Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 64
Found at i:5995712 original size:91 final size:91
Alignment explanation
Indices: 5995607--5996221 Score: 856
Period size: 91 Copynumber: 6.8 Consensus size: 91
5995597 CAATGGAATG
* ** * *
5995607 GTTCATAATAAGAAGAACTCATCCGACGAGAAAGAAGAAGTTCATAACGATAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
*
5995672 CCTGGGATCAACATTTCCAGTGGAGA
66 CCTTGGATCAACATTTCCAGTGGAGA
* * * *
5995698 GTTCATAATGAGAAGAAATCATCCAACTAGGGAGAAGAAGTTCATAATGAGAAGAACTTGCTCAA
1 GTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * *
5995763 CCTTGGATCGATATTTCCAGTAGAGA
66 CCTTGGATCAACATTTCCAGTGGAGA
* * *
5995789 GTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * *
5995854 CCTGGGATCAACATTTCCATTGGAGG
66 CCTTGGATCAACATTTCCAGTGGAGA
* *
5995880 GTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGCTCAA
1 GTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * *
5995945 CATTGGATCGACATTTCCAGTTGAGA
66 CCTTGGATCAACATTTCCAGTGGAGA
* * * *
5995971 GTTCATATTGAGAAGAACTCATCTGACGAGGTAGAAGAAGTTCATAATGTGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
*
5996036 CCTTGGATCGACATTTCCAGTAGG-GA
66 CCTTGGATCAACATTTCCAGT-GGAGA
* * **
5996062 GTTCGTAATGAGAAAAACTCATCCGACGAGGTTGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
5996127 CCTTGGATCAACATTTCCAGTAGG-GA
66 CCTTGGATCAACATTTCCAGT-GGAGA
** * * *
5996153 GTTTGTAATGAGAATAACTCATCCGACGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTTAA
1 GTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
5996218 CCTT
66 CCTT
5996222 AGCTCGTTTT
Statistics
Matches: 469, Mismatches: 54, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
91 468 1.00
92 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (91 bp):
GTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTGGATCAACATTTCCAGTGGAGA
Found at i:5995848 original size:301 final size:299
Alignment explanation
Indices: 5995289--5995856 Score: 861
Period size: 301 Copynumber: 1.9 Consensus size: 299
5995279 TAAACCAATT
**
5995289 AATATTTCCAATGGAGAGTTCATAATAAGAAAAACTCATCCAACGAGGGAGAAGAAGTTCATAAC
1 AATATTTCCAATGGAGAGTTCATAATAAGAAAAACTCATCCAACGAGAAAGAAGAAGTTCATAAC
* * * * *
5995354 GATAAGGACTTGTTCAACCTTGCATCAACATTTCCAGTGGAGATTTCATAATGAGAATAACTCAT
66 GATAAGAACTTGTTCAACCTGGCATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAAATCAT
* * * *
5995419 CCGATAAGGGAGAAAAAGTTCATAATGAGAACAACTTGTTCAACATTGGCTCAATATTTCCAATG
131 CCAATAAGGGAGAAAAAGTTCATAATGAGAACAACTTGCTCAACATTGGATCAATATTTCCAATA
* * * *
5995484 GAGAGTTCATAATGAGAAGAACTCATACGATGAGGGACAAGAAGTTCATAATGAGAAGAACTTGT
196 GAGAGTTCATAATGAGAAGAACTCATACAACGAGGAACAAGAAGTTCATAATGAAAAGAACTTGT
5995549 TCAACCTTAGCTCATTTCCATCACAGAAGGAGGTTGATC
261 TCAACCTTAGCTCATTTCCATCACAGAAGGAGGTTGATC
* *
5995588 AATATTTCCCAATGGA-ATGGTTCATAATAAGAAGAACTCATCCGACGAGAAAGAAGAAGTTCAT
1 AATATTT-CCAATGGAGA--GTTCATAATAAGAAAAACTCATCCAACGAGAAAGAAGAAGTTCAT
*
5995652 AACGATAAGAACTTGTTCAACCTGGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAAAT
63 AACGATAAGAACTTGTTCAACCTGGCATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAAAT
* * * *
5995717 CATCCAACT-AGGGAGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTGGATCGATATTTCC
128 CATCCAA-TAAGGGAGAAAAAGTTCATAATGAGAACAACTTGCTCAACATTGGATCAATATTTCC
* * *
5995781 AGTAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAAAAGAAC
192 AATAGAGAGTTCATAATGAGAAGAACTCATACAACGAGGAACAAGAAGTTCATAATGAAAAGAAC
5995846 TTGTTCAACCT
257 TTGTTCAACCT
5995857 GGGATCAACA
Statistics
Matches: 240, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
299 8 0.03
300 8 0.03
301 223 0.93
302 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (299 bp):
AATATTTCCAATGGAGAGTTCATAATAAGAAAAACTCATCCAACGAGAAAGAAGAAGTTCATAAC
GATAAGAACTTGTTCAACCTGGCATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAAATCAT
CCAATAAGGGAGAAAAAGTTCATAATGAGAACAACTTGCTCAACATTGGATCAATATTTCCAATA
GAGAGTTCATAATGAGAAGAACTCATACAACGAGGAACAAGAAGTTCATAATGAAAAGAACTTGT
TCAACCTTAGCTCATTTCCATCACAGAAGGAGGTTGATC
Found at i:5998371 original size:23 final size:24
Alignment explanation
Indices: 5998327--5998374 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
5998317 TAATAAGTAT
5998327 TAGGGCTTTGAGTTGTAATTATCC
1 TAGGGCTTTGAGTTGTAATTATCC
*
5998351 TAGGGCTTTGA-TTGTAGTTATCC
1 TAGGGCTTTGAGTTGTAATTATCC
5998374 T
1 T
5998375 TCCCCAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (24 bp):
TAGGGCTTTGAGTTGTAATTATCC
Found at i:6001821 original size:154 final size:156
Alignment explanation
Indices: 6001638--6001947 Score: 606
Period size: 154 Copynumber: 2.0 Consensus size: 156
6001628 CTAAAATAAT
6001638 CCTAATGGGCAAATTTTGAAAACTATGTTTGAAAACAATATTTAAAAATCAATATGTAGTTTTCA
1 CCTAATGGGCAAATTTTGAAAACTATGTTTGAAAACAATATTTAAAAATCAATATGTAGTTTTCA
6001703 AAAACACATAATTAAATAAAAACAACAACGATTTTAAAACCAAAACAAATTTTTTTATTTCGAAA
66 AAAACACATAATTAAATAAAAACAACAACGATTTTAAAACCAAAACAAATTTTTTTATTTCGAAA
6001768 TGTTT-AAAAAATTGATCAAATCTTG
131 TGTTTAAAAAAATTGATCAAATCTTG
6001793 CCTAATGGGCAAA-TTTGAAAACTATGTTTGAAAACAATATTTAAAAATCAATATGTAGTTTTCA
1 CCTAATGGGCAAATTTTGAAAACTATGTTTGAAAACAATATTTAAAAATCAATATGTAGTTTTCA
6001857 AAAACACATAATTAAATAAAAACAACAACGATTTTAAAACCAAAACAAATTTTTTTATTTCGAAA
66 AAAACACATAATTAAATAAAAACAACAACGATTTTAAAACCAAAACAAATTTTTTTATTTCGAAA
6001922 TGTTTAAAAAAATTGATCAAATCTTG
131 TGTTTAAAAAAATTGATCAAATCTTG
6001948 TGTTTTTGAT
Statistics
Matches: 154, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
154 121 0.79
155 33 0.21
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (156 bp):
CCTAATGGGCAAATTTTGAAAACTATGTTTGAAAACAATATTTAAAAATCAATATGTAGTTTTCA
AAAACACATAATTAAATAAAAACAACAACGATTTTAAAACCAAAACAAATTTTTTTATTTCGAAA
TGTTTAAAAAAATTGATCAAATCTTG
Found at i:6003827 original size:23 final size:23
Alignment explanation
Indices: 6003797--6003856 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
6003787 CATTTTATAT
6003797 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
6003820 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
6003843 GACACTTCGGTGCA
1 GGCACTTCGGTGCA
6003857 TTTATATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:6009437 original size:17 final size:16
Alignment explanation
Indices: 6009397--6009443 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6009387 TTATCTAAAA
6009397 ATAA-TTAAAATATAT
1 ATAATTTAAAATATAT
*
6009412 ATAATTTAAAATATTT
1 ATAATTTAAAATATAT
*
6009428 ATTTATTTAAAA-ATAT
1 A-TAATTTAAAATATAT
6009444 CAGAAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
17 9 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTTAAAATATAT
Found at i:6009625 original size:3 final size:3
Alignment explanation
Indices: 6009617--6009658 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
6009607 TACATGATTA
6009617 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6009659 TAAATATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6011299 original size:17 final size:16
Alignment explanation
Indices: 6011259--6011305 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6011249 TTATCTAAAA
6011259 ATAA-TTAAAATATAT
1 ATAATTTAAAATATAT
*
6011274 ATAATTTAAAATATTT
1 ATAATTTAAAATATAT
*
6011290 ATTTATTTAAAA-ATAT
1 A-TAATTTAAAATATAT
6011306 CAGAAAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
17 9 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTTAAAATATAT
Found at i:6011652 original size:28 final size:29
Alignment explanation
Indices: 6011602--6011657 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
6011592 ATAAATGAAA
*
6011602 ATATTAAAATTAGTGACAAAATT-ATAAC
1 ATATTAAAATTAATGACAAAATTCATAAC
*
6011630 ATATTAAAATTAAAT-ACATAATTCATAA
1 ATATTAAAATT-AATGACAAAATTCATAA
6011658 TTAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (29 bp):
ATATTAAAATTAATGACAAAATTCATAAC
Found at i:6012928 original size:3 final size:3
Alignment explanation
Indices: 6012922--6012948 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6012912 AATTTTTTAT
6012922 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
6012949 ATCAAATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6013840 original size:234 final size:234
Alignment explanation
Indices: 6013270--6013842 Score: 781
Period size: 234 Copynumber: 2.4 Consensus size: 234
6013260 ATTCAAATAT
* * *
6013270 GTGATGAATT-AAGGC--AAGGTTGAACAAGTTCTTCTTATTATGAATTTCTTC-TCTTTATTCA
1 GTGATGAATTCAA-GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTATTCA
* * * * *
6013331 GATAAGTTCTTCTCATTATAAAAACTTC--TGGAAATGTGGATGTTGATCTATCTCCTTCTGTGA
65 GATGAGTTCTTCTCA-T-TAAGAACTTCTTTGGAAATGTTGATGCTGATCTATCTACTTCTGTGA
*
6013394 TAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCAGATAAGTTCT
128 TAGAGTCATGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCAGATAAGTTCT
6013459 TCTTATTATGAACTTTCTCTGGAGAAGTTGATGTTGATCCATCAA
193 TCTTATTATGAACTTTCTCTGGAGAA---GATGTTGATCCATCAA
* *
6013504 GTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCATTTTTCAG
1 GTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTATTCAG
* * *
6013569 ATGAGTTCTTCTCATTATGAAC-ACTTCTGGAAATGTTGATGCTGATCTATCTATTTCTGTGATA
66 ATGAGTTCTTCTCATTAAGAACTTCTT-TGGAAATGTTGATGCTGATCTATCTACTTCTGTGATA
6013633 GAGTCATGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTC
130 GAGTCATGAAAAGGTTGAACAAGTTCTTCTCATTATGAA---CTTCTTCCTCTTCAGATAAGTTC
* * *
6013698 TTCTTTTTATGAACTTTCTCTGGA-AA-A-GTTGATTCATCTA
192 TTCTTATTATGAACTTTCTCTGGAGAAGATGTTGATCCATCAA
* * *
6013738 GTGATGAATTTGAA-CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 GTGATGAA-TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTATTCA
*
6013802 GATGAGTTCTTCTCATTACGAACTTCTTTGGAAATGTTGAT
