Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold211
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: 2193984
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 112243 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:1207778 original size:9 final size:9
Alignment explanation
Indices: 1207764--1207826 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
1207754 TTATTAGAAA
1207764 TGAGAGACT
1 TGAGAGACT
1207773 TGAGAGACT
1 TGAGAGACT
1207782 TGAGAGGGA-T
1 TGAGA--GACT
* *
1207792 TGATAGAATT
1 TGAGAG-ACT
*
1207802 TGAGAGAAT
1 TGAGAGACT
*
1207811 TGAGAGAGT
1 TGAGAGACT
1207820 TGAGAGA
1 TGAGAGA
1207827 AGGATGTGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 1 0.02
9 32 0.70
10 11 0.24
11 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.37, T:0.24
Consensus pattern (9 bp):
TGAGAGACT
Found at i:1209957 original size:20 final size:20
Alignment explanation
Indices: 1209934--1209972 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1209924 TATATATAAT
*
1209934 TGTTTGAAAATTTAAAAATA
1 TGTTAGAAAATTTAAAAATA
**
1209954 TGTTAGAATTTTTAAAAAT
1 TGTTAGAAAATTTAAAAAT
1209973 TGTAAAAAAT
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:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (20 bp):
TGTTAGAAAATTTAAAAATA
Found at i:1209971 original size:28 final size:27
Alignment explanation
Indices: 1209905--1209980 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
1209895 CCTAAAAAAT
* *
1209905 ATTTTTAAATAA-TTATAAATATATATA
1 ATTTTTAAA-AATTTAAAAATATATAGA
* *
1209932 ATTGTTTGAAAATTTAAAAATATGTTAGA
1 ATT-TTTAAAAATTTAAAAATAT-ATAGA
1209961 ATTTTTAAAAATTGTAAAAA
1 ATTTTTAAAAATT-TAAAAA
1209981 ATAATTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 5 0.12
28 23 0.57
29 12 0.30
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (27 bp):
ATTTTTAAAAATTTAAAAATATATAGA
Found at i:1210737 original size:17 final size:17
Alignment explanation
Indices: 1210723--1210757 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1210713 TTTATAATCT
1210723 TCCTATTTTTTTAATAA
1 TCCTATTTTTTTAATAA
*
1210740 TCCTATTTTTTAAATAA
1 TCCTATTTTTTTAATAA
1210757 T
1 T
1210758 TTTGTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (17 bp):
TCCTATTTTTTTAATAA
Found at i:1212018 original size:18 final size:18
Alignment explanation
Indices: 1211974--1212019 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1211964 TGTAATTTGA
* *
1211974 AAATAATATATTTATTAC
1 AAATTATATTTTTATTAC
*
1211992 AAA-TATATTTTTATTTC
1 AAATTATATTTTTATTAC
1212009 AAATTATATTT
1 AAATTATATTT
1212020 GCTTTGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (18 bp):
AAATTATATTTTTATTAC
Found at i:1212428 original size:293 final size:295
Alignment explanation
Indices: 1212022--1212609 Score: 1162
Period size: 293 Copynumber: 2.0 Consensus size: 295
1212012 TTATATTTGC
1212022 TTTGTAGTAAATATATTTCATTTGTCCAATTTTTATTTTATATATTTATCACGTTATTTATAGTA
1 TTTGTAGTAAATATATTTCATTTGTCCAATTTTTATTTTATATATTTATCACGTTATTTATAGTA
1212087 CTTTATTTATAGATTTAGCTAAATAAAAATAATATAATTTTATATTTAAAATATTTTGGAAGGAT
66 CTTTATTTATAGATTTAGCTAAATAAAAATAATATAATTTTATATTTAAAATATTTTGGAAGGAT
1212152 AATTTGAGAAGAAATATATACAATAATTTCTGAAAGTAAAGAAATTAAATGGATAATGAAAAATT
131 AATTTGAGAAGAAATATATACAATAATTTCTGAAAGTAAAGAAATTAAATGGATAATGAAAAATT
1212217 AAACAGATTATCTAAAAAAAGTCTAAAAAAATGGAAAATGCGTCATTTGTCACAAAATCAACTTG
196 AAACAGATTATCTAAAAAAAGTCTAAAAAAATGGAAAATGCGTCATTTGTCACAAAATCAACTTG
1212282 TATACCTTATTATATATATATATGATTACTTGATT
261 TATACCTTATTATATATATATATGATTACTTGATT
1212317 TTTGTAGT-AA-ATATTTCATTTGTCCAATTTTTATTTTATATATTTATCACGTTATTTATAGTA
1 TTTGTAGTAAATATATTTCATTTGTCCAATTTTTATTTTATATATTTATCACGTTATTTATAGTA
1212380 CTTTATTTATAGATTTAGCTAAATAAAAATAATATAATTTTATATTTAAAATATTTTGGAAGGAT
66 CTTTATTTATAGATTTAGCTAAATAAAAATAATATAATTTTATATTTAAAATATTTTGGAAGGAT
1212445 AATTTGAGAAGAAATATATACAATAATTTCTGAAAGTAAAGAAATTAAATGGATAATGAAAAATT
131 AATTTGAGAAGAAATATATACAATAATTTCTGAAAGTAAAGAAATTAAATGGATAATGAAAAATT
1212510 AAACAGATTATCTAAAAAAAGTCTAAAAAAATGGAAAATGCGTCATTTGTCACAAAATCAACTTG
196 AAACAGATTATCTAAAAAAAGTCTAAAAAAATGGAAAATGCGTCATTTGTCACAAAATCAACTTG
1212575 TATACCTTATTATATATATATATGATTACTTGATT
261 TATACCTTATTATATATATATATGATTACTTGATT
1212610 ATGGAATTTT
Statistics
Matches: 293, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
293 283 0.97
294 2 0.01
295 8 0.03
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (295 bp):
TTTGTAGTAAATATATTTCATTTGTCCAATTTTTATTTTATATATTTATCACGTTATTTATAGTA
CTTTATTTATAGATTTAGCTAAATAAAAATAATATAATTTTATATTTAAAATATTTTGGAAGGAT
AATTTGAGAAGAAATATATACAATAATTTCTGAAAGTAAAGAAATTAAATGGATAATGAAAAATT
AAACAGATTATCTAAAAAAAGTCTAAAAAAATGGAAAATGCGTCATTTGTCACAAAATCAACTTG
TATACCTTATTATATATATATATGATTACTTGATT
Found at i:1221677 original size:106 final size:106
Alignment explanation
Indices: 1221505--1221713 Score: 325
Period size: 106 Copynumber: 2.0 Consensus size: 106
1221495 CATAGCATTG
* * *
1221505 AAGAAGACCATATCGTGTAAGATAGTAACTGATGGGTTATGACATCATATGTGAAGAAGTCTATA
1 AAGAAGACCATATCGTGTAAGATAGTAACTGATAGGTTATGACATCATATGTGAAGAAGACCATA
* *
1221570 TCATGTAGGACTATAACTGGTGGGTTATGGCATCATATATA
66 TCATGTAAGACTATAACTGGTGGGTTATGACATCATATATA
1221611 AAGAAGACCATATCGTGTAAGACT-GTAACT-AGTAGGTTATGACATCATATG-GAAAGAAGACC
1 AAGAAGACCATATCGTGTAAGA-TAGTAACTGA-TAGGTTATGACATCATATGTG-AAGAAGACC
1221673 ATATCATGTAAGACTATAACTGGTGGGTTATGACATCATAT
63 ATATCATGTAAGACTATAACTGGTGGGTTATGACATCATAT
1221714 GGGGAAGTTT
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
105 2 0.02
106 92 0.97
107 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (106 bp):
AAGAAGACCATATCGTGTAAGATAGTAACTGATAGGTTATGACATCATATGTGAAGAAGACCATA
TCATGTAAGACTATAACTGGTGGGTTATGACATCATATATA
Found at i:1221715 original size:53 final size:53
Alignment explanation
Indices: 1221505--1221715 Score: 282
Period size: 53 Copynumber: 4.0 Consensus size: 53
1221495 CATAGCATTG
* *
1221505 AAGAAGACCATATCGTGTAAGA-TAGTAACTGATGGGTTATGACATCATATGTG-
1 AAGAAGACCATATCATGTAAGACTA-TAACTGGTGGGTTATGACATCATATG-GA
* * * * **
1221558 AAGAAGTCTATATCATGTAGGACTATAACTGGTGGGTTATGGCATCATATATA
1 AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGGA
* * * *
1221611 AAGAAGACCATATCGTGTAAGACTGTAACTAGTAGGTTATGACATCATATGGA
1 AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGGA
1221664 AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGG
1 AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGG
1221716 GGAAGTTTAA
Statistics
Matches: 134, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
53 132 0.99
54 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (53 bp):
AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGGA
Found at i:1222055 original size:29 final size:27
Alignment explanation
Indices: 1222010--1222098 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 27
1222000 ACTTCTGTTT
*
1222010 AAGGAAGCATTTGTGGCAAAACTCTAGA
1 AAGGAAGCCTTTGTGGCAAAACTCT-GA
* * * *
1222038 AAGGCAAGCCTTTTTGGCGAACCTCTTA
1 AAGG-AAGCCTTTGTGGCAAAACTCTGA
*
1222066 AA-GAACGCCTTTGTGGCAAATCTCTGA
1 AAGGAA-GCCTTTGTGGCAAAACTCTGA
1222093 AAGGAA
1 AAGGAA
1222099 ATGTCTTTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
26 2 0.04
27 20 0.41
28 10 0.20
29 17 0.35
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (27 bp):
AAGGAAGCCTTTGTGGCAAAACTCTGA
Found at i:1222111 original size:29 final size:28
Alignment explanation
Indices: 1222037--1222155 Score: 100
Period size: 29 Copynumber: 4.2 Consensus size: 28
1222027 AAAACTCTAG
* * *
1222037 AAAGGCAAGCCTTTTTGGCGAACCTCT-T
1 AAAGGAAAGCCTTTATGGC-AATCTCTGT
* *
1222065 AAA-GAACGCCTTTGTGGCAAATCTCTG-
1 AAAGGAAAGCCTTTATGGC-AATCTCTGT
* *
1222092 AAAGGAAATGTCTTTATGGCGATCTCTGT
1 AAAGGAAA-GCCTTTATGGCAATCTCTGT
* *
1222121 CAAAGGAAAGCCTCTATGGCCATCTCTGT
1 -AAAGGAAAGCCTTTATGGCAATCTCTGT
1222150 AAAGGA
1 AAAGGA
1222156 GTGGCTATAC
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
27 21 0.28
28 19 0.26
29 26 0.35
30 8 0.11
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (28 bp):
AAAGGAAAGCCTTTATGGCAATCTCTGT
Found at i:1225169 original size:3 final size:3
Alignment explanation
Indices: 1225161--1225227 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
1225151 TGACCCAAAC
* * * *
1225161 TAT TAT TAT TAT TAT CAT TAC TAC TAT TAT TAAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
1225207 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
1225228 CTTTTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 55 0.96
4 2 0.04
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1226087 original size:159 final size:155
Alignment explanation
Indices: 1225816--1226123 Score: 449
Period size: 159 Copynumber: 2.0 Consensus size: 155
1225806 TTTTTTAAAT
1225816 AAAAGAGAAAGTTTAGACTTTTAAAAATAAAAAAATATTTTTAGACATTTTAAAGGAAAGTTTAA
1 AAAAGAGAAAGTTTAGACTTTTAAAAATAAAAAAATATTTTTAGACATTTTAAAGGAAAGTTTAA
* * *
1225881 ATGTTTAAAACAAAGTTTTGATTTTTTTTTTAAATATTTCGAAATAAAAGCTTTAA-TCTTTAAT
66 ATGTTTAAAACAAAGTTTTGA-TTCTTTTTCAAATATTTCGAAATAAAA-CTTTAATTCTTTAAG
1225945 AAAAGTAGTGAATTTTTTAAAAGAAGAA
129 AAAAGTAGTG-ATTTTTTAAAAGAAGAA
* *
1225973 AAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATATATTTTTTAGTCATTTTAAAGGTAAAGT
1 AAAAGAGAAAGTTTAGACTTTTAAAAATAAAAA-A-ATA-TTTTTAGACATTTTAAAGG-AAAGT
* * * * *
1226038 TTAAATTTTTAAAATAAAGTTTTGA-TCTTTTTCAACTATTTCGAAATAAAACTTTAATTTTTTT
62 TTAAATGTTTAAAACAAAGTTTTGATTCTTTTTCAAATATTTCGAAATAAAACTTTAATTCTTTA
1226102 AGAAAAGTAGTGATTTTTTAAA
127 AGAAAAGTAGTGATTTTTTAAA
1226124 GGAAATTTTG
Statistics
Matches: 136, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
157 32 0.24
158 17 0.12
159 41 0.30
160 18 0.13
161 28 0.21
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (155 bp):
AAAAGAGAAAGTTTAGACTTTTAAAAATAAAAAAATATTTTTAGACATTTTAAAGGAAAGTTTAA
ATGTTTAAAACAAAGTTTTGATTCTTTTTCAAATATTTCGAAATAAAACTTTAATTCTTTAAGAA
AAGTAGTGATTTTTTAAAAGAAGAA
Found at i:1228144 original size:23 final size:24
Alignment explanation
Indices: 1228106--1228151 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1228096 GTTTGAGAGC
*
1228106 TAGATTTTTTAGTATTTGTGCATAT
