Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014498.1 Kokia drynarioides strain JFW-HI SEQ_129537, 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: 566721
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 27 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1716 original size:72 final size:72
Alignment explanation
Indices: 1595--1742 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
1585 GAAATATGGC
1595 AATT-TAATTATGTTAAACAAGGGTAAAAATGTAAATTAGTAAATAAAGCATAATAAGGAAAAAC
1 AATTATAATTATGTTAAACAAGGGTAAAAATGTAAATTAGTAAATAAAGCATAATAAGGAAAAAC
1659 CTTAGGA
66 CTTAGGA
1666 AATTATAATTATGTTAAACAAGGGTAAAAATGTAAATTAGTAAATAAAGCATAATAAGGAAAAAC
1 AATTATAATTATGTTAAACAAGGGTAAAAATGTAAATTAGTAAATAAAGCATAATAAGGAAAAAC
1731 CTTAGGA
66 CTTAGGA
1738 AATTA
1 AATTA
1743 GTCTTCTTCT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 4 0.05
72 72 0.95
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.27
Consensus pattern (72 bp):
AATTATAATTATGTTAAACAAGGGTAAAAATGTAAATTAGTAAATAAAGCATAATAAGGAAAAAC
CTTAGGA
Found at i:2516 original size:25 final size:25
Alignment explanation
Indices: 2488--2594 Score: 92
Period size: 25 Copynumber: 4.2 Consensus size: 25
2478 TTCGGCTCGA
*
2488 AAGAGCGATATTCTATCTAGCTCAT
1 AAGAGCGATATTCTATCTGGCTCAT
*
2513 AAGAGC-ATTATTCTGTCTGGCTCAT
1 AAGAGCGA-TATTCTATCTGGCTCAT
* * * *
2538 AAAAGCGTTTTTCTTTCTGGCTCAT
1 AAGAGCGATATTCTATCTGGCTCAT
* * *
2563 AAGAGTGATAATT-TATTTGGTCTCGT
1 AAGAGCGAT-ATTCTATCTGG-CTCAT
2589 AAGAGC
1 AAGAGC
2595 TAAACTTTGT
Statistics
Matches: 64, Mismatches: 14, Indels: 7
0.75 0.16 0.08
Matches are distributed among these distances:
24 1 0.02
25 52 0.81
26 11 0.17
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (25 bp):
AAGAGCGATATTCTATCTGGCTCAT
Found at i:4476 original size:21 final size:21
Alignment explanation
Indices: 4452--4491 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4442 AACCACGTCT
4452 CCACAAAATTTTTAACAATCC
1 CCACAAAATTTTTAACAATCC
*
4473 CCACTAAATTTTTAACAAT
1 CCACAAAATTTTTAACAAT
4492 TTTGCATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (21 bp):
CCACAAAATTTTTAACAATCC
Found at i:4881 original size:116 final size:116
Alignment explanation
Indices: 4677--4911 Score: 461
Period size: 116 Copynumber: 2.0 Consensus size: 116
4667 AGTTCAGGTT
4677 AATGATTTTTTTATCATCACGAAATAATTAGAAAGTAAATTCTGCGTATATTATTCAACATAGTC
1 AATGATTTTTTTATCATCACGAAATAATTAGAAAGTAAATTCTGCGTATATTATTCAACATAGTC
4742 AAAGCAATCCAACACCTTTGCGTGTCAAAATAATTAAAAATAAATTTTGAA
66 AAAGCAATCCAACACCTTTGCGTGTCAAAATAATTAAAAATAAATTTTGAA
4793 AATGATTTTTTTATCATCACGAAATAATTAGAAAGTAAATTCTGCGTATATTATTCAACATAGTC
1 AATGATTTTTTTATCATCACGAAATAATTAGAAAGTAAATTCTGCGTATATTATTCAACATAGTC
*
4858 AAAGCAATCCAACACCTTTGCGTGTCAAAATAATTAAAAATATATTTTGAA
66 AAAGCAATCCAACACCTTTGCGTGTCAAAATAATTAAAAATAAATTTTGAA
4909 AAT
1 AAT
4912 TTTTGTTGGG
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (116 bp):
AATGATTTTTTTATCATCACGAAATAATTAGAAAGTAAATTCTGCGTATATTATTCAACATAGTC
AAAGCAATCCAACACCTTTGCGTGTCAAAATAATTAAAAATAAATTTTGAA
Found at i:33483 original size:22 final size:22
Alignment explanation
Indices: 33456--33511 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
33446 GAAAAGGATT
33456 AAAATTAAATTATAATTTTTAA
1 AAAATTAAATTATAATTTTTAA
33478 AAAATTAAATTATAATTTTTAA
1 AAAATTAAATTATAATTTTTAA
33500 AAAATTAAATTA
1 AAAATTAAATTA
33512 AAATCATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTAAATTATAATTTTTAA
Found at i:33543 original size:25 final size:23
Alignment explanation
Indices: 33456--33545 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 23
33446 GAAAAGGATT
*
33456 AAAATTAAA-TTATAATTTTTAA
1 AAAATTAAATTTATCATTTTTAA
*
33478 AAAATTAAA-TTATAATTTTTAA
1 AAAATTAAATTTATCATTTTTAA
*
33500 AAAATTAAATTAAAATCATTTTTAA
1 AAAATTAAATT--TATCATTTTTAA
*
33525 AAAGTTAACATTTATTCATTT
1 AAAATTAA-ATTTA-TCATTT
33546 AAAATTTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
22 31 0.53
23 1 0.02
24 1 0.02
25 23 0.39
26 3 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (23 bp):
AAAATTAAATTTATCATTTTTAA
Found at i:33573 original size:18 final size:19
Alignment explanation
Indices: 33542--33579 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
33532 ACATTTATTC
**
33542 ATTTAAAATTTTAAA-AAA
1 ATTTAAAAACTTAAATAAA
33560 ATTTAAAAACTTAAATAAA
1 ATTTAAAAACTTAAATAAA
33579 A
1 A
33580 AATTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTTAAAAACTTAAATAAA
Found at i:33949 original size:38 final size:38
Alignment explanation
Indices: 33907--33985 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
33897 ACTTTTTTTC
*
33907 AAATATTTTTATTTTGATTTCA-CATTATATTATCATTT
1 AAATATTTTTATTTT-ATTTCAGAATTATATTATCATTT
* *
33945 AAATATTTTTATTTTATTTTAGAATTATATTATCTTTT
1 AAATATTTTTATTTTATTTCAGAATTATATTATCATTT
33983 AAA
1 AAA
33986 ATCTTTACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (38 bp):
AAATATTTTTATTTTATTTCAGAATTATATTATCATTT
Found at i:34153 original size:14 final size:14
Alignment explanation
Indices: 34129--34170 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
34119 AATTCATCAC
*
34129 TTAATTTTTCAATGT
1 TTAA-TTTTCAATAT
34144 TTAATTTTCAATAT
1 TTAATTTTCAATAT
34158 TTAAATTTTCAAT
1 TT-AATTTTCAAT
34171 TAATCAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (14 bp):
TTAATTTTCAATAT
Found at i:37184 original size:16 final size:16
Alignment explanation
Indices: 37159--37290 Score: 57
Period size: 16 Copynumber: 7.3 Consensus size: 16
37149 CTAAATAATC
37159 AGGCTATGTGCCTAGT
1 AGGCTATGTGCCTAGT
* *
37175 AGGCTTTGTGCCGGTGTATT
1 AGGCTATGTGCC----TAGT
*
37195 CAGGCTATGTGTCTAGT
1 -AGGCTATGTGCCTAGT
* *
37212 AGGCTTTGTGCCGGTGTATT
1 AGGCTATGTGCC----TAGT
37232 CAGGCTATGTGCCTAGT
1 -AGGCTATGTGCCTAGT
* * *
37249 AGGCTTTGAGCCGGTGTATT
1 AGGCTATGTGCC----TAGT
37269 CAGGCTATGTGCCTAGT
1 -AGGCTATGTGCCTAGT
37286 AGGCT
1 AGGCT
37291 TCGTGCTGGT
Statistics
Matches: 85, Mismatches: 16, Indels: 30
0.65 0.12 0.23
Matches are distributed among these distances:
16 36 0.42
17 9 0.11
20 9 0.11
21 31 0.36
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.34
Consensus pattern (16 bp):
AGGCTATGTGCCTAGT
Found at i:37198 original size:37 final size:37
Alignment explanation
Indices: 37157--37374 Score: 298
Period size: 37 Copynumber: 5.9 Consensus size: 37
37147 ATCTAAATAA
37157 TCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTAT
1 TCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTAT
*
37194 TCAGGCTATGTGTCTAGTAGGCTTTGTGCCGGTGTAT
1 TCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTAT
*
37231 TCAGGCTATGTGCCTAGTAGGCTTTGAGCCGGTGTAT
1 TCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTAT
* *
37268 TCAGGCTATGTGCCTAGTAGGCTTCGTGCTGGTGT-T
1 TCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTAT
* * ** **
37304 TCAGGCTATGAGCCTAGTAGG-TTTCATGTTGGTAAAT
1 TCAGGCTATGTGCCTAGTAGGCTTT-GTGCCGGTGTAT
*
37341 TC-GAGCTATGTGTCTAGTAGGCTTTGTGCCGGTG
1 TCAG-GCTATGTGCCTAGTAGGCTTTGTGCCGGTG
37375 ATCCAAGAAT
Statistics
Matches: 159, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
35 2 0.01
36 28 0.18
37 126 0.79
38 3 0.02
ACGTcount: A:0.15, C:0.17, G:0.32, T:0.35
Consensus pattern (37 bp):
TCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTAT
Found at i:37205 original size:21 final size:21
Alignment explanation
Indices: 37175--37281 Score: 81
Period size: 21 Copynumber: 5.6 Consensus size: 21
37165 TGTGCCTAGT
*
37175 AGGCTTTGTGCCGGTGTATTC
1 AGGCTATGTGCCGGTGTATTC
* *
37196 AGGCTATGT----GTCTAGT-
1 AGGCTATGTGCCGGTGTATTC
*
37212 AGGCTTTGTGCCGGTGTATTC
1 AGGCTATGTGCCGGTGTATTC
*
37233 AGGCTATGTGCC----TAGT-
1 AGGCTATGTGCCGGTGTATTC
* *
37249 AGGCTTTGAGCCGGTGTATTC
1 AGGCTATGTGCCGGTGTATTC
37270 AGGCTATGTGCC
1 AGGCTATGTGCC
37282 TAGTAGGCTT
Statistics
Matches: 63, Mismatches: 13, Indels: 20
0.66 0.14 0.21
Matches are distributed among these distances:
16 18 0.29
17 8 0.13
20 8 0.13
21 29 0.46
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.35
Consensus pattern (21 bp):
AGGCTATGTGCCGGTGTATTC
Found at i:44488 original size:16 final size:16
Alignment explanation
Indices: 44463--44527 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
44453 CTAAATATTC
*
44463 AGGCTATGTGCCTAGT
1 AGGCTTTGTGCCTAGT
*
44479 AGGCTTTGTGCCAGTGTATTT
1 AGGCTTTGTGCC----TA-GT
44500 AGG-TTATGTGCCTAGT
1 AGGCTT-TGTGCCTAGT
44516 AGGCTTTGTGCC
1 AGGCTTTGTGCC
44528 GGTGTATTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
16 21 0.54
17 4 0.10
20 4 0.10
21 10 0.26
ACGTcount: A:0.15, C:0.17, G:0.31, T:0.37
Consensus pattern (16 bp):
AGGCTTTGTGCCTAGT
Found at i:44508 original size:37 final size:37
Alignment explanation
Indices: 44458--44631 Score: 267
Period size: 37 Copynumber: 4.7 Consensus size: 37
44448 TGCATCTAAA
*
44458 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
44495 TATTTAGGTTATGTGCCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
** * *
44532 TATTCAGGAAATGTGCCTATTAGGCTTTGTGCCGGTA
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
44569 TATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
44606 TTTTCAGGCTATGTGCCTAGTAGGCT
1 TATTCAGGCTATGTGCCTAGTAGGCT
44632 CCATGCTGGT
Statistics
Matches: 123, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 123 1.00
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:44577 original size:21 final size:20
Alignment explanation
Indices: 44516--44622 Score: 61
Period size: 21 Copynumber: 5.6 Consensus size: 20
44506 TGTGCCTAGT
*
44516 AGGCTTTGTGCCGGTGTATTC
1 AGGCTATGTGCCGGT-TATTC
**
44537 AGGAAATGTGCC---TATT-
1 AGGCTATGTGCCGGTTATTC
*
44553 AGGCTTTGTGCCGGTATATTC
1 AGGCTATGTGCCGGT-TATTC
*
44574 AGGCTATGTGCC---TAGT-
1 AGGCTATGTGCCGGTTATTC
*
44590 AGGCT-TCGTGCCGGTGTTTTC
1 AGGCTAT-GTGCCGGT-TATTC
44611 AGGCTATGTGCC
1 AGGCTATGTGCC
44623 TAGTAGGCTC
Statistics
Matches: 64, Mismatches: 10, Indels: 24
0.65 0.10 0.24
Matches are distributed among these distances:
15 1 0.02
16 19 0.30
17 7 0.11
20 6 0.09
21 30 0.47
22 1 0.02
ACGTcount: A:0.15, C:0.20, G:0.31, T:0.35
Consensus pattern (20 bp):
AGGCTATGTGCCGGTTATTC
Found at i:44654 original size:37 final size:37
Alignment explanation
Indices: 44459--44662 Score: 149
Period size: 37 Copynumber: 5.5 Consensus size: 37
44449 GCATCTAAAT
*** * **
44459 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTGT
1 ATTCAGGCTATGTGCCTAGTAGGCTCCATGCCGGTAA
* * *** **
44496 ATTTAGGTTATGTGCCTAGTAGGCTTTGTGCCGGTGT
1 ATTCAGGCTATGTGCCTAGTAGGCTCCATGCCGGTAA
** * *** *
44533 ATTCAGGAAATGTGCCTATTAGGCTTTGTGCCGGTAT
1 ATTCAGGCTATGTGCCTAGTAGGCTCCATGCCGGTAA
* * **
44570 ATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
1 ATTCAGGCTATGTGCCTAGTAGGCTCCATGCCGGTAA
* *
44607 TTTCAGGCTATGTGCCTAGTAGGCTCCATGCTGGTAA
1 ATTCAGGCTATGTGCCTAGTAGGCTCCATGCCGGTAA
*
44644 ATTC-GAGCTATGTGTCTAG
1 ATTCAG-GCTATGTGCCTAG
44663 CAGACTTTGT
Statistics
