Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_pilon, whole genome shotgun sequence
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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:259428 original size:2 final size:2
Alignment explanation
Indices: 259421--259485 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
259411 ACTTGATTTG
259421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
259463 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
259486 GGACTTTAGC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:261788 original size:17 final size:17
Alignment explanation
Indices: 261759--261791 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
261749 TTAATGATGC
261759 AAATGAAAAAAAAATGG
1 AAATGAAAAAAAAATGG
261776 AAAT-AAAACAAAAATG
1 AAATGAAAA-AAAAATG
261792 AAAAGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (17 bp):
AAATGAAAAAAAAATGG
Found at i:263631 original size:25 final size:25
Alignment explanation
Indices: 263602--263668 Score: 93
Period size: 23 Copynumber: 2.7 Consensus size: 25
263592 AACTATATAA
263602 TATATATTTATATGTTTTCAAAAAC
1 TATATATTTATATGTTTTCAAAAAC
*
263627 TATAT-TATATATG-TTTCAAAAAC
1 TATATATTTATATGTTTTCAAAAAC
*
263650 TATATATATTATATATTTT
1 TATATAT-TTATATGTTTT
263669 TGAAATTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 15 0.42
24 8 0.22
25 10 0.28
26 3 0.08
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (25 bp):
TATATATTTATATGTTTTCAAAAAC
Found at i:263638 original size:30 final size:30
Alignment explanation
Indices: 263581--263638 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
263571 TAATAATATG
263581 TATGTATTAAAAACTATATAATATATATTTA
1 TATGTATTAAAAACTATAT-ATATATATTTA
*
263612 TATGTTTTCAAAAACTATAT-TATATAT
1 TATGTATT-AAAAACTATATATATATAT
263639 GTTTCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 7 0.28
31 7 0.28
32 11 0.44
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (30 bp):
TATGTATTAAAAACTATATATATATATTTA
Found at i:263683 original size:2 final size:2
Alignment explanation
Indices: 263678--263716 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
263668 TTGAAATTAC
263678 TA TA TA TA TA TA TA TA TA TA T- TA TCA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA TA
263717 ATGTAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 29 0.85
3 4 0.12
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:264662 original size:16 final size:17
Alignment explanation
Indices: 264618--264665 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
264608 TGATTATCGT
264618 TAAAA-ATAATTATTTA
1 TAAAATATAATTATTTA
** *
264634 TTTAATTTAATTATTTA
1 TAAAATATAATTATTTA
264651 -AAAATATAATTATTT
1 TAAAATATAATTATTT
264666 TTGGTAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAAATATAATTATTTA
Found at i:264686 original size:83 final size:84
Alignment explanation
Indices: 264591--264767 Score: 297
Period size: 84 Copynumber: 2.1 Consensus size: 84
264581 GTGATTTATC
*
264591 TTTTA-TATATCAATAAATGATTATCGTTAAAAA-TAATTATTTATTTAATTTAATTATTTAAAA
1 TTTTATTA-ATCAATAAATGATTATCGTTAAAAATTAATTAATTATTTAATTTAATTATTTAAAA
264654 ATATAATTATTTTTGGT-AA
65 ATATAATTATTTTTGGTGAA
*
264673 TTTTTATTAATCAATAAATGATTATTGTTAAAAATTAATTAATTATTTAATTTAATTATTTAAAA
1 -TTTTATTAATCAATAAATGATTATCGTTAAAAATTAATTAATTATTTAATTTAATTATTTAAAA
264738 ATATAATTATTTTTGGTGAA
65 ATATAATTATTTTTGGTGAA
264758 TTTTATTAAT
1 TTTTATTAAT
264768 TTAAATTATT
Statistics
Matches: 89, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
83 29 0.33
84 58 0.65
85 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (84 bp):
TTTTATTAATCAATAAATGATTATCGTTAAAAATTAATTAATTATTTAATTTAATTATTTAAAAA
TATAATTATTTTTGGTGAA
Found at i:264724 original size:16 final size:15
Alignment explanation
Indices: 264708--264749 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
264698 TGTTAAAAAT
264708 TAATTAATTATTTAA
1 TAATTAATTATTTAA
264723 T--TTAATTATTTAA
1 TAATTAATTATTTAA
*
264736 AAATATAATTATTT
1 TAAT-TAATTATTT
264750 TTGGTGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 12 0.52
15 2 0.09
16 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTAATTATTTAA
Found at i:273680 original size:14 final size:14
Alignment explanation
Indices: 273655--273695 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
273645 CAAATTCATG
273655 GTCAAAGTCAACGA
1 GTCAAAGTCAACGA
* * *
273669 GTTAAAGGCAACAA
1 GTCAAAGTCAACGA
273683 GTCAAAGTCAACG
1 GTCAAAGTCAACG
273696 GGTTGACTTG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (14 bp):
GTCAAAGTCAACGA
Found at i:275971 original size:11 final size:11
Alignment explanation
Indices: 275944--275979 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
275934 AATAAGAAGA
275944 ATAAAATAAA-
1 ATAAAATAAAG
275954 A-AAAATAAAG
1 ATAAAATAAAG
275964 ATAAAATAAAG
1 ATAAAATAAAG
275975 ATAAA
1 ATAAA
275980 GAAAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 2 0.08
11 14 0.58
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (11 bp):
ATAAAATAAAG
Found at i:275991 original size:3 final size:3
Alignment explanation
Indices: 275983--276022 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
275973 AGATAAAGAA
275983 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
276023 TGATAGGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:280336 original size:3 final size:3
Alignment explanation
Indices: 280328--280370 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
280318 AAAGATAAGG
280328 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
280371 TGATGATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:288200 original size:21 final size:21
Alignment explanation
Indices: 288176--288229 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
288166 GGGTTAAGAC
288176 CTTTCGATGAAAGGACCTAAT
1 CTTTCGATGAAAGGACCTAAT
* * * *
288197 CTTTCAATTAAAGGACTTATT
1 CTTTCGATGAAAGGACCTAAT
*
288218 CTTTTGATGAAA
1 CTTTCGATGAAA
288230 AGTGCTTAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
CTTTCGATGAAAGGACCTAAT
Found at i:294124 original size:23 final size:23
Alignment explanation
Indices: 294098--294164 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
294088 AACAGACGAC
294098 ACCTATTATCTTAAATAGGTGCT
1 ACCTATTATCTTAAATAGGTGCT
* * * *
294121 ACCTATTATGTTGAATAAGCGCT
1 ACCTATTATCTTAAATAGGTGCT
294144 ACCTATTA-CATTAAACTAGGT
1 ACCTATTATC-TTAAA-TAGGT
294165 ACCGGTTTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
23 31 0.91
24 3 0.09
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (23 bp):
ACCTATTATCTTAAATAGGTGCT
Found at i:294245 original size:121 final size:121
Alignment explanation
Indices: 294033--294311 Score: 310
Period size: 121 Copynumber: 2.3 Consensus size: 121
294023 GCTTATTATG
* * * ***
294033 TTAAACTACATACCGGTTTATTTGAAGGTTACTAATAATATAAATGGTAAAATAAAACAGACGAC
1 TTAAACTACATACCGGTTTGTTTAAAGGTTAATAATAATATAAACAATAAAATAAAACAGACGAC
* * * *
294098 ACCTATTATCTTAAATAGGTGCTACCTATTATGTTGAATAAGCGCTACCTATTACA
66 ACCTATTATCTAAAATAGGTGCTACCTATTACGTTAAATAAGCACTACCTATTACA
** * * * *
294154 TTAAACTAGGTACCGGTTTGTTTAAAGGTTAGTAATAATGTAAACAATAAAATAAAATAGGCG-C
1 TTAAACTACATACCGGTTTGTTTAAAGGTTAATAATAATATAAACAATAAAATAAAACAGACGAC
* * * * * *
294218 TACCTATTATGTAAAATAGGTGTTACCTATTGCGTTAAATAAGCATTATCTATTACG
66 -ACCTATTATCTAAAATAGGTGCTACCTATTACGTTAAATAAGCACTACCTATTACA
* *
294275 TTAAACTATC-TACCAGTTTGTTTAAAAGTTAATAATA
1 TTAAACTA-CATACCGGTTTGTTTAAAGGTTAATAATA
294312 TAAATGGTAA
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
120 1 0.01
121 130 0.99
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (121 bp):
TTAAACTACATACCGGTTTGTTTAAAGGTTAATAATAATATAAACAATAAAATAAAACAGACGAC
ACCTATTATCTAAAATAGGTGCTACCTATTACGTTAAATAAGCACTACCTATTACA
Found at i:294257 original size:23 final size:23
Alignment explanation
Indices: 294206--294258 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
294196 AACAATAAAA
*
294206 TAAAATAGGCGCTACCTATTATG
1 TAAAATAGGCGCTACCTATTACG
* * *
294229 TAAAATAGGTGTTACCTATTGCG
1 TAAAATAGGCGCTACCTATTACG
*
294252 TTAAATA
1 TAAAATA
294259 AGCATTATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (23 bp):
TAAAATAGGCGCTACCTATTACG
Found at i:294949 original size:111 final size:109
Alignment explanation
Indices: 294830--295044 Score: 290
Period size: 111 Copynumber: 2.0 Consensus size: 109
294820 AACACAACTT
* * *
294830 TAATATTTTAGGCGCTACCTAATATGTTAATAGTATTAATAACAAAATAAGTAATTAACTTTTTT
1 TAATATTTTAGGCGCTACCTAATATGTTAATAATATTAATAACAAAATAAGTAATTAAC--CTAT
*
294895 TTTTGTTATCGTCGGATTTCTAAGGTACC-ATCAAC-TTAAACTTTGG
64 TTTT-TTATCGTCAGATTTCTAAGG-ACCTATCAACTTTAAACTTTGG
* * * * *
294941 TAATATTTTAGGCGCTACTTAATATGTTGATAATATTGATAACAAATTAAGTTATTAACCTATTT
1 TAATATTTTAGGCGCTACCTAATATGTTAATAATATTAATAACAAAATAAGTAATTAACCTATTT
*
295006 TTTTATCGTCAGATTTCTAAGGCCCTATCAACTTTAAAC
66 TTTTATCGTCAGATTTCTAAGGACCTATCAACTTTAAAC
295045 AGACGCTACC
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
107 2 0.02
108 25 0.27
109 12 0.13
111 53 0.58
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (109 bp):
TAATATTTTAGGCGCTACCTAATATGTTAATAATATTAATAACAAAATAAGTAATTAACCTATTT
TTTTATCGTCAGATTTCTAAGGACCTATCAACTTTAAACTTTGG
Found at i:295536 original size:116 final size:117
Alignment explanation
Indices: 295312--295642 Score: 450
Period size: 116 Copynumber: 2.8 Consensus size: 117
295302 CACAGCAGAT
* *
295312 ACTCAATACACACAATTTTATGGAAATTTATTAATTTGCAAATTGCAAAAAAAAAGAAGATATTT
1 ACTCAATACACACAATTTTATGGAAACTTATTAATTTGCAAATTG---AAAAAAAGAAGACATTT
295377 TAGAAAATAATATTCAAAATAGTACACGTGAAAAGCATTGAAGGAAGATTC-CAA
63 TAGAAAATAATATTCAAAATAGTACACGTGAAAAGCATTGAAGGAAGATTCTCAA
* *
295431 GCTCAATGCACACAATTTTATGGAAACTTATTAATTTGCAAATTGTAAAAAAA-AAGACATTTTA
1 ACTCAATACACACAATTTTATGGAAACTTATTAATTTGCAAATTG-AAAAAAAGAAGACATTTTA
*
295495 GAAAATAATATTCAAAATAGTACATGTGAAAAGCATTGAAGGAAGATTCTTTGGTCAA
65 GAAAATAATATTCAAAATAGTACACGTGAAAAGCATTGAAGGAAGATTC-----TCAA
* ** **
295553 ACTCAATCCACACAATTTTATGGAAACTTATTAATTTTTAAAAAGAAAAAGAAGAAGGACATTTT
1 ACTCAATACACACAATTTTATGGAAACTTATTAATTTGCAAATTGAAAAA-AAGAA-GACATTTT
*
295618 AGAAAATAAAATTCAAAATAGTACA
64 AGAAAATAATATTCAAAATAGTACA
295643 ACTGTGTATA
Statistics
Matches: 190, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
116 58 0.31
117 7 0.04
119 42 0.22
121 5 0.03
122 44 0.23
123 2 0.01
124 32 0.17
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.29
Consensus pattern (117 bp):
