period size: 20 Copynumber: 11.7 Consensus size: 18
12974169 AAAAAATGAG
12974179 AAAAATTATAAAA-TATA
1 AAAAATTATAAAATTATA
*
12974196 AAAAATAAT-AAATGT-T-
1 AAAAATTATAAAAT-TATA
* * * *
12974212 AAATATTTTAAAATATTTG
1 AAAAATTATAAAAT-TATA
12974231 AAAAA-TATGAAAATTGATA
1 AAAAATTAT-AAAATT-ATA
** * *
12974250 TGAATTTATAAAAATGATAA
1 AAAAATTAT-AAAATTAT-A
* *
12974270 AAAAATATAAAAAAACTATA
1 AAAAAT-T-ATAAAATTATA
12974290 AAAAATTATAAAATTAATA
1 AAAAATTATAAAATT-ATA
*
12974309 AAACATATT-TAAATTTTTATAA
1 AAA-A-ATTATAAA--ATTAT-A
12974331 AAAAATT-TAAAATCCTAT-
1 AAAAATTATAAAAT--TATA
*
12974349 AAAAATCATAAAATTAT-
1 AAAAATTATAAAATTATA
*
12974366 AAAAAGTATTAAAATTGATA
1 AAAAATTA-TAAAATT-ATA
* *
12974386 TAAACTTATAAAA
1 AAAAATTATAAAA
12974399 AAATCATAAA
Statistics
Matches: 150, Mismatches: 30, Indels: 44
0.67 0.13 0.20
Matches are distributed among these distances:
16 9 0.06
17 23 0.15
18 25 0.17
19 34 0.23
20 39 0.26
21 13 0.09
22 7 0.05
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAAATTATAAAATTATA
Found at i:12974864 original size:8 final size:9
Alignment explanation
Indices: 12974816--12974871 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
12974806 TTTAAGTTTA
12974816 TTTAATAAT
1 TTTAATAAT
* *
12974825 TTTTATAAG
1 TTTAATAAT
12974834 TTTATATCAAT
1 TTTA-AT-AAT
*
12974845 TTTAATATT
1 TTTAATAAT
12974854 TTTAA-AAT
1 TTTAATAAT
*
12974862 TTTTATAAT
1 TTTAATAAT
12974871 T
1 T
12974872 CTTTACAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
8 6 0.16
9 21 0.57
10 4 0.11
11 6 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (9 bp):
TTTAATAAT
Found at i:12974870 original size:20 final size:20
Alignment explanation
Indices: 12974842--12974885 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 20
12974832 AGTTTATATC
*
12974842 AATTTTAAT-ATT-TTTA-A
1 AATTTTTATAATTCTTTACA
12974859 AATTTTTATAATTCTTTACA
1 AATTTTTATAATTCTTTACA
12974879 AATTTTT
1 AATTTTT
12974886 TATTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 3 0.13
19 4 0.17
20 8 0.35
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
AATTTTTATAATTCTTTACA
Found at i:12974895 original size:19 final size:19
Alignment explanation
Indices: 12974813--12974901 Score: 60
Period size: 20 Copynumber: 4.6 Consensus size: 19
12974803 GTTTTTAAGT
12974813 TTATTTAATAATTTTTATAA
1 TTATTTAA-AATTTTTATAA
* * *
12974833 GTT-TATATCAATTTTAAT-A
1 -TTATTTA-AAATTTTTATAA
12974852 TT-TTTAAAATTTTTATAA
1 TTATTTAAAATTTTTATAA
* *
12974870 TTCTTTACAAATTTTT-TAT
1 TTATTTA-AAATTTTTATAA
12974889 TTATTTAAGAATT
1 TTATTTAA-AATT
12974902 CTAATACCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.15
18 9 0.16
19 17 0.31
20 19 0.35
21 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATTTAAAATTTTTATAA
Found at i:12975948 original size:5 final size:5
Alignment explanation
Indices: 12975940--12975964 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12975930 TTGCAAGTGA
12975940 GGGGT GGGGT GGGGT GGGGT GGGGT
1 GGGGT GGGGT GGGGT GGGGT GGGGT
12975965 AGGGATGGGT
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:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
GGGGT
Found at i:12975974 original size:15 final size:15
Alignment explanation
Indices: 12975940--12975973 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12975930 TTGCAAGTGA
*
12975940 GGGGTGGGGTGGGGT
1 GGGGTGGGGTGGGAT
12975955 GGGGTGGGGTAGGGAT
1 GGGGTGGGGT-GGGAT
12975971 GGG
1 GGG
12975974 TTCGAAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.00, G:0.76, T:0.18
Consensus pattern (15 bp):
GGGGTGGGGTGGGAT
Found at i:12993761 original size:30 final size:30
Alignment explanation
Indices: 12993727--12993797 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
12993717 TTAATAAAGG
* *
12993727 TAAAATTATACATTGACTCC-TTCAAAATGA
1 TAAAATTATA-ATTGAATCCTTTAAAAATGA
*
12993757 TAAAACTT-TAATTTAATCCTTTAAAAATGA
1 TAAAA-TTATAATTGAATCCTTTAAAAATGA
*
12993787 TAAAAATATAA
1 TAAAATTATAA
12993798 GTTCATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 8 0.24
30 24 0.71
31 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.35
Consensus pattern (30 bp):
TAAAATTATAATTGAATCCTTTAAAAATGA
Found at i:12993877 original size:12 final size:12
Alignment explanation
Indices: 12993860--12993886 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12993850 CTTCGCCCTG
12993860 TATAACATAAAT
1 TATAACATAAAT
12993872 TATAACATAAAT
1 TATAACATAAAT
12993884 TAT
1 TAT
12993887 TATTTGCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAACATAAAT
Found at i:13007915 original size:26 final size:27
Alignment explanation
Indices: 13007858--13007924 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
13007848 ACATTGGTTG
* *
13007858 AATTCAAAATTAATCTTTAAATCAATTG
1 AATTCAAAATTAA-CTATAAATCAATTA
*
13007886 AATTCAAAATTAA-TATAAATTAATTA
1 AATTCAAAATTAACTATAAATCAATTA
13007912 AATT-AATAATTAA
1 AATTCAA-AATTAA
13007925 ACTAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.06
26 20 0.57
28 13 0.37
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (27 bp):
AATTCAAAATTAACTATAAATCAATTA
Found at i:13008726 original size:19 final size:19
Alignment explanation
Indices: 13008699--13008735 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13008689 TCAATATTAA
*
13008699 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
13008718 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
13008736 ACTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:13012047 original size:14 final size:14