Matches: 145, Mismatches: 21, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
36 1 0.01
37 144 0.99
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.35
Consensus pattern (37 bp):
ATTCAGGCTATGTGCCTAGTAGGCTCCATGCCGGTAA
Found at i:44654 original size:74 final size:74
Alignment explanation
Indices: 44458--44662 Score: 205
Period size: 74 Copynumber: 2.8 Consensus size: 74
44448 TGCATCTAAA
** *** * ** * * *
44458 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTGTATTTAGGTTATGTGCCTAGTAGGCTTT
1 TATTCAGGAAATGTGCCTAGTAGGCTCCATGCCGGTAAATTCAGGCTATGTGCCTAGTAGGCTTC
44523 GTGCCGGTG
66 GTGCCGGTG
* *** *
44532 TATTCAGGAAATGTGCCTATTAGGCTTTGTGCCGGTATATTCAGGCTATGTGCCTAGTAGGCTTC
1 TATTCAGGAAATGTGCCTAGTAGGCTCCATGCCGGTAAATTCAGGCTATGTGCCTAGTAGGCTTC
44597 GTGCCGGTG
66 GTGCCGGTG
* ** * *
44606 TTTTCAGGCTATGTGCCTAGTAGGCTCCATGCTGGTAAATTC-GAGCTATGTGTCTAG
1 TATTCAGGAAATGTGCCTAGTAGGCTCCATGCCGGTAAATTCAG-GCTATGTGCCTAG
44663 CAGACTTTGT
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
73 1 0.01
74 111 0.99
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36
Consensus pattern (74 bp):
TATTCAGGAAATGTGCCTAGTAGGCTCCATGCCGGTAAATTCAGGCTATGTGCCTAGTAGGCTTC
GTGCCGGTG
Found at i:44671 original size:111 final size:111
Alignment explanation
Indices: 44457--44679 Score: 270
Period size: 111 Copynumber: 2.0 Consensus size: 111
44447 TTGCATCTAA
* * *
44457 ATATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTGTATTTAGGTTATGTGCCTAGTAGGCTT
1 ATATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTGTATTTAGGCTATGTGCCTAGTAGGCTC
** ** ** *
44522 TGTGCCGGTGTATTCAGGAAATGTGCCTATTAGGCTTTGTGCCGGT
66 CATGCCGGTAAATTCAGGAAATGTGCCTAGCAGACTTTGTGCCGGT
*
44568 ATATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT-TTTCAGGCTATGTGCCTAGTAGGCT
1 ATATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTGTATTT-AGGCTATGTGCCTAGTAGGCT
* ** * *
44632 CCATGCTGGTAAATTC-GAGCTATGTGTCTAGCAGACTTTGTGTCGGT
65 CCATGCCGGTAAATTCAG-GAAATGTGCCTAGCAGACTTTGTGCCGGT
44679 A
1 A
44680 ATCCAAGAGT
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
110 4 0.04
111 90 0.96
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.35
Consensus pattern (111 bp):
ATATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTGTATTTAGGCTATGTGCCTAGTAGGCTC
CATGCCGGTAAATTCAGGAAATGTGCCTAGCAGACTTTGTGCCGGT
Found at i:47174 original size:21 final size:21
Alignment explanation
Indices: 47150--47201 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
47140 TGAGACAATA
47150 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
** * *
47171 CTACTAAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
47192 CTACCGATAC
1 CTACCGATAC
47202 TAAAAACTCC
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:48851 original size:123 final size:122
Alignment explanation
Indices: 48711--48940 Score: 424
Period size: 123 Copynumber: 1.9 Consensus size: 122
48701 GCAAATAAGC
*
48711 TTTTTTGGTATTCTTACAAAATTATCCTTAACTTTTCATTTTTATTCAATTTAGTCCTTTAGCTC
1 TTTTTTGGTATTCTTACAAAATTATCCTTAACTTTTCATTTTTATTCAATTTAGTCATTTAGCTC
48776 AAAACTTGCAAATTAACCATTTTATTTTAATTTTTTTAGCTTGTCATATGTCTTTTAA
66 AAAACTTGCAAATTAACCATTTTATTTTAA-TTTTTTAGCTTGTCATATGTCTTTTAA
* *
48834 TTTTTTGGTATTTTTACAAAATTGTCCTTAACTTTTCATTTTTATTCAATTTAGTCATTTAGCTC
1 TTTTTTGGTATTCTTACAAAATTATCCTTAACTTTTCATTTTTATTCAATTTAGTCATTTAGCTC
48899 AAAACTTGCAAATTAACCATTTTATTTTAATTTTTTAGCTTG
66 AAAACTTGCAAATTAACCATTTTATTTTAATTTTTTAGCTTG
48941 CCGAATATTC
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
122 12 0.12
123 92 0.88
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (122 bp):
TTTTTTGGTATTCTTACAAAATTATCCTTAACTTTTCATTTTTATTCAATTTAGTCATTTAGCTC
AAAACTTGCAAATTAACCATTTTATTTTAATTTTTTAGCTTGTCATATGTCTTTTAA
Found at i:52575 original size:21 final size:21
Alignment explanation
Indices: 52549--52637 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 21
52539 ACAATATTAT
52549 CGATACAAGTATGGCTTCTAC
1 CGATACAAGTATGGCTTCTAC
52570 CGATACAAGTATGGCTTCTAC
1 CGATACAAGTATGGCTTCTAC
* *
52591 CGATACAAGTATGACTTCTAT
1 CGATACAAGTATGGCTTCTAC
* *
52612 CGAAACATGTCAT-GCTTCTAC
1 CGATACAAGT-ATGGCTTCTAC
52633 C-ATAC
1 CGATAC
52638 TAAAAACTCC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
20 3 0.05
21 55 0.92
22 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (21 bp):
CGATACAAGTATGGCTTCTAC
Found at i:61828 original size:25 final size:22
Alignment explanation
Indices: 61788--61834 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 22
61778 TTTATTATTA
*
61788 TTATTTATATTCTAATTAATTT
1 TTATTTATATTCTAATAAATTT
61810 TTATATTATATTACTTAATAAATTT
1 TTAT-TTATATT-C-TAATAAATTT
61835 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 7 0.33
24 1 0.05
25 9 0.43
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTATATTCTAATAAATTT
Found at i:62952 original size:3 final size:3
Alignment explanation
Indices: 62944--62995 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
62934 TTCTTATTTA
* * *
62944 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TTT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
62992 TAT T
1 TAT T
62996 TAGTTTTCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:62996 original size:12 final size:12
Alignment explanation
Indices: 62899--62995 Score: 83
Period size: 12 Copynumber: 8.2 Consensus size: 12
62889 TGATTTTCGT
62899 TTATTA-TTTTA
1 TTATTATTTTTA
*
62910 TTATTTACTTTTTG
1 TTA-TTA-TTTTTA
* *
62924 TT-TT-CTTTAA
1 TTATTATTTTTA
* *
62934 TTCTTATTTATA
1 TTATTATTTTTA
*
62946 TTATTATTATTA
1 TTATTATTTTTA
*
62958 TTATTATTATTA
1 TTATTATTTTTA
62970 TTATTATTTTTA
1 TTATTATTTTTA
*
62982 TTTTTATTTTTA
1 TTATTATTTTTA
62994 TT
1 TT
62996 TAGTTTTCGT
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.07
11 5 0.07
12 53 0.77
14 6 0.09
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (12 bp):
TTATTATTTTTA
Found at i:68435 original size:17 final size:17
Alignment explanation
Indices: 68410--68443 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
68400 AGTTTTTCAA
68410 ATTTTTATG-ATTTTTT
1 ATTTTTATGAATTTTTT
68426 ATTTTATATGAATTTTTT
1 ATTTT-TATGAATTTTTT
68444 TATCTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
ATTTTTATGAATTTTTT
Found at i:68451 original size:28 final size:29
Alignment explanation
Indices: 68411--68465 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
68401 GTTTTTCAAA
*
68411 TTTTTATGATTTTT-TATTTTATATGAATT
1 TTTTTATGATTTTTAGATTTT-TATGAATT
*
68440 TTTTTAT-CTTTTTAGATTTTTATGAA
1 TTTTTATGATTTTTAGATTTTTATGAA
68466 GTACACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (29 bp):
TTTTTATGATTTTTAGATTTTTATGAATT
Found at i:68459 original size:17 final size:17
Alignment explanation
Indices: 68411--68460 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
68401 GTTTTTCAAA
68411 TTTTTATGATTTTTTAT
1 TTTTTATGATTTTTTAT
*
68428 TTTATATGAATTTTTTTAT
1 TTTTTATG-A-TTTTTTAT
68447 CTTTTTA-GATTTTT
1 -TTTTTATGATTTTT
68461 ATGAAGTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 12 0.43
18 2 0.07
19 9 0.32
20 5 0.18
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTTTATGATTTTTTAT
Found at i:87284 original size:41 final size:41
Alignment explanation
Indices: 87170--87316 Score: 186
Period size: 41 Copynumber: 3.5 Consensus size: 41
87160 ACTAGATGTA
* * *
87170 TAAATGGAAGACTCATGTCTCGGGATGAGCTTGAGATTATGT
1 TAAA-GGAAGACTCATGTCTCGGAATGAGCATGAGATTATAT
* * *
87212 ATAAATGGAAGACTCGTGACTCAGAATGAGCATGAGATTATAT
1 -TAAA-GGAAGACTCATGTCTCGGAATGAGCATGAGATTATAT
* * *
87255 TAAGGGAAGACTCATGTCTCGGAAGGAGCATGAGACTATAT
1 TAAAGGAAGACTCATGTCTCGGAATGAGCATGAGATTATAT
87296 TAAAGGAAGACTCATGTCTCG
1 TAAAGGAAGACTCATGTCTCG
87317 AAAAAAGAGT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 52 0.57
42 3 0.03
43 36 0.40
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGGAATGAGCATGAGATTATAT
Found at i:87330 original size:41 final size:41
Alignment explanation
Indices: 87240--87334 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
87230 ACTCAGAATG
* * * **
87240 AGCATGAGATTATATTAAGGGAAGACTCATGTCTCGGAAGG
1 AGCATGAGACTATATTAAAGGAAGACTCATGTCTCGAAAAA
87281 AGCATGAGACTATATTAAAGGAAGACTCATGTCTCGAAAAA
1 AGCATGAGACTATATTAAAGGAAGACTCATGTCTCGAAAAA
87322 AG-AGTGAGACTAT
1 AGCA-TGAGACTAT
87335 GTTTAATGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.02
41 47 0.98
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (41 bp):
AGCATGAGACTATATTAAAGGAAGACTCATGTCTCGAAAAA
Found at i:92161 original size:43 final size:43
Alignment explanation
Indices: 92113--92199 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
92103 TTCTTCTTCC
92113 TTCTCTTCTCTTCTCTCTTCTTCCTCTTCAACACCCATAAAGG
1 TTCTCTTCTCTTCTCTCTTCTTCCTCTTCAACACCCATAAAGG
92156 TTCTCTTCTCTTCTCTCTTCTTCCTCTTCAACACCCATAAAGG
1 TTCTCTTCTCTTCTCTCTTCTTCCTCTTCAACACCCATAAAGG
92199 T
1 T
92200 AATAGTTGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.16, C:0.37, G:0.05, T:0.43
Consensus pattern (43 bp):
TTCTCTTCTCTTCTCTCTTCTTCCTCTTCAACACCCATAAAGG
Found at i:98310 original size:18 final size:18
Alignment explanation
Indices: 98287--98332 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
98277 TGCATCTAAT
98287 TGCATCTGATTATGTGAC
1 TGCATCTGATTATGTGAC
** * *
98305 TGCATCCAAGTATGTGAT
1 TGCATCTGATTATGTGAC
98323 TGCATCTGAT
1 TGCATCTGAT
98333 CAGGCTACGC
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (18 bp):
TGCATCTGATTATGTGAC
Found at i:102343 original size:20 final size:20
Alignment explanation
Indices: 102318--102361 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
102308 AAGCATGCTA
102318 TTCCTAGTCTACTAGAATCC
1 TTCCTAGTCTACTAGAATCC
102338 TTCCTAGTCTACTAGAATCC
1 TTCCTAGTCTACTAGAATCC
102358 TTCC
1 TTCC
102362 ATAAGTGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (20 bp):
TTCCTAGTCTACTAGAATCC
Found at i:104359 original size:21 final size:20
Alignment explanation
Indices: 104334--104372 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
104324 TAGCAATATT
104334 TCTTTTTCTTTTCTCTTTTTC
1 TCTTTTTCTTTTC-CTTTTTC
104355 TCTTTTTCTTTTCCTTTT
1 TCTTTTTCTTTTCCTTTT
104373 CTCATTCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TCTTTTTCTTTTCCTTTTTC
Found at i:107342 original size:15 final size:15
Alignment explanation
Indices: 107317--107351 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
107307 GCATAAAATT
*
107317 TAAAA-TGAAACAAG
1 TAAAAGTGAAACAAA
107331 TAAAAGTGAAACAAA
1 TAAAAGTGAAACAAA
107346 TAAAAG
1 TAAAAG
107352 AAAATGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.66, C:0.06, G:0.14, T:0.14
Consensus pattern (15 bp):
TAAAAGTGAAACAAA
Found at i:125191 original size:34 final size:34
Alignment explanation
Indices: 125134--125199 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
125124 ATATATATGG
*
125134 AAATGCAATGACAATGTAGATGCAGCGACAATAA
1 AAATGCAATGACAATATAGATGCAGCGACAATAA
* *