ACTCAATACACACAATTTTATGGAAACTTATTAATTTGCAAATTGAAAAAAAGAAGACATTTTAG
AAAATAATATTCAAAATAGTACACGTGAAAAGCATTGAAGGAAGATTCTCAA
Found at i:296302 original size:60 final size:59
Alignment explanation
Indices: 296167--296331 Score: 206
Period size: 60 Copynumber: 2.8 Consensus size: 59
296157 GATGAATTTG
* * * ** * * * *
296167 GGGATGAAATTGGAAGATTCAAAATTTTGGGGACCAATTTACAATG-AGTCATATTTTT
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAAATCATAGTTTA
*
296225 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGATAATCATAGTTTA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGA-AATCATAGTTTA
* *
296285 GGGATGAAATTATAATATTCAAAAGTTTAAAGACCAATTTAAAATGA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGA
296332 GAGTTATACT
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 39 0.42
60 53 0.58
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (59 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAAATCATAGTTTA
Found at i:296313 original size:29 final size:29
Alignment explanation
Indices: 296225--296313 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
296215 TCATATTTTT
*
296225 GGGATGAAATTAGAATATTCAAAAGTTTA
1 GGGATGAAATTAAAATATTCAAAAGTTTA
* * *
296254 AGGACT-AATTTAAAATGATAATC-ATAGTTTA
1 GGGA-TGAAATTAAAAT-AT--TCAAAAGTTTA
*
296285 GGGATGAAATTATAATATTCAAAAGTTTA
1 GGGATGAAATTAAAATATTCAAAAGTTTA
296314 AAGACCAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
28 2 0.04
29 18 0.39
30 6 0.13
31 18 0.39
32 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (29 bp):
GGGATGAAATTAAAATATTCAAAAGTTTA
Found at i:301138 original size:20 final size:21
Alignment explanation
Indices: 301108--301147 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
301098 AGTCATTGGG
*
301108 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCAATACTAT
301129 GCCT-ATGGTATCAATACTA
1 GCCTGATGGTATCAATACTA
301148 CTATACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCAATACTAT
Found at i:303489 original size:3 final size:3
Alignment explanation
Indices: 303481--303523 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
303471 TTCGGCACCG
*
303481 TTA TTA TTA CTA TTA TTA TTAA TTA TTA -TA TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT
303524 GGAGGCTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:305186 original size:62 final size:61
Alignment explanation
Indices: 305071--305206 Score: 152
Period size: 62 Copynumber: 2.2 Consensus size: 61
305061 AAAAATGTTC
* * *
305071 ATTTTAGTCACTTTTGCATTTTATTTTCTTTTAATTTTTGACATGATGATTTA-TTAGTTTAT
1 ATTTTAGTCACTTTTACATGTTATTTTATTTTAATTTTTGACATGATGATTTAGTTA-TTT-T
* * *
305133 ATTTTAGTC-CTATTTACATGTTGTTTTATTTTAATTTTTG-CATGTTGCTTTTATGTTATTTT
1 ATTTTAGTCACT-TTTACATGTTATTTTATTTTAATTTTTGACATGATG-ATTTA-GTTATTTT
305195 ATTTTAGTCACT
1 ATTTTAGTCACT
305207 AATTAGTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
61 8 0.13
62 47 0.75
63 5 0.08
64 3 0.05
ACGTcount: A:0.21, C:0.09, G:0.10, T:0.60
Consensus pattern (61 bp):
ATTTTAGTCACTTTTACATGTTATTTTATTTTAATTTTTGACATGATGATTTAGTTATTTT
Found at i:305193 original size:24 final size:24
Alignment explanation
Indices: 305149--305194 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
305139 GTCCTATTTA
*
305149 CATGTTGTTTTATTTTAATTTTTG
1 CATGTTGTTTTATGTTAATTTTTG
305173 CATGTTGCTTTTATGTT-ATTTT
1 CATGTTG-TTTTATGTTAATTTT
305195 ATTTTAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.15, C:0.07, G:0.13, T:0.65
Consensus pattern (24 bp):
CATGTTGTTTTATGTTAATTTTTG
Found at i:305219 original size:62 final size:62
Alignment explanation
Indices: 305087--305231 Score: 145
Period size: 62 Copynumber: 2.3 Consensus size: 62
305077 GTCACTTTTG
* * *
305087 CATTTTATTTTCTTTTAATTTTTGACATGATGATTTATTAGTTTATATTTTAGTCCTATTTA
1 CATTTTGTTTTATTTTAATTTTTGACATGATGATTTATTAGTTTATATTTTAGTCCTAATTA
* * *
305149 CATGTTGTTTTATTTTAATTTTTG-CATGTTGCTTTTATGTTA-TTT-TATTTTAGTCACTAATT
1 CATTTTGTTTTATTTTAATTTTTGACATGATG-ATTTA--TTAGTTTATATTTTAGTC-CTAATT
305211 A
62 A
* * *
305212 -GTTTTGTTCTATATTAATTT
1 CATTTTGTTTTATTTTAATTT
305232 GCATGATACT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
61 6 0.09
62 51 0.74
63 9 0.13
64 3 0.04
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.61
Consensus pattern (62 bp):
CATTTTGTTTTATTTTAATTTTTGACATGATGATTTATTAGTTTATATTTTAGTCCTAATTA
Found at i:305877 original size:131 final size:131
Alignment explanation
Indices: 305668--306016 Score: 511
Period size: 131 Copynumber: 2.7 Consensus size: 131
305658 GTAATATATT
* * * * * * *
305668 TTCATTTCGGTTGGAGTAATAAACGACTGGTTAAAGGCATGAGAGATCATTTATTCTCGATTAGA
1 TTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* ** * *
305733 AATAATTAAATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAATAGTGACATCT
66 AATAATTAGATATTATCATTTTCTCTCGAATAAATATTGAATTTTAAGACGAAATAATGACATCT
305798 C
131 C
*
305799 TTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTTTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* *
305864 AATAATTAGATATTATCATTTTCTCTCGAATAAATATTGAATTTTAAGATGAAATAATGATATCT
66 AATAATTAGATATTATCATTTTCTCTCGAATAAATATTGAATTTTAAGACGAAATAATGACATCT
305929 C
131 C
* * *
305930 TTCATTTCGATCGTAGTAATAAATGACTT-CTTTAAGGCATGAAAGGTCATTTATTCTCGATTGG
1 TTCATTTCGATTGGAGTAATAAATGA-TTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGG
305994 AAATAATTAGATATTATCGATTT
65 AAATAATTAGATATTATC-ATTT
306017 CTTTCTTAAA
Statistics
Matches: 197, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
131 191 0.97
132 6 0.03
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (131 bp):
TTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
AATAATTAGATATTATCATTTTCTCTCGAATAAATATTGAATTTTAAGACGAAATAATGACATCT
C
Found at i:307234 original size:21 final size:21
Alignment explanation
Indices: 307209--307259 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
307199 AAGGTAGTAC
307209 CGATACCCCTTGAAAGGGTAT
1 CGATACCCCTTGAAAGGGTAT
307230 CGATACCCCTTGAAAGGGTAT
1 CGATACCCCTTGAAAGGGTAT
307251 CGATACCCC
1 CGATACCCC
307260 CTGTTATGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (21 bp):
CGATACCCCTTGAAAGGGTAT
Found at i:318538 original size:54 final size:54
Alignment explanation
Indices: 318460--318753 Score: 421
Period size: 54 Copynumber: 5.4 Consensus size: 54
318450 TATCTTTCCG
* *
318460 TGGGTTGCATACATACTGCCTATACGGTCGTTCATCAACATATGATGAA-TTCAA
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTC-A
* * * *
318514 TGGGTTGCACACATAGTGCATATACGATCGTTCATAAACATATGATGAATTTCG
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCA
* *
318568 TGGGTTGCACACATAGTGCCTATACGGTCGTTTATCAATATATGATGAATTTCA
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCA
* * * *
318622 TGGGTTGCACACAAAGTGCCTATATGGTCGTTCGTCAACATATGATGAATTTCG
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCA
**
318676 TGGGTTGCACACATAGTGCCTATATAGTCGTTCATCAACATATGATGAA-TTCTA
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTC-A
*
318730 TGGGTTACACACATAGTGCCTATA
1 TGGGTTGCACACATAGTGCCTATA
318754 GTACACATAG
Statistics
Matches: 215, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
53 3 0.01
54 209 0.97
55 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (54 bp):
TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCA
Found at i:321891 original size:14 final size:15
Alignment explanation
Indices: 321863--321935 Score: 57
Period size: 14 Copynumber: 5.1 Consensus size: 15
321853 GAATAAAAGG
321863 AAATGAAAAAGAAAA
1 AAATGAAAAAGAAAA
*
321878 AAAT-AAAAA-TAAA
1 AAATGAAAAAGAAAA
* * *
321891 AAATGATTATA-AAGA
1 AAATGA-AAAAGAAAA
*
321906 AAA-GAAAAAGAAAG
1 AAATGAAAAAGAAAA
321920 AAA-GAAAAAGAAAA
1 AAATGAAAAAGAAAA
321934 AA
1 AA
321936 GAATAAATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
13 9 0.20
14 25 0.56
15 11 0.24
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (15 bp):
AAATGAAAAAGAAAA
Found at i:321947 original size:14 final size:13
Alignment explanation
Indices: 321905--321938 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
321895 GATTATAAAG
321905 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
321918 AGAAAGAAAAAGAA
1 A-AAAGAAAAAGAA
321932 AAAAGAA
1 AAAAGAA
321939 TAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:325402 original size:21 final size:20
Alignment explanation
Indices: 325349--325402 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
325339 TCCCTCAAAG
*
325349 CTTCACTACAAGATTTTATGA
1 CTTCACTA-AAGATTTCATGA
* *
325370 CCTCGACAAAAGATTTCATGA
1 CTTC-ACTAAAGATTTCATGA
325391 CTTCAACTAAAG
1 CTTC-ACTAAAG
325403 CCTTGTTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (20 bp):
CTTCACTAAAGATTTCATGA
Found at i:328571 original size:53 final size:53
Alignment explanation
Indices: 328495--328620 Score: 236
Period size: 53 Copynumber: 2.4 Consensus size: 53
328485 TCCTTGACAC
328495 TGTAAGAGC-TTCAAGAGATTGCCTGGTGCCTAGGCAAAATATTTCTAGACCT
1 TGTAAGAGCTTTCAAGAGATTGCCTGGTGCCTAGGCAAAATATTTCTAGACCT
328547 TGTAAGAGCTTTCAAGAGATTGCCTGGTGCCTAGGCAAAATATTTCTAGACCT
1 TGTAAGAGCTTTCAAGAGATTGCCTGGTGCCTAGGCAAAATATTTCTAGACCT
*
328600 TGTAAGAGCTTTCGAGAGATT
1 TGTAAGAGCTTTCAAGAGATT
328621 ATCGTTTTTC
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
52 9 0.12
53 63 0.88
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (53 bp):
TGTAAGAGCTTTCAAGAGATTGCCTGGTGCCTAGGCAAAATATTTCTAGACCT
Found at i:330521 original size:133 final size:131
Alignment explanation
Indices: 330178--330522 Score: 413
Period size: 133 Copynumber: 2.6 Consensus size: 131
330168 GTAAATCAAA
* * *
330178 CTCGATTCAATCTTCCCTGAAGAATAGTGAAATGAATCAATG-CTCCATATTTGATTGTCCCTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACGTCTCCATATTTGATT-T-CCTAA
* * * ** * *
330242 AGAAACAGCGAAACATATCCCCTCTTTTTAGACTTGATCTTCCCCGAGTAGTAGTGGAACAAGTC
64 AGAAATAGCGGAACAAATCCCCTCTTTCGAGACTTGATATTCCCCGAGTAGCAGTGGAACAAGTC
330307 TGC
129 TGC
* * * * **
330310 CTCGATTCAATCTTCCCTAAAGAACAGTGAAATGAATCAACATCTCCAGATCTGATTTTCCTTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACGTCTCCATATTTGA-TTTCCTAAA
* * **
330375 GAAAGTAGTGGAACAAATCCCCTCTTTCGAGATTTGATATTCCTTGAGTAGCAGTGGAACAAGTC
65 GAAA-TAGCGGAACAAATCCCCTCTTTCGAGACTTGATATTCCCCGAGTAGCAGTGGAACAAGTC
330440 TGC
129 TGC
* * *
330443 CTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAGTCAACGTTTCCATATTTGATCTACTCTAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACGTCTCCATATTTGAT-TTC-CTAA
*
330508 AGAAATAACGGAACA
64 AGAAATAGCGGAACA
330523 TATCTCTTTT