1 TAGATTTTTTA-TATTCGTGCATAT
1228131 TAGATTTTTT-TATTCGTGCAT
1 TAGATTTTTTATATTCGTGCAT
1228152 TAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.57
Consensus pattern (24 bp):
TAGATTTTTTATATTCGTGCATAT
Found at i:1229419 original size:27 final size:26
Alignment explanation
Indices: 1229379--1229448 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 26
1229369 TTTGTTTAAT
1229379 TTTATAATTA-ATGATATTTAAAT-ATAA
1 TTTAT-ATTATATGATATTT--ATGATAA
1229406 TTTATATTATATGA-ATTTATGATAA
1 TTTATATTATATGATATTTATGATAA
*
1229431 -TTAAATTATAATGATATT
1 TTTATATTAT-ATGATATT
1229449 ATATTATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 10 0.26
25 8 0.21
26 11 0.29
27 9 0.24
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (26 bp):
TTTATATTATATGATATTTATGATAA
Found at i:1229429 original size:35 final size:35
Alignment explanation
Indices: 1229384--1229452 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
1229374 TTAATTTTAT
* *
1229384 AATTAATGATATTTAAA-TATAATTTATATTATATG
1 AATTAATGATAATTAAATTATAA-TGATATTATATG
*
1229419 AATTTATGATAATTAAATTATAATGATATTATAT
1 AATTAATGATAATTAAATTATAATGATATTATAT
1229453 TATTAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (35 bp):
AATTAATGATAATTAAATTATAATGATATTATATG
Found at i:1229444 original size:25 final size:23
Alignment explanation
Indices: 1229400--1229460 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
1229390 TGATATTTAA
*
1229400 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
1229424 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
1229449 ATATTATTAAAT
1 ATATAATTAAAT
1229461 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:1230456 original size:12 final size:12
Alignment explanation
Indices: 1230439--1230501 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
1230429 ATGTTAGGTA
*
1230439 AGTATTAATATT
1 AGTATTATTATT
* *
1230451 AGTATTAGTAAT
1 AGTATTATTATT
1230463 AGTATTATTATT
1 AGTATTATTATT
*
1230475 ATTATTATTATT
1 AGTATTATTATT
*
1230487 ATTATTATTATT
1 AGTATTATTATT
1230499 AGT
1 AGT
1230502 GGGAATTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
AGTATTATTATT
Found at i:1230473 original size:3 final size:3
Alignment explanation
Indices: 1230441--1230499 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
1230431 GTTAGGTAAG
* * * * *
1230441 TAT TAA TAT TAG TAT TAG TAA TAG 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
1230489 TAT TAT TAT TA
1 TAT TAT TAT TA
1230500 GTGGGAATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:1235491 original size:47 final size:48
Alignment explanation
Indices: 1235415--1235532 Score: 132
Period size: 47 Copynumber: 2.5 Consensus size: 48
1235405 TTCTAGTTGG
* * * * ** *
1235415 CCTTTGTGGTGTATTCGGTTTGTTGCCTTTGTTTCATACTCTGGTA-T
1 CCTTTGTGGCGTATTCGGTATGTTACCTTTATGGCATACTCTGATAGT
* *
1235462 CCTTTGTGGCGTATTTGGTATGTTACCTTTATGGCGTACTCTGATAGT
1 CCTTTGTGGCGTATTCGGTATGTTACCTTTATGGCATACTCTGATAGT
*
1235510 -CTTTGTGGCGTATTCAGTATGTT
1 CCTTTGTGGCGTATTCGGTATGTT
1235533 GTCTAGCGTA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 58 0.98
48 1 0.02
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (48 bp):
CCTTTGTGGCGTATTCGGTATGTTACCTTTATGGCATACTCTGATAGT
Found at i:1238416 original size:24 final size:24
Alignment explanation
Indices: 1238385--1238438 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
1238375 ATGGAGCATT
1238385 ATCA-AACAATAAAAAAAATTAA-C
1 ATCATAAC-ATAAAAAAAATTAATC
* *
1238408 ATCATAACATTAAATAAATTAATC
1 ATCATAACATAAAAAAAATTAATC
*
1238432 ATAATAA
1 ATCATAA
1238439 AAACCAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (24 bp):
ATCATAACATAAAAAAAATTAATC
Found at i:1241834 original size:46 final size:46
Alignment explanation
Indices: 1241675--1241845 Score: 134
Period size: 46 Copynumber: 3.7 Consensus size: 46
1241665 TTTGATCTTC
* **
1241675 TGCATA-GTTTGCAGACTCAAGAATATAGGAATAGGTTGTGAGCTCT
1 TGCATATG-TTGCAGACTCGAGAATATAGGAATAGGTTCCGAGCTCT
* * * * *
1241721 TGCATATGTTGC-GAACTCGAGAACACAAGAATAGGTTTCGAGCTCC
1 TGCATATGTTGCAG-ACTCGAGAATATAGGAATAGGTTCCGAGCTCT
* * * * * * *
1241767 TACATCTATTACGGAC-CTGAGAATTTAGGTATAGGTTCCGAGCTCT
1 TGCATATGTTGCAGACTC-GAGAATATAGGAATAGGTTCCGAGCTCT
*
1241813 TGCATATGTTGCAGACTTGAGAATACT-GGAATA
1 TGCATATGTTGCAGACTCGAGAATA-TAGGAATA
1241846 TTAAGCCCTA
Statistics
Matches: 93, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
45 2 0.02
46 88 0.95
47 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (46 bp):
TGCATATGTTGCAGACTCGAGAATATAGGAATAGGTTCCGAGCTCT
Found at i:1242688 original size:27 final size:27
Alignment explanation
Indices: 1242634--1242689 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1242624 TTCATCATAT
* *
1242634 ATATATACACATAACATAGCATTTATC
1 ATATATACACATAACATAGCACTCATC
1242661 ATATATACACATAACATAGCACTCATC
1 ATATATACACATAACATAGCACTCATC
1242688 AT
1 AT
1242690 TAACATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (27 bp):
ATATATACACATAACATAGCACTCATC
Found at i:1245239 original size:25 final size:25
Alignment explanation
Indices: 1245210--1245274 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
1245200 TATTGTACAT
*
1245210 GTATGCTCATATGAGCTATGAACCG
1 GTATGCTCATATGAGCTATAAACCG
* **
1245235 GTATGCTC-TCACGAGCTATAAATTG
1 GTATGCTCAT-ATGAGCTATAAACCG
*
1245260 GTAAGCTCATATGAG
1 GTATGCTCATATGAG
1245275 TTGAGAATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (25 bp):
GTATGCTCATATGAGCTATAAACCG
Found at i:1245308 original size:24 final size:24
Alignment explanation
Indices: 1245280--1245330 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1245270 ATGAGTTGAG
*
1245280 AATCGGTAAACTTTAACGAGCTAA
1 AATCGGTAAACTCTAACGAGCTAA
* * *
1245304 AATCGGTAAGCTCTCACGAGCTGA
1 AATCGGTAAACTCTAACGAGCTAA
1245328 AAT
1 AAT
1245331 AAAAAATCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (24 bp):
AATCGGTAAACTCTAACGAGCTAA
Found at i:1247312 original size:44 final size:44
Alignment explanation
Indices: 1247263--1247351 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
1247253 ATTCCCATAC
*
1247263 TTAAAGATAAACTCAAATGTATATAACTCAATTTACTTTTCAAA
1 TTAAAGATAAACTCAAATGCATATAACTCAATTTACTTTTCAAA
1247307 TTAAAGATAAACTCAAATGCATATAACTCAATTTACTTTTCAAA
1 TTAAAGATAAACTCAAATGCATATAACTCAATTTACTTTTCAAA
1247351 T
1 T
1247352 GAATAACTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (44 bp):
TTAAAGATAAACTCAAATGCATATAACTCAATTTACTTTTCAAA
Found at i:1251957 original size:19 final size:19
Alignment explanation
Indices: 1251933--1251975 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1251923 CATGTTCAAA
* *
1251933 ATTTTAATACAATTTAATT
1 ATTTTAATAAAAATTAATT
1251952 ATTTT-ATAAAAATTAATT
1 ATTTTAATAAAAATTAATT
1251970 ATTTTA
1 ATTTTA
1251976 TGAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATAAAAATTAATT
Found at i:1251969 original size:18 final size:19
Alignment explanation
Indices: 1251946--1251982 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1251936 TTAATACAAT
1251946 TTAATTATTTTAT-AAAAA
1 TTAATTATTTTATGAAAAA
1251964 TTAATTATTTTATGAAAAA
1 TTAATTATTTTATGAAAAA
1251983 AATTATATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTAATTATTTTATGAAAAA
Found at i:1251988 original size:17 final size:17
Alignment explanation
Indices: 1251947--1251988 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
1251937 TAATACAATT
1251947 TAATTATTTTATAAAAA
1 TAATTATTTTATAAAAA
1251964 TTAATTATTTTATGAAAAA
1 -TAATTATTTTAT-AAAAA
1251983 -AATTAT
1 TAATTAT
1251989 ATCGAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TAATTATTTTATAAAAA
Found at i:1266240 original size:40 final size:40
Alignment explanation
Indices: 1266178--1267213 Score: 1046
Period size: 40 Copynumber: 26.0 Consensus size: 40
1266168 GCCTTTACGA
* * * * * *
1266178 GTACCGGAGTACTAACAAGGGCACGTATGTGCTTTCAGGA
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * * *
1266218 GTACCAAAGTACAGACAGGGGCACGTATGTGCATTTAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * *
1266258 GTACCGAAGTACAAATAGGGGCACGTATGTTCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * * * * * *
1266298 GTACTGAAGTACAAATAAGGGCACATATGTGAATTTAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* *
1266338 GTATCGAAGTACAAACAGGGGGACGTGTGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* *
1266378 GTGCCGAAGTACAAACAGGGGCACTTGTGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
*
1266418 GTACCGAAGTATAAACAGGGGCACGTGTGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * *
1266458 GTACCGAAGTACAAACAGGGGAACTTGTGTTCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
*
1266498 GTACCGAAGTACAAACAAGGGCACGTGTGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * * *
1266538 GTACTGAAGTACAAATAGGGGCACGTCTGTGCATTCAAGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * * *
1266578 GTACCGAAGTAAAAACAAGGGCAAGTGTGTGCATTTAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * * * *
1266618 GTA-CTAAGTACAAACAAGGGCACGTAG-GTGAATTTAGAG
1 GTACCGAAGTACAAACAGGGGCACGT-GTGTGCATTCAGGG
* * * *
1266657 GTATCGAAGTACAAATAAGGGG-ACATGTGTGCATTTAGGG
1 GTACCGAAGTACAAA-CAGGGGCACGTGTGTGCATTCAGGG
* * * * *
1266697 TTATCAAAGTACAAACAGGGGGATGTGTGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* *
1266737 GTATCGAAGTACAGAA-AGGAGCACGTGTGTGCATTCAGGG
1 GTACCGAAGTACA-AACAGGGGCACGTGTGTGCATTCAGGG
* * *
1266777 GTACCGAAGTACAAACAAGGGCACATGTGTACATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * *
1266817 GTACCGAAGTACAAACAGGTGCACGTCTGTGCATTTAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * * *
1266857 GTACCGAAGTACAAATAGGGGCACATCTGTGCATTTAGAGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAG-GG
* * * *
1266898 GTA-CTAAGTACAAACAAGGGCACATCTGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
** * ** * *
1266937 GTATTGAAGTACAAACAAGGGCATATGTGTGCATTTATGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* *
1266977 GTATCAAAGTACAAACAGGGGCACGTGTGTGCATTCA-GG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* ** * *
1267016 GTACCAAAGTAC-AACTATTGGCATGTGTGTGCATTCGGGG
1 GTACCGAAGTACAAAC-AGGGGCACGTGTGTGCATTCAGGG
* * * ** *