125168 AAATGCAATGACATTAATA-ATGCAGGGACAAT
1 AAATGCAATGACAAT-ATAGATGCAGCGACAAT
125200 TATACTACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAGCGACAATAA
Found at i:125566 original size:97 final size:97
Alignment explanation
Indices: 125391--125593 Score: 390
Period size: 97 Copynumber: 2.1 Consensus size: 97
125381 TGTGGATTGC
*
125391 TCCTCAA-CGGCAGGCATCATAGCCTCTGCCTAACTCGCTTCAGGTGGTGCCAAATCATCAGATG
1 TCCTCAACCAGCAGGCATCATAGCCTCTGCCTAACTCGCTTCAGGTGGTGCCAAATCATCAGATG
125455 ATGCATCCACAAGTTCAAGTGCGGTGACAAAT
66 ATGCATCCACAAGTTCAAGTGCGGTGACAAAT
125487 TCCTCAACCAGCAGGCATCATAGCCTCTGCCTAACTCGCTTCAGGTGGTGCCAAATCATCAGATG
1 TCCTCAACCAGCAGGCATCATAGCCTCTGCCTAACTCGCTTCAGGTGGTGCCAAATCATCAGATG
125552 ATGCATCCACAAGTTCAAGTGCGGTGACAAAT
66 ATGCATCCACAAGTTCAAGTGCGGTGACAAAT
125584 TCCTCAACCA
1 TCCTCAACCA
125594 AATTTGTCGT
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
96 7 0.07
97 98 0.93
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (97 bp):
TCCTCAACCAGCAGGCATCATAGCCTCTGCCTAACTCGCTTCAGGTGGTGCCAAATCATCAGATG
ATGCATCCACAAGTTCAAGTGCGGTGACAAAT
Found at i:155653 original size:20 final size:20
Alignment explanation
Indices: 155628--155677 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
155618 AACACCAAAA
155628 ATATTTTTTTTCAAATTCTC
1 ATATTTTTTTTCAAATTCTC
155648 ATATTTTTTTTCAAATTCTC
1 ATATTTTTTTTCAAATTCTC
155668 ATATTTTTTT
1 ATATTTTTTT
155678 ATATCAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTTTTTTTCAAATTCTC
Found at i:164668 original size:30 final size:29
Alignment explanation
Indices: 164632--164695 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
164622 AGAAATTACA
* *
164632 ATTTAGTCATTAAATTATTC-GAAAGTTTT
1 ATTTAGTCACTAAACTATTCAG-AAGTTTT
*
164661 CATTTAGTCACTGAACTATTCAGAAGTTTT
1 -ATTTAGTCACTAAACTATTCAGAAGTTTT
164691 ATTTA
1 ATTTA
164696 ATTCTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 5 0.17
30 24 0.80
31 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (29 bp):
ATTTAGTCACTAAACTATTCAGAAGTTTT
Found at i:166033 original size:4 final size:4
Alignment explanation
Indices: 166024--166058 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
166014 TTGAAGGTAA
*
166024 AAAG AAAG AAAA AAGAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AA
166059 GAAGAAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:171028 original size:20 final size:20
Alignment explanation
Indices: 171003--171047 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
170993 AGTCAGCTTA
171003 TACAAAATACTATATGAAGG
1 TACAAAATACTATATGAAGG
171023 TACAAAATACTATATGAAGG
1 TACAAAATACTATATGAAGG
171043 TACAA
1 TACAA
171048 CCCGAATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.24
Consensus pattern (20 bp):
TACAAAATACTATATGAAGG
Found at i:176307 original size:4 final size:4
Alignment explanation
Indices: 176275--176372 Score: 52
Period size: 4 Copynumber: 25.8 Consensus size: 4
176265 ACACTTAATT
* *
176275 TTTA TTTA ATTA -TTA TTT- TTTCA -TTA TTTA TTTA TTT- TTGA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA
* * *
176320 -TT- TTTA CTTTA TATT- TATA TTTA TTTA TTT- TTTGA TTGA TAT- TTTA
1 TTTA TTTA -TTTA T-TTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA
176366 TTTA TTT
1 TTTA TTT
176373 GTTATTAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 26
0.67 0.08 0.24
Matches are distributed among these distances:
3 19 0.26
4 45 0.62
5 8 0.11
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:176352 original size:28 final size:27
Alignment explanation
Indices: 176303--176372 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
176293 TTTCATTATT
* *
176303 TATTTATTTTTGATTTATTTTT-ACTTTA
1 TATTTATATTT-ATTTATTTTTGA-TTGA
176331 TATTTATATTTATTTATTTTTTGATTGA
1 TATTTATATTTATTTA-TTTTTGATTGA
176359 TATTT-TATTTATTT
1 TATTTATATTTATTT
176373 GTTATTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 14 0.37
28 23 0.61
29 1 0.03
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.71
Consensus pattern (27 bp):
TATTTATATTTATTTATTTTTGATTGA
Found at i:178492 original size:19 final size:19
Alignment explanation
Indices: 178465--178511 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
178455 CAAAGAAAAA
*
178465 GGTTCATATATTTTCTCTC
1 GGTTTATATATTTTCTCTC
*
178484 GGTTTATATATTTTCTCTT
1 GGTTTATATATTTTCTCTC
*
178503 AGTTTATAT
1 GGTTTATAT
178512 GGATTGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (19 bp):
GGTTTATATATTTTCTCTC
Found at i:187027 original size:49 final size:49
Alignment explanation
Indices: 186972--187579 Score: 366
Period size: 49 Copynumber: 12.3 Consensus size: 49
186962 AAAGTTGAAG
* *
186972 AGGGAAAGATTAAAGCGGCAACGACGAA-CTTTACACTCTAAAATAGAAA
1 AGGGAAAGATTAAAGCCGCAACGACGAATC-TTACACCCTAAAATAGAAA
* * * * *
187021 AAGGAAATATTAAAACCGCAACGGCGAATCTTACA-CCTAAAAAATGAAGA
1 AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCTAAAATA-GAA-A
* * *
187071 A-GG-AAGATTAAAGCCACAACGACGAATCTTACACCCTAAAACCA-AAG
1 AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCTAAAA-TAGAAA
* ** * * *
187118 AGGAAAAGATTAAAGTTG-TACTG-CGAATCTTACACCCTAAAATTGAAG
1 AGGGAAAGATTAAAGCCGCAAC-GACGAATCTTACACCCTAAAATAGAAA
* * * * * *
187166 AGGGAAGGATTAAAGCCGCAATGGCGAATCTTGCACTCTAAAATCGAAA
1 AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCTAAAATAGAAA
* * *
187215 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCA-AAA
1 AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCTAAAA-TAGAAA
* * * **
187264 AGGGAAAGATTAAAGCCGTAACAACAAATCTTACACTTTAAAATCA-AAA
1 AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCTAAAAT-AGAAA
** * * * *
187313 GAGGGAAAGATTAAAGTTGTAACGATGAATCTTACA-CCTGAAAACCA-AAG
1 -AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCT-AAAA-TAGAAA
* * * * *
187363 AGGGAAAGAGTAAAGCCACAATGACTAATCTTACACCCTAAAAT--TAA
1 AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCTAAAATAGAAA
* * * ** * *
187410 AGTGGTATAGATTAAAGCCACAATGAAAAATCTTACACCTTAAAAAAACTGAAA
1 AG-GG-AAAGATTAAAGCCGCAACGACGAATCTTACACCCT-AAAATA--GAAA
* * * * * * *
187464 AGAGACATATTAAAGCCACAACGATGAATCTTACTCCTTAAAACTA-AAGA
1 AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCTAAAA-TAGAA-A
* * * * *
187514 AGGG-CAGATTAAAGCTGTAACGAC-AAGTCTTACACCCTTAAAAAATTGAAT
1 AGGGAAAGATTAAAGCCGCAACGACGAA-TCTTACACCC-T--AAAATAGAAA
*
187565 AGGGATAGATTAAAG
1 AGGGAAAGATTAAAG
187580 TTGCAATGGT
Statistics
Matches: 436, Mismatches: 91, Indels: 61
0.74 0.15 0.10
Matches are distributed among these distances:
47 4 0.01
48 79 0.18
49 241 0.55
50 53 0.12
51 9 0.02
52 45 0.10
53 1 0.00
54 4 0.01
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.19
Consensus pattern (49 bp):
AGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCCTAAAATAGAAA
Found at i:187381 original size:148 final size:145
Alignment explanation
Indices: 187002--187405 Score: 438
Period size: 148 Copynumber: 2.8 Consensus size: 145
186992 ACGACGAACT
* * * * * *
187002 TTACACTCTAAAATAGAAA-AAGGAAATATTAAAACCGCAACGGCGAATCTTACACCTAAAA-AA
1 TTACACCCTAAAATA-AAAGAGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCTAAAACCA
* * *
187065 TGAAGAAGG-AAGATTAAAGCCACAACGACGAATCTTACACCCTAAAACCAAAGAGGAAAAGATT
65 --AAGAGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGAAAAGATT
** ** *
187129 AAAGTTGTACTGCGAATC
128 AAAGCCGTACAACAAATC
** * * * * *
187147 TTACACCCTAAAATTGAAGAGGGAAGGATTAAAGCCGCAATGGCGAATCTTGCACTCTAAAATCG
1 TTACACCCTAAAATAAAAGAGGGAAAGATTAAAGCCGCAACGACGAATCTTACAC-CTAAAA-CC
*
187212 AAA-AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGGAAAGATTA
64 AAAGAGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGAAAAGATTA
187276 AAGCCGTAACAACAAATC
129 AAGCCGT-ACAACAAATC
** ** * *
187294 TTACACTTTAAAATCAAAAGAGGGAAAGATTAAAGTTGTAACGATGAATCTTACACCTGAAAACC
1 TTACACCCTAAAAT-AAAAGAGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCT-AAAACC
* *
187359 AAAGAGGGAAAGAGTAAAGCCACAATGACTAATCTTACACCCTAAAA
64 AAAGAGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAA
187406 TTAAAGTGGT
Statistics
Matches: 216, Mismatches: 34, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
144 2 0.01
145 46 0.21
146 66 0.31
147 25 0.12
148 77 0.36
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (145 bp):
TTACACCCTAAAATAAAAGAGGGAAAGATTAAAGCCGCAACGACGAATCTTACACCTAAAACCAA
AGAGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGAAAAGATTAAA
GCCGTACAACAAATC
Found at i:187393 original size:99 final size:99
Alignment explanation
Indices: 186969--187406 Score: 394
Period size: 97 Copynumber: 4.5 Consensus size: 99
186959 CCTAAAGTTG
** * *
186969 AAGAGGGAAAGATTAAAGCGGCAACGACGAA-CTTTACACTCTAAAAT-AGAAA-AAGGAAATAT
1 AAGAGGGAAAGATTAAAGCCACAACGACGAATC-TTACACTCTAAAATCA-AAAGAGGGAAAGAT
*** * * *
187031 TAAAACCGCAACGGCGAATCTTACA-CCTAAAA-AA
64 TAAAGTTGTAACGACGAATCTTACACCCTAAAACCA
* * * *
187065 TGAAGAAGG-AAGATTAAAGCCACAACGACGAATCTTACACCCTAAAA-CCAAAGAGGAAAAGAT
1 --AAGAGGGAAAGATTAAAGCCACAACGACGAATCTTACACTCTAAAATCAAAAGAGGGAAAGAT
***
187128 TAAAGTTGT-ACTG-CGAATCTTACACCCTAAAATTG
64 TAAAGTTGTAAC-GACGAATCTTACACCCTAAAACCA
* * * * * *
187163 AAGAGGGAAGGATTAAAGCCGCAATGGCGAATCTTGCACTCTAAAATCGAAA-AGGGAAAGATTA
1 AAGAGGGAAAGATTAAAGCCACAACGACGAATCTTACACTCTAAAATCAAAAGAGGGAAAGATTA
**** *
187227 AAGCCACAATGACGAATCTTACACCCTAAAACCA
66 AAGTTGTAACGACGAATCTTACACCCTAAAACCA
* ** * * *
187261 AAAAGGGAAAGATTAAAGCCGTAACAACAAATCTTACACTTTAAAATCAAAAGAGGGAAAGATTA
1 AAGAGGGAAAGATTAAAGCCACAACGACGAATCTTACACTCTAAAATCAAAAGAGGGAAAGATTA
*
187326 AAGTTGTAACGATGAATCTTACA-CCTGAAAACCA
66 AAGTTGTAACGACGAATCTTACACCCT-AAAACCA
* * * *
187360 AAGAGGGAAAGAGTAAAGCCACAATGACTAATCTTACACCCTAAAAT
1 AAGAGGGAAAGATTAAAGCCACAACGACGAATCTTACACTCTAAAAT
187407 TAAAGTGGTA
Statistics
Matches: 272, Mismatches: 56, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
96 22 0.08
97 100 0.37
98 76 0.28
99 74 0.27
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (99 bp):
AAGAGGGAAAGATTAAAGCCACAACGACGAATCTTACACTCTAAAATCAAAAGAGGGAAAGATTA
AAGTTGTAACGACGAATCTTACACCCTAAAACCA
Found at i:189227 original size:17 final size:17
Alignment explanation
Indices: 189207--189239 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
189197 TGGGATATAT
189207 TTTTAATTTA-TATTTAA
1 TTTT-ATTTATTATTTAA
189224 TTTTATTTATTATTTA
1 TTTTATTTATTATTTA
189240 TTATTGGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATTTATTATTTAA
Found at i:189476 original size:15 final size:15
Alignment explanation
Indices: 189456--189488 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
189446 TTTTGTTTCC
189456 ATTATTG-TATCTTAT
1 ATTATTGATAT-TTAT
189471 ATTATTGATATTTAT
1 ATTATTGATATTTAT
189486 ATT
1 ATT
189489 CCTAATTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTATTGATATTTAT
Found at i:189530 original size:26 final size:25
Alignment explanation
Indices: 189501--189568 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 25
189491 TAATTAACTA