Statistics
Matches: 178, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
132 47 0.26
133 122 0.69
134 9 0.05
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (131 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACGTCTCCATATTTGATTTCCTAAAG
AAATAGCGGAACAAATCCCCTCTTTCGAGACTTGATATTCCCCGAGTAGCAGTGGAACAAGTCTG
C
Found at i:333794 original size:24 final size:24
Alignment explanation
Indices: 333767--333860 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
333757 TCTTATTTGA
* *
333767 ATTCTGTTATGATACCTGACTTGG
1 ATTCTGATATGATACTTGACTTGG
* *
333791 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACTTGG
* * *
333814 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACTTGG
*
333838 ATTCTGAAATGATACTTGACTTG
1 ATTCTGATATGATACTTGACTTG
333861 AATTATGTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 21 0.36
24 38 0.64
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACTTGG
Found at i:333851 original size:47 final size:48
Alignment explanation
Indices: 333767--333857 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 48
333757 TCTTATTTGA
* * * **
333767 ATTCTGTTATGATACCTGACTTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGAAATGATACTTGACATGG
*
333814 ATTCTGATCTGATACATGACCTGGATTCTGAAATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGAAATGATACTTGAC
333858 TTGAATTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 32 0.86
48 5 0.14
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGAAATGATACTTGACATGG
Found at i:333984 original size:35 final size:35
Alignment explanation
Indices: 333935--334009 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
333925 TGGAGGAAGA
* *
333935 TTACTTGGAAGCTCCT-TGGCTTTGTGCTCAGGGCC
1 TTACTTGCAAGCTCCTCT-GCTTTGTGCTAAGGGCC
*
333970 TTACTTGCAGGCTCCTCTGCTTTGTGCTAAGGGCC
1 TTACTTGCAAGCTCCTCTGCTTTGTGCTAAGGGCC
334005 TTACT
1 TTACT
334010 GTTCGTGACG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.12, C:0.27, G:0.25, T:0.36
Consensus pattern (35 bp):
TTACTTGCAAGCTCCTCTGCTTTGTGCTAAGGGCC
Found at i:338481 original size:24 final size:24
Alignment explanation
Indices: 338454--338544 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
338444 TCTGATTTGA
* *
338454 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
338478 ATTCTGATTTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * * *
338501 ATTCTAATCTTATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
338525 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
338545 TTGAATTATG
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:338669 original size:35 final size:35
Alignment explanation
Indices: 338623--338696 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
338613 GGAGGAAGAT
* * * *
338623 TACTTGGAGGCTCCTTGGCTTTGTGCTCAGGGCCA
1 TACTTGCAGGCTCATCGGCTTTGTGCTAAGGGCCA
*
338658 TACTTGCAGGCTCATCGGCTTTGTGCTAAGGGCCT
1 TACTTGCAGGCTCATCGGCTTTGTGCTAAGGGCCA
338693 TACT
1 TACT
338697 GTTCGTGACG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.32
Consensus pattern (35 bp):
TACTTGCAGGCTCATCGGCTTTGTGCTAAGGGCCA
Found at i:339887 original size:25 final size:25
Alignment explanation
Indices: 339859--339913 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
339849 ATCAACCATG
* *
339859 CGCCAGTAGCTCTGTTGCTCCAACA
1 CGCCAGTAGCTCTGCTGCACCAACA
339884 CGCCAGTAGCTCTGCTGCACCAACA
1 CGCCAGTAGCTCTGCTGCACCAACA
339909 CGCCA
1 CGCCA
339914 CTTTAACCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.22, C:0.40, G:0.20, T:0.18
Consensus pattern (25 bp):
CGCCAGTAGCTCTGCTGCACCAACA
Found at i:341842 original size:23 final size:23
Alignment explanation
Indices: 341816--341894 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
341806 GATTTTTCCT
*
341816 GAATAACCGCATAAAATTGTCCC
1 GAATGACCGCATAAAATTGTCCC
** *
341839 GAATGACCGCATAGGATTGTCCT
1 GAATGACCGCATAAAATTGTCCC
** * *
341862 GAATGACCGCATAGGATTATCCT
1 GAATGACCGCATAAAATTGTCCC
341885 GAATGACCGC
1 GAATGACCGC
341895 GTAGAGTCCC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (23 bp):
GAATGACCGCATAAAATTGTCCC
Found at i:342580 original size:64 final size:65
Alignment explanation
Indices: 342456--342611 Score: 172
Period size: 64 Copynumber: 2.4 Consensus size: 65
342446 CACACCCATT
* ** * **
342456 TCGAATGCATTTTGTGTACTGATGCACAAGTCATGCATCGATGCACTCTTGAATATTTTG-AACA
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCAATCCAGAATATTTTGAAACA
**
342520 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCAATCCAGGCTCA-TTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCAATCCAGAAT-ATTTTGAAAC
342584 A
65 A
* * * * *
342585 TCAAATGTAATTAGTGCACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
342612 CCCTAGTGTA
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 50 0.65
65 27 0.35
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCAATCCAGAATATTTTGAAACA
Found at i:343563 original size:13 final size:13
Alignment explanation
Indices: 343545--343570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343535 GGACCAGATG
343545 AATACGGGAGAGT
1 AATACGGGAGAGT
343558 AATACGGGAGAGT
1 AATACGGGAGAGT
343571 TTCATCTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.15
Consensus pattern (13 bp):
AATACGGGAGAGT
Found at i:344455 original size:21 final size:21
Alignment explanation
Indices: 344431--344470 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
344421 AAGAATTTAT
344431 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
344452 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
344471 AAATAGCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:348346 original size:21 final size:23
Alignment explanation
Indices: 348322--348380 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 23
348312 ATGCATGCCT
348322 TGAATATGCATCGATACA-T-CG
1 TGAATATGCATCGATACATTCCG
* * *
348343 TGAAGATGCATCGATGCATTCCT
1 TGAATATGCATCGATACATTCCG
*
348366 TGAATGTGCATCGAT
1 TGAATATGCATCGAT
348381 GTACTCTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 16 0.52
22 1 0.03
23 14 0.45
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (23 bp):
TGAATATGCATCGATACATTCCG
Found at i:348375 original size:23 final size:23
Alignment explanation
Indices: 348310--348381 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
348300 GACAGTGTAC
* *
348310 CGATGCATGCCTTGAATATGCAT
1 CGATGCATTCCTTGAATGTGCAT
* *
348333 CGATACA-T-CGTGAA-GATGCAT
1 CGATGCATTCCTTGAATG-TGCAT
348354 CGATGCATTCCTTGAATGTGCAT
1 CGATGCATTCCTTGAATGTGCAT
348377 CGATG
1 CGATG
348382 TACTCTGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 16 0.41
22 1 0.03
23 21 0.54
24 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (23 bp):
CGATGCATTCCTTGAATGTGCAT
Found at i:348399 original size:20 final size:20
Alignment explanation
Indices: 348374--348420 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
348364 CTTGAATGTG
348374 CATCGATGTACTCTGTTGTA
1 CATCGATGTACTCTGTTGTA
*
348394 CATCGATGTACTCTGTTGTG
1 CATCGATGTACTCTGTTGTA
348414 CATCGAT
1 CATCGAT
348421 ACCCTCGTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
CATCGATGTACTCTGTTGTA
Found at i:358742 original size:132 final size:131
Alignment explanation
Indices: 358506--358849 Score: 546
Period size: 132 Copynumber: 2.6 Consensus size: 131
358496 TGAAAACCTT
* *
358506 TTCATTTCGGTTGGAGTAATAAATGACTGCTTAAAGGCATGAGAGGTCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* * *
358571 AATAGTTAGATATTATGGTTTTCTCTCGAATTAATATTGAATTTTAAGATGAAATAGTGATATCT
66 AATAATTAGATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCT
358636 C
131 C
*
358637 TTCATTTCGATTGGAGTAATAAATGACTTCTTTTAAGGCATGAGAGGTCATTTATTCTCGATTGG
1 TTCATTTCGATTGGAGTAATAAATGACTGC-TTTAAGGCATGAGAGGTCATTTATTCTCGATTGG
*
358702 AAATAATTAGATATTACT-GTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAATAGTGATTT
65 AAATAATTAGATATTA-TGGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAATAGTGATAT
358766 CTC
129 CTC
* * * * * *
358769 TTCATTTCGATCGAAGTAATAAATGAATGCTTTAAAGCATGAGAGTTCATTCATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
358834 AATAATTAGATATTAT
66 AATAATTAGATATTAT
358850 CGATTTCTTT
Statistics
Matches: 197, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
130 1 0.01
131 75 0.38
132 120 0.61
133 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (131 bp):
TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
AATAATTAGATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCT
C
Found at i:363441 original size:27 final size:27
Alignment explanation
Indices: 363411--363476 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
363401 ATAATAATTA
*
363411 TTACCGCCAAGGATATCGAAAATTGTC
1 TTACCACCAAGGATATCGAAAATTGTC
363438 TTACCACCAAGGATATCGAAAATTGTC
1 TTACCACCAAGGATATCGAAAATTGTC
363465 TTACCACCAAGG
1 TTACCACCAAGG
363477 TGTACGGATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (27 bp):
TTACCACCAAGGATATCGAAAATTGTC
Found at i:365003 original size:19 final size:19
Alignment explanation
Indices: 364967--365007 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
364957 ATTAACAATT
364967 ATACCCAAACCCAAAAATC
1 ATACCCAAACCCAAAAATC
*
364986 ATACCACAAACCC-TAAATC
1 ATACC-CAAACCCAAAAATC
365005 ATA
1 ATA
365008 AATCCTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (19 bp):
ATACCCAAACCCAAAAATC
Found at i:366024 original size:146 final size:147
Alignment explanation
Indices: 365857--366150 Score: 563
Period size: 146 Copynumber: 2.0 Consensus size: 147
365847 TTCTATATTA
365857 AGTATTTTTATTTTTTTTAAATTATTTTTAATTCGATTTTTATATACTTCTAGGAGTATTTTCTT
1 AGTATTTTTATTTTTTTTAAATTATTTTTAATTCGATTTTTATATACTTCTAGGAGTATTTTCTT
*
365922 TTCAATTTTGAACTTCAAATGTATTGTTAAAATGATTTTTTTATTTTTAATAGATATATGTGTAT
66 TTCAATTTTGAACTTCAAATGTATTGTTAAAATGATTATTTTATTTTTAATAGATATATGTGTAT
365987 GTTAAAAGTTACAATTT
131 GTTAAAAGTTACAATTT
366004 AGTATTTTTA-TTTTTTTAAATTATTTTTAATTCGATTTTTATATACTTCTAGGAGTATTTTCTT
1 AGTATTTTTATTTTTTTTAAATTATTTTTAATTCGATTTTTATATACTTCTAGGAGTATTTTCTT
*
366068 TTCAATTTTGAACTTCAAATGTATTGTTAAAATGATTATTTTATTTTTAATAGATATATGTGTGT
66 TTCAATTTTGAACTTCAAATGTATTGTTAAAATGATTATTTTATTTTTAATAGATATATGTGTAT
366133 GTTAAAAGTTACAATTT
131 GTTAAAAGTTACAATTT
366150 A
1 A
366151 ATAAATATAA
Statistics
Matches: 145, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
146 135 0.93
147 10 0.07
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.54
Consensus pattern (147 bp):
AGTATTTTTATTTTTTTTAAATTATTTTTAATTCGATTTTTATATACTTCTAGGAGTATTTTCTT
