Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 2 of 425
Found at i:458375 original size:40 final size:40
Alignment explanation
Indices: 458330--458410 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
458320 AAATGTTACA
458330 TACCCAGTTTCACATGTAATTAGCCTCAGCTGACTCAATT
1 TACCCAGTTTCACATGTAATTAGCCTCAGCTGACTCAATT
458370 TACCCAGTTTCACATGTAATTAGCCTCAGCTGACTCAATT
1 TACCCAGTTTCACATGTAATTAGCCTCAGCTGACTCAATT
458410 T
1 T
458411 CCTCAGGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (40 bp):
TACCCAGTTTCACATGTAATTAGCCTCAGCTGACTCAATT
Found at i:463427 original size:18 final size:17
Alignment explanation
Indices: 463404--463439 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
463394 TGTTACTATT
*
463404 ATTTTGTTGTTATTGTTA
1 ATTTTGTTATTATT-TTA
463422 ATTTTGTTATTATTTTA
1 ATTTTGTTATTATTTTA
463439 A
1 A
463440 AGGTATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (17 bp):
ATTTTGTTATTATTTTA
Found at i:473046 original size:13 final size:13
Alignment explanation
Indices: 473028--473116 Score: 116
Period size: 13 Copynumber: 7.2 Consensus size: 13
473018 AAATATCTTT
473028 ACTCCACTAAACC
1 ACTCCACTAAACC
473041 ACTCCACTAAACC
1 ACTCCACTAAACC
* *
473054 ACTACACTAAGCC
1 ACTCCACTAAACC
473067 ACTCCACTAAACC
1 ACTCCACTAAACC
473080 AC-CC-C--AACC
1 ACTCCACTAAACC
473089 AC-CCTACTAAACC
1 ACTCC-ACTAAACC
473102 ACTCCACTAAACC
1 ACTCCACTAAACC
473115 AC
1 AC
473117 CCCAACCACT
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.12
11 2 0.03
12 2 0.03
13 53 0.79
14 2 0.03
ACGTcount: A:0.38, C:0.47, G:0.01, T:0.13
Consensus pattern (13 bp):
ACTCCACTAAACC
Found at i:473538 original size:19 final size:18
Alignment explanation
Indices: 473501--473542 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
473491 GGAGAGAGTG
*
473501 TTATTTTTAATATTGTTA
1 TTATTTTTAATATTATTA
*
473519 TTATTTTCTATTATTATTA
1 TTATTTT-TAATATTATTA
473538 TTATT
1 TTATT
473543 ACTAATACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTAATATTATTA
Found at i:476427 original size:19 final size:19
Alignment explanation
Indices: 476405--476451 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
476395 CTTCCTTTCT
476405 TTTGCATT-CATTCCATACA
1 TTTGCATTACATTCCA-ACA
*
476424 TTTGCATTACATTGCAACA
1 TTTGCATTACATTCCAACA
476443 TTTGCATTA
1 TTTGCATTA
476452 AAATTTCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCAACA
Found at i:479710 original size:12 final size:12
Alignment explanation
Indices: 479684--479719 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
479674 GAGAGCCCTA
*
479684 AAAAAACACACAC
1 AAAAAACA-AAAC
479697 AAAAAACAAAAC
1 AAAAAACAAAAC
479709 AAAAAACAAAA
1 AAAAAACAAAA
479720 AATTCTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:481454 original size:205 final size:205
Alignment explanation
Indices: 481096--481584 Score: 834
Period size: 205 Copynumber: 2.4 Consensus size: 205
481086 ATCAGACGAA
* *
481096 GAGCAGATCGAAGACATAGCTGATTTAGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
481161 TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGACGGAAGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGACGGAAGGCAGA
* *
481226 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTG
481291 TGCTTACAAG
196 TGCTTACAAG
* * *
481301 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCAAATCTAAAATGAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
* * * * * *
481366 TTGGCATCTCTGTATTGTCAGAGAACAAATTGAAGTCTGGTATCTCCACTTCGATGGAGGGTAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGACGGAAGGCAGA
*
481431 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCTTTG
131 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTG
481496 TGCTTACAAG
196 TGCTTACAAG
*