*
189501 ATATTATTGTTATTATTACTATGATT
1 ATATTATT-TTATTATTACCATGATT
189527 ATATTACTATTTTATTTATTACCATGATT
1 ATA-T--TATTTTA-TTATTACCATGATT
*
189556 ATGTTATTTTATT
1 ATATTATTTTATT
189569 TAATTGTGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 2 0.06
26 10 0.28
27 1 0.03
28 4 0.11
29 19 0.53
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (25 bp):
ATATTATTTTATTATTACCATGATT
Found at i:190827 original size:32 final size:32
Alignment explanation
Indices: 190786--190849 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
190776 TAAATTCCTG
190786 AGGGTAACCTAACGTTGACGAGAAGGTAGCCT
1 AGGGTAACCTAACGTTGACGAGAAGGTAGCCT
190818 AGGGTAACCTAACGTTGACGAGAAGGTAGCCT
1 AGGGTAACCTAACGTTGACGAGAAGGTAGCCT
190850 TTCTCCTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (32 bp):
AGGGTAACCTAACGTTGACGAGAAGGTAGCCT
Found at i:196690 original size:40 final size:40
Alignment explanation
Indices: 196355--196948 Score: 405
Period size: 40 Copynumber: 14.7 Consensus size: 40
196345 ACTTTCATAA
* * * *
196355 TTCAATCTGCCCTC-TAGATGGGGTAAAAGATTGGATGG-C
1 TTCAATCTGCCC-CATGGTTGGGGTAAGAGATCGGATGGTC
* * *
196394 TTCAATATGCCCTC-TGGTT-AGGTAAAAAGATCGGATGGTC
1 TTCAATCTGCCC-CATGGTTGGGGT-AAGAGATCGGATGGTC
* * * *
196434 TTCAAGT-TACCCTC-TGGTTAGGTTAAAAGATCGGATGGTC
1 TTCAA-TCTGCCC-CATGGTTGGGGTAAGAGATCGGATGGTC
* * * * * * * *
196474 CTCAATCTACCCCATGGTTGGGATAAAAGTTTGGACGATC
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTC
* * * * *
196514 TAT-AATCTACCCCATGGTTGGGGTAATAGACCAGAGGGTC
1 T-TCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTC
* *
196554 TTCAATCTGCCTCATGGTTGGGGTAAGAGATCAGATGGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTC
* * **
196594 TTCAATTTGCGCTC-TGGTTAAGGTAAGAGATCGGATGGTC
1 TTCAATCTGC-CCCATGGTTGGGGTAAGAGATCGGATGGTC
* * *
196634 TTCAATCTGCCTCATGGTTGAGGTAAGAGATCGGAGGGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTC
* * *
196674 TTCAATCTACCCCATGGTTGGGGTAAGAGATTGAATGGTGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGAT-G-GTC
* ** * *
196716 TTCAATTTGCCCTGTGGTTGGGGTAAGAGATTGGATGGTGTT
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGAT-G-GTC
* * *
196758 TTCAATTTGCCCCATGGTTGGGGTGAGAGATCGAATGGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTC
** * * * *
196798 TTTGATCTGCCCCGTGGTTTGGGTAAGAGATTGAATGATGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATG--GTC
* ** * *
196840 TTCTATCTGCCCTGTGGTTGGGGTATGAGATCGAATGGTGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGAT-G-GTC
**** * *
196882 TTCAATCTGCGTTGTGGTTGGGGTAAAAGATC-AATGGTGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGAT-G-GTC
* *
196923 TTCAATCTGCCTCGTGGTTGGGGTAA
1 TTCAATCTGCCCCATGGTTGGGGTAA
196949 TCGAATCCGC
Statistics
Matches: 466, Mismatches: 74, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
38 3 0.01
39 35 0.08
40 251 0.54
41 42 0.09
42 134 0.29
43 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (40 bp):
TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTC
Found at i:196734 original size:42 final size:42
Alignment explanation
Indices: 196551--196948 Score: 345
Period size: 42 Copynumber: 9.7 Consensus size: 42
196541 AGACCAGAGG
* *
196551 GTCTTCAATCTG-CCTCATGGTTGGGGTAAGAGA-TCAGAT-G-
1 GTCTTCAATCTGCCCT-GTGGTTGGGGTAAGAGATTGA-ATGGT
* * * ** * *
196591 GTCTTCAATTTGCGCTCTGGTTAAGGTAAGAGATCGGAT-G-
1 GTCTTCAATCTGCCCTGTGGTTGGGGTAAGAGATTGAATGGT
* * * *
196631 GTCTTCAATCTG-CCTCATGGTTGAGGTAAGAGATCGGA-GG-
1 GTCTTCAATCTGCCCT-GTGGTTGGGGTAAGAGATTGAATGGT
* **
196671 GTCTTCAATCTACCCCATGGTTGGGGTAAGAGATTGAATGGT
1 GTCTTCAATCTGCCCTGTGGTTGGGGTAAGAGATTGAATGGT
* *
196713 GTCTTCAATTTGCCCTGTGGTTGGGGTAAGAGATTGGATGGT
1 GTCTTCAATCTGCCCTGTGGTTGGGGTAAGAGATTGAATGGT
* * ** * *
196755 GTTTTCAATTTGCCCCATGGTTGGGGTGAGAGATCGAAT-G-
1 GTCTTCAATCTGCCCTGTGGTTGGGGTAAGAGATTGAATGGT
** * * *
196795 GTCTTTGATCTGCCCCGTGGTTTGGGTAAGAGATTGAATGAT
1 GTCTTCAATCTGCCCTGTGGTTGGGGTAAGAGATTGAATGGT
* * *
196837 GTCTTCTATCTGCCCTGTGGTTGGGGTATGAGATCGAATGGT
1 GTCTTCAATCTGCCCTGTGGTTGGGGTAAGAGATTGAATGGT
** * *
196879 GTCTTCAATCTGCGTTGTGGTTGGGGTAAAAGA-TCAATGGT
1 GTCTTCAATCTGCCCTGTGGTTGGGGTAAGAGATTGAATGGT
196920 GTCTTCAATCTG-CCTCGTGGTTGGGGTAA
1 GTCTTCAATCTGCCCT-GTGGTTGGGGTAA
196949 TCGAATCCGC
Statistics
Matches: 295, Mismatches: 53, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
39 2 0.01
40 122 0.41
41 38 0.13
42 133 0.45
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.33
Consensus pattern (42 bp):
GTCTTCAATCTGCCCTGTGGTTGGGGTAAGAGATTGAATGGT
Found at i:196822 original size:124 final size:124
Alignment explanation
Indices: 196517--196948 Score: 473
Period size: 124 Copynumber: 3.5 Consensus size: 124
196507 GACGATCTAT
* * * *
196517 AATCTACCCCATGGTTGGGGTAATAGA-CCAGAGGGTCTTCAATCTGCCTCATGGTTGGGGTAAG
1 AATCTGCCCCATGGTTGGGGTAAGAGATCGA-AGGGTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * * **
196581 AGA-TCAGAT-G-GTCTTCAATTTGCGCTCTGGTTAAGGTAAGAGATCGGAT-G-GTCTTC
65 AGATTGA-ATGGTGTCTTCAATTTGCCCTGTGGTTGGGGTAAGAGATCGGATGGTGTCTTC
* * * *
196637 AATCTGCCTCATGGTTGAGGTAAGAGATCGGAGGGTCTTCAATCTACCCCATGGTTGGGGTAAGA
1 AATCTGCCCCATGGTTGGGGTAAGAGATCGAAGGGTCTTCAATCTGCCCCATGGTTGGGGTAAGA
* *
196702 GATTGAATGGTGTCTTCAATTTGCCCTGTGGTTGGGGTAAGAGATTGGATGGTGTTTTC
66 GATTGAATGGTGTCTTCAATTTGCCCTGTGGTTGGGGTAAGAGATCGGATGGTGTCTTC
* * * ** * *
196761 AATTTGCCCCATGGTTGGGGTGAGAGATCGAATGGTCTTTGATCTGCCCCGTGGTTTGGGTAAGA
1 AATCTGCCCCATGGTTGGGGTAAGAGATCGAAGGGTCTTCAATCTGCCCCATGGTTGGGGTAAGA
* * * * *
196826 GATTGAATGATGTCTTCTATCTGCCCTGTGGTTGGGGTATGAGATCGAATGGTGTCTTC
66 GATTGAATGGTGTCTTCAATTTGCCCTGTGGTTGGGGTAAGAGATCGGATGGTGTCTTC
**** * * *
196885 AATCTGCGTTGTGGTTGGGGTAAAAGATC-AATGGTGTCTTCAATCTGCCTCGTGGTTGGGGTAA
1 AATCTGCCCCATGGTTGGGGTAAGAGATCGAA-GG-GTCTTCAATCTGCCCCATGGTTGGGGTAA
196949 TCGAATCCGC
Statistics
Matches: 259, Mismatches: 45, Indels: 11
0.82 0.14 0.03
Matches are distributed among these distances:
120 59 0.23
121 4 0.02
122 34 0.13
123 3 0.01
124 134 0.52
125 25 0.10
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (124 bp):
AATCTGCCCCATGGTTGGGGTAAGAGATCGAAGGGTCTTCAATCTGCCCCATGGTTGGGGTAAGA
GATTGAATGGTGTCTTCAATTTGCCCTGTGGTTGGGGTAAGAGATCGGATGGTGTCTTC
Found at i:208925 original size:4 final size:4
Alignment explanation
Indices: 208916--208941 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
208906 AATATATCGC
208916 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
208942 CAGACTCGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:220175 original size:87 final size:86
Alignment explanation
Indices: 220030--220199 Score: 304
Period size: 87 Copynumber: 2.0 Consensus size: 86
220020 AGACGTAGTA
*
220030 AACAACTTCTAAGATAACACATTTCCAAAAGAGTTTTGAAATAGCCCTATAAAATCTATACCCCA
1 AACAACTTCTAAGATAACACATTTCCAAAAGAGTTTTGAAATAGCCCCATAAAATCTATACCCCA
220095 GACATCGAAAAGCTCTACGTC
66 GACATCGAAAAGCTCTACGTC
* *
220116 AACAACTTCTAAGATATACACATTTCCAAAAGAGTTTTGAAATGGCCCCATAAAATCTATATCCC
1 AACAACTTCTAAGATA-ACACATTTCCAAAAGAGTTTTGAAATAGCCCCATAAAATCTATACCCC
220181 AGACATCGAAAAGCTCTAC
65 AGACATCGAAAAGCTCTAC
220200 CTCCATGATG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 16 0.20
87 64 0.80
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.25
Consensus pattern (86 bp):
AACAACTTCTAAGATAACACATTTCCAAAAGAGTTTTGAAATAGCCCCATAAAATCTATACCCCA
GACATCGAAAAGCTCTACGTC
Found at i:236128 original size:76 final size:76
Alignment explanation
Indices: 236002--236154 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
235992 CTTGCGCACA
* *
236002 TATTAGAAGCCAATTGTCCTAATTGTGCTTCCAACGCTTGGATGAAAGAAGAATTTTCTTGCATA
1 TATTAGAAGCCAATTGTCCTAATTGTGCTTCCAAAGCTTGGATGAAAGAAGAATTTTCTTGCACA
236067 ATTGCTTCTGT
66 ATTGCTTCTGT
*
236078 TATTAGAAGCCAATTGTCCTAATTGTGCTTTCAAAGCTTGGATGAAAGAAGAATTTTCTTGCACA
1 TATTAGAAGCCAATTGTCCTAATTGTGCTTCCAAAGCTTGGATGAAAGAAGAATTTTCTTGCACA
236143 ATTGCTTCTGT
66 ATTGCTTCTGT
236154 T
1 T
236155 CTCGTAATAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (76 bp):
TATTAGAAGCCAATTGTCCTAATTGTGCTTCCAAAGCTTGGATGAAAGAAGAATTTTCTTGCACA
ATTGCTTCTGT
Found at i:240893 original size:21 final size:20
Alignment explanation
Indices: 240869--240915 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
240859 CGAACCGGGG
240869 ATCAAATTGTAAAAATTTAAA
1 ATCAAATTG-AAAAATTTAAA
* *
240890 ATCAAACTGATAAATTTAAA
1 ATCAAATTGAAAAATTTAAA
240910 AT-AAAT
1 ATCAAAT
240916 AAAAACTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.13
20 12 0.52
21 8 0.35
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (20 bp):
ATCAAATTGAAAAATTTAAA
Found at i:241732 original size:21 final size:20
Alignment explanation
Indices: 241708--241750 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
241698 GATTGTTTTT
241708 TGTTTT-TTCCTATTTGTCTTC
1 TGTTTTCTT-CTATTT-TCTTC
241729 TGTTTTGCTTCTATTTTCTTC
1 TGTTTT-CTTCTATTTTCTTC
241750 T
1 T
241751 TTGATGTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 12 0.60
22 6 0.30
23 2 0.10
ACGTcount: A:0.05, C:0.19, G:0.09, T:0.67
Consensus pattern (20 bp):
TGTTTTCTTCTATTTTCTTC
Found at i:258152 original size:159 final size:158
Alignment explanation
Indices: 257862--258152 Score: 456
Period size: 159 Copynumber: 1.8 Consensus size: 158
257852 GTAATGCTCA
* * *
257862 TGCTCACACGAGCTATGGGTCGAGATGTTAGGCTACACGATGCTGCTCACACAAGCTGTGGAGAA
1 TGCTCACACAAGCTATGGGTCGAGATATTAGGCTACACGATGCTGCTCACACAAGCTATGGAGAA
* *
257927 TCCGCAATAAATGTCGGATCTCAGCCATCAGTAGGACATCTAAGACCAACACACATATATCCTGT
66 TCCGCAATAAATGCCGGATCTCAGCCATCAGTAGGACATCTAAGACCAACACACATATAACCTGT
257992 AATGTTAACACGAGCTGTGAAGTGAGCC
131 AATGTTAACACGAGCTGTGAAGTGAGCC
* * *
258020 TGCTCACACAAGCTGTGGGTCTAGATATTAGGCTACACGATTGCTGCTCACACGAGCTATGGAGA
1 TGCTCACACAAGCTATGGGTCGAGATATTAGGCTACACGA-TGCTGCTCACACAAGCTATGGAGA
* * * * *
258085 ATCCGCAATAAATGCCGGATCTCAGCCATCGGTAGGACATCTAAGACTAGCACCCATATAACTTG
65 ATCCGCAATAAATGCCGGATCTCAGCCATCAGTAGGACATCTAAGACCAACACACATATAACCTG
258150 TAA
130 TAA
258153 ATCCCGAAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
158 36 0.30
159 83 0.70
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (158 bp):
TGCTCACACAAGCTATGGGTCGAGATATTAGGCTACACGATGCTGCTCACACAAGCTATGGAGAA
TCCGCAATAAATGCCGGATCTCAGCCATCAGTAGGACATCTAAGACCAACACACATATAACCTGT
AATGTTAACACGAGCTGTGAAGTGAGCC
Found at i:261575 original size:29 final size:28
Alignment explanation
Indices: 261543--261617 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
261533 AATCATAAAC
*
261543 CACAGACAGAGCACACAACAAATATGTAG
1 CACAGACAGAGCACACAAC-AACATGTAG
* * *
261572 CACAGATAAAAACACACAACAACATGTAG
1 CACAGA-CAGAGCACACAACAACATGTAG
261601 CACAGACAGAGACACAC
1 CACAGACAGAG-CACAC
261618 CTATAACAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.05
29 25 0.68
30 10 0.27
ACGTcount: A:0.51, C:0.27, G:0.15, T:0.08
Consensus pattern (28 bp):
CACAGACAGAGCACACAACAACATGTAG
Found at i:263048 original size:29 final size:29