TTCAATTTTGAACTTCAAATGTATTGTTAAAATGATTATTTTATTTTTAATAGATATATGTGTAT
GTTAAAAGTTACAATTT
Found at i:372756 original size:75 final size:76
Alignment explanation
Indices: 372672--372822 Score: 223
Period size: 77 Copynumber: 2.0 Consensus size: 76
372662 AATAAGAAAA
*
372672 GAGAGAAAACATAATTAGAGAACCTTTATTAAAGA-TTCTCTTTTATTTTTCACACTTTTAATGT
1 GAGAGAAAACATAATTAGAGAACCTTTATAAAAGACTTCTCTTTTATTTTTCACACTTTTAATGT
372736 GTAATACAATT
66 GTAATACAATT
* * * * *
372747 GAGAGAAAACATAATTAGATAACCTTTCTAAAATATCTTCTCTTTTATTTTTTACGCTTTTAATG
1 GAGAGAAAACATAATTAGAGAACCTTTATAAAAGA-CTTCTCTTTTATTTTTCACACTTTTAATG
*
372812 TGTAGTACAAT
65 TGTAATACAAT
372823 AGGAATTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 31 0.46
77 36 0.54
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (76 bp):
GAGAGAAAACATAATTAGAGAACCTTTATAAAAGACTTCTCTTTTATTTTTCACACTTTTAATGT
GTAATACAATT
Found at i:374115 original size:36 final size:36
Alignment explanation
Indices: 374068--374293 Score: 339
Period size: 36 Copynumber: 6.3 Consensus size: 36
374058 AAAGATGAAC
*
374068 ACTTGAATCGGAAGTGTCGATGCTTCCTCCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
374104 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
* * *
374140 ACTTGAATCGGAAGTGTCGATGCTTACTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
* *
374176 ATTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
*
374212 ATTTGAATCGGAAGTGCCGATGCTTCC-CTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTC-CCGTTCG
* *
374248 ACTTGAATCGGAAGTGTCGATGCTTCC-CTCTGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTC-CCGTTCG
374284 ACTTGAATCG
1 ACTTGAATCG
374294 ATGTAAACTT
Statistics
Matches: 178, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
36 178 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
Found at i:374259 original size:108 final size:108
Alignment explanation
Indices: 374068--374293 Score: 373
Period size: 108 Copynumber: 2.1 Consensus size: 108
374058 AAAGATGAAC
*
374068 ACTTGAATCGGAAGTGTCGATGCTTCCTCCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTC
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTC
*
374133 CCGTTCGACTTGAATCGGAAGTGTCGATGCTTACTTCCGTTCG
66 CCGTTCGACTTGAATCGGAAGTGTCGATGCTTACCTCCGTTCG
* * *
374176 ATTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTGCCGATGCTTCC-C
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTC
* *
374240 TCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCCCTCTGTTCG
66 -CCGTTCGACTTGAATCGGAAGTGTCGATGCTTACCTCCGTTCG
374284 ACTTGAATCG
1 ACTTGAATCG
374294 ATGTAAACTT
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
107 1 0.01
108 108 0.99
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (108 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTC
CCGTTCGACTTGAATCGGAAGTGTCGATGCTTACCTCCGTTCG
Found at i:378736 original size:60 final size:57
Alignment explanation
Indices: 378664--378776 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 57
378654 TAAATAGTCA
* *
378664 GGTGATCATTTTATAACTTTTAATAGTCGATGGAC-CAAACAAAGTAGCACTCTATAATTG
1 GGTGACCATTTTATAACTTTCAATAGT--AT-GACTC-AACAAAGTAGCACTCTATAATTG
*
378724 GGTGACCATTTTATAACTTTCAATAGTATGACTCAACAAAGTAGCACTTTATA
1 GGTGACCATTTTATAACTTTCAATAGTATGACTCAACAAAGTAGCACTCTATA
378777 GTCGGAAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
57 21 0.43
58 3 0.06
60 25 0.51
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (57 bp):
GGTGACCATTTTATAACTTTCAATAGTATGACTCAACAAAGTAGCACTCTATAATTG
Found at i:378789 original size:57 final size:59
Alignment explanation
Indices: 378670--378796 Score: 143
Period size: 57 Copynumber: 2.2 Consensus size: 59
378660 GTCAGGTGAT
* * ***
378670 CATTTTATAACTTTTAATAGTCGATGGACCAAACAAAGTAGCACTCTATAATTGGGTGAC
1 CATTTTATAACTTTCAATAGTC-ATGGACCAAACAAAGTAGCACTCTATAATCGGAAAAC
* *
378730 CATTTTATAACTTTCAATAGT-AT-GACTC-AACAAAGTAGCACTTTATAGTCGGAAAAC
1 CATTTTATAACTTTCAATAGTCATGGAC-CAAACAAAGTAGCACTCTATAATCGGAAAAC
378787 CATTTGTATA
1 CATTT-TATA
378797 CCTTACCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 31 0.53
58 7 0.12
60 20 0.34
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (59 bp):
CATTTTATAACTTTCAATAGTCATGGACCAAACAAAGTAGCACTCTATAATCGGAAAAC
Found at i:379652 original size:2 final size:2
Alignment explanation
Indices: 379645--379681 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
379635 GGATGATGGG
379645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
379682 TTTGATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:391322 original size:277 final size:281
Alignment explanation
Indices: 390951--391619 Score: 822
Period size: 277 Copynumber: 2.4 Consensus size: 281
390941 AAATTGAAAC
* * * * *
390951 AATTGTAAAATGCAAAG-TTGAAATTTATAT-AAAATGGACTAAATTGTATTCATTTACAAAGTT
1 AATTATAAAATGTAAAGATTGAAATTAATATCAAAATGGACTAAATTGCATTCATTTAAAAAGTT
* *
391014 GGTGAACAAAAGTTTATAGAGTTTGGAGATTATGATATAATTTATAAGGCTTAG-AATGAAGTTT
66 GGTGAACAAAAGTTTATAGAGTTCGGAGATTATGATATAATTTATAAGG-TTAGAAATAAAGTTT
* * * * *
391078 ATGATGTGATTTATAGGG-TT-GAGTAAATTACAAAAAATAGAAATAATTA-TGTGTCATTTTTG
130 ACGATGTGATTTATAGGGTTTAGAGTAAATTACAAAAAATAAAAATAATTACAG-GCCAATTTTG
* * * * *
391140 GATAAAAATATAATTTTAAAAATTG-AATTGAACAAACATGAAATTATAAATTAAAATTTAAATA
194 AATAAAAATATAATTTTAAAAACTGAAATTGAACAAACATGAAATTACAAAGTAAAATTAAAATA
* *
391204 AATTAAACAACACACAAATATCA
259 AAATAAACAACACACAAAGATCA
391227 AATTATAAAATGTAAAGATT-AAATTAATATCAAAATGGACTAAATTGCATTCATTTAAAAAGTT
1 AATTATAAAATGTAAAGATTGAAATTAATATCAAAATGGACTAAATTGCATTCATTTAAAAAGTT
* * *
391291 GGTGAACAAAAGTTTAT-GTAGTTCGGAGATTATGATGTAATTTATATGGTTCGAAATAAAGTTT
66 GGTGAACAAAAGTTTATAG-AGTTCGGAGATTATGATATAATTTATAAGGTTAGAAATAAAGTTT
391355 ACGATGTGATTTATAGGGTTTAGAGTAAATTACAAAAAATAAAAATAATTACAGGCCAATTTTGA
130 ACGATGTGATTTATAGGGTTTAGAGTAAATTACAAAAAATAAAAATAATTACAGGCCAATTTTGA
* * * *
391420 ATAAAAATATAGTTTTAAAGACTGAAATTTAACAAACATGAAATTACAAAGTGAAATTAAAATAA
195 ATAAAAATATAATTTTAAAAACTGAAATTGAACAAACATGAAATTACAAAGTAAAATTAAAATAA
**
391485 AATAAACAACACACATGGATCA
260 AATAAACAACACACAAAGATCA
* *
391507 AATTGA-AATAATTGTAAAATATACGTTGAAATTAATATCAAAATGGACTAAATTGCATTTATTT
1 AATT-ATAA-AA-TGT--AA-AGA--TTGAAATTAATATCAAAATGGACTAAATTGCATTCATTT
* * * * **
391571 GAAAATTTGGTAAACAAAAATTTATAGA-TTATGA-ATTTATGATATAATT
58 AAAAAGTTGGTGAACAAAAGTTTATAGAGTTCGGAGA-TTATGATATAATT
391620 CCTAGGGTTT
Statistics
Matches: 337, Mismatches: 37, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
276 28 0.08
277 103 0.31
278 2 0.01
279 57 0.17
280 60 0.18
281 3 0.01
282 3 0.01
284 2 0.01
285 2 0.01
286 1 0.00
287 18 0.05
288 57 0.17
289 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (281 bp):
AATTATAAAATGTAAAGATTGAAATTAATATCAAAATGGACTAAATTGCATTCATTTAAAAAGTT
GGTGAACAAAAGTTTATAGAGTTCGGAGATTATGATATAATTTATAAGGTTAGAAATAAAGTTTA
CGATGTGATTTATAGGGTTTAGAGTAAATTACAAAAAATAAAAATAATTACAGGCCAATTTTGAA
TAAAAATATAATTTTAAAAACTGAAATTGAACAAACATGAAATTACAAAGTAAAATTAAAATAAA
ATAAACAACACACAAAGATCA
Found at i:394896 original size:2 final size:2
Alignment explanation
Indices: 394889--394919 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
394879 CCGTACCATT
394889 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394920 ACGAGTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:397099 original size:65 final size:63
Alignment explanation
Indices: 396982--397183 Score: 214
Period size: 65 Copynumber: 3.1 Consensus size: 63
396972 AGTGATTCAC
* * * *
396982 CGATGCACCAATCCATGCATCGATGCACT-ATGA-ATTAAATTG-AACATTGAATGCATTTCATG
1 CGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGCATTTGATG
397044 CAT
61 CAT
*
397047 CGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCA
1 CGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTGATGCA
397111 T
63 T
* * * *
397112 CGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCAT
1 CGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCAT
397176 CGATGCAC
1 CGATGCAC
397184 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 48 0.40
65 63 0.52
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
CGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCAT
Found at i:397183 original size:17 final size:19
Alignment explanation
Indices: 397155--397203 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
397145 TATTTTGAAA
397155 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
397173 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
397192 CACCGATGCACT
1 CATCGATGCACT
397204 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:401301 original size:23 final size:23
Alignment explanation
Indices: 401275--401319 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
401265 CACCACAGCT
*
401275 CGTATAAACGCACCGAAGTGCCC
1 CGTAGAAACGCACCGAAGTGCCC
** *
401298 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAACGCACCGAAGTGCC
401320 ATAATGATGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (23 bp):
CGTAGAAACGCACCGAAGTGCCC
Found at i:401697 original size:148 final size:147
Alignment explanation
Indices: 401298--401741 Score: 808
Period size: 145 Copynumber: 3.0 Consensus size: 147
401288 CGAAGTGCCC
*
401298 CGTAGAATTGCACCGTAGTGCCATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 CGTAGAATTGCACCGTAGTGCCATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
401363 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTT--CACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
401426 TATGTCCCGAAGAACCG
131 TATGTCCCGAAGAACCG
401443 CGTAGAATTGCACCGTAGTGCCATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 CGTAGAATTGCACCGTAGTGCCATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
401508 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
401573 TATGTCCCGAAGAACCG
131 TATGTCCCGAAGAACCG
*
401590 CGTAGAATTGCA-CGTAATGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCC--ATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
401654 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAG-A-ATA
64 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
401717 CATATGTCCCGAAGAACCT
129 CATATGTCCCGAAGAACCG
401736 CGTAGA
1 CGTAGA
401742 CCCGACTCTT
Statistics
Matches: 292, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
145 105 0.36
146 35 0.12
147 52 0.18
148 100 0.34
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (147 bp):
CGTAGAATTGCACCGTAGTGCCATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCG
Found at i:401804 original size:148 final size:143
Alignment explanation
Indices: 401326--401741 Score: 502
Period size: 148 Copynumber: 2.8 Consensus size: 143
401316 TGCCATAATG
* *
401326 ATGTCCATAAGGACCACATAGAATTCTTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
1 ATGTCCAT-A-GACCACATAGAATGCGTT---AATCATATACATATGCTAGGGATCAAGTATGTG
**
401391 TCTTTCCAGACTT--CACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGAATTGC
61 TCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGAACCGC
* * *
401454 ACCGTAGTGCC--ATAATA
126 A-CGGAATGCCATATAACA
* *
401471 ATGTCCATAAGGACCACATAGAATTCTTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
1 ATGTCCAT-A-GACCACATAGAATGCGTT---AATCATATACATATGCTAGGGATCAAGTATGTG
**
401536 TCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGAATTGC
61 TCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGAACCGC
* *
401601 ACGTAATGCCATATAATA
126 ACGGAATGCCATATAACA
* *
401619 ATGTCCATAAGGACCACATAGAATTCTTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
1 ATGTCCAT-A-GACCACATAGAATGCGTT---AATCATATACATATGCTAGGGATCAAGTATGTG
*
401684 TCTTTCCAGACTTCACACATGTTCCAAAG-A-ATACATATGTCCCGAAGAACCTCGTAGA
61 TCTTTCCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGA
401742 CCCGACTCTT
Statistics
Matches: 265, Mismatches: 2, Indels: 7
0.97 0.01 0.03
Matches are distributed among these distances:
145 78 0.29
146 35 0.13
147 52 0.20
148 100 0.38
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (143 bp):
ATGTCCATAGACCACATAGAATGCGTTAATCATATACATATGCTAGGGATCAAGTATGTGTCTTT
CCAGACTTCACACATGTTCCAAAGAATATACATATGTCCCGAAGAACCGCGTAGAACCGCACGGA
ATGCCATATAACA
Found at i:402608 original size:18 final size:18
Alignment explanation
Indices: 402587--402621 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
402577 TCCCATCTAG
402587 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
402605 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
402622 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:403230 original size:21 final size:21
Alignment explanation
Indices: 403200--403244 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
403190 ATTTTGTCGT
* *
403200 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
403221 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
403242 TTG
1 TTG
403245 CCAGAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:404858 original size:24 final size:23
Alignment explanation
Indices: 404831--404887 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
404821 TCTATGCCTA
404831 GTGCATCGATACATC-CCTTTGAAT
1 GTGCATCGATACA-CACC-TTGAAT
* *
404855 GTGCACCGATGCACACCTTGAAT
1 GTGCATCGATACACACCTTGAAT
404878 GTGCATCGAT
1 GTGCATCGAT
404888 GCACCTGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (23 bp):
GTGCATCGATACACACCTTGAAT
Found at i:405291 original size:17 final size:18
Alignment explanation
Indices: 405259--405292 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
405249 ACCAATTTCG
*
405259 TCAAAAACAAACAATTTT
1 TCAAAAACAAAAAATTTT
405277 TCAAAAA-AAAAAATTT
1 TCAAAAACAAAAAATTT
405293 AATTTCGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (18 bp):
TCAAAAACAAAAAATTTT
Found at i:407692 original size:64 final size:61
Alignment explanation
Indices: 407484--407694 Score: 219
Period size: 65 Copynumber: 3.3 Consensus size: 61
407474 AATTTTCAGA
* * * *
407484 TTGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTGAACATCGAATGCAT
1 TTGATGCATCGATGCACCAA-CCATGCATCGATGCACTATG-ATT--TTTAAACATCGAATGCAT
* *
407549 TTCATGCATCGATGCA-CATACCATGCA-CTGATGCACTGAAGATTTTATGAAAACATCGAATGC
1 TTGATGCATCGATGCACCA-ACCATGCATC-GATGCACT-ATGATTTT-T--AAACATCGAATGC
407612 AT
60 AT
* *
407614 TTGATGCATCGATGCACCAGCCATGCATCGATGCACTATGGCTATTTTTAAACATCGAATGCAC
1 TTGATGCATCGATGCACCAACCATGCATCGATGCACTAT-G--ATTTTTAAACATCGAATGCAT
407678 TTGATGCATCGATGCAC
1 TTGATGCATCGATGCAC
407695 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 51 0.41
65 62 0.50
66 4 0.03
67 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (61 bp):
TTGATGCATCGATGCACCAACCATGCATCGATGCACTATGATTTTTAAACATCGAATGCAT
Found at i:407694 original size:17 final size:19
Alignment explanation
Indices: 407666--407714 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
407656 TATTTTTAAA
407666 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
407684 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
407703 CACCGATGCACT
1 CATCGATGCACT
407715 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:414689 original size:77 final size:77
Alignment explanation
Indices: 414601--414756 Score: 258
Period size: 77 Copynumber: 2.0 Consensus size: 77
414591 AAATAAGAAA
* *
414601 AGAGAGAAAACATAATTAGATAACCTTTATAAAAGATTTTCTCTTTTATTTTTCGCACTTTGAAT
1 AGAGAGAAAACATAATTAGATAACCTTTATAAAAGATTTTATCTTTTATTTTTCACACTTTGAAT
414666 GTGTAGTACAAT
66 GTGTAGTACAAT
* * * *
414678 AGAGATAAAACATAATTAGATAACCTTTATCAAAGATTTTATCTTTTATTTTTCACGCTTTTAAT
1 AGAGAGAAAACATAATTAGATAACCTTTATAAAAGATTTTATCTTTTATTTTTCACACTTTGAAT
414743 GTGTAGTACAAT
66 GTGTAGTACAAT
414755 AG
1 AG
414757 GAACTAAAAG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (77 bp):
AGAGAGAAAACATAATTAGATAACCTTTATAAAAGATTTTATCTTTTATTTTTCACACTTTGAAT
GTGTAGTACAAT
Found at i:417414 original size:43 final size:44
Alignment explanation
Indices: 417353--417439 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 44
417343 TCTTAGATCT
417353 TCAAATCTTTCTGGGAAATAATATA-TATATATATATATATATA
1 TCAAATCTTTCTGGGAAATAATATATTATATATATATATATATA
*
417396 TCAAATCTTTTTGGGAAATAATATATTATATATATATATATATA
1 TCAAATCTTTCTGGGAAATAATATATTATATATATATATATATA
417440 CAAGGTCACT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 24 0.57
44 18 0.43
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (44 bp):
TCAAATCTTTCTGGGAAATAATATATTATATATATATATATATA
Found at i:422234 original size:60 final size:57
Alignment explanation
Indices: 422162--422274 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 57
422152 TAAATAGTCA
* *
422162 GGTGATCATTTTATAACTTTTAATAGTCGATGGAC-CAAACAAAGTAGCACTCTATAATTG
1 GGTGACCATTTTATAACTTTCAATAGT--AT-GACTC-AACAAAGTAGCACTCTATAATTG
*
422222 GGTGACCATTTTATAACTTTCAATAGTATGACTCAACAAAGTAGCACTTTATA
1 GGTGACCATTTTATAACTTTCAATAGTATGACTCAACAAAGTAGCACTCTATA
422275 GTCGGAAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
57 21 0.43
58 3 0.06
60 25 0.51
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (57 bp):
GGTGACCATTTTATAACTTTCAATAGTATGACTCAACAAAGTAGCACTCTATAATTG
Found at i:422287 original size:57 final size:59
Alignment explanation
Indices: 422168--422294 Score: 143
Period size: 57 Copynumber: 2.2 Consensus size: 59
422158 GTCAGGTGAT
* * ***
422168 CATTTTATAACTTTTAATAGTCGATGGACCAAACAAAGTAGCACTCTATAATTGGGTGAC
1 CATTTTATAACTTTCAATAGTC-ATGGACCAAACAAAGTAGCACTCTATAATCGGAAAAC
* *
422228 CATTTTATAACTTTCAATAGT-AT-GACTC-AACAAAGTAGCACTTTATAGTCGGAAAAC
1 CATTTTATAACTTTCAATAGTCATGGAC-CAAACAAAGTAGCACTCTATAATCGGAAAAC
422285 CATTTGTATA
1 CATTT-TATA
422295 CCTTACCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 31 0.53
58 7 0.12
60 20 0.34
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (59 bp):
CATTTTATAACTTTCAATAGTCATGGACCAAACAAAGTAGCACTCTATAATCGGAAAAC
Found at i:423143 original size:2 final size:2
Alignment explanation
Indices: 423136--423176 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
423126 GGATGATGGG
423136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
423177 TTGATTTCGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:430152 original size:259 final size:258
Alignment explanation
Indices: 429694--430160 Score: 688
Period size: 259 Copynumber: 1.8 Consensus size: 258
429684 GAACAAACTA
* * *
429694 AAATTTAAATAAATTAAACAACACACATGTGTCAAATTGAAATAATTGTAAAATGCAAAGTTGAA
1 AAATTTAAATAAATTAAACAACACACAAGTATCAAATTGAAACAATTGTAAAATGCAAAGTTGAA
* **
429759 ATTTATATAAAATGGACTAAATTGCATTCATTTACAAAGTTGGTGAACAAAAGTATATAGAATTT
66 ATTAATATAAAATGGACTAAATCACATTCATTTACAAAGTTGGTGAACAAAAGTATATAGAATTT
* ** * *
429824 GGAGATTATGATATAATTTATAGGGTTTAGAATGGAGTTTATGATGTGATTTATAGGGTTTGGAG
131 GGAGATTATGATATAATTTATAGGGTTGAGAATAAAGTTTACGATGTGATTTATAGGGTATGGAG
429889 TAAATTACAAAAAAATAGAAATAATTATGTCTCATTTTTGGATAAAAATATAATTATAAATTT
196 TAAATTACAAAAAAATAGAAATAATTATGTCTCATTTTTGGATAAAAATATAATTATAAATTT
* * *
429952 AAATTTAAATAAATTAAACAACGCACAAAG-ATCAAATTGAAACGATTGTAAAATGTAAAGTTGA
1 AAATTTAAATAAATTAAACAACACAC-AAGTATCAAATTGAAACAATTGTAAAATGCAAAGTTGA
* * * *
430016 AATTAATATCAAAATGGACTAAATCACATTCATTTGA-AAAGTTGGTGAATAAAAGTTTATGGAG
65 AATTAATAT-AAAATGGACTAAATCACATTCATTT-ACAAAGTTGGTGAACAAAAGTATATAGAA
* * *
430080 TTTGGATATTATGATGTAATTTATATGGTTCGA-AATAAAGTTTACGATGTGATTTATAGGGTAT
128 TTTGGAGATTATGATATAATTTATAGGGTT-GAGAATAAAGTTTACGATGTGATTTATAGGGTAT
430144 GGAGTAAATTACAAAAA
192 GGAGTAAATTACAAAAA
430161 CAATTATAAG
Statistics
Matches: 184, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
258 63 0.34
259 119 0.65
260 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (258 bp):
AAATTTAAATAAATTAAACAACACACAAGTATCAAATTGAAACAATTGTAAAATGCAAAGTTGAA
ATTAATATAAAATGGACTAAATCACATTCATTTACAAAGTTGGTGAACAAAAGTATATAGAATTT
GGAGATTATGATATAATTTATAGGGTTGAGAATAAAGTTTACGATGTGATTTATAGGGTATGGAG
TAAATTACAAAAAAATAGAAATAATTATGTCTCATTTTTGGATAAAAATATAATTATAAATTT
Found at i:430567 original size:284 final size:283
Alignment explanation
Indices: 429952--430958 Score: 1269
Period size: 284 Copynumber: 3.5 Consensus size: 283
429942 TTATAAATTT
* * ** * * *
429952 AAATTTAAATAAATTAAACAACGCACAAAGATCAAATTGAAACGATTGTAAAATGTAAAGTTGAA
1 AAATTTAAATAAATTAAACAACACACAAGGATCAAATTGAAATAATTGTAAAATATAAAGCTAAA
**
430017 ATTAATATCAAAATGGACTAAATCACATTCATTTGAAAAGTTGGTGAATAAAAGTTTATGGAGTT
66 ATTAATATCAAAATGGACTAAATTGCATTCATTTGAAAAGTTGGTGAATAAAAGTTTATGGAGTT
* ** * * *
430082 TGGATATTATGATGTAATTTATATGGTTCGAAATAAAGTTTACGATGTGATTTATAGGGTATGGA
131 TGGAGATTATGATAAAATTTATATGGTTTGAAATGAAGTTTACGATGTGATTTATAGGGTTTGGA
* *
430147 GTAAATTAC--AAAAACAATTATAAGCCAATTTTGAATAAAAATATAATTTTAAGGATAAAATTG
196 GTAAATTACAAAAAAATAATTATAAGCCAATTTTGAATAAAAATATAATTTTAAGGATTAAATTG
* *
430210 AATAAATATGAAATTACAAACTA
261 AACAAACATGAAATTACAAACTA
430233 AAATTTAAATAAATTAAACAACACACAAGGATCAAATTGAAATAATTGTAAAATATAAAGCTAAA
1 AAATTTAAATAAATTAAACAACACACAAGGATCAAATTGAAATAATTGTAAAATATAAAGCTAAA
* * *
430298 GATTAATATAAAAATGGACTAAATTGCATTCGTTT-ACAAAGTTGGTGAACAAAAGTTTATGGAG
66 -ATTAATATCAAAATGGACTAAATTGCATTCATTTGA-AAAGTTGGTGAATAAAAGTTTATGGAG