1267056 GTATCGAAGCAC-AACAGGGGCATGCATGTGCATTCAAGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * * *
1267095 GTACCGAAGTACAAACAAGGGCATGTATGTGGATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
* * * **
1267135 GTACCGAAGTACAAATAAGGGCATGCATGTGCATTCCA-GG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATT-CAGGG
* * * * *
1267175 GTACCGAAGTACAGACAAGGGCATGTATGTACATTCAGG
1 GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGG
1267214 TAATAATTAT
Statistics
Matches: 847, Mismatches: 135, Indels: 28
0.84 0.13 0.03
Matches are distributed among these distances:
38 3 0.00
39 105 0.12
40 726 0.86
41 13 0.02
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (40 bp):
GTACCGAAGTACAAACAGGGGCACGTGTGTGCATTCAGGG
Found at i:1266476 original size:20 final size:20
Alignment explanation
Indices: 1266373--1266514 Score: 56
Period size: 20 Copynumber: 7.1 Consensus size: 20
1266363 TGTGTGCATT
*
1266373 CAGGGGTGCCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * * **
1266393 CAGGGGCACTTG-TGTGCATT
1 CAGGGGTAC-CGAAGTACAAA
*
1266413 CAGGGGTACCGAAGTATAAA
1 CAGGGGTACCGAAGTACAAA
* ** * **
1266433 CAGGGGCA-CGTGTGTGCATT
1 CAGGGGTACCG-AAGTACAAA
1266453 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * * **
1266473 CAGGGGAACTTG-TGTTCATT
1 CAGGGGTAC-CGAAGTACAAA
1266493 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
1266513 CA
1 CA
1266515 AGGGCACGTG
Statistics
Matches: 77, Mismatches: 39, Indels: 12
0.60 0.30 0.09
Matches are distributed among these distances:
19 4 0.05
20 69 0.90
21 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:1266835 original size:20 final size:20
Alignment explanation
Indices: 1266772--1266835 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1266762 TGTGTGCATT
1266772 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * * **
1266792 CAAGGGCACATG-TGTACATT
1 CAGGGGTAC-CGAAGTACAAA
1266812 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
1266832 CAGG
1 CAGG
1266836 TGCACGTCTG
Statistics
Matches: 30, Mismatches: 12, Indels: 4
0.65 0.26 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.30, T:0.14
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:1272955 original size:39 final size:39
Alignment explanation
Indices: 1272901--1272978 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1272891 AGATTATCGA
1272901 AGCGAGCTAATCCCCCATAATCAGATTTGATTTATTCTT
1 AGCGAGCTAATCCCCCATAATCAGATTTGATTTATTCTT
1272940 AGCGAGCTAATCCCCCATAATCAGATTTGATTTATTCTT
1 AGCGAGCTAATCCCCCATAATCAGATTTGATTTATTCTT
1272979 CCTTTTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (39 bp):
AGCGAGCTAATCCCCCATAATCAGATTTGATTTATTCTT
Found at i:1274638 original size:46 final size:46
Alignment explanation
Indices: 1274588--1274690 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
1274578 TGCAGAATCA
*
1274588 AGAATATAGGAATAGGTTCTAAGCTCCAACATATGTTGCGGACTTG
1 AGAATATAGGAATAGGTTCCAAGCTCCAACATATGTTGCGGACTTG
* * * * ** **
1274634 AGAATATATGTATTGGTTCCGAGCTCTTACATATGTTGCGGGGTTG
1 AGAATATAGGAATAGGTTCCAAGCTCCAACATATGTTGCGGACTTG
1274680 AGAATATAGGA
1 AGAATATAGGA
1274691 CAAAGTCCTG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (46 bp):
AGAATATAGGAATAGGTTCCAAGCTCCAACATATGTTGCGGACTTG
Found at i:1280361 original size:28 final size:29
Alignment explanation
Indices: 1280322--1280420 Score: 130
Period size: 28 Copynumber: 3.4 Consensus size: 29
1280312 CTATCGAATT
*
1280322 ATGAAAAGGGATTGTGATGACCATCAATA
1 ATGAAAAGGGATTGTGAAGACCATCAATA
* *
1280351 ATG-AAAGGGATGGTGACGACCATCAATA
1 ATGAAAAGGGATTGTGAAGACCATCAATA
*
1280379 ATGAAAAGGGATTGTGAAGGCCATCAA-A
1 ATGAAAAGGGATTGTGAAGACCATCAATA
1280407 CTATGAAAAGGGAT
1 --ATGAAAAGGGAT
1280421 GGCTTCGGCT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 27 0.44
29 23 0.37
30 12 0.19
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.20
Consensus pattern (29 bp):
ATGAAAAGGGATTGTGAAGACCATCAATA
Found at i:1280525 original size:30 final size:30
Alignment explanation
Indices: 1280318--1280594 Score: 177
Period size: 30 Copynumber: 9.4 Consensus size: 30
1280308 TCGGCTATCG
*
1280318 AATTATGAAAAGGGAT-TGTGATGACCATC-
1 AATTATGAAAAGGGATGT-TGACGACCATCA
* *
1280347 AATAATG-AAAGGGATGGTGACGACCATC-
1 AATTATGAAAAGGGATGTTGACGACCATCA
* * *
1280375 AATAATGAAAAGGGAT-TGTGAAGGCCATCA
1 AATTATGAAAAGGGATGT-TGACGACCATCA
* * *
1280405 AACTATGAAAAGGGATGGCTT--CGGCTATCA
1 AATTATGAAAAGGGAT-G-TTGACGACCATCA
* *
1280435 AATTATGAAAAGGGATGGCTT--CGACTATCG
1 AATTATGAAAAGGGAT-G-TTGACGACCATCA
** * *
1280465 AATTACAAAAAGGGATAGCTTCA-G-CTATCA
1 AATTATGAAAAGGGAT-G-TTGACGACCATCA
1280495 AATTATGAAAAGGGATGTTGACGACCATC-
1 AATTATGAAAAGGGATGTTGACGACCATCA
* * *
1280524 AATAATGAAAAGGGGTGGTGACGACCATCA
1 AATTATGAAAAGGGATGTTGACGACCATCA
** * *
1280554 ACA--ATGAGCAGGGATGGTGATGACCATCA
1 A-ATTATGAAAAGGGATGTTGACGACCATCA
1280583 AATTATGAAAAG
1 AATTATGAAAAG
1280595 AGTTTGCTTT
Statistics
Matches: 203, Mismatches: 30, Indels: 29
0.77 0.11 0.11
Matches are distributed among these distances:
28 29 0.14
29 74 0.36
30 96 0.47
31 2 0.01
32 1 0.00
33 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (30 bp):
AATTATGAAAAGGGATGTTGACGACCATCA
Found at i:1280614 original size:178 final size:177
Alignment explanation
Indices: 1280296--1280628 Score: 470
Period size: 178 Copynumber: 1.9 Consensus size: 177
1280286 CGACTAATGG
* * *
1280296 AAAGGGATAACTTCGGCTATCGAATTATGAAAAGGGATTGTGATGACCATCAATAATGAAAGGGA
1 AAAGGGATAACTTCAGCTATCAAATTATGAAAAGGGATTGTGACGACCATCAATAATGAAAGGGA
* * * *
1280361 TGGTGACGACCATCAATAATGAAAAGGGATTGTGAAGGCCATCAAACTATGAAAAGGGATGGCTT
66 TGGTGACGACCATCAACAATGAAAAGGGATGGTGAAGACCATCAAACTATGAAAAGAGATGGCTT
*
1280426 CGGCTATCAAATTATGAAAAGGGATGGCTTCGACTATCGAATTACAA
131 CGGCTATCAAAATATGAAAAGGGATGGCTTCGACTATCGAATTACAA
*
1280473 AAAGGGATAGCTTCAGCTATCAAATTATGAAAAGGGA-TGTTGACGACCATCAATAATGAAAAGG
1 AAAGGGATAACTTCAGCTATCAAATTATGAAAAGGGATTG-TGACGACCATCAATAATG-AAAGG
* ** * * * *
1280537 GGTGGTGACGACCATCAACAATGAGCAGGGATGGTGATGACCATCAAATTATGAAAAGAGTTTGC
64 GATGGTGACGACCATCAACAATGAAAAGGGATGGTGAAGACCATCAAACTATGAAAAGAGATGGC
** *
1280602 TTTTGCTATCAAAATATGGAAAGGGAT
129 TTCGGCTATCAAAATATGAAAAGGGAT
1280629 AGTTTCGGCA
Statistics
Matches: 135, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
176 2 0.01
177 51 0.38
178 82 0.61
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (177 bp):
AAAGGGATAACTTCAGCTATCAAATTATGAAAAGGGATTGTGACGACCATCAATAATGAAAGGGA
TGGTGACGACCATCAACAATGAAAAGGGATGGTGAAGACCATCAAACTATGAAAAGAGATGGCTT
CGGCTATCAAAATATGAAAAGGGATGGCTTCGACTATCGAATTACAA
Found at i:1294138 original size:3 final size:3
Alignment explanation
Indices: 1294130--1294155 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1294120 TAACAAATAT
1294130 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
1294156 TGCATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1294282 original size:22 final size:22
Alignment explanation
Indices: 1294235--1294285 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1294225 ATTAAACTAT
1294235 TTTAATTTTATAAAGACTTGTA
1 TTTAATTTTATAAAGACTTGTA
* *
1294257 -TTAATTTT-TGAATGATTTGTA
1 TTTAATTTTAT-AAAGACTTGTA
1294278 TTTAATTT
1 TTTAATTT
1294286 AGACTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 17 0.68
22 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (22 bp):
TTTAATTTTATAAAGACTTGTA
Found at i:1297220 original size:12 final size:12
Alignment explanation
Indices: 1297205--1297229 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1297195 GATCCTTATG
1297205 AAGAAAGTGATC
1 AAGAAAGTGATC
1297217 AAGAAAGTGATC
1 AAGAAAGTGATC
1297229 A
1 A
1297230 TTCATCTGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
AAGAAAGTGATC
Found at i:1307437 original size:15 final size:15
Alignment explanation
Indices: 1307417--1307447 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1307407 GTAGGATGGG
1307417 GGATTGGGTTGAGGA
1 GGATTGGGTTGAGGA
*
1307432 GGATTGGGTTGGGGA
1 GGATTGGGTTGAGGA
1307447 G
1 G
1307448 AGGAAGGTTG
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:0.16, C:0.00, G:0.58, T:0.26
Consensus pattern (15 bp):
GGATTGGGTTGAGGA
Found at i:1315634 original size:20 final size:20
Alignment explanation
Indices: 1315609--1315684 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
1315599 AAGCTTATGC
1315609 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
*
1315629 TAAGTAAAT-GAAGTAGAAAG
1 TAAGTAAATGGAA-TGGAAAG
* * *
1315649 TAAGTAAATAGAACGGTAAG
1 TAAGTAAATGGAATGGAAAG
1315669 TAAGTAAATGGAATGG
1 TAAGTAAATGGAATGG
1315685 TTCATCATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.06
20 42 0.88
21 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.28, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:1332659 original size:19 final size:19
Alignment explanation
Indices: 1332635--1332745 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
1332625 AATCATATCT
*
1332635 TCTAAGATTGCGTATCATA
1 TCTAAGATTGCATATCATA
**
1332654 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
1332673 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
1332692 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
1332711 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1332730 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
1332746 CCTGAAGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1332682 original size:38 final size:38
Alignment explanation
Indices: 1332635--1332738 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
1332625 AATCATATCT
*
1332635 TCTAAGATTGCGTATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
1332673 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1332711 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
1332739 GCATATCCCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:1332995 original size:17 final size:17
Alignment explanation
Indices: 1332952--1332999 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1332942 ATTGGTTCCA
1332952 ATTAA-AAATTAATA-T
1 ATTAATAAATTAATATT
1332967 A--AATACAA-TAATATT
1 ATTAATA-AATTAATATT