Alignment explanation
Indices: 262993--263049 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
262983 CCTAAATTTT
* * * **
262993 ACTAAATTTCCAATTTAGTCCTTAAAATC
1 ACTAAACTTACAATTTAATCCCAAAAATC
263022 ACTAAACTTACAATTTAATCCCAAAAAT
1 ACTAAACTTACAATTTAATCCCAAAAAT
263050 TTAAAAATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (29 bp):
ACTAAACTTACAATTTAATCCCAAAAATC
Found at i:264605 original size:48 final size:48
Alignment explanation
Indices: 264551--264649 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
264541 ATTTTGTTTT
264551 CTGGTTCAGACTCCATTTTCAGATGCTTCTTCATTAGCAGCATTCTCA
1 CTGGTTCAGACTCCATTTTCAGATGCTTCTTCATTAGCAGCATTCTCA
264599 CTGGTTCAGACTCCATTTTCAGATGCTTCTTCATTAGCAGCATTCTCA
1 CTGGTTCAGACTCCATTTTCAGATGCTTCTTCATTAGCAGCATTCTCA
264647 CTG
1 CTG
264650 TTTTCTTGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.37
Consensus pattern (48 bp):
CTGGTTCAGACTCCATTTTCAGATGCTTCTTCATTAGCAGCATTCTCA
Found at i:269893 original size:2 final size:2
Alignment explanation
Indices: 269886--269916 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
269876 GGTGTCGTTT
269886 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
269917 TTTTATTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:278865 original size:41 final size:41
Alignment explanation
Indices: 278630--278897 Score: 259
Period size: 42 Copynumber: 6.4 Consensus size: 41
278620 CCGAGTCTTA
* * * ** * **
278630 AGTCTTCCTTTAAGCAAAATCTCATGTTCATATCGAGTCACA
1 AGTCTTCCTTTAA-TATAATCTCATGCTCATCCCGAGACATG
* * * * * *
278672 AGTCTTCCTTTAAAATATAACCTCATACTCCTTCTGAGTCATG
1 AGTCTTCCTTT--AATATAATCTCATGCTCATCCCGAGACATG
* * * *
278715 AGTCTTCCTTAAATAATAATCTCATGCTCTTCCCAAGTCATG
1 AGTCTTCCTTTAAT-ATAATCTCATGCTCATCCCGAGACATG
* *
278757 AGTCTTCCTTTTAACATAATCTCATGCTCATCCCGAGATATG
1 AGTCTTCC-TTTAATATAATCTCATGCTCATCCCGAGACATG
*
278799 AGTCTTCCTTTTAACATAATCTCATGCTCATCCCGAGACATG
1 AGTCTTCC-TTTAATATAATCTCATGCTCATCCCGAGACATG
* *
278841 AGTCTTCCTTTAATAT-ACCTTCATGCTCATCTCGAGACATG
1 AGTCTTCCTTTAATATAATC-TCATGCTCATCCCGAGACATG
278882 AGTCTTCCTTTAATAT
1 AGTCTTCCTTTAATAT
278898 GCATCAAGTG
Statistics
Matches: 193, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
40 2 0.01
41 46 0.24
42 112 0.58
43 31 0.16
44 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (41 bp):
AGTCTTCCTTTAATATAATCTCATGCTCATCCCGAGACATG
Found at i:281611 original size:57 final size:57
Alignment explanation
Indices: 281542--281657 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
281532 TAAGCATCCA
281542 TTGCCCTCAGTGCAAACAACAACTTCCGACTTAGGGCATCAGCAACAGCATTAGGCT
1 TTGCCCTCAGTGCAAACAACAACTTCCGACTTAGGGCATCAGCAACAGCATTAGGCT
*
281599 TTGCCCTCAGTGCAAACAACAACTTCCGATTTAGGGCATCAGCAACAGCATTAGGCT
1 TTGCCCTCAGTGCAAACAACAACTTCCGACTTAGGGCATCAGCAACAGCATTAGGCT
281656 TT
1 TT
281658 CCCGGATGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (57 bp):
TTGCCCTCAGTGCAAACAACAACTTCCGACTTAGGGCATCAGCAACAGCATTAGGCT
Found at i:286616 original size:21 final size:21
Alignment explanation
Indices: 286592--286644 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
286582 CTTGTTATAG
*
286592 TTCTACCGATACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
**
286613 TTCTGTCGATACAAGTCATAC
1 TTCTACCGATACAAGTCATAC
286634 TTCTACCGATA
1 TTCTACCGATA
286645 ATAAAAACTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:287271 original size:42 final size:42
Alignment explanation
Indices: 287208--287483 Score: 277
Period size: 42 Copynumber: 6.5 Consensus size: 42
287198 ACATAATCAA
*
287208 CCGAGTCATAAGTCTTCCTTTAAACGA-AATCTCATGCTCATC
1 CCGAGTCATGAGTCTTCCTTTAAAC-ATAATCTCATGCTCATC
* * * * * * *
287250 TCGAGTCACGAGTCTTTCTTTAAAACATAACCTCATACTCCTT
1 CCGAGTCATGAGTCTTCCTTT-AAACATAATCTCATGCTCATC
* *
287293 CTGAGTCATGAGTCTTTC-TTAAATCATAATCTCATGCTCATC
1 CCGAGTCATGAGTCTTCCTTTAAA-CATAATCTCATGCTCATC
** * *
287335 CCGAGTCACAAATCTTCCTTTTAACATAATCTCATGCTCATC
1 CCGAGTCATGAGTCTTCCTTTAAACATAATCTCATGCTCATC
** * * *
287377 CCGACACATGAATCTTCCTTTCAACATAATCTCATGCTCATA
1 CCGAGTCATGAGTCTTCCTTTAAACATAATCTCATGCTCATC
* * *
287419 CCGAGACATAAGTCTTCCTTTTAACATAATCTCATGCTCATC
1 CCGAGTCATGAGTCTTCCTTTAAACATAATCTCATGCTCATC
* * * *
287461 CCGAGACACGAGTCGTCTTTTAA
1 CCGAGTCATGAGTCTTCCTTTAA
287484 TACGCATCAA
Statistics
Matches: 193, Mismatches: 37, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
41 3 0.02
42 156 0.81
43 34 0.18
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (42 bp):
CCGAGTCATGAGTCTTCCTTTAAACATAATCTCATGCTCATC
Found at i:287456 original size:126 final size:127
Alignment explanation
Indices: 287208--287465 Score: 306
Period size: 127 Copynumber: 2.0 Consensus size: 127
287198 ACATAATCAA
* * * ** * *
287208 CCGAGTCATAAGTCTTCCTTTAAACGAAATCTCATGCTCATCTCGAGTCACGAGTCTTTCTTTAA
1 CCGAGTCACAAATCTTCCTTTAAACGAAATCTCATGCTCATCCCGACACACGAATCTTCCTTTAA
* * * * * *
287273 AACATAACCTCATACTCCTTCTGAGTCATGAGTCTTTCTTAAATCATAATCTCATGCTCATC
66 AACATAACCTCATACTCATACCGAGACATAAGTCTTCCTTAAATCATAATCTCATGCTCATC
* *
287335 CCGAGTCACAAATCTTCCTTTTAAC-ATAATCTCATGCTCATCCCGACACATGAATCTTCCTTT-
1 CCGAGTCACAAATCTTCCTTTAAACGA-AATCTCATGCTCATCCCGACACACGAATCTTCCTTTA
* * * *
287398 CAACATAATCTCATGCTCATACCGAGACATAAGTCTTCCTTTTAA-CATAATCTCATGCTCATC
65 AAACATAACCTCATACTCATACCGAGACATAAGTCTTCC-TTAAATCATAATCTCATGCTCATC
287461 CCGAG
1 CCGAG
287466 ACACGAGTCG
Statistics
Matches: 110, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
126 54 0.49
127 56 0.51
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (127 bp):
CCGAGTCACAAATCTTCCTTTAAACGAAATCTCATGCTCATCCCGACACACGAATCTTCCTTTAA
AACATAACCTCATACTCATACCGAGACATAAGTCTTCCTTAAATCATAATCTCATGCTCATC
Found at i:288156 original size:160 final size:160
Alignment explanation
Indices: 287879--288196 Score: 557
Period size: 160 Copynumber: 2.0 Consensus size: 160
287869 AATATGGACA
*
287879 CAAAAACATAAAAAATACTAAAAATGATTGACATTTGCTTACCCAAATCAAAGCTCAAAGTTAGG
1 CAAAAACATAAAAAATACTAAAAATGATTAACATTTGCTTACCCAAATCAAAGCTCAAAGTTAGG
* *
287944 AGTTGGAAACACTAGTTCTTTATCTCCCTAGTCATATGGAATAAGATGAAATGAGAAAATATGAT
66 AGTTGGAAACACTAGTTCTTTATCTCCCTAGTCATATGCAAGAAGATGAAATGAGAAAATATGAT
288009 GAAAATTTTCTAATTTCTTTTCTTTTTACT
131 GAAAATTTTCTAATTTCTTTTCTTTTTACT
* *
288039 CAAAAACATAAAAATTACTAAAAATGATTAATATTTGCTTACCCAAATCAAAGCTCAAAGTTAGG
1 CAAAAACATAAAAAATACTAAAAATGATTAACATTTGCTTACCCAAATCAAAGCTCAAAGTTAGG
* *
288104 AGTTGGAAACCCTAGTTCTTTATCTCCCTAGTCGTATGCAAGAA-ATTGAAATGAGAAAATATGA
66 AGTTGGAAACACTAGTTCTTTATCTCCCTAGTCATATGCAAGAAGA-TGAAATGAGAAAATATGA
288168 TGAAAATTTTCTAATTTCTTTTCTTTTTA
130 TGAAAATTTTCTAATTTCTTTTCTTTTTA
288197 ATTCATTTAT
Statistics
Matches: 150, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
159 1 0.01
160 149 0.99
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (160 bp):
CAAAAACATAAAAAATACTAAAAATGATTAACATTTGCTTACCCAAATCAAAGCTCAAAGTTAGG
AGTTGGAAACACTAGTTCTTTATCTCCCTAGTCATATGCAAGAAGATGAAATGAGAAAATATGAT
GAAAATTTTCTAATTTCTTTTCTTTTTACT
Found at i:293681 original size:21 final size:21
Alignment explanation
Indices: 293654--293707 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
293644 CTTGTTATAG
293654 TTCTACCAATACAAGTCATGCT
1 TTCTACCAATACAAGTCATG-T
*
293676 TT-TACCAATATAAGTCATGT
1 TTCTACCAATACAAGTCATGT
*
293696 TTCTACCGATAC
1 TTCTACCAATAC
293708 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 23 0.82
22 2 0.07
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.35
Consensus pattern (21 bp):
TTCTACCAATACAAGTCATGT
Found at i:294466 original size:42 final size:42
Alignment explanation
Indices: 294336--294583 Score: 225
Period size: 42 Copynumber: 5.9 Consensus size: 42
294326 TTTTAAATGA
* * * * *
294336 AATCTCTTGCTCATCTCGAGTCACGAGTCTTCCTTTAAAACAT
1 AATCTCATGCTCATCCCGAGTCATGAGACTTCCTTT-TAACAT
* * * * * * * *
294379 AACCTCATACTCCTTCCAAGTCATGAGTCTT-CTTTAAAACCT
1 AATCTCATGCTCATCCCGAGTCATGAGACTTCCTTT-TAACAT
* ** *
294421 AATCTCATGCTCTTCCCGAGTCGCGAGACTTCCTTTTAATAT
1 AATCTCATGCTCATCCCGAGTCATGAGACTTCCTTTTAACAT
* *
294463 AATCTCATGCTCATCCCGAGACATGGGTA-TTCCTTTTAACAT
1 AATCTCATGCTCATCCCGAGTCATGAG-ACTTCCTTTTAACAT
* *
294505 AATCTCATGCTTATCCCGAGAT-ATGAGTCTTCCTTTTAACAT
1 AATCTCATGCTCATCCCGAG-TCATGAGACTTCCTTTTAACAT
* *
294547 AATCTCATGCTCATCCCGAGACATGAGTCTT-CTTTTA
1 AATCTCATGCTCATCCCGAGTCATGAGACTTCCTTTTA
294584 TTACGCATCA
Statistics
Matches: 168, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
41 6 0.04
42 134 0.80
43 28 0.17
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (42 bp):
AATCTCATGCTCATCCCGAGTCATGAGACTTCCTTTTAACAT
Found at i:296802 original size:12 final size:12
Alignment explanation
Indices: 296785--296809 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
296775 AAACCCAAAG
296785 AAAGAAAGAAAA
1 AAAGAAAGAAAA
296797 AAAGAAAGAAAA
1 AAAGAAAGAAAA
296809 A
1 A
296810 GTCAAGGGCA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:298177 original size:111 final size:111
Alignment explanation
Indices: 297983--298182 Score: 310
Period size: 111 Copynumber: 1.8 Consensus size: 111
297973 TGTTTGTCAC
* * **
297983 TTTTAATCTTTTCATTCATGTGAGCTTTGTCTCCAATAAAATTCAAATTTGTCCACCTTACAACC
1 TTTTAATCTTTTCATTCACGCGAGCTTTGTCTCCAATAAAATTCAAATTTACCCACCTTACAACC
*
298048 TTGTTCAAGCACATTTGCATTGAATAGTGGTTAGTGGACTAATGAT
66 CTGTTCAAGCACATTTGCATTGAATAGTGGTTAGTGGACTAATGAT
* * *
298094 TTTTAATCTTTTCATTCACGCGAGCTTTTTCTCCAATAAAATTCAATTTTACCCACTTTACAACC
1 TTTTAATCTTTTCATTCACGCGAGCTTTGTCTCCAATAAAATTCAAATTTACCCACCTTACAACC
**
298159 CTGTTCAAGCATTTTTGCATTGAA
66 CTGTTCAAGCACATTTGCATTGAA
298183 ATGACAGTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 79 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (111 bp):
TTTTAATCTTTTCATTCACGCGAGCTTTGTCTCCAATAAAATTCAAATTTACCCACCTTACAACC
CTGTTCAAGCACATTTGCATTGAATAGTGGTTAGTGGACTAATGAT
Found at i:298721 original size:49 final size:48
Alignment explanation
Indices: 298623--299204 Score: 425
Period size: 49 Copynumber: 11.9 Consensus size: 48
298613 ACGTTAAAAC
* * ** * * *
298623 ATGTGAAGGGAAAGATTAAAGCCGTAACGGTGAATCTTACACCCTAGAG
1 ATGTG-AGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
** ** *
298672 ATGTTGAGGGAAAGGTTGAAGTTACAACAATTAACCTTATACCTTAGAG
1 ATG-TGAGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* * * *
298721 ATATGAAGGGAAAGGTTGAAGCCGCAACAGCGAACCTTATACCTTAGAG
1 ATGTG-AGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* * ** * * *
298770 ATGTGA-TGAGAAGGATTGAAGTCACAACGACGAATCTTATACCCTAAAG
1 ATGTGAGGGA-AAGG-TTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* *
298819 ATGTGAAGCAGAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
1 ATGTGAGGGA-AAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* * *
298868 ATATGATGGG-AAGGTTGAAGCTACAACGGTGAAACTTATACCTTAGAG
1 ATGTGA-GGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* * * * *
298916 ATGTGATGGG-AAGGATTGAAGTCGCAACGGTTAATCTTATACCCTAGAG