65 GATGAGTTCTTCTCATTAAGAACTTCTTTGGAAATGTTGAT
6013843 CCATTGAGTA
Statistics
Matches: 304, Mismatches: 23, Indels: 24
0.87 0.07 0.07
Matches are distributed among these distances:
234 114 0.38
235 15 0.05
236 34 0.11
237 93 0.31
239 2 0.01
240 46 0.15
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (234 bp):
GTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTATTCAG
ATGAGTTCTTCTCATTAAGAACTTCTTTGGAAATGTTGATGCTGATCTATCTACTTCTGTGATAG
AGTCATGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCAGATAAGTTCTTCT
TATTATGAACTTTCTCTGGAGAAGATGTTGATCCATCAA
Found at i:6013841 original size:112 final size:112
Alignment explanation
Indices: 6013641--6013842 Score: 334
Period size: 112 Copynumber: 1.8 Consensus size: 112
6013631 TAGAGTCATG
**
6013641 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTTTT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
*
6013706 ATGAACTTTCTCTGGAAAAGTTGATTCATCTAGTGATGAATTTGAAC
66 ACGAACTTTCTCTGGAAAAGTTGATTCATCTAGTGATGAATTTGAAC
*
6013753 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCAT
* *
6013818 TACGAAC-TTCTTTGGAAATGTTGAT
65 TACGAACTTTCTCTGGAAAAGTTGAT
6013843 CCATTGAGTA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 58 0.70
113 25 0.30
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (112 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
ACGAACTTTCTCTGGAAAAGTTGATTCATCTAGTGATGAATTTGAAC
Found at i:6015051 original size:18 final size:18
Alignment explanation
Indices: 6015014--6015051 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6015004 TATGTGAAAG
*
6015014 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCAAA
6015032 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
6015050 AA
1 AA
6015052 GATAATCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:6015436 original size:22 final size:22
Alignment explanation
Indices: 6015411--6015453 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6015401 CTATATATTT
*
6015411 TTTTC-TTTTTTTATCATTTTTC
1 TTTTCATTTCTTT-TCATTTTTC
6015433 TTTTCATTTCTTTTCATTTTT
1 TTTTCATTTCTTTTCATTTTT
6015454 TTTCTTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTCATTTCTTTTCATTTTTC
Found at i:6015456 original size:10 final size:10
Alignment explanation
Indices: 6015408--6015457 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
6015398 TTTCTATATA
6015408 TTTTTTTC-T
1 TTTTTTTCAT
6015417 TTTTTTATCATT
1 TTTTTT-TCA-T
6015429 TTTCTTTTCAT
1 TTT-TTTTCAT
*
6015440 TTCTTTTCAT
1 TTTTTTTCAT
6015450 TTTTTTTC
1 TTTTTTTC
6015458 TTCAAGCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 6 0.17
10 16 0.46
11 3 0.09
12 7 0.20
13 3 0.09
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:6025561 original size:16 final size:17
Alignment explanation
Indices: 6025540--6025582 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
6025530 CTAAAACTAA
6025540 TTAAAATATATA-TAAT
1 TTAAAATATATATTAAT
* *
6025556 TTAAAATATTTATTTAT
1 TTAAAATATATATTAAT
6025573 TTAAAA-ATAT
1 TTAAAATATAT
6025583 CAGAAAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAAATATATATTAAT
Found at i:6027235 original size:3 final size:3
Alignment explanation
Indices: 6027221--6027271 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
6027211 AATTTTTTAT
* * * * *
6027221 TAA TAT TAA TAA TAA TTA TTA TTA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6027269 TAA
1 TAA
6027272 ATCAAATGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:6028942 original size:17 final size:17
Alignment explanation
Indices: 6028920--6028955 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
6028910 TTTAAATACA
*
6028920 CCTTGGATTGATTGTAG
1 CCTTGGATTGATTATAG
6028937 CCTTGGATTGATTATAG
1 CCTTGGATTGATTATAG
6028954 CC
1 CC
6028956 GTTGTGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (17 bp):
CCTTGGATTGATTATAG
Found at i:6029208 original size:71 final size:74
Alignment explanation
Indices: 6029101--6029236 Score: 206
Period size: 71 Copynumber: 1.9 Consensus size: 74
6029091 TGTTATATGG
* * *
6029101 ATAGAGGTATCGGTACCCATAAGGGGTATCGGTACCCATAGGGCATTCTGTTA-TTTTCGAAGCC
1 ATAGAGGCATCGGTACCCATAAGGGGTATCGGTACCCACAGGGCAATCTGTTATTTTTCGAAGCC
6029165 AAATCTTGC
66 AAATCTTGC
* *
6029174 ATAGAGGCATCGGTACTC-T-AGGGGTATCGGTACCCACGGGGCAATCTGTTATTTTTCGAAGCC
1 ATAGAGGCATCGGTACCCATAAGGGGTATCGGTACCCACAGGGCAATCTGTTATTTTTCGAAGCC
6029237 CTTCTATTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 29 0.51
72 12 0.21
73 16 0.28
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (74 bp):
ATAGAGGCATCGGTACCCATAAGGGGTATCGGTACCCACAGGGCAATCTGTTATTTTTCGAAGCC
AAATCTTGC
Found at i:6031536 original size:25 final size:22
Alignment explanation
Indices: 6031475--6031536 Score: 52
Period size: 26 Copynumber: 2.5 Consensus size: 22
6031465 TATATATATA
*
6031475 ATTTTTAACTTTAAAAATAAATT
1 ATTTTTAA-TTTAAAAAAAAATT
6031498 ATTTTCATATATTTAAAAAAAAAATT
1 ATTTT--TA-ATTT-AAAAAAAAATT
6031524 AGATTTTTAATTT
1 --ATTTTTAATTT
6031537 CTTTTTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
23 5 0.16
25 9 0.28
26 13 0.41
28 5 0.16
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTTAATTTAAAAAAAAATT
Found at i:6036155 original size:31 final size:31
Alignment explanation
Indices: 6036120--6036341 Score: 381
Period size: 31 Copynumber: 7.2 Consensus size: 31
6036110 GGTCACAATA
6036120 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
6036151 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
6036182 TAAACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
6036213 TAAAATGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
6036244 TAAACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
6036275 TAAACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
6036306 TAAATTGTTCATTTGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
6036337 TAAAC
1 TAAAC
6036342 CCTCGACTCT
Statistics
Matches: 180, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 180 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:6036243 original size:16 final size:16
Alignment explanation
Indices: 6036222--6036306 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
6036212 GTAAAATGTT
6036222 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
6036238 CATATGTAAACTATT---
1 CATATGT-GCCT-TTAAA
6036253 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
6036269 CATATGTAAACTATT---
1 CATATGT-GCCT-TTAAA
6036284 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
6036300 CATATGT
1 CATATGT
6036307 AAATTGTTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 14 0.27
16 21 0.41
17 4 0.08
18 4 0.08
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:6036957 original size:64 final size:65
Alignment explanation
Indices: 6036851--6037073 Score: 195
Period size: 64 Copynumber: 3.5 Consensus size: 65
6036841 TGAAGGTATG
* * * ** ** * **
6036851 CATCAATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAAT-ATTATTGTTGGGATA
1 CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTAATCATTATTAATGGGATA
*
6036915 CATCGATGCACT-CATTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGGAT
1 CATCGATGCACTAC-TTATGCATCGATGCACCAATTGCATTCGATGTAATCATTATTAATGGGAT
*
6036978 G
65 A
** * * **
6036979 CATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAA-AAGAGT
1 CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTAATCATTATTAATGGGA-T
*
6037042 G
65 A
** *
6037043 CATCGATGCACTACCAATGCATCGATACACC
1 CATCGATGCACTACTTATGCATCGATGCACC
6037074 TTCAAACAAA
Statistics
Matches: 132, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
63 4 0.03
64 122 0.92
65 6 0.05
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (65 bp):
CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTAATCATTATTAATGGGATA
Found at i:6036959 original size:18 final size:19
Alignment explanation
Indices: 6036915--6036959 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
6036905 TGTTGGGATA
*
6036915 CATCGATGCACTCATTATG
1 CATCGATGCACTCAATATG
6036934 CATCGATGCAC-CAAT-TG
1 CATCGATGCACTCAATATG
6036951 CATTCGATG
1 CA-TCGATG
6036960 TTTCATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 11 0.46
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCAATATG
Found at i:6040303 original size:31 final size:31
Alignment explanation
Indices: 6040243--6040555 Score: 549
Period size: 31 Copynumber: 10.2 Consensus size: 31
6040233 GGTCACAATA
6040243 TAAACTGTTCATATGTGCCTTT-AACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
6040273 TAAAATGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
6040304 TAAATTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
6040335 TAAACTGTTCATATGTGCCTTT-AACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
6040365 TAAAATGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
6040396 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
6040427 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
6040458 TAAACTGTTCATATATGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
6040489 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
6040520 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
6040551 TAAAC
1 TAAAC
6040556 CTCGACTCTG
Statistics
Matches: 268, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
30 49 0.18
31 219 0.82
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:6040405 original size:92 final size:93
Alignment explanation
Indices: 6040240--6040554 Score: 562
Period size: 92 Copynumber: 3.4 Consensus size: 93
6040230 AGAGGTCACA
6040240 ATATAAACTGTTCATATGTGCCTTT-AACATATGTAAAATGTTCATATGTGCCTTTAAACATATG
1 ATATAAACTGTTCATATGTGCCTTTAAACATATGTAAAATGTTCATATGTGCCTTTAAACATATG