1332982 ATTAATAAATTAATATT
1 ATTAATAAATTAATATT
1332999 A
1 A
1333000 ATAGAAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.07
14 6 0.22
15 5 0.19
16 2 0.07
17 12 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAATAAATTAATATT
Found at i:1332998 original size:14 final size:14
Alignment explanation
Indices: 1332952--1333002 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
1332942 ATTGGTTCCA
1332952 ATTAA-AAATTAAT
1 ATTAATAAATTAAT
* *
1332965 ATAAATACAATAATATT
1 ATTAATA-AAT--TAAT
1332982 ATTAATAAATTAAT
1 ATTAATAAATTAAT
1332996 ATTAATA
1 ATTAATA
1333003 GAAACATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 4 0.13
14 11 0.37
15 3 0.10
16 3 0.10
17 9 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTAATAAATTAAT
Found at i:1333725 original size:13 final size:13
Alignment explanation
Indices: 1333707--1333739 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1333697 GAGGCCTGCG
1333707 CATTATGGGTAAT
1 CATTATGGGTAAT
1333720 CATTATGGGTAAT
1 CATTATGGGTAAT
1333733 CATTATG
1 CATTATG
1333740 CAAAGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (13 bp):
CATTATGGGTAAT
Found at i:1347144 original size:17 final size:17
Alignment explanation
Indices: 1347092--1347144 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1347082 ATTTTTCCGG
*
1347092 ACTCGAATTTATTATAA
1 ACTCAAATTTATTATAA
* *
1347109 ACTCAAGCTTT-CT-TAA
1 ACTCAA-ATTTATTATAA
1347125 ACTCAAATTTATTATAA
1 ACTCAAATTTATTATAA
1347142 ACT
1 ACT
1347145 TGGGTTATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 12 0.43
18 3 0.11
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (17 bp):
ACTCAAATTTATTATAA
Found at i:1370500 original size:3 final size:3
Alignment explanation
Indices: 1370487--1370531 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1370477 GAGATACATC
*
1370487 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1370532 TTACAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1371900 original size:42 final size:41
Alignment explanation
Indices: 1371759--1371999 Score: 191
Period size: 42 Copynumber: 5.7 Consensus size: 41
1371749 CTCGGTGGAT
* * * *
1371759 TCAGCACTTAGCAAGCACC-TTAAATTCAGTGATACGAGGAA
1 TCAGCACTTAGCAA-CCCCTTTAAATTCAATAATACGGGGAA
* * * * * * * *
1371800 TCAACACATAGCAACCCCTTTCACAGTAAAAAAAACGGTGGAT
1 TCAGCACTTAGCAACCCCTTT-AAATTCAATAATACGG-GGAA
* *
1371843 TCAGCACTTAGCAACCACCTTTATATTCAGTAATACGGGGAA
1 TCAGCACTTAGCAACC-CCTTTAAATTCAATAATACGGGGAA
* *
1371885 TCAGCACATATCAACCCCTTTCACAA-TCAA-AGATACGGTGGAA
1 TCAGCACTTAGCAACCCCTTT-A-AATTCAATA-ATACGG-GGAA
* * *
1371928 TCAGCACTTAGCAACCACCTTTAAAGTCAATAATTCAGGGAA
1 TCAGCACTTAGCAACC-CCTTTAAATTCAATAATACGGGGAA
**
1371970 TCAGCACTTAGCAACCCCTTTTTATTCAAT
1 TCAGCACTTAGCAACCCCTTTAAATTCAAT
1372000 GTTTTTGGGT
Statistics
Matches: 157, Mismatches: 32, Indels: 22
0.74 0.15 0.10
Matches are distributed among these distances:
40 3 0.02
41 31 0.20
42 57 0.36
43 55 0.35
44 11 0.07
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (41 bp):
TCAGCACTTAGCAACCCCTTTAAATTCAATAATACGGGGAA
Found at i:1371900 original size:85 final size:85
Alignment explanation
Indices: 1371751--1371990 Score: 329
Period size: 85 Copynumber: 2.8 Consensus size: 85
1371741 ATCCGTTACT
* * * *
1371751 CGGTGGATTCAGCACTTAGCAAGCACC-TTAAATTCAGTGATACGAGGAATCAACACATAGCAAC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAAC
*
1371815 CCCTTTCACAGTAAAAAAAA
66 CCCTTTCACAATAAAAAAAA
* *
1371835 CGGTGGATTCAGCACTTAGCAACCACCTTTATATTCAGTAATACGGGGAATCAGCACATATCAAC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAAC
* * *
1371900 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATAAAAAAAA
* * * * * *
1371920 CGGTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAATAATTCAGGGAATCAGCACTTAGCAAC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAAC
1371985 CCCTTT
66 CCCTTT
1371991 TTATTCAATG
Statistics
Matches: 137, Mismatches: 18, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
84 26 0.19
85 111 0.81
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (85 bp):
CGGTGGATTCAGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAAC
CCCTTTCACAATAAAAAAAA
Found at i:1379460 original size:54 final size:54
Alignment explanation
Indices: 1379398--1379507 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
1379388 CTAACCTAAG
1379398 TATGCTCAAAATTAAATTAAACATATAATAATTAAATATGCAACTTTTAAGAGT
1 TATGCTCAAAATTAAATTAAACATATAATAATTAAATATGCAACTTTTAAGAGT
1379452 TATGCTCAAAATTAAATTAAACATATAATAATTAAATATGCAACTTTTAAGAGT
1 TATGCTCAAAATTAAATTAAACATATAATAATTAAATATGCAACTTTTAAGAGT
1379506 TA
1 TA
1379508 ATCACAATAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (54 bp):
TATGCTCAAAATTAAATTAAACATATAATAATTAAATATGCAACTTTTAAGAGT
Found at i:1385087 original size:27 final size:27
Alignment explanation
Indices: 1385042--1385194 Score: 155
Period size: 27 Copynumber: 5.7 Consensus size: 27
1385032 AACACGCTAA
* *
1385042 AAAAGGAAGCCTTCATGGTGATCTATG
1 AAAAGGAAGCCTTCGTGGCGATCTATG
* * * *
1385069 AAGAGGAAGCCTTTGTGGTGATCTATA
1 AAAAGGAAGCCTTCGTGGCGATCTATG
* *
1385096 AAAAGGAAGCCTTCATTGCGATCTATG
1 AAAAGGAAGCCTTCGTGGCGATCTATG
* * ** *
1385123 -AAAGGAAATCCTTTGTGGAAATTTATG
1 AAAAGG-AAGCCTTCGTGGCGATCTATG
*
1385150 AAAAAGAAGCCTTCGTGGCGATCTATG
1 AAAAGGAAGCCTTCGTGGCGATCTATG
*
1385177 AAAAGGAAGCCTTTGTGG
1 AAAAGGAAGCCTTCGTGG
1385195 AAATTGATGA
Statistics
Matches: 99, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
26 5 0.05
27 90 0.91
28 4 0.04
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (27 bp):
AAAAGGAAGCCTTCGTGGCGATCTATG
Found at i:1385199 original size:54 final size:55
Alignment explanation
Indices: 1385041--1385209 Score: 218
Period size: 54 Copynumber: 3.1 Consensus size: 55
1385031 GAACACGCTA
* * ** *
1385041 AAAAAGGAAGCCTTCATGGTGATCTATGAAGAGGAAGCCTTTGTGGTGATCTAT-
1 AAAAAGGAAGCCTTCATGGCGATCTATGAAAAGGAAGCCTTTGTGGAAATTTATG
* *
1385095 AAAAAGGAAGCCTTCATTGCGATCTATG-AAAGGAAATCCTTTGTGGAAATTTATG
1 AAAAAGGAAGCCTTCATGGCGATCTATGAAAAGG-AAGCCTTTGTGGAAATTTATG
* *
1385150 AAAAA-GAAGCCTTCGTGGCGATCTATGAAAAGGAAGCCTTTGTGGAAATTGATG
1 AAAAAGGAAGCCTTCATGGCGATCTATGAAAAGGAAGCCTTTGTGGAAATTTATG
*
1385204 ATAAAG
1 AAAAAG
1385210 AAATCCTATG
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
53 4 0.04
54 85 0.86
55 10 0.10
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (55 bp):
AAAAAGGAAGCCTTCATGGCGATCTATGAAAAGGAAGCCTTTGTGGAAATTTATG
Found at i:1386544 original size:27 final size:27
Alignment explanation
Indices: 1386506--1386559 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1386496 TACTTATGGC
1386506 TAGTTTGCTTTAACCATTAATGATCAT
1 TAGTTTGCTTTAACCATTAATGATCAT
1386533 TAGTTTGCTTTAACCATTAATGATCAT
1 TAGTTTGCTTTAACCATTAATGATCAT
1386560 GTTGAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (27 bp):
TAGTTTGCTTTAACCATTAATGATCAT
Found at i:1400371 original size:42 final size:42
Alignment explanation
Indices: 1400221--1400355 Score: 243
Period size: 42 Copynumber: 3.2 Consensus size: 42
1400211 ACCAGCACTT
* *
1400221 AGCCTGCTAAACATATAGTCTGAAATTGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATTGTTTCACCGGCATTA
1400263 AGCCTGCTAGACATAAAGTCTGAAATTGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATTGTTTCACCGGCATTA
*
1400305 AGCCTGCTAGACATAAAGTCTGAAATTGTTTCACTGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATTGTTTCACCGGCATTA
1400347 AGCCTGCTA
1 AGCCTGCTA
1400356 AGCGCTAAGC
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (42 bp):
AGCCTGCTAGACATAAAGTCTGAAATTGTTTCACCGGCATTA
Found at i:1415451 original size:101 final size:101
Alignment explanation
Indices: 1415276--1415473 Score: 315
Period size: 101 Copynumber: 2.0 Consensus size: 101
1415266 TTGACAGATA
* * * *
1415276 AGACCATGGTTGGACCATGGCAATGTTTATATGTAACACCATAGTTGGGCTATGGCATTTTAATG
1 AGACCAGGGTTGGACCATGGCAATATTTATAAGTAACACCATAGTTGGGCTATGGCATTCTAATG
*
1415341 AAAAGACCATAACTGGGTTATGGCACTTTGAACCTG
66 AAAAGACCATAACTGGGTTATGGCACTATGAACCTG
* * *
1415377 AGACCAGGGTTGGACTATGGCAATATTTATAAGTAAGACCATAGTTGGGCTATGGCATTCTGATG
1 AGACCAGGGTTGGACCATGGCAATATTTATAAGTAACACCATAGTTGGGCTATGGCATTCTAATG
*
1415442 ATAAGACCATAACTGGGTTATGGCACTATGAA
66 AAAAGACCATAACTGGGTTATGGCACTATGAA
1415474 TGTAAGACCA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 88 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (101 bp):
AGACCAGGGTTGGACCATGGCAATATTTATAAGTAACACCATAGTTGGGCTATGGCATTCTAATG
AAAAGACCATAACTGGGTTATGGCACTATGAACCTG
Found at i:1415452 original size:33 final size:32
Alignment explanation
Indices: 1415313--1415532 Score: 106
Period size: 33 Copynumber: 6.6 Consensus size: 32
1415303 TATATGTAAC
* *
1415313 ACCATAGTTGGGCTATGGCATTTTAATGAAAAG
1 ACCATAGTTGGGCTATGGCA-TTTGATGATAAG
** * *** *
1415346 ACCATAACTGGGTTATGGCACTTTGAACCTGAG
1 ACCATAGTTGGGCTATGGCA-TTTGATGATAAG
** * * *
1415379 ACCAGGGTTGGACTATGGCAATATTTATAAGTAAG
1 ACCATAGTTGGGCTATGGC-AT-TTGATGA-TAAG
1415414 ACCATAGTTGGGCTATGGCATTCTGATGATAAG
1 ACCATAGTTGGGCTATGGCATT-TGATGATAAG
** * *
1415447 ACCATAACTGGGTTATGGCACTATGAATG-TAAG
1 ACCATAGTTGGGCTATGGCA-TTTG-ATGATAAG
* * *
1415480 ACCAT-GACTGGG-TCATGGCA-ATGCATGTGTAAG
1 ACCATAG-TTGGGCT-ATGGCATTTG-ATG-ATAAG
*
1415513 ACCATAGTTGGACTATGGCA
1 ACCATAGTTGGGCTATGGCA
1415533 CAAAGAAAAT
Statistics
Matches: 141, Mismatches: 34, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
31 6 0.04
32 1 0.01
33 99 0.70
34 16 0.11
35 19 0.13
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (32 bp):
ACCATAGTTGGGCTATGGCATTTGATGATAAG
Found at i:1415498 original size:101 final size:100
Alignment explanation
Indices: 1415291--1415532 Score: 290
Period size: 101 Copynumber: 2.4 Consensus size: 100
1415281 ATGGTTGGAC
* * *
1415291 CATGGCAATGTTTATATGTAACACCATAGTTGGGCTATGGCATTTTAATGAAAAGACCATAACTG
1 CATGGCAATATTTATATGTAAGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACTG
* * ** *
1415356 GGTTATGGCACTTTGAACCTGAGACCAGGGTTGGA
66 GGTTATGGCACTATGAACCTAAGACCAGACTGGGA
* * *
1415391 CTATGGCAATATTTATAAGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACT
1 C-ATGGCAATATTTATATGTAAGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACT
** *
1415456 GGGTTATGGCACTATGAATGTAAGACCATGACTGGGT
65 GGGTTATGGCACTATGAACCTAAGACCA-GACTGGGA
** * *
1415493 CATGGC-A-ATGCATGTGTAAGACCATAGTTGGACTATGGCA
1 CATGGCAATATTTATATGTAAGACCATAGTTGGGCTATGGCA
1415533 CAAAGAAAAT
Statistics
Matches: 121, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
99 28 0.23
100 2 0.02
101 86 0.71
102 5 0.04
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (100 bp):
CATGGCAATATTTATATGTAAGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACTG
GGTTATGGCACTATGAACCTAAGACCAGACTGGGA
Found at i:1419787 original size:54 final size:54
Alignment explanation
Indices: 1419609--1419769 Score: 313
Period size: 54 Copynumber: 3.0 Consensus size: 54
1419599 TTTAGATGTC
*
1419609 TTTTTGTCATGACATATTGAGCTTACACTTGATATAAACTTGAATTTATATGCT
1 TTTTTGCCATGACATATTGAGCTTACACTTGATATAAACTTGAATTTATATGCT
1419663 TTTTTGCCATGACATATTGAGCTTACACTTGATATAAACTTGAATTTATATGCT
1 TTTTTGCCATGACATATTGAGCTTACACTTGATATAAACTTGAATTTATATGCT
1419717 TTTTTGCCATGACATATTGAGCTTACACTTGATATAAACTTGAATTTATATGC
1 TTTTTGCCATGACATATTGAGCTTACACTTGATATAAACTTGAATTTATATGC
1419770 CATGTTCATC
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (54 bp):
TTTTTGCCATGACATATTGAGCTTACACTTGATATAAACTTGAATTTATATGCT
Found at i:1420727 original size:9 final size:8
Alignment explanation
Indices: 1420711--1420740 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1420701 AAAAGTCCTC
1420711 AGAAAAAA
1 AGAAAAAA
1420719 AGAAAAAA
1 AGAAAAAA
1420727 AG-AAAAA
1 AGAAAAAA
1420734 AGAAAAA
1 AGAAAAA
1420741 CTTGCACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:1430022 original size:21 final size:21
Alignment explanation
Indices: 1429996--1430038 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1429986 TCTAAACATA
1429996 AACCAAGTCCACTAGGCAAAG
1 AACCAAGTCCACTAGGCAAAG
1430017 AACCAAGTCCACTAGGCAAAG
1 AACCAAGTCCACTAGGCAAAG
1430038 A
1 A
1430039 TAAATTATAT
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:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (21 bp):
AACCAAGTCCACTAGGCAAAG
Found at i:1438937 original size:17 final size:17
Alignment explanation
Indices: 1438917--1438964 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
1438907 GTATAATATG
*
1438917 AAATAGAAAATAATTTT
1 AAATGGAAAATAATTTT
*
1438934 AAATGGAAAACAATTTT
1 AAATGGAAAATAATTTT
1438951 AAATGGAAAATAAT
1 AAATGGAAAATAAT
1438965 CCATTGTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.29
Consensus pattern (17 bp):
AAATGGAAAATAATTTT
Found at i:1439477 original size:227 final size:228
Alignment explanation
Indices: 1439071--1439525 Score: 903
Period size: 227 Copynumber: 2.0 Consensus size: 228
1439061 AAGAAAGAAA
1439071 AAGAAAAGATGATTGTTTATAATTTAAAAAAATTAATTATTTTAAGTAATTTAATTAAAGTGAAA
1 AAGAAAAGATGATTGTTTATAATTTAAAAAAATTAATTATTTTAAGTAATTTAATTAAAGTGAAA
1439136 TTAAATTGAAGAAGATAGTAGATATAAACAACTGTATAATAATTTGTTATCTTTAAAATTTAATG
66 TTAAATTGAAGAAGATAGTAGATATAAACAACTGTATAATAATTTGTTATCTTTAAAATTTAATG
1439201 ACATGAAACTATTAATTTATTGGTGCCTAAAAACTATACTTTCTAGGATGATCCTAATATAAGTT
131 ACATGAAACTATTAATTTATTGGTGCCTAAAAACTATACTTTCTAGGATGATCCTAATATAAGTT
1439266 ATTCCCTTTATTTTAACCCTTTATAACAAATTT
196 ATTCCCTTTATTTTAACCCTTTATAACAAATTT
1439299 AAGAAAAGAT-ATTGTTTATAATTTAAAAAAATTAATTATTTTAAGTAATTTAATTAAAGTGAAA
1 AAGAAAAGATGATTGTTTATAATTTAAAAAAATTAATTATTTTAAGTAATTTAATTAAAGTGAAA
1439363 TTAAATTGAAGAAGATAGTAGATATAAACAACTGTATAATAATTTGTTATCTTTAAAATTTAATG
66 TTAAATTGAAGAAGATAGTAGATATAAACAACTGTATAATAATTTGTTATCTTTAAAATTTAATG
1439428 ACATGAAACTATTAATTTATTGGTGCCTAAAAACTATACTTTCTAGGATGATCCTAATATAAGTT
131 ACATGAAACTATTAATTTATTGGTGCCTAAAAACTATACTTTCTAGGATGATCCTAATATAAGTT
1439493 ATTCCCTTTATTTTAACCCTTTATAACAAATTT
196 ATTCCCTTTATTTTAACCCTTTATAACAAATTT
1439526 CACTTATAAC
Statistics
Matches: 227, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
227 217 0.96
228 10 0.04
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (228 bp):
AAGAAAAGATGATTGTTTATAATTTAAAAAAATTAATTATTTTAAGTAATTTAATTAAAGTGAAA
TTAAATTGAAGAAGATAGTAGATATAAACAACTGTATAATAATTTGTTATCTTTAAAATTTAATG
ACATGAAACTATTAATTTATTGGTGCCTAAAAACTATACTTTCTAGGATGATCCTAATATAAGTT
ATTCCCTTTATTTTAACCCTTTATAACAAATTT
Found at i:1445973 original size:15 final size:15
Alignment explanation
Indices: 1445953--1445985 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1445943 ATATAAAATA
1445953 TTAACTAAATATTAT
1 TTAACTAAATATTAT
*
1445968 TTAACTAAATATTGT
1 TTAACTAAATATTAT
1445983 TTA
1 TTA
1445986 CCAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (15 bp):
TTAACTAAATATTAT
Found at i:1448054 original size:16 final size:17
Alignment explanation
Indices: 1448033--1448066 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1448023 TTAAAATTAA
1448033 AATTTTATTA-TTTATT
1 AATTTTATTATTTTATT
*
1448049 AATTTTTTTATTTTATT
1 AATTTTATTATTTTATT
1448066 A
1 A
1448067 TTGTTGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
AATTTTATTATTTTATT
Found at i:1455965 original size:18 final size:19
Alignment explanation
Indices: 1455920--1455968 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1455910 GAATATTTAC
*
1455920 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
1455940 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
1455958 ATAAAAATAAA
1 ATAAAAATAAA
1455969 AATAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:1457655 original size:40 final size:40
Alignment explanation
Indices: 1457579--1457655 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
1457569 ATGTGTGACC
* *
1457579 AGGGGCACCGAAGTACAAACAGGGGCACAGATGTGCATTT
1 AGGGGCACCGAAGTACAAACAAGGGCACAGAAGTGCATTT
* *
1457619 AGGGGTACTGAAGTACAAACAAGGGCAC-GTAAGTGCA
1 AGGGGCACCGAAGTACAAACAAGGGCACAG-AAGTGCA
1457656 ATCATTCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.14
Consensus pattern (40 bp):
AGGGGCACCGAAGTACAAACAAGGGCACAGAAGTGCATTT
Found at i:1460376 original size:50 final size:49
Alignment explanation
Indices: 1460307--1460451 Score: 146
Period size: 50 Copynumber: 2.9 Consensus size: 49
1460297 TATTGAGGTT
* * * * * *
1460307 ATGAGAGGTCACGCATAAGACCATGTCTCGGACATAGCATTGGCACTGAG
1 ATGAGAGGTCCCACGTAAGACCATATCTGGGACAT-GCATTGGCACCGAG
* * * *
1460357 ATGAGAGGTCCCCCGTAAGACAATATCTGGGACATGACATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATATCTGGGACATG-CATTGGCACCGAG
* * *
1460407 ATGAGAGCTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGAGAGGTCCCACGTAAGACCATATCTGGGACAT-GCATTGGCA
1460452 GTTTAGGAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
49 1 0.01
50 76 0.97
51 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.21
Consensus pattern (49 bp):
ATGAGAGGTCCCACGTAAGACCATATCTGGGACATGCATTGGCACCGAG
Found at i:1460727 original size:20 final size:20
Alignment explanation
Indices: 1460702--1460740 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1460692 AGAGTTATTT
1460702 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
1460722 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
1460741 GAAGAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:1469247 original size:50 final size:50
Alignment explanation
Indices: 1469193--1469287 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
1469183 TATTGAGGTT
* * * *
1469193 ATGAGAGGTCACACATAAGACTATGTCTCGGACATAGCATTGGCACCAAG
1 ATGAGAGGTCACACATAAGACAATATCTAGGACATAGCATGGGCACCAAG
* * *
1469243 ATGAGAGGTCACCCGTAAGACAATATCTAGGACATGGCATGGGCA
1 ATGAGAGGTCACACATAAGACAATATCTAGGACATAGCATGGGCA
1469288 ACGATATGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (50 bp):
ATGAGAGGTCACACATAAGACAATATCTAGGACATAGCATGGGCACCAAG
Found at i:1469297 original size:50 final size:50
Alignment explanation
Indices: 1469192--1469298 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
1469182 TTATTGAGGT
* * * * *
1469192 TATGAGAGGTCACACATAAGACTATGTCTCGGACATAGCATTGGCACCAA
1 TATGAGAGGTCACACATAAGACAATATCTAGGACATAGCATGGGCAACAA
* * * * *
1469242 GATGAGAGGTCACCCGTAAGACAATATCTAGGACATGGCATGGGCAACGA
1 TATGAGAGGTCACACATAAGACAATATCTAGGACATAGCATGGGCAACAA
1469292 TATGAGA
1 TATGAGA
1469299 ACTCCTATGT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (50 bp):
TATGAGAGGTCACACATAAGACAATATCTAGGACATAGCATGGGCAACAA
Found at i:1469613 original size:20 final size:20
Alignment explanation
Indices: 1469588--1469636 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1469578 TGAGTTATTT
*
1469588 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAACTAAAC
*
1469608 AAGTAAG-AGAGTAACTAAAG
1 AAGTAAGCA-AGTAACTAAAC
1469628 AAG-AAGCAA
1 AAGTAAGCAA
1469637 AGACCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAACTAAAC
Found at i:1475348 original size:40 final size:40
Alignment explanation
Indices: 1475263--1475501 Score: 175
Period size: 40 Copynumber: 6.0 Consensus size: 40
1475253 AATGTGTGAC
* * *
1475263 CAGGGGCACCAAAGTACAAACAGGGGCA--TAAATGTGCATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACGT-AA-GTGCAAT
* * *
1475303 TAGGGGTACTGAAGTACAAACAGGGGCACGTAAGTGTAAT
1 CAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAAT
* * * * *
1475343 CAGGGGTACCGAAGCACCAACAAGGGCACGTAACTGAAAT
1 CAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAAT
* * * * * *
1475383 CAGGGGTACCAAAGTACAAACAAGGGCATGCACGTCCAAT
1 CAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAAT
* *
1475423 CAGGGGGT--CGAAGTAGAAACAGGGGCAGGTAA--GCAAT
1 CA-GGGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAAT
* * *** * *
1475460 TAAGGGTATTAAAATACAAACAGGGGCATGTAAGTGCAAT
1 CAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAAT
1475500 CA
1 CA
1475502 TTCAATAATT
Statistics
Matches: 155, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
36 4 0.03
37 5 0.03
38 19 0.12
39 18 0.12
40 101 0.65
41 7 0.05
42 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (40 bp):
CAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAAT
Found at i:1476628 original size:21 final size:21
Alignment explanation
Indices: 1476602--1476655 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1476592 TTTCTAAAAT
*
1476602 CACTTGACCTTGGGGTCTTAC