1 ATGTGA-GGGAAAGG-TTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* * * * **
298965 ATGTGAAGGGAAAGGTTAAAGTCGCAATGGTGAATGTTATACCTTAGAG
1 ATGTG-AGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* * **
299014 ATGTGGAGGGAAAGGTTAAAGCCGCAACGACGAACCTTATACCTTAGAG
1 ATGT-GAGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* * * * * * * * *
299063 ATGTGATGGGAAAGATTAAAGCTACGACGGCGAATCTTATTCCCTAAAG
1 ATGTGA-GGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
* ** * * * *
299112 ATGTGATGGGAAAGATTGAAGCCGTAAC-GCGAATCTTGTACCATAGAG
1 ATGTGA-GGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
** * * * *
299160 ATGTGAAGGGAAATATTGAGGCCATAATGGTGAATCTTATACCTT
1 ATGTG-AGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTT
299205 GAAAATGAAG
Statistics
Matches: 436, Mismatches: 84, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
47 2 0.00
48 96 0.22
49 323 0.74
50 15 0.03
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (48 bp):
ATGTGAGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
Found at i:298797 original size:98 final size:97
Alignment explanation
Indices: 298623--299171 Score: 498
Period size: 98 Copynumber: 5.6 Consensus size: 97
298613 ACGTTAAAAC
* * * * * *
298623 ATGTGAAGGGAAAGATTAAAGCCGTAACGGTGAATCTTACACCCTAGAGATGTTGA-GGGAAAGG
1 ATGTGAAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATG-TGATGGG-AAGG
* * * *
298687 TTGAAGTTACAACAATTAACCTTATACCTTAGAG
64 TTGAAGTCACAACGATGAATCTTATACCTTAGAG
* * * *
298721 ATATGAAGGGAAAGGTTGAAGCCGCAACAGCGAACCTTATACCTTAGAGATGTGATGAGAAGGAT
1 ATGTGAAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGGAAGG-T
* * *
298786 TGAAGTCACAACGACGAATCTTATACCCTAAAG
65 TGAAGTCACAACGATGAATCTTATACCTTAGAG
* * *
298819 ATGTGAA-GCAGAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAGATATGATGGGAAGGT
1 ATGTGAAGGGA-AAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGGAAGGT
* *
298883 TGAAG-CTACAACGGTGAAACTTATACCTTAGAG
65 TGAAGTC-ACAACGATGAATCTTATACCTTAGAG
* * * * * *
298916 ATGTGATGGG-AAGGATTGAAGTCGCAACGGTTAATCTTATACCCTAGAGATGTGAAGGGAAAGG
1 ATGTGAAGGGAAAGG-TTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGG-AAGG
* * * * *
298980 TTAAAGTCGCAATGGTGAATGTTATACCTTAGAG
64 TTGAAGTCACAACGATGAATCTTATACCTTAGAG
* * ** *
299014 ATGTGGAGGGAAAGGTTAAAGCCGCAACGACGAACCTTATACCTTAGAGATGTGATGGGAAAGAT
1 ATGTGAAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGG-AAGGT
* * ** * * *
299079 TAAAG-CTACGACGGCGAATCTTATTCCCTAAAG
65 TGAAGTC-ACAACGATGAATCTTATACCTTAGAG
* * * * * * * *
299112 ATGTGATGGGAAAGATTGAAGCCGTAAC-GCGAATCTTGTACCATAGAGATGTGAAGGGAA
1 ATGTGAAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGGAA
299172 ATATTGAGGC
Statistics
Matches: 369, Mismatches: 72, Indels: 22
0.80 0.16 0.05
Matches are distributed among these distances:
96 7 0.02
97 105 0.28
98 252 0.68
99 5 0.01
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (97 bp):
ATGTGAAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGGAAGGTT
GAAGTCACAACGATGAATCTTATACCTTAGAG
Found at i:299161 original size:244 final size:243
Alignment explanation
Indices: 298623--299171 Score: 586
Period size: 244 Copynumber: 2.2 Consensus size: 243
298613 ACGTTAAAAC
* * * *
298623 ATGTGAAGGGAAAGATTAAAGCCGTAACGGTGAATCTTACACCCTAGAGATGTTGAGGGAAAGGT
1 ATGTGATGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCATAGAGATG-TGAGGG-AAGGT
* * *
298688 TGAAGTTACAACAATTAACCTTATACCTTAGAGATATGAAGGGAAAGGTTGAAGCCGCAACAGCG
64 TGAAGTCACAACAATTAACCTTATACCCTAGAGATATGAAGGGAAAGGTTAAAGCCGCAACAGCG
* * * *
298753 AACCTTATACCTTAGAGATGTGATGAGAAGGATTGAAGTCACAACGACGAATCTTATACCCTAAA
129 AACCTTATACCTTAGAGATGTGAGGAGAAGGATTAAAGCCACAACGACGAACCTTATACCCTAAA
* * * * *
298818 GATGTGAAGCAGAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAG
194 GATGTGAAGCAGAAGATTAAAGCCACAACGGCGAACCTTATACCCTAAAG
* * *** * *
298868 ATATGATGGG-AAGGTTGAAGCTACAACGGTGAAACTTATACCTTAGAGATGTGATGGGAAGGAT
1 ATGTGATGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCATAGAGATGTGA-GGGAAGG-T
* ** * * * ** *
298932 TGAAGTCGCAACGGTTAATCTTATACCCTAGAGATGTGAAGGGAAAGGTTAAAGTCGCAATGGTG
64 TGAAGTCACAACAATTAACCTTATACCCTAGAGATATGAAGGGAAAGGTTAAAGCCGCAACAGCG
** * *
298997 AATGTTATACCTTAGAGATGTGGAGG-GAAAGG-TTAAAGCCGCAACGACGAACCTTATACCTTA
129 AACCTTATACCTTAGAGATGT-GAGGAG-AAGGATTAAAGCCACAACGACGAACCTTATACCCTA
* * * * * * *
299060 GAGATGTGATG-GGAAAGATTAAAGCTACGACGGCGAATCTTATTCCCTAAAG
192 AAGATGTGAAGCAG-AAGATTAAAGCCACAACGGCGAACCTTATACCCTAAAG
* *
299112 ATGTGATGGGAAAGATTGAAGCCGTAAC-GCGAATCTTGTACCATAGAGATGTGAAGGGAA
1 ATGTGATGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCATAGAGATGTG-AGGGAA
299172 ATATTGAGGC
Statistics
Matches: 246, Mismatches: 51, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
243 8 0.03
244 209 0.85
245 29 0.12
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (243 bp):
ATGTGATGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCATAGAGATGTGAGGGAAGGTTG
AAGTCACAACAATTAACCTTATACCCTAGAGATATGAAGGGAAAGGTTAAAGCCGCAACAGCGAA
CCTTATACCTTAGAGATGTGAGGAGAAGGATTAAAGCCACAACGACGAACCTTATACCCTAAAGA
TGTGAAGCAGAAGATTAAAGCCACAACGGCGAACCTTATACCCTAAAG
Found at i:299191 original size:195 final size:194
Alignment explanation
Indices: 298707--299204 Score: 516
Period size: 195 Copynumber: 2.6 Consensus size: 194
298697 AACAATTAAC
* * * * * * *
298707 CTTATACCTTAGAGATATGAAGGGAAAGGTTGAAGCCGCAACAGCG-AACCTTATACCTTAGAGA
1 CTTATACCCTAAAGATGTGATGGGAAAGATTGAAGCCGCAAC-G-GTAATCTTATACCATAGAGA
* * * * * * ** * * * *
298771 TGTGATGAGAAGGATTGAAGTCACAACGACGAATCTTATACCCTAAAGATGT-GAAGCAGAAGGT
64 TGTGAAGGGAAAGATTAAAGCCACAATGGTGAATCTTATACCTTAGAGATGTGGAGGGA-AAGGT
* ** * * *
298835 TGAAGCCACAACGGTGAACCTTATACCTTAGAGATATGATGGGAAGGTTGAAGCTACAACGGTGA
128 TAAAGCCACAACGACGAACCTTATACCTTAGAGATATGATGGGAAGATTAAAGCTACAACGGCGA
298900 AA
193 AA
* * * * *
298902 CTTATACCTTAGAGATGTGATGGGAAGGATTGAAGTCGCAACGGTTAATCTTATACCCTAGAGAT
1 CTTATACCCTAAAGATGTGATGGGAAAGATTGAAGCCGCAACGG-TAATCTTATACCATAGAGAT
* * * *
298967 GTGAAGGGAAAGGTTAAAGTCGCAATGGTGAATGTTATACCTTAGAGATGTGGAGGGAAAGGTTA
65 GTGAAGGGAAAGATTAAAGCCACAATGGTGAATCTTATACCTTAGAGATGTGGAGGGAAAGGTTA
* * *
299032 AAGCCGCAACGACGAACCTTATACCTTAGAGATGTGATGGGAAAGATTAAAGCTACGACGGCGAA
130 AAGCCACAACGACGAACCTTATACCTTAGAGATATGATGGG-AAGATTAAAGCTACAACGGCGAA
*
299097 T
194 A
* * *
299098 CTTATTCCCTAAAGATGTGATGGGAAAGATTGAAGCCGTAACGCG-AATCTTGTACCATAGAGAT
1 CTTATACCCTAAAGATGTGATGGGAAAGATTGAAGCCGCAACG-GTAATCTTATACCATAGAGAT
* * * *
299162 GTGAAGGGAAATATTGAGGCCATAATGGTGAATCTTATACCTT
65 GTGAAGGGAAAGATTAAAGCCACAATGGTGAATCTTATACCTT
299205 GAAAATGAAG
Statistics
Matches: 251, Mismatches: 47, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
193 1 0.00
194 1 0.00
195 188 0.75
196 60 0.24
197 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.24
Consensus pattern (194 bp):
CTTATACCCTAAAGATGTGATGGGAAAGATTGAAGCCGCAACGGTAATCTTATACCATAGAGATG
TGAAGGGAAAGATTAAAGCCACAATGGTGAATCTTATACCTTAGAGATGTGGAGGGAAAGGTTAA
AGCCACAACGACGAACCTTATACCTTAGAGATATGATGGGAAGATTAAAGCTACAACGGCGAAA
Found at i:299554 original size:37 final size:38
Alignment explanation
Indices: 299513--299796 Score: 220
Period size: 37 Copynumber: 7.7 Consensus size: 38
299503 CTCGATCATG
* *
299513 GGGCAGATGGAAG-CATCCAATCTTTTACCCATTCAGA
1 GGGCAGATTGAAGCCATGCAATCTTTTACCCATTCAGA
*
299550 GGGCAGATTGAAGCCATGCAA--TTTTACCCCGA-TC-GTG
1 GGGCAGATTGAAGCCATGCAATCTTTTA-CCC-ATTCAG-A
* * * * *
299587 GGGCAAATGGAAG-CATCCAATCTTTTACTCATTTAGA
1 GGGCAGATTGAAGCCATGCAATCTTTTACCCATTCAGA
*
299624 GCGCAGATTGAAGCCATGCAA--TTTTACCCCGA-TCATG-
1 GGGCAGATTGAAGCCATGCAATCTTTTA-CCC-ATTCA-GA
* * *
299661 GGGCAAATAGAAG-CATTCAATCTTTTACCCATTCAGA
1 GGGCAGATTGAAGCCATGCAATCTTTTACCCATTCAGA
* * *
299698 GGGTAGATTGAAGCCATGCAATC--TTACCCCGTTC-GTG
1 GGGCAGATTGAAGCCATGCAATCTTTTA-CCCATTCAG-A
* * *
299735 GGGCAAATGGAAG-CATCCAATCTTTTACCCATTCAGA
1 GGGCAGATTGAAGCCATGCAATCTTTTACCCATTCAGA
*
299772 GGGTAGATTGAAGCCATGCAATCTT
1 GGGCAGATTGAAGCCATGCAATCTT
299797 ACCCCAACCA
Statistics
Matches: 189, Mismatches: 35, Indels: 45
0.70 0.13 0.17
Matches are distributed among these distances:
36 38 0.20
37 103 0.54
38 48 0.25
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (38 bp):
GGGCAGATTGAAGCCATGCAATCTTTTACCCATTCAGA
Found at i:299589 original size:74 final size:74
Alignment explanation
Indices: 299406--299801 Score: 488
Period size: 74 Copynumber: 5.2 Consensus size: 74
299396 CAAAGCGAAA
* * * ** *
299406 CCATGCAATCTTACCTCGATCGTGGGGGCAGATTGAAGACCATCTGATCTTTTACCCTAAGTCAA
1 CCATGCAATCTTACCCCGATCGT-GGGGCAAATGGAAG--CATCCAATCTTTTACCC--ATTC-A
*
299471 GAAGGTCAGATTGAAG
60 G-AGGGCAGATTGAAG
* * * * *
299487 ACTAT-CGATCTCTTACCTCGATCATGGGGCAGATGGAAGCATCCAATCTTTTACCCATTCAGAG
1 -CCATGC-A-ATCTTACCCCGATCGTGGGGCAAATGGAAGCATCCAATCTTTTACCCATTCAGAG
299551 GGCAGATTGAAG
63 GGCAGATTGAAG
* * * *
299563 CCATGCAATTTTACCCCGATCGTGGGGCAAATGGAAGCATCCAATCTTTTACTCATTTAGAGCGC
1 CCATGCAATCTTACCCCGATCGTGGGGCAAATGGAAGCATCCAATCTTTTACCCATTCAGAGGGC
299628 AGATTGAAG
66 AGATTGAAG
* * * * *
299637 CCATGCAATTTTACCCCGATCATGGGGCAAATAGAAGCATTCAATCTTTTACCCATTCAGAGGGT
1 CCATGCAATCTTACCCCGATCGTGGGGCAAATGGAAGCATCCAATCTTTTACCCATTCAGAGGGC
299702 AGATTGAAG
66 AGATTGAAG
* *
299711 CCATGCAATCTTACCCCGTTCGTGGGGCAAATGGAAGCATCCAATCTTTTACCCATTCAGAGGGT
1 CCATGCAATCTTACCCCGATCGTGGGGCAAATGGAAGCATCCAATCTTTTACCCATTCAGAGGGC
299776 AGATTGAAG
66 AGATTGAAG
299785 CCATGCAATCTTACCCC
1 CCATGCAATCTTACCCC
299802 AACCATGAAG
Statistics
Matches: 282, Mismatches: 29, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
74 212 0.75
75 4 0.01
76 14 0.05
77 2 0.01
78 3 0.01
80 15 0.05
81 1 0.00
82 17 0.06
83 14 0.05
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (74 bp):
CCATGCAATCTTACCCCGATCGTGGGGCAAATGGAAGCATCCAATCTTTTACCCATTCAGAGGGC
AGATTGAAG
Found at i:299935 original size:76 final size:75
Alignment explanation
Indices: 299522--299941 Score: 212
Period size: 74 Copynumber: 5.6 Consensus size: 75
299512 GGGGCAGATG
* * * * * * * * * * *
299522 GAAGCATCCAATCTTTTACCCATTCAGAGGGCAGATTGAAGCCATGCAATTTTACCCCGATCGTG
1 GAAGCATACTATCTCTTACCCAATCAGAGGTCAGATTGAAGACATTCAATCTTACCCCAACCATG
* *
299587 -GGGCAAATG
66 AAGGCAAATT
* * * * * * * * * * *
299596 GAAGCATCCAATCTTTTACTCATTTAGAGCG-CAGATTGAAGCCATGCAATTTTACCCCGATCAT
1 GAAGCATACTATCTCTTACCCAATCAGAG-GTCAGATTGAAGACATTCAATCTTACCCCAACCAT
* *
299660 G-GGGCAAATA
65 GAAGGCAAATT
* * * * * * *** *
299670 GAAGCATTCAATCTTTTACCCATTCAGAGGGT-AGATTGAAGCCATGCAATCTTACCCCGTTCGT
1 GAAGCATACTATCTCTTACCCAATCAGA-GGTCAGATTGAAGACATTCAATCTTACCCCAACCAT
* *
299734 G-GGGCAAATG
65 GAAGGCAAATT
* * * * * *
299744 GAAGCATCCAATCTTTTACCCATTCAGAGGGT-AGATTGAAGCCATGCAATCTTACCCCAACCAT
1 GAAGCATACTATCTCTTACCCAATCAGA-GGTCAGATTGAAGACATTCAATCTTACCCCAACCAT
299808 GAA-GCAAATT
65 GAAGGCAAATT
* * ** * * * *
299818 GAAG-ATCACTAATTTCTTACCCCGATCATTGGGCAGGTTGAAGTCATTCAATCTTTTA-CCCAT