*
430362 TTTGGAGATTATGATAAAATTTATATGGTTTGAAATGAAGTTTACGATGTGATTTATAGTGTTTG
129 TTTGGAGATTATGATAAAATTTATATGGTTTGAAATGAAGTTTACGATGTGATTTATAGGGTTTG
430427 GAGTAAATTACAAAAAAATAATTATAAGCCAATTTTGAATAAAAATATAATTTTAAGGATTAAAT
194 GAGTAAATTACAAAAAAATAATTATAAGCCAATTTTGAATAAAAATATAATTTTAAGGATTAAAT
*
430492 TGAACAAACATGAAATTACAAACAA
259 TGAACAAACATGAAATTACAAACTA
* *
430517 AAATTTAAATAAATTAAACAACACACAAGGATCAAATTGAAATAATTGTAAAATGTAAAACTGAA
1 AAATTTAAATAAATTAAACAACACACAAGGATCAAATTGAAATAATTGTAAAATATAAAGCT-AA
*
430582 AATTAATATCAAAATAGACT-AATTGCATTCATTT-ACAAAGTTGGTGAATAAAAGTTTAT-GAG
65 AATTAATATCAAAATGGACTAAATTGCATTCATTTGA-AAAGTTGGTGAATAAAAGTTTATGGAG
* * *
430644 ATTTGGAGATTATGATCCAATTTATAGGGTTTAAAATAGGGTTTAAAAATGAAGTTTACAATGTG
129 -TTTGGAGATTATGAT--AA---A-A---TTT---ATATGGTTT-GAAATGAAGTTTACGATGTG
*
430709 ATTTATAGGGTTTGAAGTAAATTACAAAAGTATAAAAATAATTAT-AGACCAATTTTGAATAAAA
180 ATTTATAGGGTTTGGAGTAAATTAC---A--A-AAAAATAATTATAAG-CCAATTTTGAATAAAA
* * * * * *
430773 ATATAATTTTAAAGACTAAATTTAACAAACATGAAATTATAAAGTG
238 ATATAATTTTAAGGATTAAATTGAACAAACATGAAATTACAAACTA
* ** * * * *
430819 AAATTAAAATAAATTAAACAGTACACATGAATCAAATTGAAATAATTGTAAAATAT-ACGCTGAA
1 AAATTTAAATAAATTAAACAACACACAAGGATCAAATTGAAATAATTGTAAAATATAAAGCTAAA
* * *
430883 ATTAATATCAAAATGGTCTAAATTGCATTTATTTGAAAA-TTGGTAAATAAAAGTTTATAGG-GT
66 ATTAATATCAAAATGGACTAAATTGCATTCATTTGAAAAGTTGGTGAATAAAAGTTTAT-GGAGT
**
430946 TTATAGATTATGA
130 TTGGAGATTATGA
430959 ATTTATGATA
Statistics
Matches: 639, Mismatches: 57, Indels: 41
0.87 0.08 0.06
Matches are distributed among these distances:
281 59 0.09
282 128 0.20
283 52 0.08
284 149 0.23
285 5 0.01
288 1 0.00
289 1 0.00
292 3 0.00
295 8 0.01
296 41 0.06
299 1 0.00
300 49 0.08
301 23 0.04
302 119 0.19
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (283 bp):
AAATTTAAATAAATTAAACAACACACAAGGATCAAATTGAAATAATTGTAAAATATAAAGCTAAA
ATTAATATCAAAATGGACTAAATTGCATTCATTTGAAAAGTTGGTGAATAAAAGTTTATGGAGTT
TGGAGATTATGATAAAATTTATATGGTTTGAAATGAAGTTTACGATGTGATTTATAGGGTTTGGA
GTAAATTACAAAAAAATAATTATAAGCCAATTTTGAATAAAAATATAATTTTAAGGATTAAATTG
AACAAACATGAAATTACAAACTA
Found at i:430682 original size:12 final size:12
Alignment explanation
Indices: 430667--430691 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
430657 GATCCAATTT
430667 ATAGGGTTTAAA
1 ATAGGGTTTAAA
430679 ATAGGGTTTAAA
1 ATAGGGTTTAAA
430691 A
1 A
430692 ATGAAGTTTA
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:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATAGGGTTTAAA
Found at i:431124 original size:4 final size:4
Alignment explanation
Indices: 431117--431351 Score: 87
Period size: 4 Copynumber: 57.8 Consensus size: 4
431107 ATAATAAATT
* * * * * *
431117 ATAC ATAC ATAC AT-G ATAT ATAT ATAT ATAT ATATC ATAC ATAT ATATC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA-C ATAC ATAC ATA-C
* * *
431166 ATAC ATTA- ATAC ATAC ATAG AT-- ATAC ATATC ATAC ATAT ATATG ATAC
1 ATAC A-TAC ATAC ATAC ATAC ATAC ATAC ATA-C ATAC ATAC ATA-C ATAC
* * * * * *
431214 ACAC ATATC ATAT ATATC ATTC ATAC ATAC ATGC ATGC ATTA- ATA- ATAT
1 ATAC ATA-C ATAC ATA-C ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATAC
* * *
431263 ATAC ATAC ATATC ATAC ATA- AT-G ATAC ATAC ATTA- ATAA AT-T ATAC
1 ATAC ATAC ATA-C ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATAC ATAC
*
431309 ATAC ATAC ATA- GTAC ATATC ATAAC ATATC ATAAC ATATC ATA
1 ATAC ATAC ATAC ATAC ATA-C AT-AC ATA-C AT-AC ATA-C ATA
431352 ATTAAATTTA
Statistics
Matches: 183, Mismatches: 23, Indels: 49
0.72 0.09 0.19
Matches are distributed among these distances:
2 2 0.01
3 19 0.10
4 116 0.63
5 44 0.24
6 2 0.01
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (4 bp):
ATAC
Found at i:431196 original size:44 final size:44
Alignment explanation
Indices: 431138--431300 Score: 150
Period size: 44 Copynumber: 3.9 Consensus size: 44
431128 CATGATATAT
*
431138 ATATATATATATATCATACATATATATCATACATTAATACATAC
1 ATATATATACATATCATACATATATATCATACATTAATACATAC
* * *
431182 ATAGATATACATATCATACATATATATGATAC----ACACATATC
1 ATATATATACATATCATACATATATATCATACATTAATACATA-C
* * *
431223 ATATATAT-CAT-TCATACATACAT-GCATGCATTAATA-AT--
1 ATATATATACATATCATACATATATATCATACATTAATACATAC
*
431261 ATATACATACATATCATACATA-ATGATACATACATTAATA
1 ATATATATACATATCATACATATAT-AT-CATACATTAATA
431301 AATTATACAT
Statistics
Matches: 96, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
38 10 0.10
39 16 0.17
40 18 0.19
41 10 0.10
42 13 0.14
44 29 0.30
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (44 bp):
ATATATATACATATCATACATATATATCATACATTAATACATAC
Found at i:431228 original size:2 final size:2
Alignment explanation
Indices: 431132--431208 Score: 50
Period size: 2 Copynumber: 38.0 Consensus size: 2
431122 TACATACATG
* *
431132 AT AT AT AT AT AT AT AT AT AT CAT AC AT AT AT AT CAT AC AT -T A-
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT -AT AT AT AT AT
* * * * *
431174 AT AC AT AC AT AG AT AT AC AT AT CAT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
431209 GATACACACA
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
1 2 0.04
2 48 0.86
3 6 0.11
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:431280 original size:66 final size:65
Alignment explanation
Indices: 431152--431346 Score: 159
Period size: 66 Copynumber: 2.9 Consensus size: 65
431142 ATATATATAT
* *
431152 CATACATATATATCATACATTAATACATACATAGATATACATATCATACATATATATGATACACA
1 CATACATATATATCATACATTAATACATACATAGATATACATATCATACATACATATCATACACA
* *
431217 CATATCATATATATCATTCA-TACATACATGCAT-GCATTAATA-ATAT-ATACATACATATCAT
1 CATA-CATATATATCATACATTA-ATACATACATAG-A-T-ATACATATCATACATACATATCAT
*
431278 ACATAA
61 ACA-CA
* * * * * *
431284 TGATACATACAT-TAATAAATT-ATACATACATACATAGTACATATCATAACATATCATAACATA
1 -CATACATATATATCATACATTAATACATACATAGATA-TACATATCAT-ACATA-CATATCATA
431347 TCATAATTAA
Statistics
Matches: 103, Mismatches: 13, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
63 1 0.01
64 3 0.03
65 21 0.20
66 46 0.45
67 18 0.17
68 14 0.14
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (65 bp):
CATACATATATATCATACATTAATACATACATAGATATACATATCATACATACATATCATACACA
Found at i:439683 original size:2 final size:2
Alignment explanation
Indices: 439676--439723 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
439666 TAAAAACATA
439676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
439718 AT AT AT
1 AT AT AT
439724 GTATGTATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:440254 original size:21 final size:20
Alignment explanation
Indices: 440228--440272 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
440218 CAGTTGAGCT
*
440228 TTCTGTTACAAGCTGTTATGC
1 TTCTGTT-CAAGCTGTTATGA
*
440249 TTCTGTTTAAGCTGTTATGA
1 TTCTGTTCAAGCTGTTATGA
440269 TTCT
1 TTCT
440273 ATTTCAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.49
Consensus pattern (20 bp):
TTCTGTTCAAGCTGTTATGA
Found at i:443186 original size:54 final size:54
Alignment explanation
Indices: 443127--443239 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 54
443117 TCAGTATTAC
*
443127 TAATAACTCTGCCCCCGATACTGGTCACAGTCAGCAAGCA-GTTGCTCCATCAAA
1 TAATAACTCTGCCCCCGATACTGGTCACAGTCAGCAAG-ATGTTACTCCATCAAA
443181 TAATAACTCTGCCCCCGATACTGGTCACAGTCAGCAAGATGTTACTCCATCAAA
1 TAATAACTCTGCCCCCGATACTGGTCACAGTCAGCAAGATGTTACTCCATCAAA
443235 TAATA
1 TAATA
443240 CAAGAGTACT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
53 1 0.02
54 56 0.98
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (54 bp):
TAATAACTCTGCCCCCGATACTGGTCACAGTCAGCAAGATGTTACTCCATCAAA
Found at i:445345 original size:21 final size:20
Alignment explanation
Indices: 445320--445364 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
445310 CAGTTGAGCT
445320 TTCTGTTACAAGCTGTTATGC
1 TTCTGTT-CAAGCTGTTATGC
*
445341 TTCTGTTTAAGCTGTTATGC
1 TTCTGTTCAAGCTGTTATGC
445361 TTCT
1 TTCT
445365 ATTTTAGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (20 bp):
TTCTGTTCAAGCTGTTATGC
Found at i:445768 original size:2 final size:2
Alignment explanation
Indices: 445761--445799 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
445751 TAACATCGGA
445761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
445800 CACTAGTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:446559 original size:17 final size:17
Alignment explanation
Indices: 446537--446570 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
446527 TCATAATGGT
446537 CCTTCACCATTATGATC
1 CCTTCACCATTATGATC
446554 CCTTCACCATTATGATC
1 CCTTCACCATTATGATC
446571 ATTGCACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.35
Consensus pattern (17 bp):
CCTTCACCATTATGATC
Found at i:453140 original size:2 final size:2
Alignment explanation
Indices: 453131--453163 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
453121 CATTTAAAAA
453131 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
453164 TATGCATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:463428 original size:45 final size:47
Alignment explanation
Indices: 463377--463465 Score: 146
Period size: 45 Copynumber: 1.9 Consensus size: 47
463367 TCGAATAAAT
*
463377 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGATTAGGATTTATTTTTGTGAACAA
*
463422 GCATGCGAATTAGATATCATGCGATTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGATTAGGATTTATTTTTGTGAA
463466 TAACAAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 27 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGATTAGGATTTATTTTTGTGAACAA
Found at i:473120 original size:17 final size:18
Alignment explanation
Indices: 473085--473122 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
473075 AGAAAAAATG
**
473085 AAAACAAAAATGATGGAA
1 AAAACAAAAATGAAAGAA
473103 AAAACAAAAA-GAAAGAA
1 AAAACAAAAATGAAAGAA
473120 AAA
1 AAA
473123 GAAGAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAACAAAAATGAAAGAA
Found at i:473162 original size:6 final size:7
Alignment explanation
Indices: 473145--473178 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
473135 AAAGGGAATA
473145 AAAAATG
1 AAAAATG
473152 AAAAATG
1 AAAAATG
*
473159 AAAAAGAG
1 AAAAA-TG
473167 AAAAATG
1 AAAAATG
473174 AAAAA
1 AAAAA
473179 AAGAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:473169 original size:15 final size:15
Alignment explanation
Indices: 473144--473184 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
473134 AAAAGGGAAT
*