6040304 TAAATTGTTCATATGTGCCTTTAAACAT
66 TAAATTGTTCATATGTGCCTTTAAACAT
*
6040332 ATATAAACTGTTCATATGTGCCTTT-AACATATGTAAAATGTTCATATGTGCCTTTAAACATATA
1 ATATAAACTGTTCATATGTGCCTTTAAACATATGTAAAATGTTCATATGTGCCTTTAAACATATG
*
6040396 TAAACTGTTCATATGTGCCTTTAAACAT
66 TAAATTGTTCATATGTGCCTTTAAACAT
* * *
6040424 ATGTAAACTGTTCATATGTGCCTTTAAACATATGTAAACTGTTCATATATGCCTTTAAACATATG
1 ATATAAACTGTTCATATGTGCCTTTAAACATATGTAAAATGTTCATATGTGCCTTTAAACATATG
6040489 TAAATTGTTCATATGTGCCTTTAAACAT
66 TAAATTGTTCATATGTGCCTTTAAACAT
*
6040517 ATGTAAACTGTTCATATGTGCCTTTAAACATATGTAAA
1 ATATAAACTGTTCATATGTGCCTTTAAACATATGTAAA
6040555 CCTCGACTCT
Statistics
Matches: 215, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
92 114 0.53
93 101 0.47
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (93 bp):
ATATAAACTGTTCATATGTGCCTTTAAACATATGTAAAATGTTCATATGTGCCTTTAAACATATG
TAAATTGTTCATATGTGCCTTTAAACAT
Found at i:6041261 original size:64 final size:64
Alignment explanation
Indices: 6041064--6041271 Score: 197
Period size: 64 Copynumber: 3.2 Consensus size: 64
6041054 AATGAAGGTA
* ** * * *** *
6041064 TGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTA-ATATTATTGCTGGG
1 TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTATTATTAAAGAG
* * * ** * * *
6041127 ATGCATCAATGCACTCCTTATCCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 -TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTATTATTAAAGAG
* *
6041191 ACGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAAAAGA
1 -TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTATTATT-AAAGA
6041255 G
64 G
6041256 TGCATCGATGCACTAC
1 TGCATCGATGCACTAC
6041272 CAATGGATCG
Statistics
Matches: 118, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
64 109 0.92
65 9 0.08
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTATTATTAAAGAG
Found at i:6041282 original size:64 final size:64
Alignment explanation
Indices: 6041149--6041288 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 64
6041139 ACTCCTTATC
* * **
6041149 CATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGACGCATCGATGCACTACTTATG
1 CATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGACGCATCGATGCACTACCAATG
** * *
6041213 CATCGATGCATGAATTGCATTCGATGTATTTATT-TTAAA-AGAGTGCATCGATGCACTACCAAT
1 CATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAGA-CGCATCGATGCACTACCAAT
6041276 G
64 G
* *
6041277 GATCGATACACC
1 CATCGATGCACC
6041289 TTCAAACAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
63 2 0.03
64 55 0.89
65 5 0.08
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (64 bp):
CATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGACGCATCGATGCACTACCAATG
Found at i:6049884 original size:20 final size:22
Alignment explanation
Indices: 6049862--6049902 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6049852 ATAATTATTT
6049862 AAAAA-ATTAAATAAAAATATA
1 AAAAATATTAAATAAAAATATA
*
6049883 AAAAATATTTAATAAAAATA
1 AAAAATATTAAATAAAAATA
6049903 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAATATTAAATAAAAATATA
Found at i:6050043 original size:17 final size:17
Alignment explanation
Indices: 6050023--6050067 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
6050013 AGTAAAACAT
*
6050023 ATTAAATAATAAATATG
1 ATTAAATAATAAATATA
6050040 ATT--AT-ATAAATATA
1 ATTAAATAATAAATATA
*
6050054 ATTAAAAAATAAAT
1 ATTAAATAATAAAT
6050068 TTGGGGCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 1 0.04
17 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTAAATAATAAATATA
Found at i:6050217 original size:23 final size:21
Alignment explanation
Indices: 6050179--6050221 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
6050169 ATAGTTATTT
6050179 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
6050200 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
6050221 A
1 A
6050222 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:6052244 original size:32 final size:32
Alignment explanation
Indices: 6052203--6052266 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
6052193 ATTCAATTTT
* *
6052203 ATTTAATTTATGATTATTTTATTTTCCTTCGA
1 ATTTAATTTATGATTATTTTAATTCCCTTCGA
6052235 ATTTAATTTATGATTATTTTAATTCCCTTCGA
1 ATTTAATTTATGATTATTTTAATTCCCTTCGA
6052267 GTCTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.11, G:0.06, T:0.56
Consensus pattern (32 bp):
ATTTAATTTATGATTATTTTAATTCCCTTCGA
Found at i:6052255 original size:16 final size:16
Alignment explanation
Indices: 6052204--6052258 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
6052194 TTCAATTTTA
6052204 TTTAATTTATGATTAT
1 TTTAATTTATGATTAT
** *
6052220 TTT-ATTT-TCCTTCGAA
1 TTTAATTTATGATT--AT
6052236 TTTAATTTATGATTAT
1 TTTAATTTATGATTAT
6052252 TTTAATT
1 TTTAATT
6052259 CCCTTCGAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 3 0.10
15 4 0.14
16 15 0.52
17 4 0.14
18 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTAATTTATGATTAT
Found at i:6053962 original size:30 final size:31
Alignment explanation
Indices: 6053907--6053967 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6053897 ACATCCTTTA
*
6053907 GCCAAGAACCCACACATCCTTCGGGTTTCAC
1 GCCAAGAACCCACACATCCTCCGGGTTTCAC
* *
6053938 GCCAAG-ACCCTCATATCCTCCGGGTTTCAC
1 GCCAAGAACCCACACATCCTCCGGGTTTCAC
6053968 ACTCATTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.21
Consensus pattern (31 bp):
GCCAAGAACCCACACATCCTCCGGGTTTCAC
Found at i:6055574 original size:23 final size:23
Alignment explanation
Indices: 6055548--6055613 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
6055538 TAAAACCTGG
*
6055548 CCCAGAGCCCAAATTAAACCCGA
1 CCCAGAGCCCAAACTAAACCCGA
* * *
6055571 CCCAAAGCCTAACCTAAACCCGA
1 CCCAGAGCCCAAACTAAACCCGA
* * *
6055594 CCCAGAACCTAACCTAAACC
1 CCCAGAGCCCAAACTAAACC
6055614 TAAACCTAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.39, C:0.42, G:0.09, T:0.09
Consensus pattern (23 bp):
CCCAGAGCCCAAACTAAACCCGA
Found at i:6056829 original size:6 final size:6
Alignment explanation
Indices: 6056818--6056860 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
6056808 AACCTTTGTA
* *
6056818 TTTATT TTTATT TAT-TT TTTATT TTTATTT TTTATT TTAATT T
1 TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT T
6056861 GTTTAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.12
6 22 0.69
7 6 0.19
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:6056840 original size:17 final size:17
Alignment explanation
Indices: 6056818--6056887 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
6056808 AACCTTTGTA
6056818 TTTATTTTTATTTATTT
1 TTTATTTTTATTTATTT
*
6056835 TTTATTTTTATTTTTTAT
1 TTTATTTTTATTTATT-T
* * *
6056853 TTTA-ATTTGTTTAATT
1 TTTATTTTTATTTATTT
*
6056869 TTTGTTTATTATTATATTT
1 TTTATTT-TTATT-TATTT
6056888 AATATTTCAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.10
17 23 0.57
18 9 0.22
19 4 0.10
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTATTTTTATTTATTT
Found at i:6056846 original size:13 final size:13
Alignment explanation
Indices: 6056828--6056881 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
6056818 TTTATTTTTA
6056828 TTTATTTTTTATT
1 TTTATTTTTTATT
6056841 TTTATTTTTTATT
1 TTTATTTTTTATT
*
6056854 TTAATTTGTTTAATT
1 TTTATTT-TTT-ATT
* *
6056869 TTTGTTTATTATT
1 TTTATTTTTTATT
6056882 ATATTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 22 0.63
14 5 0.14
15 8 0.23
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:6067681 original size:139 final size:139
Alignment explanation
Indices: 6067359--6067945 Score: 829
Period size: 139 Copynumber: 4.2 Consensus size: 139
6067349 TGATAGACCA
* * * * *
6067359 ACCAACATTTCCCATGAAGAGTTAATAATGAGAATAACTCATCCGATGAGGTAGAAGAACTTCAT
1 ACCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * *
6067424 AATGAGAAGAACTTGTTCAACCTTAGCTAGATTCATCGCATATAGAGTTGAATCA-TGACGCCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGTGACACCTC
6067488 ACTCGAGGG
131 ACTCGAGGG
* * * * *
6067497 ACCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAATAAGTTTAT
1 ACCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * * * * ** *
6067562 AATGAGAAGAACTTGTTCAATCTTAGCTTGATTCATCGCATATGGAGTTGTATCAGTGATGCCTT
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGTGACACCTC
6067627 ACTCGAGGG
131 ACTCGAGGG
* *
6067636 ACCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGATGATGGAGAAGAAGTTCAA
1 ACCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * * *
6067701 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATCACATATAGAGTTAAATCAGTGACACTTT
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGTGACACCTC
*
6067766 ACTTGAGGG
131 ACTCGAGGG
*
6067775 ACCAACATTTCCAATGGAGAGTTCATAATGAGAATACCTCATCCGATGAGGGAGAAGAAGTTCAT
1 ACCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCAT
***
6067840 AATGAGAAGAACTTGTTCATTATTAGCTCGATTCATCACATATAGAGTTGAATCAGTGACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGTGACACCTC
*
6067905 ACTCGAGGT
131 ACTCGAGGG
* * *
6067914 ATCAACATTTTCAAT--AGGGTTCATAATGAGAA
1 ACCAACATTTCCAATGGAGAGTTCATAATGAGAA
6067946 GAAACTCGTT
Statistics
Matches: 399, Mismatches: 49, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
137 16 0.04
138 106 0.27
139 277 0.69
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (139 bp):
ACCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGTGACACCTC
ACTCGAGGG
Found at i:6080626 original size:28 final size:28
Alignment explanation
Indices: 6080583--6080637 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
6080573 TCAACATGTG
* *
6080583 TATTGAATAGTGGTTTGAGGAATTCCCT
1 TATTGAATAGTGGTTTGAAGAAGTCCCT
*
6080611 TATTGAATAGTTGTTTGAAGAAGTCCC
1 TATTGAATAGTGGTTTGAAGAAGTCCC