1 GAAGCAT-ACT-ATCTCTTA-CCCAATCAGAGGTCAGATTGAAGACATTCAATC--TTACCCCAA
*
299881 TCA-GAAGGCAAATT
61 CCATGAAGGCAAATT
299895 GAAGCATACTATCTCTTACCCTAATCAGAGGTCAGATTGAAGACATT
1 GAAGCATACTATCTCTTACCC-AATCAGAGGTCAGATTGAAGACATT
299942 AACCAATCAT
Statistics
Matches: 294, Mismatches: 39, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
73 2 0.01
74 203 0.69
75 13 0.04
76 51 0.17
77 20 0.07
78 5 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (75 bp):
GAAGCATACTATCTCTTACCCAATCAGAGGTCAGATTGAAGACATTCAATCTTACCCCAACCATG
AAGGCAAATT
Found at i:301254 original size:14 final size:14
Alignment explanation
Indices: 301235--301261 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
301225 TATTTTTTGA
301235 AATAAAAAAAGAAT
1 AATAAAAAAAGAAT
301249 AATAAAAAAAGAA
1 AATAAAAAAAGAA
301262 ATCTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (14 bp):
AATAAAAAAAGAAT
Found at i:304873 original size:62 final size:68
Alignment explanation
Indices: 304782--304952 Score: 185
Period size: 72 Copynumber: 2.5 Consensus size: 68
304772 GATGGAACGG
* * * **
304782 AGTCATCGGACCT-TTAATCCATAATAAGATTCAT-T-T-C-T-CATTTA-ATACTCATGATGAC
1 AGTCATCGGACCTCATAATCCGTAA-AAGATTCATATATACATACATTCATATACTCACAATGAC
*
304840 ACAT
65 AAAT
304844 AGTCATCGGACCTCATAATCCGTAAAAGATTCATATACTCACAATGACATTCATATACTCACAAT
1 AGTCATCGGACCTCATAATCCGTAAAAGATTCATATA-T-AC-AT-ACATTCATATACTCACAAT
304909 GACAAAT
62 GACAAAT
*
304916 AGTCATCGGACCTCATAATCTGTAAAAGATTCATATA
1 AGTCATCGGACCTCATAATCCGTAAAAGATTCATATA
304953 CTCACGATGA
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
62 22 0.24
63 10 0.11
65 1 0.01
67 1 0.01
69 1 0.01
71 5 0.05
72 51 0.56
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (68 bp):
AGTCATCGGACCTCATAATCCGTAAAAGATTCATATATACATACATTCATATACTCACAATGACA
AAT
Found at i:304897 original size:20 final size:20
Alignment explanation
Indices: 304872--304912 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
304862 TCCGTAAAAG
304872 ATTCATATACTCACAATGAC
1 ATTCATATACTCACAATGAC
304892 ATTCATATACTCACAATGAC
1 ATTCATATACTCACAATGAC
304912 A
1 A
304913 AATAGTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
ATTCATATACTCACAATGAC
Found at i:304943 original size:72 final size:72
Alignment explanation
Indices: 304826--304964 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
304816 TTCTCATTTA
** *
304826 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCATATACTCACAATGA
1 ATACTCACAATGACAAATAGTCATCGGACCTCATAATCCGTAAAAGATTCATATACTCACAATGA
304891 CATTCAT
66 CATTCAT
* *
304898 ATACTCACAATGACAAATAGTCATCGGACCTCATAATCTGTAAAAGATTCATATACTCACGATGA
1 ATACTCACAATGACAAATAGTCATCGGACCTCATAATCCGTAAAAGATTCATATACTCACAATGA
304963 CA
66 CA
304965 CATAGTCATC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.27
Consensus pattern (72 bp):
ATACTCACAATGACAAATAGTCATCGGACCTCATAATCCGTAAAAGATTCATATACTCACAATGA
CATTCAT
Found at i:314992 original size:21 final size:21
Alignment explanation
Indices: 314966--315021 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
314956 CAGTGCAGAT
* *
314966 TTCTACTGATACTTGTGATAG-
1 TTCTACTGATACTAGTCAT-GC
* *
314987 TTCTACCGATACAAGTCATGC
1 TTCTACTGATACTAGTCATGC
315008 TTCTACTGATACTA
1 TTCTACTGATACTA
315022 AAAACTCCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (21 bp):
TTCTACTGATACTAGTCATGC
Found at i:321389 original size:42 final size:43
Alignment explanation
Indices: 321257--321529 Score: 188
Period size: 42 Copynumber: 6.5 Consensus size: 43
321247 GTAATCAACC
* * *
321257 GAGTCATAAGTCTTCCTTTAAATGA-AATCCCATGCTCAT-CT
1 GAGTCATAAGTCTTCCTTTAAATCATAATCTCATGCTCTTCCT
* * * * *
321298 CGAGTCATAAGTCTTCTTTTAAAACATTACCTCATACTCCTTCC-
1 -GAGTCATAAGTCTTCCTTTAAATCATAATCTCATGCT-CTTCCT
*
321342 GAGTCATATGTCTTCC-TTAAATCATAATCTCATGCTCTTCCT
1 GAGTCATAAGTCTTCCTTTAAATCATAATCTCATGCTCTTCCT
* ** * * *
321384 AAGTCACGAGTCTTCCTTTTAA-CATAATCTCATGCTCATCCC
1 GAGTCATAAGTCTTCCTTTAAATCATAATCTCATGCTCTTCCT
* * * * *
321426 GAGACATGAGTCTTCCTTTCAA-CATAATTTCATGCTCAT-CT
1 GAGTCATAAGTCTTCCTTTAAATCATAATCTCATGCTCTTCCT
** * ** * *
321467 CGAAACATGAA-TCTTTCTTT-AAT-ATACCCTCATGCTCATCCC
1 -GAGTCAT-AAGTCTTCCTTTAAATCATAATCTCATGCTCTTCCT
*
321509 GAGACATAAGTCTTCCTTTAA
1 GAGTCATAAGTCTTCCTTTAA
321530 TACGCATCAA
Statistics
Matches: 184, Mismatches: 36, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
40 2 0.01
41 35 0.19
42 118 0.64
43 26 0.14
44 2 0.01
45 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (43 bp):
GAGTCATAAGTCTTCCTTTAAATCATAATCTCATGCTCTTCCT
Found at i:321441 original size:84 final size:82
Alignment explanation
Indices: 321255--321526 Score: 217
Period size: 84 Copynumber: 3.2 Consensus size: 82
321245 ACGTAATCAA
* * * ** * *
321255 CCGAGTCATAAGTCTTCCTTTAA-ATGAAATCCCATGCTCATCTCGAGTCA-TAAGTCTTCTTTT
1 CCGAGACATAAGTCTTCCTTAAACAT--AATCTCATGCTCATCTCGAAACACGAA-TCTTCCTTT
* * * *
321318 AAAACATTACCTCATACTCCTT
63 --AACATAACCTCATGCTCATC
* * * * * *
321340 CCGAGTCATATGTCTTCCTTAAATCATAATCTCATGCTCTTC-CTAAGTCACGAGTCTTCCTTTT
1 CCGAGACATAAGTCTTCCTTAAA-CATAATCTCATGCTCATCTCGAA-ACACGAATCTTCC-TTT
*
321404 AACATAATCTCATGCTCATC
63 AACATAACCTCATGCTCATC
* * * * *
321424 CCGAGACATGAGTCTTCCTTTCAACATAATTTCATGCTCATCTCGAAACATGAATCTTTCTTTAA
1 CCGAGACATAAGTCTTCC-TTAAACATAATCTCATGCTCATCTCGAAACACGAATCTTCCTTTAA
* *
321489 TATACCCTCATGCTCATC
65 CATAACCTCATGCTCATC
321507 CCGAGACATAAGTCTTCCTT
1 CCGAGACATAAGTCTTCCTT
321527 TAATACGCAT
Statistics
Matches: 151, Mismatches: 29, Indels: 17
0.77 0.15 0.09
Matches are distributed among these distances:
82 2 0.01
83 37 0.25
84 57 0.38
85 49 0.32
86 4 0.03
87 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (82 bp):
CCGAGACATAAGTCTTCCTTAAACATAATCTCATGCTCATCTCGAAACACGAATCTTCCTTTAAC
ATAACCTCATGCTCATC
Found at i:322198 original size:24 final size:25
Alignment explanation
Indices: 322144--322193 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
322134 AAAACATAAA
322144 AATTACTAAAAATGATTGATATTTG
1 AATTACTAAAAATGATTGATATTTG
322169 AATTACTAAAAATGATTGATATTTG
1 AATTACTAAAAATGATTGATATTTG
322194 CTTACCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (25 bp):
AATTACTAAAAATGATTGATATTTG
Found at i:335376 original size:18 final size:18
Alignment explanation
Indices: 335350--335401 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
335340 AAAATACGAG
* *
335350 AAATAATGTTCACATTTT
1 AAATGATGTTCACATTTC
335368 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
335386 AAATGATGTTCACATT
1 AAATGATGTTCACATT
335402 GATGGAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:337298 original size:3 final size:3
Alignment explanation
Indices: 337290--337314 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
337280 ATGGAGAAAG
337290 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
337315 AATGGTAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:338587 original size:23 final size:22
Alignment explanation
Indices: 338560--338603 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
338550 AAGCTTATAG
*
338560 ATATTCTTAATATTTATTTTTAT
1 ATATTCTTAATATAT-TTTTTAT
*
338583 ATATTTTTAATATATTTTTTA
1 ATATTCTTAATATATTTTTTA
338604 ATAGTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
ATATTCTTAATATATTTTTTAT
Found at i:338589 original size:10 final size:11
Alignment explanation
Indices: 338560--338606 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
338550 AAGCTTATAG
*
338560 ATATTCTTAAT
1 ATATTTTTAAT
338571 ATTTATTTTT-AT
1 A--TATTTTTAAT
338583 ATATTTTTAAT
1 ATATTTTTAAT
338594 ATATTTTTTAAT
1 ATA-TTTTTAAT
338606 A
1 A
338607 GTTTGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.23
11 6 0.19
12 12 0.39
13 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTTTTAAT
Found at i:338810 original size:17 final size:16
Alignment explanation
Indices: 338770--338811 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
338760 AATTGAAGTG
338770 TTTA-TATTTTAAATA
1 TTTATTATTTTAAATA
*
338785 TTTATTTATTTTTAATA
1 TTTA-TTATTTTAAATA
338802 TTTTATTATT
1 -TTTATTATT
338812 GATCCAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTATTTTAAATA
Found at i:339969 original size:14 final size:15
Alignment explanation
Indices: 339950--339983 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
339940 TTTTGAACGT
*
339950 CAATT-ATTTAATAA
1 CAATTAATTAAATAA
339964 CAATTAATTAAATAA
1 CAATTAATTAAATAA
339979 CAATT
1 CAATT
339984 TGAAAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
CAATTAATTAAATAA
Found at i:341534 original size:19 final size:19
Alignment explanation
Indices: 341512--341552 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
341502 TGTTCAAATG
*
341512 CATAACTAGTATTACACCA
1 CATAACTAGTACTACACCA
*
341531 CATAATTAGTACTACACCA
1 CATAACTAGTACTACACCA
341550 CAT
1 CAT
341553 TAAAGCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (19 bp):
CATAACTAGTACTACACCA
Found at i:342525 original size:32 final size:31
Alignment explanation
Indices: 342486--342570 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 31
342476 TGCCATTGTC
* *
342486 AATAATTTCGATATCAAACAAGCTTAAAGCAT
1 AATAATTTC-ATATCCAACAAGCTTAAAACAT
*
342518 AATAATTTCATCACCCAACAAGCTTAAAACAT
1 AATAATTTCAT-ATCCAACAAGCTTAAAACAT
342550 AATAATTTCAATATCCAACAA
1 AATAATTTC-ATATCCAACAA
342571 TAATTTCAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
31 2 0.04
32 43 0.91
33 2 0.04
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (31 bp):
AATAATTTCATATCCAACAAGCTTAAAACAT
Found at i:346785 original size:18 final size:18
Alignment explanation
Indices: 346752--346786 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
346742 TAAGATGAAA
* *
346752 CATAAAAATAACAAAACC
1 CATAAAAAGAAAAAAACC
346770 CATAAAAAGAAAAAAAC
1 CATAAAAAGAAAAAAAC
346787 AGGGATTAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.17, G:0.03, T:0.09
Consensus pattern (18 bp):
CATAAAAAGAAAAAAACC
Found at i:357757 original size:24 final size:23
Alignment explanation
Indices: 357723--357775 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
357713 CAGTCGTTTG
*
357723 AAAAA-GAAAAATGAGAAAAAGGAA
1 AAAAATGAAAAA-GAAAAAAA-GAA
*
357747 GAAAATGAAAAAGAAAAAAAGAA
1 AAAAATGAAAAAGAAAAAAAGAA
357770 AAAAAT
1 AAAAAT
357776 TTTAAATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 8 0.32
24 11 0.44
25 6 0.24
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (23 bp):
AAAAATGAAAAAGAAAAAAAGAA
Found at i:357766 original size:15 final size:14
Alignment explanation
Indices: 357722--357772 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
357712 TCAGTCGTTT
*
357722 GAAAAAGAAAAATGA
1 GAAAAAGAAAAA-AA
*
357737 GAAAAAGGAAGAAAAT
1 GAAAAA-GAA-AAAAA
357753 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
357767 GAAAAA
1 GAAAAA
357773 AATTTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.32
15 9 0.29
16 9 0.29