Alignment explanation
Indices: 13012028--13012059 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
13012018 AGGTCATTTA
13012028 GCCCAACCAAACTG
1 GCCCAACCAAACTG
13012042 GCCCAACCAAACTG
1 GCCCAACCAAACTG
13012056 GCCC
1 GCCC
13012060 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:13018340 original size:25 final size:26
Alignment explanation
Indices: 13018311--13018367 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
13018301 GCAAAACTTT
* *
13018311 TTTTTATATTAAAATATT-TTTTTTG
1 TTTTTAAAATAAAATATTATTTTTTG
13018336 TTTTTAAAATAAAATATTATTTTTTG
1 TTTTTAAAATAAAATATTATTTTTTG
13018362 TCTTTT
1 T-TTTT
13018368 TTTTTATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 16 0.57
26 8 0.29
27 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTTAAAATAAAATATTATTTTTTG
Found at i:13019062 original size:60 final size:58
Alignment explanation
Indices: 13018990--13019112 Score: 219
Period size: 60 Copynumber: 2.1 Consensus size: 58
13018980 ATACTAAACT
13018990 AAACATAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA
1 AAACATAACAATTTATAACATAATCCTAAATTACTAA-AAATTAATTTTAAAATAATTA
*
13019049 CAAACATAACAATTTATAACATAATCCTAAATTACTAACAATTAATTTTAAAATAATTA
1 -AAACATAACAATTTATAACATAATCCTAAATTACTAAAAATTAATTTTAAAATAATTA
13019108 AAACA
1 AAACA
13019113 ATATTTTTAG
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 5 0.08
59 20 0.32
60 37 0.60
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACATAACAATTTATAACATAATCCTAAATTACTAAAAATTAATTTTAAAATAATTA
Found at i:13034758 original size:22 final size:24
Alignment explanation
Indices: 13034721--13034765 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
13034711 TTACTTTTGA
*
13034721 TCTCTTTAATTGTTT-ATTTCTAC
1 TCTCTTTAATTATTTAATTTCTAC
13034744 TCTC-TTAATTATTTAATTTCTA
1 TCTCTTTAATTATTTAATTTCTA
13034766 GACATTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.22, C:0.16, G:0.02, T:0.60
Consensus pattern (24 bp):
TCTCTTTAATTATTTAATTTCTAC
Found at i:13036209 original size:27 final size:26
Alignment explanation
Indices: 13036163--13036215 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
13036153 CACCACTGAA
* *
13036163 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
13036189 TCGGGGAAATCAGCACATAGCAACCCC
1 TCGGGG-AATCAGCACATAGCAACCCC
13036216 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:13036295 original size:70 final size:71
Alignment explanation
Indices: 13036175--13036324 Score: 232
Period size: 70 Copynumber: 2.1 Consensus size: 71
13036165 GGGGAATCAT
* *
13036175 CACTTAGCAACCCCTCGGGGAAATCAGCACATAGCAACCCCCTTTTCATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGAAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATGG
13036240 ATATCG
66 ATATCG
***
13036246 CACTTAGCAACCCCTCGGGG-AATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGAAATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATACAATG
13036309 GATATCG
65 GATATCG
13036316 CACTTAGCA
1 CACTTAGCA
13036325 CCACCAATGA
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 7 0.10
70 46 0.63
71 20 0.27
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGAAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATGG
ATATCG
Found at i:13036428 original size:104 final size:102
Alignment explanation
Indices: 13036245--13036466 Score: 356
Period size: 104 Copynumber: 2.2 Consensus size: 102
13036235 AATGGATATC
13036245 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATATGGTGG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATATGGTGG
* *
13036310 ATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 ATATCGCACATAGCACCACCAATAAACCGGGGAATCA
13036347 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGT
* *
13036412 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
64 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
13036451 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
13036467 TTTATATACA
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
102 17 0.15
103 20 0.18
104 73 0.66
105 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (102 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATATGGTGG
ATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:13036828 original size:29 final size:29
Alignment explanation
Indices: 13036795--13036858 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
13036785 TAATCCACCA
13036795 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
13036824 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
13036854 CCCAA
1 CCCAA
13036859 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:13036832 original size:30 final size:30
Alignment explanation
Indices: 13036802--13036858 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13036792 CCACCCAACT
13036802 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
13036831 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
13036859 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:13041957 original size:27 final size:26
Alignment explanation
Indices: 13041911--13041963 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
13041901 CACCACTGAA
* *
13041911 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
13041937 TCGGGGAAATCAGCACATAGCAACCCC
1 TCGGGG-AATCAGCACATAGCAACCCC
13041964 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:13042066 original size:72 final size:71
Alignment explanation
Indices: 13041923--13042074 Score: 241
Period size: 71 Copynumber: 2.1 Consensus size: 71