6080638 ACCAATCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (28 bp):
TATTGAATAGTGGTTTGAAGAAGTCCCT
Found at i:6081486 original size:18 final size:18
Alignment explanation
Indices: 6081446--6081484 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
6081436 AAGTATAAGG
6081446 ATTTATTTAAAATTAATC
1 ATTTATTTAAAATTAATC
*
6081464 ATTTA-TTAAAATTAATT
1 ATTTATTTAAAATTAATC
6081481 ATTT
1 ATTT
6081485 TAATAGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTATTTAAAATTAATC
Found at i:6087871 original size:12 final size:12
Alignment explanation
Indices: 6087854--6087883 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
6087844 ATATTACATT
6087854 TTATTATATATA
1 TTATTATATATA
6087866 TTATTATATATA
1 TTATTATATATA
6087878 TATATT
1 T-TATT
6087884 TATTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTATATATA
Found at i:6087877 original size:14 final size:13
Alignment explanation
Indices: 6087838--6087886 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
6087828 ATTGTTAATT
*
6087838 TTTTATATATTACA
1 TTTTATATA-TATA
6087852 TTTTATTATATATA
1 TTTTA-TATATATA
6087866 TTATTATATATATA
1 TT-TTATATATATA
6087880 TATTTAT
1 T-TTTAT
6087887 TTTCTTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 23 0.74
15 8 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTATATATATA
Found at i:6088454 original size:12 final size:12
Alignment explanation
Indices: 6088437--6088500 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
6088427 TCATTTATTG
6088437 TTTATTGTTTAT
1 TTTATTGTTTAT
6088449 TTTATTTGTTTAT
1 TTTA-TTGTTTAT
* * *
6088462 TATCTTATTTAT
1 TTTATTGTTTAT
* *
6088474 TGT-TTGTTT-G
1 TTTATTGTTTAT
6088484 TTTATTTGTTTAT
1 TTTA-TTGTTTAT
6088497 TTTA
1 TTTA
6088501 CTTCATGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
10 2 0.05
11 5 0.12
12 19 0.47
13 14 0.35
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (12 bp):
TTTATTGTTTAT
Found at i:6088454 original size:19 final size:19
Alignment explanation
Indices: 6088430--6088490 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
6088420 ACTTTATTCA
6088430 TTTATTGTTTATTGTTTAT
1 TTTATTGTTTATTGTTTAT
*
6088449 TTTATTTGTTTATTATCTTA-
1 TTTA-TTGTTTATTGT-TTAT
*
6088469 TTTATTGTTTGTTTGTTTAT
1 TTTATTGTTT-ATTGTTTAT
6088489 TT
1 TT
6088491 GTTTATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 13 0.37
20 19 0.54
21 3 0.09
ACGTcount: A:0.15, C:0.02, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTATTGTTTATTGTTTAT
Found at i:6088470 original size:35 final size:35
Alignment explanation
Indices: 6088422--6088497 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
6088412 ATTCATTTAC
*
6088422 TTTATTCATTTATTGT-TT-ATTGTTTATTTTATTTG
1 TTTATTCATTTATT-TATTGATTGTTT-GTTTATTTG
*
6088457 TTTATT-ATCTTATTTATTGTTTGTTTGTTTATTTG
1 TTTATTCAT-TTATTTATTGATTGTTTGTTTATTTG
6088492 TTTATT
1 TTTATT
6088498 TTACTTCATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
34 3 0.08
35 27 0.75
36 6 0.17
ACGTcount: A:0.16, C:0.03, G:0.09, T:0.72
Consensus pattern (35 bp):
TTTATTCATTTATTTATTGATTGTTTGTTTATTTG
Found at i:6089519 original size:15 final size:15
Alignment explanation
Indices: 6089501--6089529 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6089491 TCTTTCATCA
6089501 TTTTTT-TATTTACT
1 TTTTTTATATTTACT
6089515 TTTTTTATATTTACT
1 TTTTTTATATTTACT
6089530 AACTCTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTATATTTACT
Found at i:6090054 original size:14 final size:14
Alignment explanation
Indices: 6090035--6090064 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6090025 ATTAAACACA
6090035 TTAAAAGTCAGCCT
1 TTAAAAGTCAGCCT
6090049 TTAAAAGTCAGCCT
1 TTAAAAGTCAGCCT
6090063 TT
1 TT
6090065 CAAGAATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (14 bp):
TTAAAAGTCAGCCT
Found at i:6090805 original size:17 final size:17
Alignment explanation
Indices: 6090780--6090819 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
6090770 TAAGAAGATG
* *
6090780 ATCAAGGAAGCAGCTGA
1 ATCATGGAAGCAGCCGA
6090797 ATCATGGAAGCAGCCGA
1 ATCATGGAAGCAGCCGA
6090814 ATCATG
1 ATCATG
6090820 AAAGAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.15
Consensus pattern (17 bp):
ATCATGGAAGCAGCCGA
Found at i:6092706 original size:2 final size:2
Alignment explanation
Indices: 6092701--6092725 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6092691 TTTTTTAGAT
6092701 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6092726 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6092777 original size:47 final size:46
Alignment explanation
Indices: 6092705--6092832 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 46
6092695 TTAGATTATA
*
6092705 TATATATATATATATATATATTATTTTTTTATTATCAGTTTTATTAAT
1 TATATATATATATATATTTATTATTTTTTTATTAT--GTTTTATTAAT
* * *
6092753 T-TATATATATATATATTTACTATTTTTTTATT-TTTTTTATTTAT
1 TATATATATATATATATTTATTATTTTTTTATTATGTTTTATTAAT
6092797 TATATATATATATATTATTT-TTACTTTTTTTATTAT
1 TATATATATATATA-TATTTATTA-TTTTTTTATTAT
6092833 TTTATTTATT
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
44 10 0.14
45 14 0.20
46 16 0.23
47 30 0.42
48 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (46 bp):
TATATATATATATATATTTATTATTTTTTTATTATGTTTTATTAAT
Found at i:6092789 original size:9 final size:9
Alignment explanation
Indices: 6092775--6092907 Score: 54
Period size: 9 Copynumber: 13.9 Consensus size: 9
6092765 ATATTTACTA
6092775 TTTTTTTAT
1 TTTTTTTAT
6092784 TTTTTTTAT
1 TTTTTTTAT
* *
6092793 TTATTATAT
1 TTTTTTTAT
* * *
6092802 ATATATATAT
1 -TTTTTTTAT
*
6092812 TATTTTTACTT
1 TTTTTTTA--T
6092823 TTTTTATTAT
1 TTTTT-TTAT
*
6092833 TTTATTTAT
1 TTTTTTTAT
*
6092842 TTGTTTTA-
1 TTTTTTTAT
* *
6092850 TTTATATAT
1 TTTTTTTAT
*
6092859 TTTCTTCTTCT
1 TTT-TT-TTAT
6092870 TTTTCTTTA-
1 TTTT-TTTAT
*
6092879 TTTCTTTAT
1 TTTTTTTAT
6092888 TCTTTTTTAT
1 T-TTTTTTAT
6092898 ATTTATTTTA
1 -TTT-TTTTA
6092908 CTTACTATTT
Statistics
Matches: 92, Mismatches: 20, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
8 9 0.10
9 39 0.42
10 24 0.26
11 17 0.18
12 3 0.03
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:6092825 original size:45 final size:44
Alignment explanation
Indices: 6092677--6092842 Score: 141
Period size: 45 Copynumber: 3.8 Consensus size: 44
6092667 TTTTACTTTA
** * *
6092677 ATATA-TATTTTTATTTTTT-TAGATTATATATATATATATATAT
1 ATATATTATTTTTATTTTTTATTTATTTTATTTAT-TATATATAT
* * *
6092720 ATATATTA-TTTT-TTTATTA-TCAGTTTTATTAATT-TATATAT
1 ATATATTATTTTTATTTTTTATTTA-TTTTATTTATTATATATAT
* *
6092761 ATATA-TATTTACTATTTTTTTATTTTTTTTATTTATTATATATAT
1 ATATATTATTT-TTA-TTTTTTATTTATTTTATTTATTATATATAT
6092806 ATATATTATTTTTACTTTTTT-TATTATTTTATTTATT
1 ATATATTATTTTTA-TTTTTTAT-TTATTTTATTTATT
6092843 TGTTTTATTT
Statistics
Matches: 98, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
40 2 0.02
41 14 0.14
42 8 0.08
43 16 0.16
44 19 0.19
45 34 0.35
46 5 0.05
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (44 bp):
ATATATTATTTTTATTTTTTATTTATTTTATTTATTATATATAT
Found at i:6092852 original size:36 final size:37
Alignment explanation
Indices: 6092752--6092830 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
6092742 GTTTTATTAA
* * *
6092752 TTTATATA-TATATATATTTACTATT-TTTTTATTTTT
1 TTTATTTATTATATATATATA-TATTATTTTTACTTTT
6092788 TTTATTTATTATATATATATATATTATTTTTACTTTT
1 TTTATTTATTATATATATATATATTATTTTTACTTTT
6092825 TTTATT
1 TTTATT
6092831 ATTTTATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 11 0.29
37 27 0.71
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (37 bp):
TTTATTTATTATATATATATATATTATTTTTACTTTT
Found at i:6092856 original size:45 final size:44
Alignment explanation
Indices: 6092726--6092906 Score: 118
Period size: 49 Copynumber: 3.9 Consensus size: 44
6092716 ATATATATAT
* * * *
6092726 TATTTTTTTATTATCAGTTT-TATTAATTTATATATATATATATTTAC
1 TATTTTTTTATT-TTA-TTTAT-TTATTTTATTTATAT-TATTTTTAC
*
6092773 TATTTTTTTATTTTTTTTATTTATTATATATATATATATTATTTTTAC
1 TATTTTTTTATTTTATTTATTTATT-T-TAT-T-TATATTATTTTTAC
* * *
6092821 TTTTTTTATTATTTTATTTATTTGTTTTATTTATA-TATTTTCTTC
1 TATTTTT-TTATTTTATTTATTTATTTTATTTATATTATTTT-TAC
* * * *
6092866 T-TCTTTTT-CTTTATTTCTTTATTCTTTTTTATATTTATTTT
1 TATTTTTTTATTTTATTTATTTATT-TTATTTATA-TTATTTT
6092907 ACTTACTATT
Statistics
Matches: 110, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
42 12 0.11
43 10 0.09
44 10 0.09
45 20 0.18
46 4 0.04
47 18 0.16
48 15 0.14
49 21 0.19
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (44 bp):
TATTTTTTTATTTTATTTATTTATTTTATTTATATTATTTTTAC
Found at i:6100112 original size:61 final size:58
Alignment explanation
Indices: 6100029--6100144 Score: 135
Period size: 61 Copynumber: 1.9 Consensus size: 58
6100019 AATACTTCGC
* ** *
6100029 TTAGGATGATAACCCAAGAGGGCGTCCTAAGTCGGAAAAAAAACGAAAAAAGAAAAAACGT
1 TTAGGATGAAAACCCAAGAGGGCACCCTAAAT-GG-AAAAAAA-GAAAAAAGAAAAAACGT
* *
6100090 TTAGGGTGAAAACCCGAA-AGGGCACCCTAAATTGAAAAAAAGAAAAAAGAAAAAA
1 TTAGGATGAAAACCC-AAGAGGGCACCCTAAATGGAAAAAAAGAAAAAAGAAAAAA
6100145 AGAGAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
58 14 0.29
59 7 0.15
60 1 0.02
61 24 0.50
62 2 0.04
ACGTcount: A:0.53, C:0.14, G:0.22, T:0.12
Consensus pattern (58 bp):
TTAGGATGAAAACCCAAGAGGGCACCCTAAATGGAAAAAAAGAAAAAAGAAAAAACGT
Found at i:6100136 original size:8 final size:8
Alignment explanation
Indices: 6100123--6100184 Score: 74
Period size: 9 Copynumber: 7.6 Consensus size: 8
6100113 ACCCTAAATT
6100123 GAAAAAAA
1 GAAAAAAA
6100131 G-AAAAAA
1 GAAAAAAA
6100138 GAAAAAAA
1 GAAAAAAA
6100146 GAGAAAAAA
1 GA-AAAAAA
6100155 GAGAAAAAA
1 GA-AAAAAA
6100164 GGAAAAAAA
1 -GAAAAAAA
*
6100173 -AGAAAAA