481506 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATAAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
*
481571 TTGGCGTCTCTGTA
66 TTGGCATCTCTGTA
481585 GCGACGGAGA
Statistics
Matches: 265, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
205 265 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (205 bp):
GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGACGGAAGGCAGA
CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTG
TGCTTACAAG
Found at i:483124 original size:132 final size:132
Alignment explanation
Indices: 481611--483093 Score: 2453
Period size: 132 Copynumber: 11.2 Consensus size: 132
481601 CGAAGATTGT
* * * *
481611 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGTAGATCTGACATTCTTGTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* *
481676 ATAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAAGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
*
481741 GT
131 GC
* ** *
481743 AGATTTGGCATCCCTGTGCTTATAGGGAATAGATCGAAGATAATAGATCTGACATTCTTGTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
481808 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
481873 GC
131 GC
* *
481875 AGATTTGGTATCCTTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* *
481940 ACAGTAAAGAAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
482005 GC
131 GC
* * *
482007 AGATTTGGTATCCCTGTGCTTATAGGGAACATATCGAAGATAGCAGATCTGACATTCCTGTACTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
482072 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
482137 GC
131 GC
482139 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
*
482204 ACAGTGAAGCAGATCGAAGATTTCAACATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
482269 GC
131 GC
* * * *
482271 AGATTTGGCATCCCTGTACTTATAGGGAATAGATCGAATATAACAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
** * * *
482336 ATGGTGAAGTAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
482401 GC
131 GC
* * * *
482403 ATATTTGGTATCCCTGTGCTTATAGGGAACAGATTGAAGATAGCAGATCTGACATTCCTTTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* * *
482468 ACAGTGAAACAAATCGAAGATTTCAGTATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
482533 GC
131 GC
*
482535 AGATTTGGCATCCCTGTACTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* * *
482600 ACAGTGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
482665 GC
131 GC
* * * *
482667 ATATTTGGTATCCCTGTGCTTATAGGGAACAGATTGAAGATAGCAGATCTGACATTCCTTTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* * *
482732 ACAGTGAAACAGATCGAAGATTTCAGTATGGCATCCCTATGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
482797 GC
131 GC
*
482799 AGATTTGGCATCCCTGTACTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
*
482864 ACAGTGAAGCAGATTGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
482929 GC
131 GC
*
482931 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTTCTGTGCTT
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* * * * *
482996 ACGGTGAAGCAGATCGAAGATTTCAGCATGGAATCCTTGTGCTTATAGGGAACAAGTTGAAGATA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
483061 GC
131 GC
* * *
483063 AGATTTGACATCTCTGTGTTTATAGGGAACA
1 AGATTTGGCATCCCTGTGCTTATAGGGAACA
483094 AGTTGAAGAC
Statistics
Matches: 1259, Mismatches: 92, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 1259 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
GC
Found at i:483435 original size:22 final size:22
Alignment explanation
Indices: 483410--483520 Score: 141
Period size: 22 Copynumber: 4.9 Consensus size: 22
483400 AAATATCTTT
483410 ACTCTACTAAACCACTCCAACC
1 ACTCTACTAAACCACTCCAACC
*
483432 ACTCTACTAAACCATTCCAACC
1 ACTCTACTAAACCACTCCAACC
*
483454 ACTCCACTAAACCACTACACTAAACC