13041913 GGGGAATCAT
* *
13041923 CACTTAGCAACCCCTCGGGGAAATCAGCACATAGCAACCCCCTTTTCATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGAAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATGG
13041988 ATATCG
66 ATATCG
* ***
13041994 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGAAATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATACAATG
13042059 GATATCG
65 GATATCG
13042066 CACTTAGCA
1 CACTTAGCA
13042075 CCACCAATGA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
71 44 0.59
72 30 0.41
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGAAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATGG
ATATCG
Found at i:13042115 original size:104 final size:104
Alignment explanation
Indices: 13041993--13042216 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
13041983 AATGGATATC
13041993 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
13042058 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
13042097 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
13042162 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
13042201 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
13042217 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:13042578 original size:29 final size:29
Alignment explanation
Indices: 13042545--13042608 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
13042535 TAATCCACCA
13042545 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
13042574 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
13042604 CCCAA
1 CCCAA
13042609 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:13042582 original size:30 final size:30
Alignment explanation
Indices: 13042552--13042608 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13042542 CCACCCAACT
13042552 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
13042581 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
13042609 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:13048794 original size:5 final size:5
Alignment explanation
Indices: 13048786--13048815 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
13048776 ATTTGTGTTT
13048786 TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA
13048816 ACTTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:13055900 original size:5 final size:5
Alignment explanation
Indices: 13055892--13055926 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
13055882 ATTTATGTTT
13055892 TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA
13055927 ACTTAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:13057558 original size:32 final size:32
Alignment explanation
Indices: 13057519--13057592 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 32
13057509 ATTTAAAAAA
13057519 TAATAAATAAATTAACAAAATACTGGTATTAG
1 TAATAAATAAATTAACAAAATACTGGTATTAG
* *
13057551 ---T-AATAAATTAACAAAATATTGTTATTAG
1 TAATAAATAAATTAACAAAATACTGGTATTAG
13057579 TAATAAATTAAATT
1 TAATAAA-TAAATT
13057593 TAAAAATTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
28 25 0.71
29 1 0.03
31 1 0.03
32 2 0.06
33 6 0.17
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (32 bp):
TAATAAATAAATTAACAAAATACTGGTATTAG
Found at i:13057559 original size:28 final size:28
Alignment explanation
Indices: 13057524--13057589 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
13057514 AAAAATAATA
13057524 AATAAATTAACAAAATACTGGTATTAGT
1 AATAAATTAACAAAATACTGGTATTAGT
* *
13057552 AATAAATTAACAAAATATTGTTATTAGT
1 AATAAATTAACAAAATACTGGTATTAGT
13057580 AATAAATTAA
1 AATAAATTAA
13057590 ATTTAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.35
Consensus pattern (28 bp):
AATAAATTAACAAAATACTGGTATTAGT
Found at i:13058556 original size:6 final size:6
Alignment explanation
Indices: 13058547--13058574 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13058537 TGTTATTTTT
13058547 ATAATG ATAATG ATAATG ATAATG ATAA
1 ATAATG ATAATG ATAATG ATAATG ATAA
13058575 CAAAATTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (6 bp):
ATAATG
Found at i:13078276 original size:23 final size:23
Alignment explanation
Indices: 13078246--13078295 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
13078236 TTGTTTAAAC
*
13078246 ATTTTTA-CCTAATAAAACTAAT
1 ATTTTTACCCTAAAAAAACTAAT
13078268 ATTTCTTACCCTAAAAAAACTAAT
1 ATTT-TTACCCTAAAAAAACTAAT
13078292 ATTT
1 ATTT
13078296 ATGTTTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.16
23 3 0.12
24 18 0.72
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTTTACCCTAAAAAAACTAAT
Found at i:13085014 original size:6 final size:6
Alignment explanation
Indices: 13085003--13085041 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
13084993 CAAACAACAG
* * *
13085003 CCTTCT CCTTCT GCTTCT CCTTCT CCTTTT CCTCCT CCT
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCT
13085042 CCACCACCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (6 bp):
CCTTCT
Found at i:13093360 original size:23 final size:23
Alignment explanation
Indices: 13093329--13093418 Score: 117
Period size: 23 Copynumber: 3.9 Consensus size: 23
13093319 TAGAAGAGTG
13093329 AAGAGACTTGAATATGAAAAGTA
1 AAGAGACTTGAATATGAAAAGTA
* * * *
13093352 AAAAAACTTGAATATGAATAGTG
1 AAGAGACTTGAATATGAAAAGTA
* *
13093375 AAGAGACTTGAAGATGAAAAGTT
1 AAGAGACTTGAATATGAAAAGTA
*
13093398 AAGAGGCTTGAATATGAAAAG
1 AAGAGACTTGAATATGAAAAG
13093419 ATACACACAT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.50, C:0.04, G:0.23, T:0.22
Consensus pattern (23 bp):
AAGAGACTTGAATATGAAAAGTA