1 GAAAAAAA
6100180 GAAAA
1 GAAAA
6100185 GTGGTTCAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
7 13 0.27
8 12 0.25
9 21 0.44
10 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:6100137 original size:7 final size:7
Alignment explanation
Indices: 6100125--6100184 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
6100115 CCTAAATTGA
6100125 AAAAAAG
1 AAAAAAG
6100132 AAAAAAG
1 AAAAAAG
6100139 AAAAAA-
1 AAAAAAG
* *
6100145 AGAGAA-
1 AAAAAAG
*
6100151 AAAAGAG
1 AAAAAAG
6100158 AAAAAAGG
1 AAAAAA-G
*
6100166 AAAAAAA
1 AAAAAAG
6100173 AGAAAAAG
1 A-AAAAAG
6100181 AAAA
1 AAAA
6100185 GTGGTTCAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 7 0.17
7 22 0.52
8 13 0.31
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:6100150 original size:17 final size:17
Alignment explanation
Indices: 6100124--6100179 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 17
6100114 CCCTAAATTG
6100124 AAAAAA-AGAAAAAAGA
1 AAAAAAGAGAAAAAAGA
6100140 AAAAAAGAGAAAAAAGA
1 AAAAAAGAGAAAAAAGA
*
6100157 GAAAAAAGGAAAAAAAAGA
1 -AAAAAA-GAGAAAAAAGA
6100176 AAAA
1 AAAA
6100180 GAAAAGTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 6 0.17
17 10 0.28
18 10 0.28
19 10 0.28
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAGAGAAAAAAGA
Found at i:6100153 original size:26 final size:26
Alignment explanation
Indices: 6100124--6100179 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
6100114 CCCTAAATTG
6100124 AAAAAAAGAAAAAA-GAAAAAAAGAGA
1 AAAAAAAGAAAAAAGGAAAAAAA-AGA
*
6100150 AAAAAGAGAAAAAAGGAAAAAAAAGA
1 AAAAAAAGAAAAAAGGAAAAAAAAGA
6100176 AAAA
1 AAAA
6100180 GAAAAGTGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (26 bp):
AAAAAAAGAAAAAAGGAAAAAAAAGA
Found at i:6101131 original size:110 final size:110
Alignment explanation
Indices: 6100938--6101297 Score: 446
Period size: 110 Copynumber: 3.3 Consensus size: 110
6100928 AGCTAGAGCT
* * **
6100938 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGTACAAGCTCAACTTCACAGCGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGG
* * *
6101003 GGCGACTGAGTGTTAACAAATAACTTTTCAGTTTCATTCAGGGTC
66 GGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
**
6101048 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAATGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGG
* *
6101113 GGCAACTGACTGTCAACAATTAACTCTTT-AGTTTCATTCAGAGTC
66 GGCGACTGACTGTCAACAAATAACT-TTTCAGTTTCATTCAGAGTC
* * * * * *
6101158 AATTTTAACTTCACAGCGAAGGATATTGGACTCGGGACAACATAAGCTCAACGTCGCAGCGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGG
* * * *
6101223 GGCGACTGGCTGTCAACAAACAA-TTTCCCAG-TTC--T-AGAGCC
66 GGCGACTGACTGTCAACAAATAACTTT-TCAGTTTCATTCAGAGTC
*
6101264 AATTTCAACTTCACGGC-AGAGGATATTAGACTCG
1 AATTTCAACTTCACAGCGA-AGGATATTAGACTCG
6101298 GAACAATACA
Statistics
Matches: 218, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
105 1 0.00
106 34 0.16
107 1 0.00
108 2 0.01
109 4 0.02
110 173 0.79
111 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (110 bp):
AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGG
GGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
Found at i:6102107 original size:23 final size:21
Alignment explanation
Indices: 6102072--6102121 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
6102062 TTTATGTCCA
6102072 AAATATATTTATATATTATAT
1 AAATATATTTATATATTATAT
* *
6102093 ATATATATCTATATATATTGTAT
1 AAATATAT-T-TATATATTATAT
6102116 AAATAT
1 AAATAT
6102122 TATTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.29
22 1 0.04
23 16 0.67
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATATATTTATATATTATAT
Found at i:6103357 original size:2 final size:2
Alignment explanation
Indices: 6103352--6103387 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6103342 TACATTTTAT
6103352 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6103388 TTCTTTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6103369 original size:17 final size:17
Alignment explanation
Indices: 6103349--6103385 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
6103339 TATTACATTT
6103349 TATTATATATATATATA
1 TATTATATATATATATA
6103366 TATTATATATATATATA
1 TATTATATATATATATA
6103383 TAT
1 TAT
6103386 ATTTCTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTATATATATATATA
Found at i:6103382 original size:19 final size:19
Alignment explanation
Indices: 6103352--6103388 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6103342 TACATTTTAT
6103352 TATATATATATATATATTA
1 TATATATATATATATATTA
6103371 TATATATATATATATATT
1 TATATATATATATATATT
6103389 TCTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATATATATATATATTA
Found at i:6103441 original size:5 final size:5
Alignment explanation
Indices: 6103409--6103465 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
6103399 TTTTTGAATC
* *
6103409 ATTTT ATTAT -TTTT CTTATT ATTTTT ATTTT ATTTT ATTTT ATTTT ATTTTT
1 ATTTT ATTTT ATTTT ATT-TT A-TTTT ATTTT ATTTT ATTTT ATTTT A-TTTT
6103461 ATTTT
1 ATTTT
6103466 CTTTGTTCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
4 3 0.07
5 30 0.67
6 10 0.22
7 2 0.04
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:6103456 original size:26 final size:26
Alignment explanation
Indices: 6103409--6103465 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
6103399 TTTTTGAATC
*
6103409 ATTTTATTATTTTTCTTATTATTTTT
1 ATTTTATTATTTTTATTATTATTTTT
*
6103435 ATTTTATTTTATTTTATT-TTATTTTT
1 ATTTTATTAT-TTTTATTATTATTTTT
6103461 ATTTT
1 ATTTT
6103466 CTTTGTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (26 bp):
ATTTTATTATTTTTATTATTATTTTT
Found at i:6103484 original size:21 final size:20
Alignment explanation
Indices: 6103460--6103504 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
6103450 ATTTTATTTT
* *
6103460 TATTTTCTTTGTTCATATGTA
1 TATTTTATTTGTT-ATATATA
6103481 TATTTTTATTTGTTATATATA
1 TA-TTTTATTTGTTATATATA
6103502 TAT
1 TAT
6103505 ATATATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.05
21 10 0.48
22 10 0.48
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.64
Consensus pattern (20 bp):
TATTTTATTTGTTATATATA
Found at i:6103849 original size:14 final size:13
Alignment explanation
Indices: 6103822--6103995 Score: 79
Period size: 13 Copynumber: 12.5 Consensus size: 13
6103812 TAGTTTTTCA
*
6103822 TATTTTATTATTT
1 TATTTTATTTTTT
6103835 TATTATTATTTTTT
1 TATT-TTATTTTTT
*
6103849 TATTCTATTTAATTT
1 TATTTTATTT--TTT
*
6103864 T-TTGTATTTGTATT
1 TATTTTATTT-T-TT
6103878 T-TTTTATTTTTT
1 TATTTTATTTTTT
*
6103890 TATTTTCGCTTGGTTTTT
1 TATTTT---AT--TTTTT
* *
6103908 CTAATTCATTTATTT
1 -TATTTTATTT-TTT
*
6103923 TA-TTTATTTGTT
1 TATTTTATTTTTT
6103935 TATTTTATTTGTTTAT
1 TATTTTA-TT-TTT-T
* *
6103951 TATCTTATTTATT
1 TATTTTATTTTTT
6103964 TA-TTTATTTTGTT
1 TATTTTATTTT-TT
*
6103977 T-TTTTATTTGTT
1 TATTTTATTTTTT
6103989 TATTTTA
1 TATTTTA
6103996 CTTCCTGTTT
Statistics
Matches: 125, Mismatches: 17, Indels: 38
0.69 0.09 0.21
Matches are distributed among these distances:
12 16 0.13
13 43 0.34
14 37 0.30
15 11 0.09
16 9 0.07
18 5 0.04
19 4 0.03
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (13 bp):
TATTTTATTTTTT
Found at i:6103878 original size:20 final size:18
Alignment explanation
Indices: 6103823--6103871 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
6103813 AGTTTTTCAT
* * *
6103823 ATTTTATTATTTTATTATT
1 ATTTTTTTATTCTATT-TA
6103842 ATTTTTTTATTCTATTTA
1 ATTTTTTTATTCTATTTA
6103860 ATTTTTTGTATT
1 ATTTTTT-TATT
6103872 TGTATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTTATTCTATTTA
Found at i:6103894 original size:8 final size:8
Alignment explanation
Indices: 6103808--6103994 Score: 74
Period size: 8 Copynumber: 22.2 Consensus size: 8
6103798 TATATTATCA
6103808 TTTTTAGTT
1 TTTTTA-TT
*
6103817 TTTCATATT
1 TTT-TTATT
*
6103826 TTATTATTT
1 TTTTTA-TT
6103835 TATTATTATT
1 T-TT-TTATT
6103845 TTTTTATT
1 TTTTTATT
* *
6103853 CTATTTAAT
1 -TTTTTATT
* *
6103862 TTTTTGTA
1 TTTTTATT
*
6103870 TTTGTATT
1 TTTTTATT
6103878 TTTTTATT
1 TTTTTATT
6103886 TTTTTATT
1 TTTTTATT
**
6103894 TTCGCTTGGTT
1 TT---TTTATT
*
6103905 TTTCTAATT
1 TTT-TTATT
**
6103914 CATTTATT
1 TTTTTATT
6103922 TTATTTATT
1 TT-TTTATT
*
6103931 TGTTTA--
1 TTTTTATT
6103937 -TTTTATT
1 TTTTTATT
*
6103944 TGTTTATT
1 TTTTTATT
* *
6103952 ATCTTATT
1 TTTTTATT
*
6103960 TATTTATT
1 TTTTTATT
*
6103968 TATTTTGTT
1 T-TTTTATT
6103977 TTTTTATT
1 TTTTTATT
*
6103985 TGTTTATT
1 TTTTTATT
6103993 TT
1 TT
6103995 ACTTCCTGTT
Statistics
Matches: 127, Mismatches: 37, Indels: 29
0.66 0.19 0.15
Matches are distributed among these distances:
5 4 0.03
8 73 0.57
9 35 0.28
10 6 0.05
11 9 0.07
ACGTcount: A:0.17, C:0.04, G:0.05, T:0.74
Consensus pattern (8 bp):
TTTTTATT
Found at i:6103928 original size:4 final size:4
Alignment explanation
Indices: 6103915--6103993 Score: 70
Period size: 4 Copynumber: 19.0 Consensus size: 4
6103905 TTTCTAATTC
* *
6103915 ATTT ATTTT ATTT ATTT GTTT ATTTT ATTT GTTT A-TT ATCTT ATTT ATTT
1 ATTT A-TTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT AT-TT ATTT ATTT
* * *
6103965 ATTT ATTTT GTTT TTTT ATTT GTTT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT
6103994 TACTTCCTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
3 3 0.05
4 43 0.70
5 15 0.25
ACGTcount: A:0.18, C:0.01, G:0.05, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:6103992 original size:33 final size:33
Alignment explanation
Indices: 6103917--6103993 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
6103907 TCTAATTCAT
*
6103917 TTATTTTATTTATTTGTTTATTTTATTTGTTTA
1 TTATTTTATTTATTTATTTATTTTATTTGTTTA
* * *