473144 AAAAAATGAAAAATG
1 AAAAAAAGAAAAATG
*
473159 AAAAAGAGAAAAATG
1 AAAAAAAGAAAAATG
473174 AAAAAAAGAAA
1 AAAAAAAGAAA
473185 TAAAATGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (15 bp):
AAAAAAAGAAAAATG
Found at i:473189 original size:18 final size:17
Alignment explanation
Indices: 473159--473192 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
473149 ATGAAAAATG
*
473159 AAAAAGAGAAAAATGAA
1 AAAAAGAAAAAAATGAA
473176 AAAAAGAAATAAAATGA
1 AAAAAGAAA-AAAATGA
473193 GGGTTCAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAAAAATGAA
Found at i:474569 original size:51 final size:51
Alignment explanation
Indices: 474508--474987 Score: 527
Period size: 51 Copynumber: 9.2 Consensus size: 51
474498 AAATTCGTTT
*
474508 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
474559 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * *
474610 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGATAATTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
474661 GTTGAAGATTGAGTCATATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* ** *
474712 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* ** *
474763 GTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * * **
474819 GTTGAAGATTGTTCGAGTTCTGTACTCTCTGATA-GAATAGAGAGCGGACCCGTTC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGA-AGGAATAGGGAGCGGACAAGTTC
* * *
474874 GTTGAAGATTGTTTGAGTCC--TGCTCTCTGAAGGAATAGGGAGCGGACATGTTT
1 GTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * * * * *
474927 ATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGAC-ACTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
474977 GTTGAAGATTG
1 GTTGAAGATTG
474988 TTTGAGTCTT
Statistics
Matches: 384, Mismatches: 35, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
49 6 0.02
50 12 0.03
51 222 0.58
52 1 0.00
53 33 0.09
54 2 0.01
55 53 0.14
56 54 0.14
57 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:475049 original size:53 final size:53
Alignment explanation
Indices: 474938--475072 Score: 157
Period size: 53 Copynumber: 2.5 Consensus size: 53
474928 TTGAAGATCG
* ** **
474938 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACACTTTGTTGAAGATTGTTTG
1 AGTCTTATACTCCCTGAACGAATA-GGAGAAGACACTTTGTCCAAGATTGTTCA
*
474992 AGTCTTATACTCCCTGAATG-ATAGGAGAAGACACGTTTG-CCAAGGATTGTTCA
1 AGTCTTATACTCCCTGAACGAATAGGAGAAGACAC-TTTGTCCAA-GATTGTTCA
* *
475045 AGTCTTATACTTCCTGAAGGAATAGGAG
1 AGTCTTATACTCCCTGAACGAATAGGAG
475073 CAGCTCGTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
52 12 0.17
53 32 0.46
54 26 0.37
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (53 bp):
AGTCTTATACTCCCTGAACGAATAGGAGAAGACACTTTGTCCAAGATTGTTCA
Found at i:488378 original size:12 final size:14
Alignment explanation
Indices: 488355--488387 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
488345 TTTGTTGGTT
488355 TTTGTGACATACA-
1 TTTGTGACATACAG
488368 TTTGT-ACATACAG
1 TTTGTGACATACAG
488381 TTTGTGA
1 TTTGTGA
488388 TATGGGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 10 0.56
14 1 0.06
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (14 bp):
TTTGTGACATACAG
Found at i:488737 original size:32 final size:32
Alignment explanation
Indices: 488701--488763 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
488691 TATATGATAC
*
488701 TCATCAC-TTTAAGTGATATGGCACATACCATA
1 TCATCACTTTTAA-TGACATGGCACATACCATA
*
488733 TCATCACTTTTAATGACATGTCACATACCAT
1 TCATCACTTTTAATGACATGGCACATACCAT
488764 GTTAACATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (32 bp):
TCATCACTTTTAATGACATGGCACATACCATA
Found at i:493364 original size:57 final size:57
Alignment explanation
Indices: 493260--493373 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 57
493250 CTCTACTCCA
** *
493260 ACATTTACAGTTTCACCTCCATTTATTTGAACAGAGGCAGGGATTTTCTTCAGCTGC
1 ACATTTACAGTTTCACCTCCATTTATTTGAACAGAACCAGGGATTTTCCTCAGCTGC
* * * *
493317 ACATTTTCAGTTTCACCTCCATTTGTTTGAACAGATACCA-GGCTTTTCCTCGGCTGC
1 ACATTTACAGTTTCACCTCCATTTATTTGAACAGA-ACCAGGGATTTTCCTCAGCTGC
493374 TCTTCAACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
57 47 0.96
58 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (57 bp):
ACATTTACAGTTTCACCTCCATTTATTTGAACAGAACCAGGGATTTTCCTCAGCTGC
Found at i:496988 original size:22 final size:21
Alignment explanation
Indices: 496974--497016 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
496964 ATATTGTTTA
*
496974 TATACATATAT-TATATTAAT
1 TATAAATATATATATATTAAT
*
496994 TATAAATATATATATATTTAT
1 TATAAATATATATATATTAAT
497015 TA
1 TA
497017 CTTATTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TATAAATATATATATATTAAT
Found at i:498375 original size:23 final size:23
Alignment explanation
Indices: 498344--498409 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
498334 TTTTATTATT
* *
498344 TTTATTTTATTTATACATATTCTA
1 TTTA-TTTATATATATATATTCTA
* * *
498368 TTTATTTATCTATTTTTATTCTA
1 TTTATTTATATATATATATTCTA
*
498391 CTTATTTATATATATATAT
1 TTTATTTATATATATATAT
498410 ATATATATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 30 0.88
24 4 0.12
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTATTTATATATATATATTCTA
Found at i:498868 original size:12 final size:12
Alignment explanation
Indices: 498851--498875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
498841 TATTTCCTCT
498851 TTATTATTATCA
1 TTATTATTATCA
498863 TTATTATTATCA
1 TTATTATTATCA
498875 T
1 T
498876 AGACTTTTTA
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:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTATTATCA
Found at i:501448 original size:31 final size:31
Alignment explanation
Indices: 501413--501472 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
501403 CTTAAAAATC
501413 ATTTAACTTAATTTGTTATATCGAAATATTT
1 ATTTAACTTAATTTGTTATATCGAAATATTT
501444 ATTTAACTTAATTTGTTATATCGAAATAT
1 ATTTAACTTAATTTGTTATATCGAAATAT
501473 CAAAATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (31 bp):
ATTTAACTTAATTTGTTATATCGAAATATTT
Found at i:503782 original size:95 final size:95
Alignment explanation
Indices: 503666--503928 Score: 350
Period size: 95 Copynumber: 2.7 Consensus size: 95
503656 AGATTATAAT
* *
503666 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGCCTCAGCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTA
*
503731 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
65 TGGATAAGATTCAGCTAACCTGATAAAGGTG
* *
503762 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCAGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTAT
*
503827 GGATAATATTCAGCTAACCTGATAAAGGTG
66 GGATAAGATTCAGCTAACCTGATAAAGGTG
* * * * **
503857 ATTATAATATCTATACAATTATA--TTAAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGC
1 ATTAT-A-A--TATACAA-TAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGC
503920 TTTATGGAT
61 TTTATGGAT
503929 TCAGCTAGCC
Statistics
Matches: 150, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
95 88 0.59
96 7 0.05
97 1 0.01
98 44 0.29
99 7 0.05
100 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTAT
GGATAAGATTCAGCTAACCTGATAAAGGTG
Found at i:505147 original size:84 final size:84
Alignment explanation
Indices: 505006--506218 Score: 1452
Period size: 84 Copynumber: 14.5 Consensus size: 84
504996 TTCATTATTT
* * *
505006 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
* * *
505071 CTCAGCTCTAAGGCGCAAC
66 CTCAGCTCCAAGGCACATC
* * *
505090 ATTTGCAGCATAGCTCAAGGCTATAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
505155 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * *
505174 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAAAACCTTCGAGTTTGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
*
505239 ATCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * ** * * *
505258 ATTTACATCATAACTAAAGGCTAGAAGGGTAATCTATCAA-TAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
* *
505322 CTCAGCTCAAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * * * * * *
505341 ATTTGTAGCATTACTTAAGTCGAGAAGGGCTATATGCCAACCAAAGACCTTCAAGTTCGACTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
505406 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
*
505425 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
*
505490 CTCAGCTCCAAGGAACATC
66 CTCAGCTCCAAGGCACATC
* * * * * * *
505509 ATTTACAGCATAACTAAAGGCTAGAAGGGTTATCTGTCAAC-AAATACCTTCAAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
505573 CTCAGCT-CAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * * * *
505591 A-TTGCAGCA-AAGCTTAAGTCGAGAAGGGCTATCTACCAACCAAAGACCTTCGAGTTTGACTAC
1 ATTTGCAGCATAA-CTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
* *
505654 GCTCAACTCCAAGGCACATT
65 GCTCAGCTCCAAGGCACATC
* *
505674 ATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
*
505739 CTCAGCTCCAAGGAACATC
66 CTCAGCTCCAAGGCACATC
* ** * * * ** *
505758 ATTTGTAGCATAGTTTAAGTCGAGAAGGACTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
505823 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* *
505842 ATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
* *
505907 CTCAGCTCCAAGGAAGATC
66 CTCAGCTCCAAGGCACATC
* * * * *
505926 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAA-ACCTTTGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
*
505990 CTCAGCTCAAAGGCACAT-
66 CTCAGCTCCAAGGCACATC
* * * * * * * * *
506008 ATTTGCAGTATAGCTTAAGTCAAGAAGGGCTATCTGCCATC-AAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
* * *
506072 TTCAGCTCAAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * *
506091 ATTTGCATCATAACTCAAGGCTAGAAGAGTTATCTGCCAATAAAAGACCTGCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
*
506156 CTCAGCTCAAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * * * *
506175 ATTTACAACATAGCTTAAGGCAAGAAGGGCTATCTGTCAACAAA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
506219 TTTATCGAGT
Statistics
Matches: 959, Mismatches: 161, Indels: 18
0.84 0.14 0.02
Matches are distributed among these distances:
80 2 0.00
81 32 0.03
82 101 0.11
83 162 0.17
84 660 0.69
85 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (84 bp):
ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:505817 original size:417 final size:417
Alignment explanation
Indices: 505006--506215 Score: 1696
Period size: 417 Copynumber: 2.9 Consensus size: 417
504996 TTCATTATTT
* * *
505006 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
* ** * * * * * *