Found at i:13093392 original size:46 final size:46
Alignment explanation
Indices: 13093325--13093415 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
13093315 AAGTTAGAAG
*
13093325 AGTGAAGAGACTTGAATATGAAAAGTAAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAAGATGAAAAGTAAAAAAACTTGAATATGAAT
* * **
13093371 AGTGAAGAGACTTGAAGATGAAAAGTTAAGAGGCTTGAATATGAA
1 AGTGAAGAGACTTGAAGATGAAAAGTAAAAAAACTTGAATATGAA
13093416 AAGATACACA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.23
Consensus pattern (46 bp):
AGTGAAGAGACTTGAAGATGAAAAGTAAAAAAACTTGAATATGAAT
Found at i:13097861 original size:23 final size:23
Alignment explanation
Indices: 13097835--13097928 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
13097825 AAGTTAGAAG
13097835 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
13097858 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
13097881 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
13097904 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
13097927 AG
1 AG
13097929 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:13099092 original size:16 final size:15
Alignment explanation
Indices: 13099049--13099092 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
13099039 GAAAAAAAAG
*
13099049 AGAAATAAGATTGTAA
1 AGAAA-AAGATGGTAA
13099065 AGAAAAATGATGGTAA
1 AGAAAAA-GATGGTAA
13099081 AGAAAGAAGATG
1 AGAAA-AAGATG
13099093 AGATAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (15 bp):
AGAAAAAGATGGTAA
Found at i:13099567 original size:29 final size:29
Alignment explanation
Indices: 13099524--13099581 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
13099514 CCGAGTGATT
*
13099524 GACTATAAAATACTAGTTGTTGCTTAGGC
1 GACTATAAAACACTAGTTGTTGCTTAGGC
13099553 GACTATAAAACACTAGTTGTTGCTTAGGC
1 GACTATAAAACACTAGTTGTTGCTTAGGC
13099582 CTCTTTTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (29 bp):
GACTATAAAACACTAGTTGTTGCTTAGGC
Found at i:13125809 original size:18 final size:19
Alignment explanation
Indices: 13125786--13125888 Score: 81
Period size: 18 Copynumber: 5.4 Consensus size: 19
13125776 ACATCGTGAT
13125786 CTGAAGCCCGAAGT-CTAA
1 CTGAAGCCCGAAGTGCTAA
* *
13125804 CTGAAGCAAAC-AAGTGTTAAA
1 CTGAAGC--CCGAAGTGCT-AA
*
13125825 CGGAAGCCCGAAG-GCTAA
1 CTGAAGCCCGAAGTGCTAA
13125843 CTGAAGCACAC-AAGTGCTAA
1 CTGAAGC-C-CGAAGTGCTAA
*
13125863 ATGGAAGCCCGAA-TGCTAA
1 CT-GAAGCCCGAAGTGCTAA
13125882 CTGAAGC
1 CTGAAGC
13125889 TCATCAGAGC
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
18 20 0.30
19 19 0.28
20 15 0.22
21 13 0.19
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (19 bp):
CTGAAGCCCGAAGTGCTAA
Found at i:13125843 original size:39 final size:39
Alignment explanation
Indices: 13125788--13125888 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
13125778 ATCGTGATCT
* *
13125788 GAAGCCCGAAGTCTAACTGAAGCAAACAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCAAACAAGTGCTAAACG
* *
13125827 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCAAACAAGTGCTAAACG
*
13125866 GAAGCCCGAATGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
13125889 TCATCAGAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCAAACAAGTGCTAAACG
Found at i:13125870 original size:21 final size:21
Alignment explanation
Indices: 13125806--13125870 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
13125796 AAGTCTAACT
* * *
13125806 GAAGCAAACAAGTGTTAAACG
1 GAAGCACACAAGTGCTAAATG
*
13125827 GAAGC-C-CGAAG-GCTAACT-
1 GAAGCACAC-AAGTGCTAAATG
13125845 GAAGCACACAAGTGCTAAATG
1 GAAGCACACAAGTGCTAAATG
13125866 GAAGC
1 GAAGC
13125871 CCGAATGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
18 5 0.15
19 9 0.26
20 10 0.29
21 10 0.29
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAATG
Found at i:13125881 original size:19 final size:19
Alignment explanation
Indices: 13125821--13125881 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
13125811 AAACAAGTGT
* *
13125821 TAAACGGAAGCCCGAAGGC
1 TAAATGGAAGCCCGAATGC
*
13125840 TAACT-GAAGCACAC-AAGTGC
1 TAAATGGAAGC-C-CGAA-TGC
13125860 TAAATGGAAGCCCGAATGC
1 TAAATGGAAGCCCGAATGC
13125879 TAA
1 TAA
13125882 CTGAAGCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
18 5 0.15
19 13 0.39
20 10 0.30
21 5 0.15
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (19 bp):
TAAATGGAAGCCCGAATGC
Found at i:13127991 original size:126 final size:126
Alignment explanation
Indices: 13127830--13128073 Score: 434
Period size: 126 Copynumber: 1.9 Consensus size: 126
13127820 GTTTTAGCCT
* *
13127830 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGTGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAAGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
13127895 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAAATTTTGAGAGTGAACTGG
66 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAAATTTTGAGAGTGAACTGG
* * *
13127956 TAAGAAGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACTTTAGGGCATGATT
1 TAAGAAGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
*
13128021 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAG
66 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAAATTTTGAGAG
13128074 AAGATCAATG
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 112 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (126 bp):
TAAGAAGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAAATTTTGAGAGTGAACTGG
Found at i:13128980 original size:18 final size:18
Alignment explanation