6103950 TTATCTTATTTATTTATTTATTTTGTTTTTTTA
1 TTATTTTATTTATTTATTTATTTTATTTGTTTA
6103983 TT-TGTTTATTT
1 TTAT-TTTATTT
6103994 TACTTCCTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.03
33 37 0.97
ACGTcount: A:0.17, C:0.01, G:0.05, T:0.77
Consensus pattern (33 bp):
TTATTTTATTTATTTATTTATTTTATTTGTTTA
Found at i:6108563 original size:18 final size:18
Alignment explanation
Indices: 6108540--6108586 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
6108530 TACATAATAT
*
6108540 AATAATTTTTTCAA-TTAA
1 AATAATTTTTT-AACTAAA
*
6108558 AATAATATTTTAACTAAA
1 AATAATTTTTTAACTAAA
6108576 AACTAATTTTT
1 AA-TAATTTTT
6108587 AAATGAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 15 0.62
19 7 0.29
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAATTTTTTAACTAAA
Found at i:6109360 original size:35 final size:35
Alignment explanation
Indices: 6109315--6109440 Score: 180
Period size: 35 Copynumber: 3.6 Consensus size: 35
6109305 ACACACATAA
*
6109315 AAAAAGTACAACTAAAAACATACATAAACTTAGTT
1 AAAAAGTACAACTAAAAACACACATAAACTTAGTT
*
6109350 AAAAAGTACAACTAAAAACACACATAAGCTTAGTT
1 AAAAAGTACAACTAAAAACACACATAAACTTAGTT
* * *
6109385 AAAAAATATAGCTAAAAACACACATAAACTTAGTT
1 AAAAAGTACAACTAAAAACACACATAAACTTAGTT
* *
6109420 AAAATATTACAACTTAAAACA
1 AAAA-AGTACAACTAAAAACA
6109441 TAACATAACA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 68 0.85
36 12 0.15
ACGTcount: A:0.57, C:0.15, G:0.06, T:0.22
Consensus pattern (35 bp):
AAAAAGTACAACTAAAAACACACATAAACTTAGTT
Found at i:6110206 original size:14 final size:15
Alignment explanation
Indices: 6110188--6110271 Score: 68
Period size: 14 Copynumber: 5.7 Consensus size: 15
6110178 ATAGCATATA
6110188 GCATATTATATAATT
1 GCATATTATATAATT
*
6110203 -CATATTAAATAATT
1 GCATATTATATAATT
*
6110217 GCATATTATAGT-GTT
1 GCATATTATA-TAATT
* * *
6110232 -CATGTTAAATAGTT
1 GCATATTATATAATT
6110246 AGCATATTAT-TAGATT
1 -GCATATTATATA-ATT
6110262 GCATATTATA
1 GCATATTATA
6110272 AATAATAGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
13 1 0.02
14 23 0.43
15 21 0.39
16 9 0.17
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (15 bp):
GCATATTATATAATT
Found at i:6110222 original size:29 final size:30
Alignment explanation
Indices: 6110186--6110269 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 30
6110176 ATATAGCATA
6110186 TAGCATATTATATAATTCATATTAAATAAT
1 TAGCATATTATATAATTCATATTAAATAAT
* * *
6110216 T-GCATATTATAGT-GTTCATGTTAAATAGT
1 TAGCATATTATA-TAATTCATATTAAATAAT
6110245 TAGCATATTAT-TAGATTGCATATTA
1 TAGCATATTATATA-ATT-CATATTA
6110270 TAAATAATAG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
28 1 0.02
29 24 0.55
30 13 0.30
31 6 0.14
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (30 bp):
TAGCATATTATATAATTCATATTAAATAAT
Found at i:6111520 original size:18 final size:19
Alignment explanation
Indices: 6111485--6111521 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6111475 CACGGAATGT
6111485 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
6111505 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
6111522 GGATTAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:6116948 original size:28 final size:27
Alignment explanation
Indices: 6116877--6116993 Score: 119
Period size: 27 Copynumber: 4.3 Consensus size: 27
6116867 ATTTCTGTCT
6116877 CTTTTAATTTCTTTTTAATCTTTATT-
1 CTTTTAATTTCTTTTTAATCTTTATTC
*** * *
6116903 CTTTTAATTTCCACTTAATATTTTTTTC
1 CTTTTAATTTCTTTTTAAT-CTTTATTC
*
6116931 CTTTTGATTTCTTTTTAATCTTTATTC
1 CTTTTAATTTCTTTTTAATCTTTATTC
* * * *
6116958 CTTTTAATTCCCTTTAAATCTTTATTT
1 CTTTTAATTTCTTTTTAATCTTTATTC
*
6116985 ATTTTAATT
1 CTTTTAATT
6116994 CTTATAAATA
Statistics
Matches: 72, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
26 16 0.22
27 41 0.57
28 15 0.21
ACGTcount: A:0.21, C:0.15, G:0.01, T:0.64
Consensus pattern (27 bp):
CTTTTAATTTCTTTTTAATCTTTATTC
Found at i:6128001 original size:5 final size:5
Alignment explanation
Indices: 6127984--6128045 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
6127974 TATAACGGTT
* *
6127984 GAAAA G-AAA -AAAA GAAAA GAAAAAA GAAAA AAAAA TATAAA GAAAAA
1 GAAAA GAAAA GAAAA GAAAA G--AAAA GAAAA GAAAA GA-AAA G-AAAA
6128031 GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA
6128046 TACAGAAGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 6 0.12
5 29 0.60
6 7 0.15
7 6 0.12
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (5 bp):
GAAAA
Found at i:6128025 original size:16 final size:16
Alignment explanation
Indices: 6127992--6128045 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
6127982 TTGAAAAGAA
6127992 AAAAAGAAAAGAAAAAAG
1 AAAAAGAAAAG--AAAAG
*
6128010 AAAAA-AAAATATAAAG
1 AAAAAGAAAAGA-AAAG
6128026 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
6128042 AAAA
1 AAAA
6128046 TACAGAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 1 0.03
16 17 0.53
17 9 0.28
18 5 0.16
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:6129554 original size:18 final size:18
Alignment explanation
Indices: 6129527--6129568 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
6129517 AAAGTTTGGG
*
6129527 TATATAGTATATA-TTATT
1 TATATTGTATATACTT-TT
6129545 TATATTGTATATACTTTT
1 TATATTGTATATACTTTT
6129563 TATATT
1 TATATT
6129569 AAATAGACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATTGTATATACTTTT
Found at i:6129601 original size:14 final size:14
Alignment explanation
Indices: 6129582--6129665 Score: 71
Period size: 14 Copynumber: 5.7 Consensus size: 14
6129572 TAGACATATA
*
6129582 TCATATTATATAGC
1 TCATATTATATAGT
* *
6129596 TCATATTAAATAAT
1 TCATATTATATAGT
6129610 TGCATATTATATAGT
1 T-CATATTATATAGT
* *
6129625 TCATGTTAAATAGT
1 TCATATTATATAGT
6129639 TAGCATATTAT-TAGAT
1 T--CATATTATATAG-T
6129655 TGCATATTATA
1 T-CATATTATA
6129666 AATAATATCC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
14 24 0.43
15 24 0.43
16 8 0.14
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (14 bp):
TCATATTATATAGT
Found at i:6129616 original size:29 final size:30
Alignment explanation
Indices: 6129583--6129649 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
6129573 AGACATATAT
6129583 CATATTATATAGCTCATATTAAATAATT-G
1 CATATTATATAGCTCATATTAAATAATTAG
* * *
6129612 CATATTATATAGTTCATGTTAAATAGTTAG
1 CATATTATATAGCTCATATTAAATAATTAG
6129642 CATATTAT
1 CATATTAT
6129650 TAGATTGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (30 bp):
CATATTATATAGCTCATATTAAATAATTAG
Found at i:6129617 original size:15 final size:15
Alignment explanation
Indices: 6129597--6129663 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
6129587 TTATATAGCT
6129597 CATATTAAATAATTG
1 CATATTAAATAATTG
* *
6129612 CATATTATATAGTT-
1 CATATTAAATAATTG
* *
6129626 CATGTTAAATAGTTAG
1 CATATTAAATAATT-G
*
6129642 CATATT-ATTAGATTG
1 CATATTAAATA-ATTG
6129657 CATATTA
1 CATATTA
6129664 TAAATAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
14 12 0.29
15 22 0.54
16 7 0.17
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
CATATTAAATAATTG
Found at i:6130387 original size:18 final size:19
Alignment explanation
Indices: 6130359--6130395 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
6130349 TTAGAATATG
6130359 AAAAATAAGAAAAAAAGAA
1 AAAAATAAGAAAAAAAGAA
6130378 AAAAAT-AGAAAAAAAGAA
1 AAAAATAAGAAAAAAAGAA
6130396 TGTTCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (19 bp):
AAAAATAAGAAAAAAAGAA
Found at i:6134613 original size:85 final size:84
Alignment explanation
Indices: 6134465--6134856 Score: 380
Period size: 85 Copynumber: 4.6 Consensus size: 84
6134455 TAAATTTTAT
* ** * ** *
6134465 AGAATCTTAACTGTTCATGTCCTTTTCTTTTCAGACAAATATCACCTCAAATCAGATCGAGTAAA
1 AGAATCTTAACTATTCACATCCTTTACTTTTCA-TTAAATATCACCTCAAATCAGATCAAGTAAA
6134530 A-AATTAATTTCAAATGACAG
65 ATAA-TAATTTCAAATGACAG
* * *
6134550 AGAATCTTAACTATTCACATCAC-TTGCTTTCCATTAAAATATCACCTCAAATTAGATCAAGTAA
1 AGAATCTTAACTATTCACATC-CTTTACTTTTCATT-AAATATCACCTCAAATCAGATCAAGTAA
*** *
6134614 AATAATAATTTCAAATTTTAT
64 AATAATAATTTCAAATGACAG
* * * *
6134635 AGAATCTTAACTATTCACAACCTTTTCTTTTAAGTTAAATATCACCTCAAATCAAATCAAGTACA
1 AGAATCTTAACTATTCACATCCTTTACTTTTCA-TTAAATATCACCTCAAATCAGATCAAGTA-A
* *
6134700 CAAT--TACTTTCAAATGACAT
64 -AATAATAATTTCAAATGACAG
* * ** *
6134720 AGAATCTTTACTATTAATGTCCTTTATTTTTCATTGAAATATCACCTCAAATCAGATCAAGTAAA
1 AGAATCTTAACTATTCACATCCTTTACTTTTCATT-AAATATCACCTCAAATCAGATCAAGTAAA
*
6134785 ATAATAATTTCAAAT-TCTAG
65 ATAATAATTTCAAATGAC-AG
* * * * *
6134805 AGAATCTTAACTATTCACGTCATTTATTTTTCAATCAAATATCATCTCAAAT
1 AGAATCTTAACTATTCACATCCTTTACTTTTC-ATTAAATATCACCTCAAAT
6134857 GAATTAGGGT
Statistics
Matches: 254, Mismatches: 41, Indels: 24
0.80 0.13 0.08
Matches are distributed among these distances:
83 3 0.01
84 5 0.02
85 235 0.93
86 8 0.03
87 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (84 bp):
AGAATCTTAACTATTCACATCCTTTACTTTTCATTAAATATCACCTCAAATCAGATCAAGTAAAA
TAATAATTTCAAATGACAG
Found at i:6134847 original size:170 final size:170
Alignment explanation
Indices: 6134456--6134856 Score: 522
Period size: 170 Copynumber: 2.4 Consensus size: 170
6134446 TAATATTTAT
* * *
6134456 AAATTTTATAGAATCTTAACTGTTCATGTCCTTTTCTTTTCAGA-CAAATATCACCTCAAATCAG
1 AAATTTTATAGAATCTTAACTATTCACGTCCTTTTCTTTTCA-ATCAAATATCACCTCAAATCAA
* * *
6134520 ATCGAGTAAAAAATTAATTTCAAATGACAGAGAATCTTAACTATTCACATCACTTGCTTTCCATT
65 ATCAAGTAAAAAATTAATTTCAAATGACAGAGAATCTTAACTATTAACATCACTTACTTTCCATT
*
6134585 AAAATATCACCTCAAATTAGATCAAGTAAAATAATAATTTC
130 AAAATATCACCTCAAATCAGATCAAGTAAAATAATAATTTC
** *
6134626 AAATTTTATAGAATCTTAACTATTCACAACCTTTTCTTTT-AAGTTAAATATCACCTCAAATCAA
1 AAATTTTATAGAATCTTAACTATTCACGTCCTTTTCTTTTCAA-TCAAATATCACCTCAAATCAA