1 CACTTGACCTTAGGGTCTTAC
1476623 CACTTGACCTTAGGGTCTTAC
1 CACTTGACCTTAGGGTCTTAC
*
1476644 CACTTGAACTTA
1 CACTTGACCTTA
1476656 ATAAATCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (21 bp):
CACTTGACCTTAGGGTCTTAC
Found at i:1491328 original size:15 final size:15
Alignment explanation
Indices: 1491291--1491328 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
1491281 AACTCGACAT
1491291 TTACTTGTTAGTTTA
1 TTACTTGTTAGTTTA
1491306 TTAC-TGTTAGTTTA
1 TTACTTGTTAGTTTA
1491320 TTACTTGTT
1 TTACTTGTT
1491329 GCGATTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.61
Consensus pattern (15 bp):
TTACTTGTTAGTTTA
Found at i:1494606 original size:29 final size:29
Alignment explanation
Indices: 1494570--1495022 Score: 443
Period size: 29 Copynumber: 15.8 Consensus size: 29
1494560 CGATGGTGAA
**
1494570 ACCATCCCTTTTCATATTAAATGGTCGTC
1 ACCATCCCTTTTCATATTTGATGGTCGTC
* * **
1494599 ACTATCCCTTTTCGTATTCAATGGTCGTC
1 ACCATCCCTTTTCATATTTGATGGTCGTC
* * ** **
1494628 ACTATCCTTTTTCATATTCAATGGTCGAA
1 ACCATCCCTTTTCATATTTGATGGTCGTC
1494657 ACCATCCCTTTTCATATTTGATGGTCGTC
1 ACCATCCCTTTTCATATTTGATGGTCGTC
1494686 ACCATCCCTTTTCATATTTGATGGTCGTC
1 ACCATCCCTTTTCATATTTGATGGTCGTC
** * * *
1494715 AGAATCCCTTTTCATAGTCGATGGTCATC
1 ACCATCCCTTTTCATATTTGATGGTCGTC
* **
1494744 ACCATCCCTTTTCATATTTGATGGTTGGA
1 ACCATCCCTTTTCATATTTGATGGTCGTC
* *
1494773 ACCATCTCTTTGCATATTTGATGGTCGTC
1 ACCATCCCTTTTCATATTTGATGGTCGTC
* * *** **
1494802 ACCA----TGTGC-TAAACGATGGTCGAA
1 ACCATCCCTTTTCATATTTGATGGTCGTC
* * **
1494826 ACCATCCTTTTTCATATTCGATGGTCGAA
1 ACCATCCCTTTTCATATTTGATGGTCGTC
* *
1494855 ACCATCCTTTTTCATATTTGATGGTCATC
1 ACCATCCCTTTTCATATTTGATGGTCGTC
1494884 ACCATCCCTTTTCATATTTGATGGTCGTC
1 ACCATCCCTTTTCATATTTGATGGTCGTC
* * **
1494913 ACCATCCCTTTTCATATTTTAGGGTCGAA
1 ACCATCCCTTTTCATATTTGATGGTCGTC
*
1494942 ACTAT-CCTTTTGCATATTTGATGGTCGTC
1 ACCATCCCTTTT-CATATTTGATGGTCGTC
* * * *
1494971 ACTATCCCTTTTCATATTCGATTGTCG-A
1 ACCATCCCTTTTCATATTTGATGGTCGTC
*
1494999 ACCGTCCCTTTTCATATTTGATGG
1 ACCATCCCTTTTCATATTTGATGG
1495023 GTGTCGATAT
Statistics
Matches: 354, Mismatches: 63, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
24 14 0.04
25 4 0.01
28 29 0.08
29 301 0.85
30 6 0.02
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTTGATGGTCGTC
Found at i:1494713 original size:87 final size:87
Alignment explanation
Indices: 1494560--1495022 Score: 503
Period size: 87 Copynumber: 5.4 Consensus size: 87
1494550 GTGTGCTAAA
** ** * * **
1494560 CGATGGT-GAAACCATCCCTTTTCATATTAAATGGTCGTCACTATCCCTTTTCGTATTCAATGGT
1 CGATGGTCGAAACCATCCCTTTTCATATTTGATGGTCGAAACCATCCCTTTTCATATTTGATGGT
*
1494624 CGTCACTATCCTTTTTCATATT
66 CGTCACTATCCCTTTTCATATT
* **
1494646 CAATGGTCGAAACCATCCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTCATATTTGATGGT
1 CGATGGTCGAAACCATCCCTTTTCATATTTGATGGTCGAAACCATCCCTTTTCATATTTGATGGT
** *
1494711 CGTCAGAATCCCTTTTCATAGT
66 CGTCACTATCCCTTTTCATATT
* * * * *
1494733 CGATGGTC-ATCACCATCCCTTTTCATATTTGATGGTTGGAACCATCTCTTTGCATATTTGATGG
1 CGATGGTCGA-AACCATCCCTTTTCATATTTGATGGTCGAAACCATCCCTTTTCATATTTGATGG
* * * **
1494797 TCGT--C-A-CCATGTGC-TAAA
65 TCGTCACTATCCCTTTTCATATT
* * *
1494815 CGATGGTCGAAACCATCCTTTTTCATATTCGATGGTCGAAACCATCCTTTTTCATATTTGATGGT
1 CGATGGTCGAAACCATCCCTTTTCATATTTGATGGTCGAAACCATCCCTTTTCATATTTGATGGT
* *
1494880 CATCACCATCCCTTTTCATATT
66 CGTCACTATCCCTTTTCATATT
* ** * * *
1494902 TGATGGTCGTCACCATCCCTTTTCATATTTTAGGGTCGAAACTAT-CCTTTTGCATATTTGATGG
1 CGATGGTCGAAACCATCCCTTTTCATATTTGATGGTCGAAACCATCCCTTTT-CATATTTGATGG
1494966 TCGTCACTATCCCTTTTCATATT
65 TCGTCACTATCCCTTTTCATATT
* *
1494989 CGATTGTCG-AACCGTCCCTTTTCATATTTGATGG
1 CGATGGTCGAAACCATCCCTTTTCATATTTGATGG
1495023 GTGTCGATAT
Statistics
Matches: 313, Mismatches: 55, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
82 59 0.19
83 6 0.02
84 2 0.01
85 1 0.00
86 38 0.12
87 207 0.66
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (87 bp):
CGATGGTCGAAACCATCCCTTTTCATATTTGATGGTCGAAACCATCCCTTTTCATATTTGATGGT
CGTCACTATCCCTTTTCATATT
Found at i:1494861 original size:169 final size:169
Alignment explanation
Indices: 1494648--1494972 Score: 490
Period size: 169 Copynumber: 1.9 Consensus size: 169
1494638 TTCATATTCA
* ** *
1494648 ATGGTCGAAACCATCCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTCATATTTGATGGTCG
1 ATGGTCGAAACCATCCCTTTTCATATTCGATGGTCGAAACCATCCCTTTTCATATTTGATGGTCA
* * * *
1494713 TCAGAATCCCTTTTCATAGTCGATGGTCATCACCATCCCTTTTCATATTTGATGGTTGGAACCAT
66 TCACAATCCCTTTTCATAGTCGATGGTCATCACCATCCCTTTTCATATTTGAGGGTCGAAACCAT
1494778 -CTCTTTGCATATTTGATGGTCGTCACCATGTGCTAAACG
131 CCT-TTTGCATATTTGATGGTCGTCACCATGTGCTAAACG
* *
1494817 ATGGTCGAAACCATCCTTTTTCATATTCGATGGTCGAAACCATCCTTTTTCATATTTGATGGTCA
1 ATGGTCGAAACCATCCCTTTTCATATTCGATGGTCGAAACCATCCCTTTTCATATTTGATGGTCA
* * * * * *
1494882 TCACCATCCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTCATATTTTAGGGTCGAAACTAT
66 TCACAATCCCTTTTCATAGTCGATGGTCATCACCATCCCTTTTCATATTTGAGGGTCGAAACCAT
1494947 CCTTTTGCATATTTGATGGTCGTCAC
131 CCTTTTGCATATTTGATGGTCGTCAC
1494973 TATCCCTTTT
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
169 137 0.99
170 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (169 bp):
ATGGTCGAAACCATCCCTTTTCATATTCGATGGTCGAAACCATCCCTTTTCATATTTGATGGTCA
TCACAATCCCTTTTCATAGTCGATGGTCATCACCATCCCTTTTCATATTTGAGGGTCGAAACCAT
CCTTTTGCATATTTGATGGTCGTCACCATGTGCTAAACG
Found at i:1494874 original size:111 final size:111
Alignment explanation
Indices: 1494602--1494917 Score: 294
Period size: 111 Copynumber: 2.8 Consensus size: 111
1494592 GGTCGTCACT
* * * * * * * **
1494602 ATCCCTTTTCGTATTCAATGGTCGTCACTATCCTTTTTCATATTCAATGGTC-GAAACCATCCCT
1 ATCCCTTTTCATAGTCGATGGTCATAACCATCCCTTTTCATATTTGATGGTCAG-AACCATCCCT
* * * *** ** **
1494666 TTTCATATTTGATGGTCGTCACCATCCCTTTTCATATTTGATGGTCGTCAGA
65 TTGCATATTTGATGGTCGTCACCA----TGTGC-TAAACGATGGTCGAAACC
* ** *
1494718 ATCCCTTTTCATAGTCGATGGTCATCACCATCCCTTTTCATATTTGATGGTTGGAACCATCTCTT
1 ATCCCTTTTCATAGTCGATGGTCATAACCATCCCTTTTCATATTTGATGGTCAGAACCATCCCTT
1494783 TGCATATTTGATGGTCGTCACCATGTGCTAAACGATGGTCGAAACC
66 TGCATATTTGATGGTCGTCACCATGTGCTAAACGATGGTCGAAACC
* * * **
1494829 ATCCTTTTTCATATTCGATGGTCGA-AACCATCCTTTTTCATATTTGATGGTCATCACCATCCCT
1 ATCCCTTTTCATAGTCGATGGTC-ATAACCATCCCTTTTCATATTTGATGGTCAGAACCATCCCT
*
1494893 TTTCATATTTGATGGTCGTCACCAT
65 TTGCATATTTGATGGTCGTCACCAT
1494918 CCCTTTTCAT
Statistics
Matches: 168, Mismatches: 30, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
111 88 0.52
112 4 0.02
116 75 0.45
117 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (111 bp):
ATCCCTTTTCATAGTCGATGGTCATAACCATCCCTTTTCATATTTGATGGTCAGAACCATCCCTT
TGCATATTTGATGGTCGTCACCATGTGCTAAACGATGGTCGAAACC
Found at i:1494878 original size:140 final size:140
Alignment explanation
Indices: 1494676--1494931 Score: 368
Period size: 140 Copynumber: 1.8 Consensus size: 140
1494666 TTTCATATTT
** * ** *
1494676 GATGGTCGTCACCATCCCTTTTCATATTTGATGGTCGTCAGAATCCCTTTTCATAGTCGATGGTC
1 GATGGTCGAAACCATCCCTTTTCATATTCGATGGTCGAAACAATCCCTTTTCATAGTCGATGGTC
* *
1494741 ATCACCATCCCTTTTCATATTTGATGGTTGGAACCATCTCTTTGCATATTTGATGGTCGTCACCA
66 ATCACCATCCCTTTTCATATTTGATGGTCGGAACCATCCCTTTGCATATTTGATGGTCGTCACCA
1494806 TGTGCTAAAC
131 TGTGCTAAAC
* * * * *
1494816 GATGGTCGAAACCATCCTTTTTCATATTCGATGGTCGAAACCATCCTTTTTCATATTTGATGGTC
1 GATGGTCGAAACCATCCCTTTTCATATTCGATGGTCGAAACAATCCCTTTTCATAGTCGATGGTC
** *
1494881 ATCACCATCCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTCATATTT
66 ATCACCATCCCTTTTCATATTTGATGGTCGGAACCATCCCTTTGCATATTT
1494932 TAGGGTCGAA
Statistics
Matches: 100, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
140 100 1.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.39
Consensus pattern (140 bp):
GATGGTCGAAACCATCCCTTTTCATATTCGATGGTCGAAACAATCCCTTTTCATAGTCGATGGTC
ATCACCATCCCTTTTCATATTTGATGGTCGGAACCATCCCTTTGCATATTTGATGGTCGTCACCA
TGTGCTAAAC
Found at i:1501475 original size:22 final size:22
Alignment explanation
Indices: 1501433--1501481 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1501423 CATAATAGCC
1501433 ACATACCAAAATCACATTCAA-
1 ACATACCAAAATCACATTCAAT
**
1501454 ACATACCAAAAGTGTCATTCAAT
1 ACATACCAAAA-TCACATTCAAT
1501477 ACATA
1 ACATA
1501482 TCATCACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 8 0.33
23 5 0.21
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.22
Consensus pattern (22 bp):
ACATACCAAAATCACATTCAAT
Found at i:1502107 original size:29 final size:29
Alignment explanation
Indices: 1502044--1502214 Score: 175
Period size: 29 Copynumber: 5.9 Consensus size: 29
1502034 GTGTGCTAAA
** *
1502044 TGATGGTCGAAACCATCCCCTTTTCATATT
1 TGATGGTCGTCACCAT-CCCTTTTTATATT
1502074 TGATGGTCGTCACCATCCCTTTTTATATT
1 TGATGGTCGTCACCATCCCTTTTTATATT
* * ** * *
1502103 CGATGGTTGAAACCATCCCTTTTCACATT
1 TGATGGTCGTCACCATCCCTTTTTATATT
* *
1502132 TGATAGTCGTCACCAT-CCTTTTTCATTTT
1 TGATGGTCGTCACCATCCCTTTTT-ATATT
*
1502161 TGATGGTCATCACCAT-CCTTTTTCATATT
1 TGATGGTCGTCACCATCCCTTTTT-ATATT
* *
1502190 CGATGGTTGTCACCATCCCTTTTTA
1 TGATGGTCGTCACCATCCCTTTTTA
1502215 AGTCATCACC
Statistics
Matches: 116, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
28 6 0.05
29 89 0.77
30 21 0.18
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.42
Consensus pattern (29 bp):
TGATGGTCGTCACCATCCCTTTTTATATT
Found at i:1502141 original size:58 final size:58
Alignment explanation
Indices: 1502045--1502214 Score: 209
Period size: 58 Copynumber: 2.9 Consensus size: 58
1502035 TGTGCTAAAT
*
1502045 GATGGTCGAAACCATCCCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTTATATTC
1 GATGGTTGAAACCAT-CCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTTATATTC
* * * *
1502104 GATGGTTGAAACCATCCCTTTTCACATTTGATAGTCGTCACCAT-CCTTTTTCATTTTT
1 GATGGTTGAAACCATCCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTT-ATATTC
* * * * *
1502162 GATGG-TCATCACCATCCTTTTTCATATTCGATGGTTGTCACCATCCCTTTTTA
1 GATGGTTGA-AACCATCCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTTA
1502215 AGTCATCACC
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