Indices: 13128957--13128992 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13128947 ATAACAAGTA
*
13128957 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
13128975 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
13128993 ATGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.58, T:0.25
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:13129022 original size:37 final size:38
Alignment explanation
Indices: 13128972--13129049 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 38
13128962 ATGGAGTTAG
*
13128972 TGGGGGTGATGGAGGTAGTGGATGGTTTAGTAAGGT-A
1 TGGGGGTGATGGAGATAGTGGATGGTTTAGTAAGGTGA
*
13129009 TGGGGGTGATGGAGATAGTGGATGGTTTAGTAGGGTGA
1 TGGGGGTGATGGAGATAGTGGATGGTTTAGTAAGGTGA
13129047 TGG
1 TGG
13129050 AGTTAGTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 34 0.89
38 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.50, T:0.29
Consensus pattern (38 bp):
TGGGGGTGATGGAGATAGTGGATGGTTTAGTAAGGTGA
Found at i:13129045 original size:29 final size:29
Alignment explanation
Indices: 13129012--13129074 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
13129002 TAAGGTATGG
13129012 GGGTGATGGAGATAGTGGAT-GGTTTAGTA
1 GGGTGATGGAGATAGTGG-TCGGTTTAGTA
* *
13129041 GGGTGATGGAGTTAGTGGTCGGTTTAGTG
1 GGGTGATGGAGATAGTGGTCGGTTTAGTA
13129070 GGGTG
1 GGGTG
13129075 TTTAATTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.17, C:0.02, G:0.49, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGATAGTGGTCGGTTTAGTA
Found at i:13129605 original size:170 final size:170
Alignment explanation
Indices: 13129314--13129809 Score: 721
Period size: 170 Copynumber: 2.9 Consensus size: 170
13129304 CGAAAATAAG
* *
13129314 ATCTGT-AATTTTAGCCTGTTACCCTACTGTTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCA
1 ATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCG
* * * *
13129378 CCACTGCTCGGAGAGCCAGGATCTGTAAATTTTAGCCTGTTACCCCATTGCTTAGGGGGCTAAGG
66 CCACTGCTCGGCGAGCCA-GATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* *
13129443 CGAG-TCTTTGACCTGCTCCACCACTGCTCGGCGAGCCCAA
130 CGTGATCTTTGATCTGCTCCACCACTGCTCGGCGAGCCCAA
* *
13129483 GTCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCG
1 ATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCG
13129548 CCACTGCTCGGCGAGCCTAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
66 CCACTGCTCGGCGAGCC-AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* *
13129613 CGTGTATCTTTGATCTGCTCCGCCACTGCTTGGCGAGCCCAA
130 CGTG-ATCTTTGATCTGCTCCACCACTGCTCGGCGAGCCCAA
* * *
13129655 ATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGTCTA-TCTTTGATCTGCT
1 ATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG---AGTCTTCGACCTGCT
* *
13129719 -CGACCACTGCTCGGCGAGCCCAGATCTGTAAATTTTAACCTGTTACCCTACTGCTTAGAGGGTT
63 CCG-CCACTGCTCGGCGAG-CCAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTT
*
13129783 AAGGTGTGTATCTTTGATCTGCTCCAC
126 AAGGCGTG-ATCTTTGATCTGCTCCAC
13129810 TATTACTTAA
Statistics
Matches: 297, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
169 5 0.02
170 117 0.39
171 1 0.00
172 77 0.26
173 2 0.01
174 92 0.31
175 3 0.01
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.30
Consensus pattern (170 bp):
ATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCG
CCACTGCTCGGCGAGCCAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
GTGATCTTTGATCTGCTCCACCACTGCTCGGCGAGCCCAA
Found at i:13129982 original size:87 final size:88
Alignment explanation
Indices: 13129311--13129959 Score: 729
Period size: 87 Copynumber: 7.5 Consensus size: 88
13129301 CAACGAAAAT
* * * *
13129311 AAGATCTGT-AATTTTAGCCTGTTACCCTACTGTTTAGGGGGTTAAGGCGAG--TCTTCGACCTG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
* *
13129373 CTCCACCACTGC-TCGGAGAGCC
66 CTCCACCACTGCTTAGGCGAGCC
* * * * * *
13129395 AGGATCTGTAAATTTTAGCCTGTTACCCCATTGCTTAGGGGGCTAAGGCGAG--TCTTTGACCTG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
*
13129458 CTCCACCACTGC-TCGGCGAGCCC
66 CTCCACCACTGCTTAGGCGAG-CC
* * * *
13129481 AAG-TCTGTAAACTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAG--TCTTCGACCTG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
* *
13129543 CTCCGCCACTGC-TCGGCGAGCC
66 CTCCACCACTGCTTAGGCGAGCC
*
13129565 TAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
*
13129630 CTCCGCCACTGCTT-GGCGAGCCC
66 CTCCACCACTGCTTAGGCGAG-CC
* *
13129653 AA-ATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCGTCTATCTTTGATCTG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
* *
13129717 CTCGACCACTGC-TCGGCGAGCC
66 CTCCACCACTGCTTAGGCGAGCC
* * * *
13129739 CAGATCTGTAAATTTTAACCTGTTACCCTACTGCTTAGAGGGTTAAGGTGTGTATCTTTGATCTG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
* * * * **
13129804 CTCCACTATTACTTAAG-GAGAT
66 CTCCACCACTGCTTAGGCGAGCC
* * * * * *
13129826 AAGATCTAT-AATCTTCAGCTTGTTACCCTATTGCTTAGGGAGTTAAAGCGTGTATCTTTGATCT
1 AAGATCTGTAAAT-TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCT
* * * *
13129890 GCTCCACTACCGCTTAAG-GAGAC
65 GCTCCACCACTGCTTAGGCGAGCC
**
13129913 AAGATCTGTAGTTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
1 AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
13129960 ACTGGTGGTT
Statistics
Matches: 495, Mismatches: 58, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
84 12 0.02
85 186 0.38
86 11 0.02
87 279 0.56
88 7 0.01
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (88 bp):
AAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTG
CTCCACCACTGCTTAGGCGAGCC