* * * * * ** * *
6134690 ATCAAGTACACAATTACTTTCAAATGACATAGAATCTTTACTATTAATGTC-CTTTATTTTTCAT
65 ATCAAGTAAAAAATTAATTTCAAATGACAGAGAATCTTAACTATTAACATCAC-TTACTTTCCAT
*
6134754 TGAAATATCACCTCAAATCAGATCAAGTAAAATAATAATTTC
129 TAAAATATCACCTCAAATCAGATCAAGTAAAATAATAATTTC
* * * *
6134796 AAATTCTAGAGAATCTTAACTATTCACGTCATTTAT-TTTTCAATCAAATATCATCTCAAAT
1 AAATTTTATAGAATCTTAACTATTCACGTCCTTT-TCTTTTCAATCAAATATCACCTCAAAT
6134857 GAATTAGGGT
Statistics
Matches: 199, Mismatches: 27, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
168 1 0.01
169 2 0.01
170 193 0.97
171 3 0.02
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (170 bp):
AAATTTTATAGAATCTTAACTATTCACGTCCTTTTCTTTTCAATCAAATATCACCTCAAATCAAA
TCAAGTAAAAAATTAATTTCAAATGACAGAGAATCTTAACTATTAACATCACTTACTTTCCATTA
AAATATCACCTCAAATCAGATCAAGTAAAATAATAATTTC
Found at i:6134879 original size:18 final size:18
Alignment explanation
Indices: 6134854--6135060 Score: 242
Period size: 18 Copynumber: 11.6 Consensus size: 18
6134844 TATCATCTCA
*
6134854 AATGAATTAGGGTTTTTT
1 AATGAATTAGGGTTTCTT
*
6134872 AGTGAATTAGGGTTT-TAT
1 AATGAATTAGGGTTTCT-T
* * *
6134890 AGTGCATTAAGGTTTCTT
1 AATGAATTAGGGTTTCTT
6134908 AATGAATTAGGGTTT-TT
1 AATGAATTAGGGTTTCTT
*
6134925 AGTGAATTAGGGTTTCTT
1 AATGAATTAGGGTTTCTT
* *
6134943 AGTTAATTAGGGTTTCTT
1 AATGAATTAGGGTTTCTT
*
6134961 AATAAATTAGGGTTT-TT
1 AATGAATTAGGGTTTCTT
* *
6134978 AATGACTTACGAGTTTCTT
1 AATGAATTA-GGGTTTCTT
*
6134997 AATGAATTAGGGTCTCTT
1 AATGAATTAGGGTTTCTT
6135015 AATGAATTAGGGTTTCTT
1 AATGAATTAGGGTTTCTT
* *
6135033 AGTGACTTAGGGTTT-TT
1 AATGAATTAGGGTTTCTT
6135050 AATGAATTAGG
1 AATGAATTAGG
6135061 ATTAATGGTT
Statistics
Matches: 163, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
17 37 0.23
18 115 0.71
19 11 0.07
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.44
Consensus pattern (18 bp):
AATGAATTAGGGTTTCTT
Found at i:6134936 original size:53 final size:53
Alignment explanation
Indices: 6134854--6135060 Score: 265
Period size: 53 Copynumber: 3.9 Consensus size: 53
6134844 TATCATCTCA
* *
6134854 AATGAATTAGGGTTTTTTAGTGAATTAGGGTTT-TATAGTGCATTAAGGTTTCTT
1 AATGAATTAGGG-TTTTTAGTGAATTAGGGTTTCT-TAGTGAATTAGGGTTTCTT
*
6134908 AATGAATTAGGGTTTTTAGTGAATTAGGGTTTCTTAGTTAATTAGGGTTTCTT
1 AATGAATTAGGGTTTTTAGTGAATTAGGGTTTCTTAGTGAATTAGGGTTTCTT
* * * * * *
6134961 AATAAATTAGGGTTTTTAATGACTTACGAGTTTCTTAATGAATTAGGGTCTCTT
1 AATGAATTAGGGTTTTTAGTGAATTA-GGGTTTCTTAGTGAATTAGGGTTTCTT
* *
6135015 AATGAATTAGGGTTTCTTAGTGACTTAGGGTTT-TTAATGAATTAGG
1 AATGAATTAGGGTTT-TTAGTGAATTAGGGTTTCTTAGTGAATTAGG
6135061 ATTAATGGTT
Statistics
Matches: 137, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
53 72 0.53
54 55 0.40
55 10 0.07
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.44
Consensus pattern (53 bp):
AATGAATTAGGGTTTTTAGTGAATTAGGGTTTCTTAGTGAATTAGGGTTTCTT
Found at i:6136924 original size:42 final size:42
Alignment explanation
Indices: 6136860--6136956 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
6136850 CCCCACTTCA
* * * * *
6136860 AGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACACCC
1 AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
*
6136902 AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACG
1 AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
6136944 AGAGCCATCACCT
1 AGAGCCATCACCT
6136957 ATTCCATCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.30, C:0.37, G:0.16, T:0.16
Consensus pattern (42 bp):
AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
Found at i:6137552 original size:21 final size:21
Alignment explanation
Indices: 6137522--6137619 Score: 115
Period size: 21 Copynumber: 4.7 Consensus size: 21
6137512 GATTCACCTA
*
6137522 TCATCGTTCAAGAGGCCCCTT
1 TCATCGTTCAAGAGGCCCCTC
*
6137543 TCATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
6137564 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
*
6137585 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
6137606 CCACCGATCAAGAG
1 TCATCGTTCAAGAG
6137620 CTCGATTCAC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:6137573 original size:42 final size:42
Alignment explanation
Indices: 6137526--6137619 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
6137516 CACCTATCAT
*
6137526 CGTTCAAGAGGCCCCTTTCATCATTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTGTCATCATTCAAGAGGCCCCTCCCAC
* *
6137568 CGTTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTGTCATCATTCAAGAGGCCCCTCCCAC
*
6137610 CGATCAAGAG
1 CGTTCAAGAG
6137620 CTCGATTCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTGTCATCATTCAAGAGGCCCCTCCCAC
Found at i:6139345 original size:15 final size:15
Alignment explanation
Indices: 6139322--6139354 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6139312 GCCGGTTGTG
6139322 ATTGGGATTTTTTTT
1 ATTGGGATTTTTTTT
*
6139337 ATTGTGATTTTTTTT
1 ATTGGGATTTTTTTT
6139352 ATT
1 ATT
6139355 ACGATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (15 bp):
ATTGGGATTTTTTTT
Found at i:6139362 original size:14 final size:15
Alignment explanation
Indices: 6139327--6139362 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6139317 TTGTGATTGG
**
6139327 GATTTTTTTTATTGT
1 GATTTTTTTTATTAC
6139342 GATTTTTTTTATTAC
1 GATTTTTTTTATTAC
6139357 GATTTT
1 GATTTT
6139363 GATTTCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.11, T:0.69
Consensus pattern (15 bp):
GATTTTTTTTATTAC
Found at i:6141656 original size:24 final size:24
Alignment explanation
Indices: 6141629--6141682 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6141619 TTGAAACATC
6141629 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* * *
6141653 ATCAAAGTTTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
6141677 ATCAAA
1 ATCAAA
6141683 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:6141696 original size:24 final size:24
Alignment explanation
Indices: 6141645--6141696 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
6141635 ATCTGAGTAT
** *
6141645 TGACCAAGATCAAAGTTTGGGTAT
1 TGACCAAGATCAAAGTTTGAATAC
6141669 TGACCAAGATCAAA-TTTCGAATAC
1 TGACCAAGATCAAAGTTT-GAATAC
6141693 TGAC
1 TGAC
6141697 TAGTACTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTTGAATAC
Found at i:6142461 original size:14 final size:16
Alignment explanation
Indices: 6142426--6142462 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6142416 GAAATCATTG
6142426 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
6142442 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
6142456 AAAATTA
1 AAAATTA
6142463 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:6142646 original size:20 final size:20
Alignment explanation
Indices: 6142621--6142686 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
6142611 TAAAACCTGG
6142621 TGCGAAATTAAAATTCGTGT
1 TGCGAAATTAAAATTCGTGT
*
6142641 TGCG-AATTCGAAAA-TCGAGT
1 TGCGAAATT--AAAATTCGTGT
**
6142661 TGCGAAAACAAAATTCGTGT
1 TGCGAAATTAAAATTCGTGT
6142681 TGCGAA
1 TGCGAA
6142687 TTCAGAAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.21
20 24 0.63
21 6 0.16
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGAAATTAAAATTCGTGT
Found at i:6142666 original size:40 final size:40
Alignment explanation
Indices: 6142621--6142768 Score: 149
Period size: 40 Copynumber: 3.7 Consensus size: 40
6142611 TAAAACCTGG
**
6142621 TGCGAAATTAAAATTCGTGTTGCGAATTC-GAAAATCGAGT
1 TGCGAAAACAAAATTCGTGTTGCGAATTCAG-AAATCGAGT
6142661 TGCGAAAACAAAATTCGTGTTGCGAATTCAGAAATCGAGT
1 TGCGAAAACAAAATTCGTGTTGCGAATTCAGAAATCGAGT
** * ** *
6142701 TGCGAATTCGGAAA-TCACGTTGCGAATTCAGAAATCGCGT
1 TGCGAAAAC-AAAATTCGTGTTGCGAATTCAGAAATCGAGT
** *
6142741 TGCGAATTCAGAAA-TCGCGTTGCGAATT
1 TGCGAAAACA-AAATTCGTGTTGCGAATT
6142769 TGGAAACTGT
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 91 0.96
41 4 0.04
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (40 bp):
TGCGAAAACAAAATTCGTGTTGCGAATTCAGAAATCGAGT
Found at i:6142774 original size:20 final size:20
Alignment explanation
Indices: 6142639--6142768 Score: 165
Period size: 20 Copynumber: 6.5 Consensus size: 20
6142629 TAAAATTCGT
*
6142639 GTTGCGAATTC-GAAAATCGA
1 GTTGCGAATTCAG-AAATCGC
** *
6142659 GTTGCGAAAACA-AAATTCGT
1 GTTGCGAATTCAGAAA-TCGC
*
6142679 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGC
* *
6142699 GTTGCGAATTCGGAAATCAC
1 GTTGCGAATTCAGAAATCGC
6142719 GTTGCGAATTCAGAAATCGC
1 GTTGCGAATTCAGAAATCGC
6142739 GTTGCGAATTCAGAAATCGC
1 GTTGCGAATTCAGAAATCGC
6142759 GTTGCGAATT
1 GTTGCGAATT
6142769 TGGAAACTGT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 90 0.94
21 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATCGC
Found at i:6142774 original size:60 final size:60
Alignment explanation
Indices: 6142639--6142774 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 60
6142629 TAAAATTCGT
* *
6142639 GTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTCGTGTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCGGAAATCGAGTTGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGA
** *
6142699 GTTGCGAATTCGGAAATC-ACGTTGCGAATTCAGAAA-TCGCGTTGCGAATTCAGAAATCGC
1 GTTGCGAATTCGGAAATCGA-GTTGCGAAAACA-AAATTCGCGTTGCGAATTCAGAAATCGA
*
6142759 GTTGCGAATTTGGAAA
1 GTTGCGAATTCGGAAA
6142775 CTGTGTTGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
59 1 0.01
60 64 0.94
61 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (60 bp):
GTTGCGAATTCGGAAATCGAGTTGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGA
Found at i:6143621 original size:14 final size:15
Alignment explanation
Indices: 6143597--6143630 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6143587 TTTCATTTGA
6143597 TTTTTCATTTAATTT