57 9 0.09
58 66 0.69
59 21 0.22
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (58 bp):
GATGGTTGAAACCATCCCTTTTCATATTTGATGGTCGTCACCATCCCTTTTTATATTC
Found at i:1502257 original size:28 final size:28
Alignment explanation
Indices: 1502222--1502278 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1502212 TTAAGTCATC
*
1502222 ACCATCCCTTTTCATATTCGATGGTCAA
1 ACCATCCCTTATCATATTCGATGGTCAA
*
1502250 ACCATCCCTTATCATATTTGATGGTCAA
1 ACCATCCCTTATCATATTCGATGGTCAA
1502278 A
1 A
1502279 ACATTGGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (28 bp):
ACCATCCCTTATCATATTCGATGGTCAA
Found at i:1506964 original size:25 final size:26
Alignment explanation
Indices: 1506922--1506975 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
1506912 TTCTCCTAAA
*
1506922 TTTCAATTTTATTTAATTATTTAAT-T
1 TTTCAATTTTATTGAATTA-TTAATAT
1506948 TTTCAA-TTTATTGAATTATTAATAT
1 TTTCAATTTTATTGAATTATTAATAT
1506973 TTT
1 TTT
1506976 ATGCAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTAATAT
Found at i:1507875 original size:3 final size:3
Alignment explanation
Indices: 1507867--1508105 Score: 478
Period size: 3 Copynumber: 79.7 Consensus size: 3
1507857 TGAGGATCGC
1507867 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1507915 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1507963 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1508011 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1508059 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1508106 TCCTATAGAG
Statistics
Matches: 236, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 236 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1514984 original size:60 final size:61
Alignment explanation
Indices: 1514890--1515010 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 61
1514880 CTACTCCAAG
1514890 AGTTCGATCTAGGAATTTAGGATCGAAAGGGAGTAGAAAACCAAGTAGCAGACTAGTTGTC
1 AGTTCGATCTAGGAATTTAGGATCGAAAGGGAGTAGAAAACCAAGTAGCAGACTAGTTGTC
1514951 AGTTCGATCT-GGAATTTAGGATCGAAAGGGAGTAGAAAACCAAGTAGCAGACTAGTTGTC
1 AGTTCGATCTAGGAATTTAGGATCGAAAGGGAGTAGAAAACCAAGTAGCAGACTAGTTGTC
1515011 CAGATTAGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 50 0.83
61 10 0.17
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (61 bp):
AGTTCGATCTAGGAATTTAGGATCGAAAGGGAGTAGAAAACCAAGTAGCAGACTAGTTGTC
Found at i:1517557 original size:25 final size:26
Alignment explanation
Indices: 1517515--1517568 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
1517505 TTCTACTAAA
*
1517515 TTTCAATTTTATTTAATTATTTAAT-T
1 TTTCAATTTTATTGAATTA-TTAATAT
1517541 TTTCAA-TTTATTGAATTATTAATAT
1 TTTCAATTTTATTGAATTATTAATAT
1517566 TTT
1 TTT
1517569 ATGCAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTAATAT
Found at i:1527131 original size:27 final size:25
Alignment explanation
Indices: 1527101--1527169 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
1527091 CGTTCCGACC
*
1527101 CACAGCTCGTGTGAGCAGACCCATTTT
1 CACAGCTCGTGTGAGCA-ACCCA-ATT
** *
1527128 CACAGCTCGTGTGAGCATTCTAATT
1 CACAGCTCGTGTGAGCAACCCAATT
1527153 CACAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
1527170 TACATGTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 19 0.50
26 2 0.05
27 17 0.45
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCAACCCAATT
Found at i:1534310 original size:29 final size:29
Alignment explanation
Indices: 1534264--1534391 Score: 202
Period size: 29 Copynumber: 4.4 Consensus size: 29
1534254 CCCTCAGATA
*
1534264 ATGAAAAGGGATAGCTTCGGTTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* * *
1534293 ATGAAAAGAGATAACTTCAGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1534322 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* *
1534351 ATAAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1534380 ATGAAAAGGGAT
1 ATGAAAAGGGAT
1534392 GGTGACGACC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAAT
Found at i:1534411 original size:29 final size:29
Alignment explanation
Indices: 1534315--1534493 Score: 121
Period size: 29 Copynumber: 6.1 Consensus size: 29
1534305 AACTTCAGCT
* * * *
1534315 ATCGAATATGAAAAGGGATAGCT-TCGGCT
1 ATCGAATATGAAAAGGGAT-GGTGACGACC
* * * * *
1534344 ATCGAATATAAAAAGGGATAGCT-TCGGCT
1 ATCGAATATGAAAAGGGAT-GGTGACGACC
*
1534373 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
**
1534402 ATC-AACTATGAAAAGATATGGTGACGACC
1 ATCGAA-TATGAAAAGGGATGGTGACGACC
**
1534431 ATCGAATATGAAAAGGGATGGTTTCGACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
* * * * * *
1534460 GTTGATTAAAGAAAAGGGATGTTTACGACC
1 ATCGAAT-ATGAAAAGGGATGGTGACGACC
1534490 ATCG
1 ATCG
1534494 TTTAGCACAC
Statistics
Matches: 124, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
28 3 0.02
29 98 0.79
30 23 0.19
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23
Consensus pattern (29 bp):
ATCGAATATGAAAAGGGATGGTGACGACC
Found at i:1534416 original size:58 final size:58
Alignment explanation
Indices: 1534264--1534417 Score: 159
Period size: 58 Copynumber: 2.7 Consensus size: 58
1534254 CCCTCAGATA
* ***
1534264 ATGAAAAGGGATAGCTTCGGTTATCGAATATGAAAAGAGATAACTTCAGCTATCGAAT
1 ATGAAAAGGGATAGCTACGACCATCGAATATGAAAAGAGATAACTTCAGCTATCGAAT
* * * * * * * *
1534322 ATGAAAAGGGATAGCTTCGGCTATCGAATATAAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTACGACCATCGAATATGAAAAGAGATAACTTCAGCTATCGAAT
*
1534380 ATGAAAAGGGAT-GGTGACGACCATC-AACTATGAAAAGA
1 ATGAAAAGGGATAGCT-ACGACCATCGAA-TATGAAAAGA
1534418 TATGGTGACG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 4 0.05
58 78 0.95
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (58 bp):
ATGAAAAGGGATAGCTACGACCATCGAATATGAAAAGAGATAACTTCAGCTATCGAAT
Found at i:1537326 original size:9 final size:9
Alignment explanation
Indices: 1537312--1537359 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
1537302 TTATTAATTC
1537312 TAATTATTT
1 TAATTATTT
1537321 TAATTATTT
1 TAATTATTT
*
1537330 TAATTA-AT
1 TAATTATTT
1537338 T-A--ATTT
1 TAATTATTT
1537344 TAATTATTT
1 TAATTATTT
1537353 TAATTAT
1 TAATTAT
1537360 CTAACCCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
5 1 0.03
6 2 0.06
7 2 0.06
8 2 0.06
9 26 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TAATTATTT
Found at i:1537336 original size:13 final size:14
Alignment explanation
Indices: 1537320--1537349 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1537310 TCTAATTATT
1537320 TTAATT-ATTTTAA
1 TTAATTAATTTTAA
1537333 TTAATTAATTTTAA
1 TTAATTAATTTTAA
1537347 TTA
1 TTA
1537350 TTTTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAATTAATTTTAA
Found at i:1537347 original size:23 final size:22
Alignment explanation
Indices: 1537312--1537358 Score: 85
Period size: 23 Copynumber: 2.1 Consensus size: 22
1537302 TTATTAATTC
1537312 TAATTATTTTAATTATTTTAAT
1 TAATTATTTTAATTATTTTAAT
1537334 TAATTAATTTTAATTATTTTAAT
1 TAATT-ATTTTAATTATTTTAAT
1537357 TA
1 TA
1537359 TCTAACCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TAATTATTTTAATTATTTTAAT
Found at i:1537348 original size:32 final size:31
Alignment explanation
Indices: 1537300--1537359 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
1537290 CCTAACAAAA
1537300 AATTATTAATTCTAATTATTTTAATTATTTT
1 AATTATTAATTCTAATTATTTTAATTATTTT
*
1537331 AATTAATTAATTTTAATTATTTTAATTAT
1 AATT-ATTAATTCTAATTATTTTAATTAT
1537360 CTAACCCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (31 bp):
AATTATTAATTCTAATTATTTTAATTATTTT
Found at i:1537371 original size:32 final size:32
Alignment explanation
Indices: 1537304--1537371 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1537294 ACAAAAAATT
* **
1537304 ATTAATTCTAATTATTTTAATTATTTTAATTA
1 ATTAATTCTAATTATTTTAATTATTCTAACCA
*
1537336 ATTAATTTTAATTATTTTAATTA-TCTAACCCA
1 ATTAATTCTAATTATTTTAATTATTCTAA-CCA
1537368 ATTA
1 ATTA
1537372 CGGTTTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 4 0.13
32 27 0.87
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.54
Consensus pattern (32 bp):
ATTAATTCTAATTATTTTAATTATTCTAACCA
Found at i:1549724 original size:19 final size:20
Alignment explanation
Indices: 1549685--1549726 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1549675 GTGACCCCTG
*
1549685 TTTTGAAAATTTTTAGGTTT
1 TTTTGAAAATTTTTAGATTT
*
1549705 TTTTG-AAATTTTTTGATTT
1 TTTTGAAAATTTTTAGATTT
1549724 TTT
1 TTT
1549727 CTGACTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTTGAAAATTTTTAGATTT
Found at i:1553731 original size:13 final size:14
Alignment explanation
Indices: 1553715--1553743 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1553705 GGATTTTAAC
1553715 TTTTATTTT-TGGA
1 TTTTATTTTGTGGA
1553728 TTTTATTTTGTGGA
1 TTTTATTTTGTGGA
1553742 TT
1 TT
1553744 ACTATTGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (14 bp):
TTTTATTTTGTGGA
Found at i:1561584 original size:22 final size:21
Alignment explanation
Indices: 1561533--1561589 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1561523 GTACTATGCA
* *
1561533 AATGAAACGGGTAAGAAAAGG
1 AATGGAACGGGTAAGAAAAAG
*
1561554 AATGTAACGGGTAAGAAAAAG
1 AATGGAACGGGTAAGAAAAAG
1561575 ATATGGAAC-GGTAAG
1 A-ATGGAACGGGTAAG
1561590 TGACTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 26 0.81
22 6 0.19
ACGTcount: A:0.49, C:0.05, G:0.32, T:0.14
Consensus pattern (21 bp):
AATGGAACGGGTAAGAAAAAG
Found at i:1563883 original size:10 final size:10
Alignment explanation
Indices: 1563870--1563916 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
1563860 ATTTATTAGC
*
1563870 AAACACATTA
1 AAACACATTT
1563880 AAACACATTT
1 AAACACATTT
1563890 AAACACA-TT
1 AAACACATTT
*
1563899 AAATACATTT
1 AAACACATTT
1563909 AAACACAT
1 AAACACAT
1563917 ATTAGACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (10 bp):
AAACACATTT
Found at i:1563884 original size:74 final size:74
Alignment explanation
Indices: 1563763--1563901 Score: 215
Period size: 74 Copynumber: 1.9 Consensus size: 74
1563753 TAACTGATTC
* * *
1563763 CAACTAAATAGTCACCTGAAAATATTTATTAACAAACACCTTTAAACACATTTAAACACACTAAA
1 CAACTAAATAGTCACCTGAAAACATTTATTAACAAACACATTAAAACACATTTAAACACACTAAA
1563828 CTTAATAAG
66 CTTAATAAG