Found at i:13130151 original size:132 final size:131
Alignment explanation
Indices: 13129914--13130432 Score: 618
Period size: 132 Copynumber: 3.9 Consensus size: 131
13129904 TAAGGAGACA
* * * * * *
13129914 AGATCTGTAGTTTTTAGCCTGTTACC-CTACTGCTTAGGGGGTTAAGACTGGTGGTTTG-AATCT
1 AGATCTGTA-TATTTAGCCTGTT-CCACTCCTGCTCAGTGGGATAAGGCTGGTGG-TTGAAATCT
* * *
13129977 GCTCCATTGCCGATACATTGAGATAAGATCCGCTAAAATTTGATATGTTCCACTCTTGCCAGTGG
63 GCTCCATTGCCGATACATGGAGATAAGATCCGCTAAAATTTGATCTGTTCCACTCCTGCCAGTGG
13130042 GATG
128 GATG
* *
13130046 AGATCTGCTATATTTAGCCTGTTCCACTCTTGCTCAGTGGGATAACGCTGGTGGTTTG-AATCTG
1 AGATCTG-TATATTTAGCCTGTTCCACTCCTGCTCAGTGGGATAAGGCTGGTGG-TTGAAATCTG
* *
13130110 CTCCATTGCCGATACATGGAGATAAGATTCG-TCAAAATTTGATCTGCTCCACTCCTGCTCAGTG
64 CTCCATTGCCGATACATGGAGATAAGATCCGCT-AAAATTTGATCTGTTCCACTCCTGC-CAGTG
* *
13130174 AAGATA
127 -GGATG
* * * *
13130180 AGATCTAG-A-GTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGTTGAAATTTG
1 AGATCT-GTATATTTAGCCTGTTCCACTCCTGCTCAGTG-GGATAAGGCTGGTGGTTGAAATCTG
* * * *
13130243 CTCTATTGCCGATACATGGAGACAAAATCCGCTGAAATTTGATCTGTTCCACTCCTGCCAGTGGG
64 CTCCATTGCCGATACATGGAGATAAGATCCGCTAAAATTTGATCTGTTCCACTCCTGCCAGTGGG
13130308 ATG
129 ATG
* *
13130311 AGATCTGATATATTTAGCCTGTTCCACTCCTGCTCAGTGGGATAAGGCTTGTGGCTGAAATCTGC
1 AGATCTG-TATATTTAGCCTGTTCCACTCCTGCTCAGTGGGATAAGGCTGGTGGTTGAAATCTGC
* ** * * *
13130376 TCCATTACCGATACATGGAGATAAGATTTGCCAAAATTTGATCTGCTCCGCTCCTGC
65 TCCATTGCCGATACATGGAGATAAGATCCGCTAAAATTTGATCTGTTCCACTCCTGC
13130433 TTAGCGAAGA
Statistics
Matches: 330, Mismatches: 45, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
130 1 0.00
131 12 0.04
132 204 0.62
133 102 0.31
134 10 0.03
135 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (131 bp):
AGATCTGTATATTTAGCCTGTTCCACTCCTGCTCAGTGGGATAAGGCTGGTGGTTGAAATCTGCT
CCATTGCCGATACATGGAGATAAGATCCGCTAAAATTTGATCTGTTCCACTCCTGCCAGTGGGAT
G
Found at i:13130355 original size:265 final size:265
Alignment explanation
Indices: 13129956--13130450 Score: 778
Period size: 265 Copynumber: 1.9 Consensus size: 265
13129946 CTTAGGGGGT
* * *
13129956 TAAGACTGGTGGTTTGAATCTGCTCCATTGCCGATACATTGAGATAAGATCCGCTAAAATTTGAT
1 TAAGACTGGTGGTTTGAATCTGCTCCATTGCCGATACATGGAGACAAAATCCGCTAAAATTTGAT
* * *
13130021 ATGTTCCACTCTTGCCAGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCTTGCTCAGTGG
66 ATGTTCCACTCCTGCCAGTGGGATGAGATCTGATATATTTAGCCTGTTCCACTCCTGCTCAGTGG
* * *
13130086 GATAACGCTGGTGGTTTG-AATCTGCTCCATTGCCGATACATGGAGATAAGATTCGTCAAAATTT
131 GATAACGCTGGTGG-CTGAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCAAAATTT
*
13130150 GATCTGCTCCACTCCTGCTCAGTGAAGATAAGATCTAGAGTTTAGCCTGCTCCACTCCTGCTCAG
195 GATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGAGTTTAGCCTGCTCCACTCCTGCTCAG
13130215 TGAAGA
260 TGAAGA
* * * *
13130221 TAAGGCTGGTGG-TTGAAATTTGCTCTATTGCCGATACATGGAGACAAAATCCGCTGAAATTTGA
1 TAAGACTGGTGGTTTG-AATCTGCTCCATTGCCGATACATGGAGACAAAATCCGCTAAAATTTGA
*
13130285 TCTGTTCCACTCCTGCCAGTGGGATGAGATCTGATATATTTAGCCTGTTCCACTCCTGCTCAGTG
65 TATGTTCCACTCCTGCCAGTGGGATGAGATCTGATATATTTAGCCTGTTCCACTCCTGCTCAGTG
* * *
13130350 GGATAAGGCTTGTGGCTGAAATCTGCTCCATTACCGATACATGGAGATAAGATTTGCCAAAATTT
130 GGATAACGCTGGTGGCTGAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCAAAATTT
* *
13130415 GATCTGCTCCGCTCCTGCTTAGCGAAGATAAGATCT
195 GATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCT
13130451 GTCGAAATTT
Statistics
Matches: 208, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
264 5 0.02
265 203 0.98
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (265 bp):
TAAGACTGGTGGTTTGAATCTGCTCCATTGCCGATACATGGAGACAAAATCCGCTAAAATTTGAT
ATGTTCCACTCCTGCCAGTGGGATGAGATCTGATATATTTAGCCTGTTCCACTCCTGCTCAGTGG
GATAACGCTGGTGGCTGAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCAAAATTTG
ATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGAGTTTAGCCTGCTCCACTCCTGCTCAGT
GAAGA
Found at i:13130486 original size:178 final size:178
Alignment explanation
Indices: 13130276--13130718 Score: 681
Period size: 179 Copynumber: 2.5 Consensus size: 178
13130266 AAAATCCGCT
*
13130276 GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGATATATTTAGCCTGTTCCACTCC
1 GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCC
*
13130341 TGCTCAGTGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTACCGATACATGGAGATAAGATTTG
66 TGCTCAGTGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTACCGATACATGGAGATAAGATTCG
** *
13130406 CCAAAATTTGATCTGCTCCGCTCCTGCTTAGCGAAGATAAGATCTGTC
131 CCAAAATTTGATCTGCTCCGCTCCTAATCAGCGAAGATAAGATCTGTC
* * *
13130454 GAAATTTGATCTGTTCCACTCCAGCCAGTGGGATGAGATTTGCTCTATTTAGCCTGCTT-CACTC
1 GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGCTATATTTAGCCTG-TTCCACTC
* ** * * * *
13130518 CTGTTCAGTAAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCTGATACATGGAGGTAAGATT
65 CTGCTCAGT-GGGATAAGGCTTGTGGCTGAAATCTGCTCCATTACCGATACATGGAGATAAGATT
*
13130583 CGCCAAAATTTGATCTGCTCCGCTCCTAATCAGCGGAGATAAGATCTGTC
129 CGCCAAAATTTGATCTGCTCCGCTCCTAATCAGCGAAGATAAGATCTGTC
* *
13130633 GAAATTTGATCTATTCCACTCCTGCCAGTAGGATGAGATCTGCTATATTTAGCCTGTTCCACTCC
1 GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCC
**
13130698 TGCTCAGTGGTTTAAGGCTTG
66 TGCTCAGTGGGATAAGGCTTG
13130719 CTGAAATCTG
Statistics
Matches: 235, Mismatches: 27, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
178 75 0.32
179 160 0.68
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (178 bp):
GAAATTTGATCTGTTCCACTCCTGCCAGTGGGATGAGATCTGCTATATTTAGCCTGTTCCACTCC
TGCTCAGTGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTACCGATACATGGAGATAAGATTCG
CCAAAATTTGATCTGCTCCGCTCCTAATCAGCGAAGATAAGATCTGTC
Found at i:13131992 original size:24 final size:24
Alignment explanation
Indices: 13131965--13132012 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13131955 TCGCCTTGGC
*
13131965 CTCTCCTTTGCTTTTCTTTTCTTT
1 CTCTCCTTTGCTTTTCTCTTCTTT
** *
13131989 CTCTTTTTTGTTTTTCTCTTCTTT
1 CTCTCCTTTGCTTTTCTCTTCTTT
13132013 TTCTTTTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (24 bp):
CTCTCCTTTGCTTTTCTCTTCTTT
Found at i:13132004 original size:15 final size:15
Alignment explanation
Indices: 13131986--13132049 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
13131976 TTTTCTTTTC
*
13131986 TTTCTCTTTTTTGTT
1 TTTCTCTTTTTTCTT
13132001 TTTCTCTTCTTTTTCTT
1 TTTCTC-T-TTTTTCTT
*
13132018 TTTC-CTTTTTTCTC
1 TTTCTCTTTTTTCTT
*
13132032 TTTCAT-TTTTCTCTT
1 TTTC-TCTTTTTTCTT
13132047 TTT
1 TTT
13132050 TTTTGTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.27
15 17 0.41
16 2 0.05
17 11 0.27
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTCTCTTTTTTCTT
Found at i:13132016 original size:6 final size:6
Alignment explanation
Indices: 13131976--13132059 Score: 57
Period size: 6 Copynumber: 13.7 Consensus size: 6
13131966 TCTCCTTTGC
* * *
13131976 TTTTC- TTTTCT TTCTCTT TTTTGT TTTTC- TCTTCT TTTTCT TTTTCCTT
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTT-C-T
* *
13132025 TTTTCT CTTTCAT TTTTCT CTTTT-T TTTTGT TTTT
1 TTTTCT TTTTC-T TTTTCT -TTTTCT TTTTCT TTTT
13132060 GAAAGTGAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
5 13 0.21
6 30 0.48
7 15 0.24
8 5 0.08
ACGTcount: A:0.01, C:0.18, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:13132017 original size:24 final size:23
Alignment explanation
Indices: 13131976--13132053 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 23
13131966 TCTCCTTTGC
* *
13131976 TTTTCTTTTCTTTCTCTTTTTTGT
1 TTTTCTCTTCTTTTTCTTTTTT-T
13132000 TTTTCTCTTCTTTTTCTTTTTCCTT
1 TTTTCTCTTCTTTTTCTTTTT--TT
*
13132025 TTTTCTCTTTCATTTTTCTCTTTTT
1 TTTTCTC-TTC-TTTTTCTTTTTTT
13132050 TTTT
1 TTTT
13132054 GTTTTTGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 19 0.40
25 14 0.30
26 4 0.09
27 10 0.21
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (23 bp):
TTTTCTCTTCTTTTTCTTTTTTT
Found at i:13132033 original size:16 final size:17
Alignment explanation
Indices: 13131993--13132034 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
13131983 TTCTTTCTCT
*
13131993 TTTTTGTTTTTCTCTTC
1 TTTTTCTTTTTCTCTTC
13132010 TTTTTCTTTTTC-CTT-
1 TTTTTCTTTTTCTCTTC
13132025 TTTTCTCTTT
1 TTTT-TCTTT
13132035 CATTTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 11 0.48
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTCTCTTC
Found at i:13132053 original size:13 final size:13
Alignment explanation
Indices: 13131981--13132053 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
13131971 TTTGCTTTTC
*
13131981 TTTTCTTTCTCTT
1 TTTTTTTTCTCTT
*
13131994 TTTTGTTTT-TCTC
1 TTTT-TTTTCTCTT
*
13132007 TTCTTTTTCT-TT
1 TTTTTTTTCTCTT
13132019 TTCCTTTTTTCTCTT
1 TT--TTTTTTCTCTT
**
13132034 TCATTTTTCTCTT
1 TTTTTTTTCTCTT
13132047 TTTTTTT
1 TTTTTTT
13132054 GTTTTTGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
12 7 0.15
13 26 0.57
14 10 0.22
15 3 0.07
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:13135819 original size:46 final size:46
Alignment explanation
Indices: 13135749--13135915 Score: 155
Period size: 46 Copynumber: 3.6 Consensus size: 46
13135739 TGTAACCTGC
* *
13135749 CCATAAGTAAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACGTTCGCAT
* * * *
13135795 CCATAAGTGAACTCGGACTTAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC--A-GAC--GTTCGCAT
* * * *
13135845 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAG-ACGTTCGCAT
13135888 CCATAAGTGAACTCGGACTCAACTCAAC
1 CCATAAGTGAACTCGGACTCAACTCAAC
13135916 AAGTTCGGAT
Statistics
Matches: 96, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 51 0.53
47 23 0.24
48 3 0.03
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACGTTCGCAT
Found at i:13135924 original size:93 final size:93
Alignment explanation
Indices: 13135758--13135927 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
13135748 CCCATAAGTA
* * * *
13135758 AACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTTAACTCAAT
1 AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
*
13135823 GAGCTCGGATGCCTAGTTACATCTCACG
66 AAGCTCGGATGCCTAGTTACATCTCACG
*
13135851 AACTCGGACTCAACTCAACGAGTTC-GAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCGGACTCAACTCAACGAGCTCAG-ACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
13135915 CAAGTTCGGATGC
65 CAAGCTCGGATGC
13135928 TCAACCATCC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
92 1 0.01
93 68 0.99
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
AAGCTCGGATGCCTAGTTACATCTCACG
Found at i:13135943 original size:46 final size:45
Alignment explanation
Indices: 13135850--13135935 Score: 111
Period size: 46 Copynumber: 1.9 Consensus size: 45
13135840 TACATCTCAC
* * *
13135850 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACAAGTTCG-ACATGCGCAACCATAAGT
* *
13135896 GAACTCGGACTCAACTCAACAAGTTCG-GATGCTCAACCAT
1 GAACTCGGACTCAACTCAACAAGTTCGACATGCGCAACCAT
13135936 CCTAGTGACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 9 0.26
46 26 0.74
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACAAGTTCGACATGCGCAACCATAAGT