1 TTTTTCATTTAATTT
*
6143612 TTTTTC-TTTAGTTT
1 TTTTTCATTTAATTT
6143626 TTTTT
1 TTTTT
6143631 TTGTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTCATTTAATTT
Found at i:6145926 original size:15 final size:16
Alignment explanation
Indices: 6145906--6145935 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6145896 TCTAGTTTTT
6145906 CCGAGTA-CCGGTTAC
1 CCGAGTACCCGGTTAC
6145921 CCGAGTACCCGGTTA
1 CCGAGTACCCGGTTA
6145936 ATTTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (16 bp):
CCGAGTACCCGGTTAC
Found at i:6149334 original size:30 final size:30
Alignment explanation
Indices: 6149254--6149340 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
6149244 GTGGTATTAA
* * *
6149254 TACTCTTAATATCTTTACTCTCAATATATG
1 TACTCTTAGTATCTATACTCCCAATATATG
** *
6149284 TACT-TGTAGTAAT-TGCACTCCCAATATCTG
1 TACTCT-TAGT-ATCTATACTCCCAATATATG
6149314 TACTCTTAGTATCTATACTCCCAATAT
1 TACTCTTAGTATCTATACTCCCAATAT
6149341 TTACACTACC
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
29 3 0.07
30 40 0.87
31 3 0.07
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (30 bp):
TACTCTTAGTATCTATACTCCCAATATATG
Found at i:6150317 original size:15 final size:15
Alignment explanation
Indices: 6150277--6150400 Score: 117
Period size: 15 Copynumber: 8.3 Consensus size: 15
6150267 TGTGATATTG
* *
6150277 ATACTCTAAGTATCA
1 ATACTCTTAGTATCT
6150292 ATACTCTTAGTATCT
1 ATACTCTTAGTATCT
*
6150307 ATACTCCTAGTATCT
1 ATACTCTTAGTATCT
* * *
6150322 ATATTATTAGTATTT
1 ATACTCTTAGTATCT
* * *
6150337 ATACTCTCAATATTT
1 ATACTCTTAGTATCT
*
6150352 ATACTCTTAATA-CTT
1 ATACTCTTAGTATC-T
6150367 ATACTCTTAGTATCT
1 ATACTCTTAGTATCT
* *
6150382 ATACT-TCAATATCT
1 ATACTCTTAGTATCT
6150396 ATACT
1 ATACT
6150401 ACCGGGTTGA
Statistics
Matches: 91, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
14 12 0.13
15 78 0.86
16 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (15 bp):
ATACTCTTAGTATCT
Found at i:6150998 original size:60 final size:60
Alignment explanation
Indices: 6150934--6151181 Score: 381
Period size: 60 Copynumber: 4.1 Consensus size: 60
6150924 CCAATATAAA
*
6150934 TATGTGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTATATCGGTGTAAG
1 TATGTGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACATCGGTGTAAG
* *
6150994 TATGTGTTTATTTTTAGGTACCAAGATATTGAGATATGTACATACTTACATCTGTGTAAG
1 TATGTGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACATCGGTGTAAG
* * * * * *
6151054 TATGTGTTTGTTTTTAGGTAACAAGATATTGAGAGATGTACATACTTACACCAGTATAAA
1 TATGTGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACATCGGTGTAAG
* *
6151114 TATGTGTTTATTTTTAGGTACCAAGATAATGAGAGATGTACATACTTACA-CTGATGTAAG
1 TATGTGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACATC-GGTGTAAG
6151174 TATGTGTT
1 TATGTGTT
6151182 AATTGGTATA
Statistics
Matches: 170, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
59 1 0.01
60 169 0.99
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (60 bp):
TATGTGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACATCGGTGTAAG
Found at i:6154756 original size:163 final size:166
Alignment explanation
Indices: 6154486--6154816 Score: 623
Period size: 163 Copynumber: 2.0 Consensus size: 166
6154476 AAAATCAACG
6154486 ATTAACGGTTCGGGTTTGATTTGGTCAATGATTCAAAATTGGTTTGGCCAGACTGGTTCAGGACG
1 ATTAACGGTTCGGGTTTGATTTGGTCAATGATTCAAAATTGGTTTGGCCAGACTGGTTCAGGACG
6154551 GGTTTAACCCTCTGAATCGGTTTGACCAATTGTCAAGAAAAACAA-TTCCACACGCGTA-GCGGC
66 GGTTTAACCCTCTGAATCGGTTTGACCAATTGTCAAGAAAAACAATTTCCACACGCGTAGGCGGC
6154614 GCGTGTAGCATATGGGATGACCTTCTGT-GCAAAAA
131 GCGTGTAGCATATGGGATGACCTTCTGTGGCAAAAA
6154649 ATTAACGGTTCGGGTTTGATTTGGTCAATGATTCAAAATTGGTTTGGCCAGACTGGTTCAGGACG
1 ATTAACGGTTCGGGTTTGATTTGGTCAATGATTCAAAATTGGTTTGGCCAGACTGGTTCAGGACG
6154714 GGTTTAACCCTCTGAATCGGTTTGACCAATTGTCAAGAAAAACAATTTCCACACGCGTAGCGGCG
66 GGTTTAACCCTCTGAATCGGTTTGACCAATTGTCAAGAAAAACAATTTCCACACGCGTA--GGCG
6154779 GCGCGTGTAGCATATGGGATGACCTTCTGTGGCAAAAA
129 GCGCGTGTAGCATATGGGATGACCTTCTGTGGCAAAAA
6154817 TTGTACCATT
Statistics
Matches: 163, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
163 110 0.67
164 13 0.08
167 33 0.20
168 7 0.04
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (166 bp):
ATTAACGGTTCGGGTTTGATTTGGTCAATGATTCAAAATTGGTTTGGCCAGACTGGTTCAGGACG
GGTTTAACCCTCTGAATCGGTTTGACCAATTGTCAAGAAAAACAATTTCCACACGCGTAGGCGGC
GCGTGTAGCATATGGGATGACCTTCTGTGGCAAAAA
Found at i:6160461 original size:20 final size:19
Alignment explanation
Indices: 6160436--6160483 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 19
6160426 TTATTACCTG
6160436 GTAATCTTTTATTCCCACTT
1 GTAATCTTTTATTCCCAC-T
6160456 GTAATCTTTTATTCCCACT
1 GTAATCTTTTATTCCCACT
6160475 GATAATCTT
1 G-TAATCTT
6160484 ACATTCCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (19 bp):
GTAATCTTTTATTCCCACT
Found at i:6160489 original size:20 final size:20
Alignment explanation
Indices: 6160436--6160490 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
6160426 TTATTACCTG
**
6160436 GTAATCTTTTATTCCCACTT
1 GTAATCTTACATTCCCACTT
**
6160456 GTAATCTTTTATTCCCAC-T
1 GTAATCTTACATTCCCACTT
6160475 GATAATCTTACATTCC
1 G-TAATCTTACATTCC
6160491 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.24, C:0.25, G:0.05, T:0.45
Consensus pattern (20 bp):
GTAATCTTACATTCCCACTT
Found at i:6162063 original size:28 final size:28
Alignment explanation
Indices: 6162028--6162085 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
6162018 TAAACTTATC
* *
6162028 TTTTTGGTCAAAATATGCACCTAAAGTA
1 TTTTTGGTCAAAATAGGCACATAAAGTA
*
6162056 TTTTTGGTCAAAATAGGTACATAAAGTA
1 TTTTTGGTCAAAATAGGCACATAAAGTA
6162084 TT
1 TT
6162086 CAATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (28 bp):
TTTTTGGTCAAAATAGGCACATAAAGTA
Found at i:6162720 original size:28 final size:28
Alignment explanation
Indices: 6162666--6162721 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
6162656 ATATTGTGTT
* * *
6162666 CAGAGATGTTCTTTCGAGGCCTCAATTG
1 CAGAGATGTTCTCTAGAGGCATCAATTG
6162694 CAGAGATGTTCTCTAGAGGTCAT-AATTG
1 CAGAGATGTTCTCTAGAGG-CATCAATTG
6162722 TGTGAAGCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (28 bp):
CAGAGATGTTCTCTAGAGGCATCAATTG
Found at i:6164833 original size:20 final size:20
Alignment explanation
Indices: 6164808--6164846 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6164798 AATAATGAAA
6164808 AGATAATTCCTAAAAACAAG
1 AGATAATTCCTAAAAACAAG
*
6164828 AGATAATTCCTAAAGACAA
1 AGATAATTCCTAAAAACAA
6164847 TTCTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (20 bp):
AGATAATTCCTAAAAACAAG
Found at i:6165106 original size:29 final size:29
Alignment explanation
Indices: 6165073--6165131 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6165063 TTAGTGCAAT
6165073 TTCGAGAATCTAATGTCATGCACAGAAAA
1 TTCGAGAATCTAATGTCATGCACAGAAAA
6165102 TTCGAGAATCTAATGTCATGCACAGAAAA
1 TTCGAGAATCTAATGTCATGCACAGAAAA
6165131 T
1 T
6165132 GTATCAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (29 bp):
TTCGAGAATCTAATGTCATGCACAGAAAA
Found at i:6168401 original size:19 final size:19
Alignment explanation
Indices: 6168377--6168418 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
6168367 AAAGTAATTG
6168377 GGGCTTGTTATTTTGTTTA
1 GGGCTTGTTATTTTGTTTA
6168396 GGGCTTGTTATTTTGTTTA
1 GGGCTTGTTATTTTGTTTA
6168415 GGGC
1 GGGC
6168419 ATGTGGAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.07, G:0.31, T:0.52
Consensus pattern (19 bp):
GGGCTTGTTATTTTGTTTA
Found at i:6169825 original size:16 final size:16
Alignment explanation
Indices: 6169801--6169865 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
6169791 CCAACGTTTA
*
6169801 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
6169817 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCG
*
6169833 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
6169849 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6169865 T
1 T
6169866 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:6169954 original size:16 final size:16
Alignment explanation
Indices: 6169933--6169965 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6169923 CAAAAAAAAT
6169933 TGTTCGTTTATGATCG
1 TGTTCGTTTATGATCG
*
6169949 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGATCG
6169965 T
1 T
6169966 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGATCG
Found at i:6176703 original size:18 final size:18
Alignment explanation
Indices: 6176680--6176714 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6176670 AAAAATAATG
6176680 AAAAGATAATTCCTAAAA
1 AAAAGATAATTCCTAAAA
6176698 AAAAGATAATTCCTAAA
1 AAAAGATAATTCCTAAA
6176715 GATAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (18 bp):
AAAAGATAATTCCTAAAA
Found at i:6185478 original size:14 final size:15
Alignment explanation
Indices: 6185461--6185495 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
6185451 AAATGAATTG
*
6185461 AATAAAAATAA-ATA
1 AATAAAAATAAGAAA
6185475 AATAAAAATAAGAAA
1 AATAAAAATAAGAAA
6185490 AATAAA
1 AATAAA
6185496 TGATTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
AATAAAAATAAGAAA
Found at i:6198710 original size:20 final size:22
Alignment explanation
Indices: 6198664--6198718 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
6198654 ACCGAAGGGG
*
6198664 GTATCGATACAATAGAAGGGAA
1 GTATCGATACTATAGAAGGGAA
*
6198686 GTATCGGTACTATAGAA-GG-A
1 GTATCGATACTATAGAAGGGAA
6198706 GTATCGATACTAT
1 GTATCGATACTAT
6198719 TATGTCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 13 0.43
21 2 0.07
22 15 0.50
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.25
Consensus pattern (22 bp):
GTATCGATACTATAGAAGGGAA
Done.