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:358922 original size:14 final size:14
Alignment explanation
Indices: 358903--358935 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
358893 GGAGTAGGCC
358903 TAGTAGTCTAGAGA
1 TAGTAGTCTAGAGA
358917 TAGTAGTCTAGAGA
1 TAGTAGTCTAGAGA
358931 TAGTA
1 TAGTA
358936 AGCTTCGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.30
Consensus pattern (14 bp):
TAGTAGTCTAGAGA
Found at i:370887 original size:26 final size:25
Alignment explanation
Indices: 370830--370881 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
370820 ATTCAAAAAT
* *
370830 AAACTTAAAAGTAAAATTGCATTGTT
1 AAACTTAAAAG-AAAATTGCAATGTC
370856 AAACTTAAAA-AAAATTGCAATGTC
1 AAACTTAAAAGAAAATTGCAATGTC
370880 AA
1 AA
370882 TTACTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.58
26 10 0.42
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (25 bp):
AAACTTAAAAGAAAATTGCAATGTC
Found at i:375705 original size:7 final size:7
Alignment explanation
Indices: 375693--375725 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
375683 ATTTTATATG
375693 GAATTTT
1 GAATTTT
375700 GAATTTT
1 GAATTTT
375707 GAATTTT
1 GAATTTT
375714 -AATTATT
1 GAATT-TT
375721 GAATT
1 GAATT
375726 AAAAGTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.17
7 16 0.67
8 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (7 bp):
GAATTTT
Found at i:383063 original size:13 final size:13
Alignment explanation
Indices: 383045--383069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
383035 CCCATTTTAT
383045 CATTTTTAGCATG
1 CATTTTTAGCATG
383058 CATTTTTAGCAT
1 CATTTTTAGCAT
383070 TTTTAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:395754 original size:76 final size:76
Alignment explanation
Indices: 395625--395775 Score: 257
Period size: 76 Copynumber: 2.0 Consensus size: 76
395615 AATCATCAAA
* * *
395625 TGGTTGGATGCGGGCATAATATACTCTATTTCTGACAGCAATTGGTCAAACCCATTCAATGTGTT
1 TGGTTGGATACGGGCATAATATACCCTATTTCTGACAGCAATTAGTCAAACCCATTCAATGTGTT
395690 CCAAAAAAAAG
66 CCAAAAAAAAG
* *
395701 TGGTTGGATACGGGCATAATATACCCTATTTCTGATAGCAATTAGTCAGACCCATTCAATGTGTT
1 TGGTTGGATACGGGCATAATATACCCTATTTCTGACAGCAATTAGTCAAACCCATTCAATGTGTT
395766 CCAAAAAAAA
66 CCAAAAAAAA
395776 ATTGGTTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (76 bp):
TGGTTGGATACGGGCATAATATACCCTATTTCTGACAGCAATTAGTCAAACCCATTCAATGTGTT
CCAAAAAAAAG
Found at i:400139 original size:24 final size:25
Alignment explanation
Indices: 400112--400162 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
400102 GAAGCCAATC
400112 AAGGAGATGA-ATAAGAGAAGG-AGA
1 AAGGAGATGAGA-AAGAGAAGGAAGA
*
400136 AAGGAGATGAGAATGAGAAGGAAGA
1 AAGGAGATGAGAAAGAGAAGGAAGA
400161 AA
1 AA
400163 CAGAGCCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.37, T:0.08
Consensus pattern (25 bp):
AAGGAGATGAGAAAGAGAAGGAAGA
Found at i:403590 original size:23 final size:23
Alignment explanation
Indices: 403555--403610 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
403545 ACCAGTTATT
403555 AGTAT-TTTGTAACTCTCCTGCC
1 AGTATGTTTGTAACTCTCCTGCC
* *
403577 ATTATGTTTGTAACTCTCTTGCC
1 AGTATGTTTGTAACTCTCCTGCC
403600 AGTATGTTTGT
1 AGTATGTTTGT
403611 TTTAATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.46
Consensus pattern (23 bp):
AGTATGTTTGTAACTCTCCTGCC
Found at i:404004 original size:18 final size:18
Alignment explanation
Indices: 403977--404019 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
403967 TGTTTATTTG
403977 ATTT-TTATT-AATTTACA
1 ATTTATTATTAAATTTA-A
403994 ATTTATTATTAAATTTAA
1 ATTTATTATTAAATTTAA
404012 ATTGTATT
1 ATT-TATT
404020 TATATTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTTATTATTAAATTTAA
Found at i:407281 original size:25 final size:24
Alignment explanation
Indices: 407232--407305 Score: 87
Period size: 23 Copynumber: 3.1 Consensus size: 24
407222 TTTGCTTTTA
* * *
407232 ATTTTTTGTAACTCACCAATTATT
1 ATTTTTTGTAACTCTCCTATCATT
*
407256 ATTATTTTGTAACTCTCCTGTCATT
1 ATT-TTTTGTAACTCTCCTATCATT
*
407281 A-TGTTTGTAACTCTCCTATCATT
1 ATTTTTTGTAACTCTCCTATCATT
407304 AT
1 AT
407306 GCTTGTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
23 20 0.48
24 4 0.10
25 18 0.43
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (24 bp):
ATTTTTTGTAACTCTCCTATCATT
Found at i:407291 original size:23 final size:23
Alignment explanation
Indices: 407256--407311 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
407246 ACCAATTATT
*
407256 ATTAT-TTTGTAACTCTCCTGTC
1 ATTATGTTTGTAACTCTCCTATC
407278 ATTATGTTTGTAACTCTCCTATC
1 ATTATGTTTGTAACTCTCCTATC
*
407301 ATTATGCTTGT
1 ATTATGTTTGT
407312 TTTAATTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.50
Consensus pattern (23 bp):
ATTATGTTTGTAACTCTCCTATC
Found at i:407717 original size:19 final size:18
Alignment explanation
Indices: 407675--407713 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
407665 TGTTTATTTG
407675 ATTT-TTATTAATTTATA
1 ATTTATTATTAATTTATA
407692 ATTTATTATTAAATTTA-A
1 ATTTATTATT-AATTTATA
407710 ATTT
1 ATTT
407714 TATTTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 10 0.50
19 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTATTATTAATTTATA
Found at i:419921 original size:13 final size:13
Alignment explanation
Indices: 419887--419912 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
419877 GATAATGCTT
419887 ATTATTTTACTAA
1 ATTATTTTACTAA
419900 ATTATTTTACTAA
1 ATTATTTTACTAA
419913 TTTCTTTTAT
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:0.00, T:0.54
Consensus pattern (13 bp):
ATTATTTTACTAA
Found at i:433618 original size:42 final size:42
Alignment explanation
Indices: 433571--433656 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
433561 AATGGTCATT
433571 TCTAATGCCATCACACCTCAAAACTTGAGTTTTTACTTGTCC
1 TCTAATGCCATCACACCTCAAAACTTGAGTTTTTACTTGTCC
433613 TCTAATGCCATCACACCTCAAAACTTGAGTTTTTACTTGTCC
1 TCTAATGCCATCACACCTCAAAACTTGAGTTTTTACTTGTCC
433655 TC
1 TC
433657 AAGTAAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.36
Consensus pattern (42 bp):
TCTAATGCCATCACACCTCAAAACTTGAGTTTTTACTTGTCC
Found at i:434998 original size:25 final size:23
Alignment explanation
Indices: 434963--435008 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
434953 CTTCTTCATT
*
434963 TTCTTTTTCTTTTCTTTTCTTCC
1 TTCTTTTTCTTTTCTCTTCTTCC
434986 TTCTTCTTCTCTTTTCTCTTCTT
1 TTCTT-TT-TCTTTTCTCTTCTT
435009 TCTATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 2 0.10
25 13 0.65
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
TTCTTTTTCTTTTCTCTTCTTCC
Found at i:439288 original size:19 final size:17
Alignment explanation
Indices: 439264--439299 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
439254 TCACTACCTC
439264 CTTTATTTTCTCATTTAAT
1 CTTTATTTT-T-ATTTAAT
439283 CTTTATTTTTATTTAAT
1 CTTTATTTTTATTTAAT
439300 TGGTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTATTTTTATTTAAT
Found at i:450275 original size:55 final size:55
Alignment explanation
Indices: 450166--450273 Score: 130
Period size: 54 Copynumber: 2.0 Consensus size: 55
450156 GCCTAATAAC
* *
450166 AAATTTAGTCATCTAATATTTACACATTTGATCAATTTGATCTCAAATCTAAAAT
1 AAATTTAGTCATCTAATATTTACACATTTGATCAATTTAATCTCAAATATAAAAT
* * * * *
450221 AAATTTAGTCCTC-AATATTTACGAGATTTG-TCATTTTAATCTTAATTATAAAA
1 AAATTTAGTCATCTAATATTTAC-ACATTTGATCAATTTAATCTCAAATATAAAA
450274 ATTATAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
54 27 0.60
55 18 0.40
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (55 bp):
AAATTTAGTCATCTAATATTTACACATTTGATCAATTTAATCTCAAATATAAAAT
Found at i:453976 original size:17 final size:18
Alignment explanation
Indices: 453956--453990 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
453946 TAAAAAAAAT
453956 AAAAATAAG-AAAATAAG
1 AAAAATAAGAAAAATAAG
453973 AAAAATAAGAAAAATAAG
1 AAAAATAAGAAAAATAAG
453991 TTAAATCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAATAAGAAAAATAAG
Found at i:453990 original size:9 final size:9
Alignment explanation
Indices: 453956--453990 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
453946 TAAAAAAAAT
453956 AAAAATAAG
1 AAAAATAAG
453965 -AAAATAAG
1 AAAAATAAG
453973 AAAAATAAG
1 AAAAATAAG
453982 AAAAATAAG
1 AAAAATAAG
453991 TTAAATCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAATAAG
Found at i:456523 original size:21 final size:21
Alignment explanation
Indices: 456499--456552 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
456489 CTTATGATAG
*
456499 TTCTACCGATACAAGTGTAAC
1 TTCTACCGATACAAGTCTAAC
* * *
456520 TTCTACCTAAACAAGTCTTAC
1 TTCTACCGATACAAGTCTAAC
456541 TTCTACCGATAC
1 TTCTACCGATAC
456553 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAGTCTAAC
Found at i:457288 original size:85 final size:82
Alignment explanation
Indices: 457192--457447 Score: 268
Period size: 85 Copynumber: 3.0 Consensus size: 82
457182 AATCTTCCTT
* * *
457192 TTTAAAC--AATCTTATGCTCTACCGAGGCATAAGTCTTCCTTTTTAAACATAATCTCACGTTCA
1 TTTAAACATAATCTAAT-CTCTACCGAGACATGAGTCTTCC-TTTTAAACATAATCTCA-GTTCA
457255 TTCCGAGACATGAGTCTTCC
63 TTCCGAGACATGAGTCTTCC
* * * *
457275 TTTAAACATAATCTCATTCTCATCCCGAGACATGAGTCTTCCTTTTAAACATTATCTCATTCTCA
1 TTTAAACATAATCT-AATCTC-TACCGAGACATGAGTCTTCCTTTTAAACATAATCTCAGT-TCA
*
457340 TCCCGAGACATGAGTCTTCC
63 TTCCGAGACATGAGTCTTCC
* *
457360 TTTAAACATAATCTCAATCTC-ATCTCGAGACATGAGTCTTCCTTTTAAACATATTGC-CATGCT
1 TTTAAACATAATCT-AATCTCTA-C-CGAGACATGAGTCTTCCTTTTAAACATAAT-CTCA-GTT
* * *
457423 CATTCTGAGTCAAGAGTCTTCC
61 CATTCCGAGACATGAGTCTTCC
457445 TTT
1 TTT
457448 TTATACATAA
Statistics
Matches: 146, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
83 7 0.05
84 2 0.01
85 118 0.81
86 19 0.13
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (82 bp):
TTTAAACATAATCTAATCTCTACCGAGACATGAGTCTTCCTTTTAAACATAATCTCAGTTCATTC
CGAGACATGAGTCTTCC
Found at i:457290 original size:42 final size:43
Alignment explanation
Indices: 457213--457457 Score: 277
Period size: 42 Copynumber: 5.7 Consensus size: 43
457203 TTATGCTCTA
* *
457213 CCGAGGCATAAGTCTTCCTTTTTAAACATAATCTCACGT-TCATT
1 CCGAGACATGAGTCTTCC-TTTTAAACATAATCTCA-GTCTCATT
* *
457257 CCGAGACATGAGTCTTCC-TTTAAACATAATCTCATTCTCATC
1 CCGAGACATGAGTCTTCCTTTTAAACATAATCTCAGTCTCATT
* * *
457299 CCGAGACATGAGTCTTCCTTTTAAACATTATCTCATTCTCATC
1 CCGAGACATGAGTCTTCCTTTTAAACATAATCTCAGTCTCATT
*
457342 CCGAGACATGAGTCTTCC-TTTAAACATAATCTCAATCTCA-T
1 CCGAGACATGAGTCTTCCTTTTAAACATAATCTCAGTCTCATT
*
457383 CTCGAGACATGAGTCTTCCTTTTAAACATATTGC-CA-TGCTCATT
1 C-CGAGACATGAGTCTTCCTTTTAAACATAAT-CTCAGT-CTCATT
* * * *
457427 CTGAGTCAAGAGTCTTCCTTTTTATACATAA
1 CCGAGACATGAGTCTTCC-TTTTAAACATAA
457458 AGTGTTCAAG
Statistics
Matches: 179, Mismatches: 14, Indels: 16
0.86 0.07 0.08
Matches are distributed among these distances:
41 2 0.01
42 76 0.42
43 72 0.40
44 29 0.16
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (43 bp):
CCGAGACATGAGTCTTCCTTTTAAACATAATCTCAGTCTCATT
Done.