Found at i:13139386 original size:46 final size:44
Alignment explanation
Indices: 13139296--13139460 Score: 161
Period size: 46 Copynumber: 3.6 Consensus size: 44
13139286 GTCGATGCCG
* * * * * *
13139296 TGTCCCAGACAGGTCTTACACTGACACATGTAACCGTGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGGCTCGTCTAA--ATGCCGATGCA
*
13139342 TGTCCCAGACATGTCTTACACTGGCTC-TCATAATATGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTGGCTCGTC-TAA-AT-GCCGATGCA
* *
13139388 TGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGATGCCA
1 TGTCCCAGACATGTCTTACACT-G-GCTCGTCTAAATGCCGATG-CA
13139435 TGTCCCAGACATGGTCTTACACTGGC
1 TGTCCCAGACAT-GTCTTACACTGGC
13139461 ACACAAATCT
Statistics
Matches: 101, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
45 2 0.02
46 64 0.63
47 18 0.18
48 15 0.15
49 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (44 bp):
TGTCCCAGACATGTCTTACACTGGCTCGTCTAAATGCCGATGCA
Found at i:13142136 original size:19 final size:17
Alignment explanation
Indices: 13142104--13142146 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
13142094 CTACTTGTGC
*
13142104 ATTTATGTTTTGAACTTG
1 ATTTATGTTATGAA-TTG
13142122 ATTTGATGTTATGAATTG
1 ATTT-ATGTTATGAATTG
*
13142140 AATTATG
1 ATTTATG
13142147 ATAATACCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 10 0.45
19 9 0.41
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (17 bp):
ATTTATGTTATGAATTG
Found at i:13145042 original size:46 final size:46
Alignment explanation
Indices: 13144884--13145113 Score: 171
Period size: 46 Copynumber: 4.8 Consensus size: 46
13144874 TGTAACCCGC
** * * ** *
13144884 CCATAAGTGAACTCGTTCTCAACTCAACAAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTCACAT
* * *
13144930 CCATAAGTGAACTCGGACTTAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GA--AC-A-TTCACAT
* * *
13144980 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTCACAT
*
13145023 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC----G---AA-CATTC-A-CAT
13145079 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
13145114 GATGCTCAAC
Statistics
Matches: 148, Mismatches: 17, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 2 0.01
45 2 0.01
46 58 0.39
47 25 0.17
48 2 0.01
49 2 0.01
50 5 0.03
51 2 0.01
52 1 0.01
53 2 0.01
54 4 0.03
56 37 0.25
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTCACAT
Found at i:13145084 original size:56 final size:56
Alignment explanation
Indices: 13145019--13145131 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
13145009 TCGAACATTC
13145019 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTA
1 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTA
13145075 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTA
1 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTA
13145131 G
1 G
13145132 TGACATGTCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (56 bp):
GCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTA
Found at i:13146635 original size:21 final size:21
Alignment explanation
Indices: 13146609--13146653 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
13146599 GCTGGCTTAT
*
13146609 CATGTTGTTT-TGTGACTCCAG
1 CATGTT-TTTCTGGGACTCCAG
13146630 CATGTTTTTCTGGGACTCCAG
1 CATGTTTTTCTGGGACTCCAG
13146651 CAT
1 CAT
13146654 TTGATCCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (21 bp):
CATGTTTTTCTGGGACTCCAG
Found at i:13148014 original size:15 final size:15
Alignment explanation
Indices: 13147994--13148023 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13147984 GTATAAATTT
13147994 TCTCGATCTATATTG
1 TCTCGATCTATATTG
13148009 TCTCGATCTATATTG
1 TCTCGATCTATATTG
13148024 CCTTAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (15 bp):
TCTCGATCTATATTG
Found at i:13150336 original size:126 final size:126
Alignment explanation
Indices: 13150175--13150414 Score: 435
Period size: 126 Copynumber: 1.9 Consensus size: 126
13150165 TAGCCTTAAA
*
13150175 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCAAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
* *
13150240 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTGAGAGTGAACTGGTAAG
66 GAATTCTTTAAATACCGAACATTACCTTTATTTTGAAAAATTTTGAGAGTGAACTGGTAAG
* *
13150301 AGGATATTCAAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCATGATTCTTC
1 AGGATATTCAAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
13150366 GAATTCTTTAAATACCGAACATTACCTTTATTTTGAAAAATTTTGAGAG
66 GAATTCTTTAAATACCGAACATTACCTTTATTTTGAAAAATTTTGAGAG
13150415 AAGATCAATG
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 109 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
AGGATATTCAAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
GAATTCTTTAAATACCGAACATTACCTTTATTTTGAAAAATTTTGAGAGTGAACTGGTAAG
Found at i:13150892 original size:14 final size:14
Alignment explanation
Indices: 13150873--13150903 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13150863 ATATATTTAC
*
13150873 ATAATAAATATATA
1 ATAATAAATAAATA
13150887 ATAATAAATAAATA
1 ATAATAAATAAATA
13150901 ATA
1 ATA
13150904 TAATAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAATAAATA
Found at i:13150904 original size:19 final size:18
Alignment explanation
Indices: 13150875--13150911 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
13150865 ATATTTACAT
13150875 AATAAATATATAATAATA
1 AATAAATATATAATAATA
13150893 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
13150912 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Done.