505071 CTCAGCTCTAAGGCGCAACATTTGCAGCATAGCTCAAGGCTATAAGGGCTATCTGCCAACAAAAG
66 CTCAGCTCCAAGGAACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAA-
* * * * * *
505136 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAA-CTCAAGGCTAGAA
130 ACCTTCGAGTTCGATTACACTCAGCT-CAAGGCACATCATTTGCAGCA-AAGCTTAAGTCAAGAA
* * * * *
505200 GGGTTATATGCCAACAAAAAACCTTCGAGTTTGACTACGATCAGCTCCAAGGCACATCATTTACA
193 GGGCTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGATCAGCTCCAAGGCACATCATTTGCA
* * * *
505265 TCATAACTAAAGGCTAGAAGGGTAATCTATCAATAAAGACCTTCGAGTTCGATTACACTCAGCTC
258 TCATAACTCAAGGCTAGAAGGGTTATCTACCAAAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
505330 AAAGGCATATCATTTGTAGCATTA-CTTAAGTCGAGAAGGGCTATATGCCAACCAAAGACCTTCA
323 AAAGGCACATCATTTGTAGCA-TAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCA
505394 AGTTCGACTACACTCAGCTCCAAGGCACATC
387 AGTTCGACTACACTCAGCTCCAAGGCACATC
*
505425 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
* *
505490 CTCAGCTCCAAGGAACATCATTTACAGCATAACTAAAGGCTAGAAGGGTTATCTGTCAACAAATA
66 CTCAGCTCCAAGGAACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAA
* *
505555 CCTTCAAGTTCGATTACACTCAGCTCAAGGCACATCA-TTGCAGCAAAGCTTAAGTCGAGAAGGG
131 CCTTCGAGTTCGATTACACTCAGCTCAAGGCACATCATTTGCAGCAAAGCTTAAGTCAAGAAGGG
* * * *
505619 CTATCTACCAACCAAAGACCTTCGAGTTTGACTACGCTCAACTCCAAGGCACATTATTTGCAGT-
196 CTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGATCAGCTCCAAGGCACATCATTTGCA-TC
* * *
505683 ATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
260 ATAACTCAAGGCTAGAAGGGTTATCTACCAA-AAAAGACCTTCGAGTTCGATTACACTCAGCTCA
* * * *
505748 AAGGAACATCATTTGTAGCATAGTTTAAGTCGAGAAGGACTATCTGCCAACCAAAGACCTTCGAG
324 AAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCAAG
*
505813 TTCGACTACGCTCAGCTCCAAGGCACATC
389 TTCGACTACACTCAGCTCCAAGGCACATC
* *
505842 ATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
*
505907 CTCAGCTCCAAGGAAGATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAA
66 CTCAGCTCCAAGGAACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAA
* * *
505972 CCTTTGAGTTCGATTACACTCAGCTCAAAGGCACAT-ATTTGCAGTATAGCTTAAGTCAAGAAGG
131 CCTTCGAGTTCGATTACACTCAGCTC-AAGGCACATCATTTGCAGCAAAGCTTAAGTCAAGAAGG
* * * * *
506036 GCTATCTGCC-ATCAAAGACCTTCGAGTTCGATTAC-ATTCAGCTCAAAGGCATATCATTTGCAT
195 GCTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGA-TCAGCTCCAAGGCACATCATTTGCAT
* * *
506099 CATAACTCAAGGCTAGAAGAGTTATCTGCCAATAAAAGACCTGCGAGTTCGATTACACTCAGCTC
259 CATAACTCAAGGCTAGAAGGGTTATCTACCAA-AAAAGACCTTCGAGTTCGATTACACTCAGCTC
** * * * *
506164 AAAGGCACATCATTTACAACATAGCTTAAGGCAAGAAGGGCTATCTGTCAAC
323 AAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAC
506216 AAATTTATCG
Statistics
Matches: 702, Mismatches: 81, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
415 2 0.00
416 104 0.15
417 418 0.60
418 64 0.09
419 114 0.16
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (417 bp):
ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGAACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAA
CCTTCGAGTTCGATTACACTCAGCTCAAGGCACATCATTTGCAGCAAAGCTTAAGTCAAGAAGGG
CTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGATCAGCTCCAAGGCACATCATTTGCATCA
TAACTCAAGGCTAGAAGGGTTATCTACCAAAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAA
GGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCAAGTT
CGACTACACTCAGCTCCAAGGCACATC
Found at i:506728 original size:22 final size:21
Alignment explanation
Indices: 506703--506744 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
506693 CATATATTGT
*
506703 TTATATACATATATTATATTAA
1 TTATAAACATATATT-TATTAA
*
506725 TTATAAATATATATTTATTA
1 TTATAAACATATATTTATTA
506745 CTTGTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAAACATATATTTATTAA
Found at i:507826 original size:13 final size:14
Alignment explanation
Indices: 507808--507838 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
507798 CCCTTAACAG
507808 TTTAATTTCTT-TT
1 TTTAATTTCTTATT
507821 TTTAATTTCTTATT
1 TTTAATTTCTTATT
507835 TTTA
1 TTTA
507839 TCTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTAATTTCTTATT
Found at i:507951 original size:25 final size:24
Alignment explanation
Indices: 507874--507945 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 24
507864 TTTTATTTCA
507874 TTTTTCATTAGTATTTATATATT-TT
1 TTTTTCATT--TATTTATATATTATT
* *
507899 TTTTT-ATTTATTTTCTGTATTATT
1 TTTTTCATTTA-TTTATATATTATT
507923 TTTTTCATTTATTTAT-TATTATT
1 TTTTTCATTTATTTATATATTATT
507946 ACTTTTCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.05
23 15 0.37
24 14 0.34
25 10 0.24
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.72
Consensus pattern (24 bp):
TTTTTCATTTATTTATATATTATT
Found at i:507994 original size:17 final size:17
Alignment explanation
Indices: 507973--508019 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
507963 TATATTATAC
507973 ATATATATATATTTGGT
1 ATATATATATATTTGGT
* *
507990 TTATATCAT-TATTTTGT
1 ATATAT-ATATATTTGGT
508007 ATATATATATATT
1 ATATATATATATT
508020 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 2 0.08
17 21 0.84
18 2 0.08
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (17 bp):
ATATATATATATTTGGT
Found at i:508078 original size:2 final size:2
Alignment explanation
Indices: 508066--508105 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
508056 CTATTTTTAT
508066 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
508106 TACTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:508426 original size:9 final size:9
Alignment explanation
Indices: 508412--508493 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 9
508402 ACATTCTTTG
508412 TATTTTTTT
1 TATTTTTTT
508421 TA-TTTTTT
1 TATTTTTTT
*
508429 TATGTTTATTCC
1 TAT-TTT-TT-T
*
508441 TATTTCTTT
1 TATTTTTTT
*
508450 TATTTATTT
1 TATTTTTTT
* *
508459 CATTTGTTT
1 TATTTTTTT
*
508468 TAGTTTTTT
1 TATTTTTTT
*
508477 TA-ATTTTT
1 TATTTTTTT
*
508485 AATTTTTTT
1 TATTTTTTT
508494 GTACATATGT
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
8 14 0.25
9 30 0.54
10 5 0.09
11 4 0.07
12 3 0.05
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.76
Consensus pattern (9 bp):
TATTTTTTT
Found at i:509571 original size:11 final size:11
Alignment explanation
Indices: 509555--509587 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
509545 TAAGAGTTTG
509555 TCTCTTCTCCT
1 TCTCTTCTCCT
509566 TCTCTTCTCCCT
1 TCTCTTCT-CCT
509578 T-TCTTCTCCT
1 TCTCTTCTCCT
509588 CTCCCTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 14 0.67
12 4 0.19
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (11 bp):
TCTCTTCTCCT
Found at i:509583 original size:16 final size:16
Alignment explanation
Indices: 509564--509596 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
509554 GTCTCTTCTC
*
509564 CTTCTCTTCTCCCTTT
1 CTTCTCCTCTCCCTTT
509580 CTTCTCCTCTCCCTTT
1 CTTCTCCTCTCCCTTT
509596 C
1 C
509597 GTTGATCGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (16 bp):
CTTCTCCTCTCCCTTT
Found at i:512984 original size:28 final size:26
Alignment explanation
Indices: 512940--512995 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
512930 TATGCAGAAT
*
512940 TAAATATAAATATAAAAGATAAATAAA
1 TAAATATAAATAGAAAAGAT-AATAAA
* *
512967 TAAATTATATATAGAAAATATAATAAA
1 TAAA-TATAAATAGAAAAGATAATAAA
512994 TA
1 TA
512996 TTATATCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (26 bp):
TAAATATAAATAGAAAAGATAATAAA
Found at i:513805 original size:20 final size:21
Alignment explanation
Indices: 513761--513820 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
513751 TAATATTTCT
* * *
513761 AATAATATAATATTATAATAA
1 AATAAAATAAGATTATATTAA
* *
513782 AATAAAATCA-ATTATATTAT
1 AATAAAATAAGATTATATTAA
*
513802 AATAATATAAGATTATATT
1 AATAAAATAAGATTATATT
513821 TTTATTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AATAAAATAAGATTATATTAA
Found at i:513923 original size:26 final size:25
Alignment explanation
Indices: 513877--513928 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
513867 AATTTCATAG
513877 AAATAATATTATTAAATTATTATAAT
1 AAATAATATTATTAAATTATT-TAAT
*
513903 AAATAATATTATT-TATATATTTAAT
1 AAATAATATTATTAAAT-TATTTAAT
513928 A
1 A
513929 TTAATCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATAATATTATTAAATTATTTAAT
Found at i:513973 original size:23 final size:23
Alignment explanation
Indices: 513953--513997 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
513943 TAATATATTT
513953 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
513976 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
513998 TATAACACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:514098 original size:31 final size:33
Alignment explanation
Indices: 514034--514098 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 33
514024 TTAATATAAT
* *
514034 TTAATATTTTTATTTCAATAAAATATACCAATA
1 TTAATATTTTTAATTCAATAAAATATACAAATA
514067 TTAATA-TTTTAATT-AATAAAATTATA-AAATA
1 TTAATATTTTTAATTCAATAAAA-TATACAAATA
514098 T
1 T
514099 ATTTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 12 0.41
32 11 0.38
33 6 0.21
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (33 bp):
TTAATATTTTTAATTCAATAAAATATACAAATA
Found at i:514101 original size:33 final size:34
Alignment explanation
Indices: 514032--514106 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 34
514022 AATTAATATA
* **
514032 ATTTAATATTTTTATTTCAATAAAATATACCAAT
1 ATTTAATATTTTTAATTCAATAAAATATAAAAAT
514066 A-TTAATA-TTTTAATT-AATAAAATTATAAAATAT
1 ATTTAATATTTTTAATTCAATAAAA-TATAAAA-AT
514099 ATTTAATA
1 ATTTAATA
514107 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
31 7 0.20
32 12 0.34
33 9 0.26
34 7 0.20
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (34 bp):
ATTTAATATTTTTAATTCAATAAAATATAAAAAT
Found at i:514192 original size:23 final size:21
Alignment explanation
Indices: 514110--514190 Score: 56
Period size: 26 Copynumber: 3.6 Consensus size: 21
514100 TTTAATAATA
* *
514110 AATAAATTATTTTAATATTTT
1 AATAAATAATTTTATTATTTT
* *
514131 AA-AAACAATTATATTATTTAT
1 AATAAATAATTTTATTATTT-T
*
514152 GATAAAATAATTATTTTATTATTTGT
1 AAT-AAAT-A--ATTTTATTATTT-T
514178 AATAAATAATTTT
1 AATAAATAATTTT
514191 TAAAAAAACT
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
20 13 0.29
21 4 0.09
22 5 0.11
23 3 0.07
24 2 0.04
25 4 0.09
26 14 0.31
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (21 bp):
AATAAATAATTTTATTATTTT
Done.