* * * *
1563837 CAACTAAATAGTCACCTGCAAGCATTTATTAGCAAACACATTAAAACACATTTAAACACATTAAA
1 CAACTAAATAGTCACCTGAAAACATTTATTAACAAACACATTAAAACACATTTAAACACACTAAA
1563902 TACATTTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 58 1.00
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (74 bp):
CAACTAAATAGTCACCTGAAAACATTTATTAACAAACACATTAAAACACATTTAAACACACTAAA
CTTAATAAG
Found at i:1563908 original size:19 final size:20
Alignment explanation
Indices: 1563870--1563916 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
1563860 ATTTATTAGC
1563870 AAACACATTAAAACACATTT
1 AAACACATTAAAACACATTT
*
1563890 AAACACATT-AAATACATTT
1 AAACACATTAAAACACATTT
1563909 AAACACAT
1 AAACACAT
1563917 ATTAGACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (20 bp):
AAACACATTAAAACACATTT
Found at i:1564041 original size:19 final size:19
Alignment explanation
Indices: 1564014--1564052 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1564004 TTATTCCAAC
1564014 AACTAAATTAACTAAGATG
1 AACTAAATTAACTAAGATG
*
1564033 AACTCAATTAACTAAGATG
1 AACTAAATTAACTAAGATG
1564052 A
1 A
1564053 GAAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (19 bp):
AACTAAATTAACTAAGATG
Found at i:1567840 original size:10 final size:10
Alignment explanation
Indices: 1567825--1567849 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1567815 ATTTATGAAC
1567825 AAACACATTA
1 AAACACATTA
1567835 AAACACATTA
1 AAACACATTA
1567845 AAACA
1 AAACA
1567850 AACTAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (10 bp):
AAACACATTA
Found at i:1567882 original size:74 final size:76
Alignment explanation
Indices: 1567792--1567941 Score: 214
Period size: 74 Copynumber: 2.0 Consensus size: 76
1567782 TAACTGATTC
*
1567792 CAACTAAATAGGCACCTGCAAATATTTATGAACAAACACATTAAAACACA-TTAAA-ACAAACTA
1 CAACTAAATAGGCACCTGCAAACATTTATGAACAAACACATTAAAACACATTTAAACACAAACTA
1567855 AACTTAATAAG
66 AACTTAATAAG
* * * * * *
1567866 CAACTAAATAGTCACCTGCAAGCATTTATTAACAAACACGTTAAAACACATTTAAACACATATTA
1 CAACTAAATAGGCACCTGCAAACATTTATGAACAAACACATTAAAACACATTTAAACACAAACTA
*
1567931 GACTTAATAAG
66 AACTTAATAAG
1567942 TTTAATTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
74 45 0.68
75 5 0.08
76 16 0.24
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.24
Consensus pattern (76 bp):
CAACTAAATAGGCACCTGCAAACATTTATGAACAAACACATTAAAACACATTTAAACACAAACTA
AACTTAATAAG
Found at i:1569161 original size:26 final size:28
Alignment explanation
Indices: 1569092--1569164 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
1569082 TTAACTCCAT
*
1569092 GGGTATTTCGGTCATTTT-CCCCTTCAG
1 GGGTATTTCGATCATTTTACCCCTTCAG
* * *
1569119 GGGTATTTCGATAATTTTACCCTTTGA-
1 GGGTATTTCGATCATTTTACCCCTTCAG
1569146 GGG-ATTTCGATCATTTTAC
1 GGGTATTTCGATCATTTTAC
1569165 GCTATAGGGC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 15 0.38
27 19 0.47
28 6 0.15
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (28 bp):
GGGTATTTCGATCATTTTACCCCTTCAG
Found at i:1571335 original size:19 final size:19
Alignment explanation
Indices: 1571308--1571400 Score: 79
Period size: 19 Copynumber: 5.1 Consensus size: 19
1571298 TTATTCCAGC
*
1571308 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
1571327 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
* * *
1571346 -A-GTAATTTATTCT-AG--C
1 AACTTAA-TTA-ACTAAGATG
*
1571362 AACTTAATTAATTAAGATG
1 AACTTAATTAACTAAGATG
*
1571381 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
1571400 A
1 A
1571401 GTAATTTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
16 1 0.02
17 9 0.16
18 9 0.16
19 38 0.67
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:1571363 original size:54 final size:54
Alignment explanation
Indices: 1571298--1571425 Score: 220
Period size: 54 Copynumber: 2.4 Consensus size: 54
1571288 CAACAATAAA
*
1571298 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
* * *
1571352 TTATTCTAGCAACTTAATTAATTAAGATGAACTCAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
1571406 TTATTCCAGCAACTAAATTA
1 TTATTCCAGCAACTAAATTA
1571426 CTTATTCCGC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (54 bp):
TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
Found at i:1574304 original size:37 final size:37
Alignment explanation
Indices: 1574254--1574328 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1574244 TCTAAAAGTC
1574254 AAAATTAAAAAGAGGCGAGCTTTAAAAGCCCAATGTG
1 AAAATTAAAAAGAGGCGAGCTTTAAAAGCCCAATGTG
1574291 AAAATTAAAAAGAGGCGAGCTTTAAAAGCCCAATGTG
1 AAAATTAAAAAGAGGCGAGCTTTAAAAGCCCAATGTG
1574328 A
1 A
1574329 GATCAACACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (37 bp):
AAAATTAAAAAGAGGCGAGCTTTAAAAGCCCAATGTG
Found at i:1575380 original size:25 final size:25
Alignment explanation
Indices: 1575342--1575390 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1575332 ATTAATTGGT
1575342 TCCAATGTAAGTTCAGCCGAATCTA
1 TCCAATGTAAGTTCAGCCGAATCTA
* *
1575367 TCCAATGTATGTTCAGTCGAATCT
1 TCCAATGTAAGTTCAGCCGAATCT
1575391 GTAGAAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCCAATGTAAGTTCAGCCGAATCTA
Found at i:1587953 original size:23 final size:23
Alignment explanation
Indices: 1587927--1587972 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1587917 CTTTCTCACT
* *
1587927 GTAGGAATTTTTGGGGTATTACA
1 GTAGGAATTTTCGGGATATTACA
*
1587950 GTAGTAATTTTCGGGATATTACA
1 GTAGGAATTTTCGGGATATTACA
1587973 AAGCTACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.39
Consensus pattern (23 bp):
GTAGGAATTTTCGGGATATTACA
Found at i:1588330 original size:50 final size:50
Alignment explanation
Indices: 1588256--1588355 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
1588246 CGGACTGATC
*
1588256 ATCAGTCTGAGGATTAAATGCAGTGCTAAAATGCAACCGCGTACCAAGAG
1 ATCAGTCTAAGGATTAAATGCAGTGCTAAAATGCAACCGCGTACCAAGAG
1588306 ATCAGTCTAAGGATTAAATGCAGTGCTAAAATGCAACCGCGTACCAAGAG
1 ATCAGTCTAAGGATTAAATGCAGTGCTAAAATGCAACCGCGTACCAAGAG
1588356 CTTCCTGTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (50 bp):
ATCAGTCTAAGGATTAAATGCAGTGCTAAAATGCAACCGCGTACCAAGAG
Found at i:1600020 original size:41 final size:41
Alignment explanation
Indices: 1599970--1600085 Score: 171
Period size: 40 Copynumber: 2.9 Consensus size: 41
1599960 ATAATTAATT
1599970 ATACCCCTGAATTGCACATACGTGCCCCTATTTGTAATTCG
1 ATACCCCTGAATTGCACATACGTGCCCCTATTTGTAATTCG
** * * *
1600011 ATACCCCTGAATTGCACATATATGCCCC-GTTTGTACTTTG
1 ATACCCCTGAATTGCACATACGTGCCCCTATTTGTAATTCG
*
1600051 ATACCCCTGAATTGCACATACGTGCCCCTTTTTGT
1 ATACCCCTGAATTGCACATACGTGCCCCTATTTGT
1600086 GCTTTAGTGA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
40 35 0.53
41 31 0.47
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (41 bp):
ATACCCCTGAATTGCACATACGTGCCCCTATTTGTAATTCG
Found at i:1600108 original size:81 final size:82
Alignment explanation
Indices: 1599970--1600124 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 82
1599960 ATAATTAATT
* * * *
1599970 ATACCCCTGAATTGCACATACGTGCCCCTATTTGTAATTCGATACCCCTGAATTGCACATATATG
1 ATACCCCTGAATTGCACATACGTGCCCCTATTTGTAATTAGATACCACTAAAGTGCACATATATG
1600035 CCCC-GTTTGTACTTTG
66 CCCCTGTTTGTACTTTG
* ** *
1600051 ATACCCCTGAATTGCACATACGTGCCCCTTTTTGTGCTTTAG-TGA-CACTAAAGTGCACATATG
1 ATACCCCTGAATTGCACATACGTGCCCCTATTTGT-AATTAGAT-ACCACTAAAGTGCACATATA
1600114 TGCCCCTGTTT
64 TGCCCCTGTTT
1600125 ACACTCAGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
81 55 0.87
82 8 0.13
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.34
Consensus pattern (82 bp):
ATACCCCTGAATTGCACATACGTGCCCCTATTTGTAATTAGATACCACTAAAGTGCACATATATG
CCCCTGTTTGTACTTTG
Found at i:1600547 original size:20 final size:21
Alignment explanation
Indices: 1600524--1600563 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1600514 ACCATATTCT
*
1600524 TTCAT-TTTTTTCTCATTTAC
1 TTCATCTTCTTTCTCATTTAC
*
1600544 TTCATCTTCTTTCTCTTTTA
1 TTCATCTTCTTTCTCATTTA
1600564 GTTTGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (21 bp):
TTCATCTTCTTTCTCATTTAC
Found at i:1617526 original size:5 final size:5
Alignment explanation
Indices: 1617516--1617583 Score: 82
Period size: 5 Copynumber: 13.6 Consensus size: 5
1617506 GTATATATAT
* * * * * *
1617516 ATTCC ATTCC ATACC ATTTC ATTCC ATACT ATTCC ATTTC ATACC ATTCC
1 ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC
1617566 ATTCC ATTCC ATTCC ATT
1 ATTCC ATTCC ATTCC ATT
1617584 TCATCAAGCA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTCC
Found at i:1617540 original size:15 final size:15
Alignment explanation
Indices: 1617516--1617583 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 15
1617506 GTATATATAT
1617516 ATTCCATTCCATACC
1 ATTCCATTCCATACC
* *
1617531 ATTTCATTCCATACT
1 ATTCCATTCCATACC
*
1617546 ATTCCATTTCATACC
1 ATTCCATTCCATACC
*
1617561 ATTCCATTCCATTCC
1 ATTCCATTCCATACC
1617576 ATTCCATT
1 ATTCCATT
1617584 TCATCAAGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTCCATTCCATACC
Found at i:1621971 original size:12 final size:12
Alignment explanation
Indices: 1621956--1621985 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1621946 TTAGGTTGTT
1621956 ACACGGCCTAGC
1 ACACGGCCTAGC
*
1621968 ACACGGCCTGGC
1 ACACGGCCTAGC
1621980 ACACGG
1 ACACGG
1621986 GCGTGTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:1623716 original size:40 final size:41
Alignment explanation
Indices: 1623658--1623822 Score: 190
Period size: 41 Copynumber: 4.1 Consensus size: 41
1623648 AAAATGTCGT
* * * * *
1623658 AAAAGGTAAAGTATTAGCGACATTTTT-GCATAAACGCCGC
1 AAAAGGTAAAGCAATAGCGGCATTTTTCTCATAAACACCGC
* *
1623698 AAAAAGTAAAGCAATAGCGGCATTTTTCTCATAAACACCGT
1 AAAAGGTAAAGCAATAGCGGCATTTTTCTCATAAACACCGC
* * * *
1623739 AAAAGGTAAATCAATAGCGGCGTTTTTCTCATAAACGCTGC
1 AAAAGGTAAAGCAATAGCGGCATTTTTCTCATAAACACCGC
* * *
1623780 TAAAGGCAAAGCAATAGCGGCATTTTT-ACATAAACACCGC
1 AAAAGGTAAAGCAATAGCGGCATTTTTCTCATAAACACCGC
1623820 AAA
1 AAA
1623823 TATTTTTTAC
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
40 35 0.34
41 68 0.66
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (41 bp):
AAAAGGTAAAGCAATAGCGGCATTTTTCTCATAAACACCGC
Done.