1 ACTCTACTAAACCACT-C-C--AACC
* *
483480 ACTCCACTAAACCACCCCAACC
1 ACTCTACTAAACCACTCCAACC
*
483502 ACCCTACTAAACCACTCCA
1 ACTCTACTAAACCACTCCA
483521 CTAAACCACC
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
22 55 0.71
23 1 0.01
24 2 0.03
25 1 0.01
26 19 0.24
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.16
Consensus pattern (22 bp):
ACTCTACTAAACCACTCCAACC
Found at i:483444 original size:13 final size:13
Alignment explanation
Indices: 483410--483529 Score: 86
Period size: 13 Copynumber: 10.2 Consensus size: 13
483400 AAATATCTTT
483410 ACTCTACTAAACC
1 ACTCTACTAAACC
483423 ACTC--C--AACC
1 ACTCTACTAAACC
483432 ACTCTACTAAACC
1 ACTCTACTAAACC
*
483445 A-T-T-C-CAACC
1 ACTCTACTAAACC
*
483454 ACTCCACTAAACC
1 ACTCTACTAAACC
483467 ACTAC-ACTAAACC
1 ACT-CTACTAAACC
*
483480 ACTCCACTAAACC
1 ACTCTACTAAACC
*
483493 AC-C--C-CAACC
1 ACTCTACTAAACC
*
483502 ACCCTACTAAACC
1 ACTCTACTAAACC
*
483515 ACTCCACTAAACC
1 ACTCTACTAAACC
483528 AC
1 AC
483530 CCCAACCACT
Statistics
Matches: 86, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
9 19 0.22
10 4 0.05
11 3 0.03
12 5 0.06
13 54 0.63
14 1 0.01
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.16
Consensus pattern (13 bp):
ACTCTACTAAACC
Found at i:483489 original size:48 final size:48
Alignment explanation
Indices: 483413--483529 Score: 154
Period size: 48 Copynumber: 2.5 Consensus size: 48
483403 TATCTTTACT
* **
483413 CTACTAAACCACT-C-C--AACCACTCTACTAAACCATTCCAACCACTC
1 CTACTAAACCACTACACTAAACCACTCCACTAAACCACCCCAACCAC-C
483458 C-ACTAAACCACTACACTAAACCACTCCACTAAACCACCCCAACCACC
1 CTACTAAACCACTACACTAAACCACTCCACTAAACCACCCCAACCACC
*
483505 CTACTAAACCACTCCACTAAACCAC
1 CTACTAAACCACTACACTAAACCAC
483530 CCCAACCACT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
44 11 0.17
45 2 0.03
46 1 0.02
47 2 0.03
48 47 0.75
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (48 bp):
CTACTAAACCACTACACTAAACCACTCCACTAAACCACCCCAACCACC
Found at i:483502 original size:35 final size:36
Alignment explanation
Indices: 483410--483541 Score: 146
Period size: 35 Copynumber: 3.8 Consensus size: 36
483400 AAATATCTTT
* *
483410 ACTCTACTAAACCACTCCAACCACT-CTACTAAACC
1 ACTCCACTAAACCACCCCAACCACTCCTACTAAACC
* * ** ** *
483445 ATTCCAACCACTCCA-CTAAACCACTAC-ACTAAACC
1 ACTCC-ACTAAACCACCCCAACCACTCCTACTAAACC
483480 ACTCCACTAAACCACCCCAACCAC-CCTACTAAACC
1 ACTCCACTAAACCACCCCAACCACTCCTACTAAACC
483515 ACTCCACTAAACCACCCCAACCACTCC
1 ACTCCACTAAACCACCCCAACCACTCC
483542 ACTTGCCTAC
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
34 7 0.09
35 61 0.79
36 9 0.12
ACGTcount: A:0.37, C:0.48, G:0.00, T:0.15
Consensus pattern (36 bp):
ACTCCACTAAACCACCCCAACCACTCCTACTAAACC
Found at i:483950 original size:19 final size:18
Alignment explanation
Indices: 483913--483954 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
483903 GGAGAGAGTG
*
483913 TTATTTTTAATATTGTTA
1 TTATTTTTAATATTATTA
*
483931 TTATTTTCTATTATTATTA
1 TTATTTT-TAATATTATTA
483950 TTATT
1 TTATT
483955 ACTAATACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTAATATTATTA
Found at i:484672 original size:49 final size:49
Alignment explanation
Indices: 484600--484698 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
484590 TCGAAGTAAG
484600 AATTTGTTTTAAAATAAAGGCAGTATTCGGTATTAGGAAATTTGAGAAA
1 AATTTGTTTTAAAATAAAGGCAGTATTCGGTATTAGGAAATTTGAGAAA
484649 AATTTGTTTTAAAATAAAGGCAGTATTCGGTATTAGGAAATTTGAGAAA
1 AATTTGTTTTAAAATAAAGGCAGTATTCGGTATTAGGAAATTTGAGAAA
484698 A
1 A
484699 CGTGCCCTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.34
Consensus pattern (49 bp):
AATTTGTTTTAAAATAAAGGCAGTATTCGGTATTAGGAAATTTGAGAAA
Found at i:486186 original size:2 final size:2
Alignment explanation
Indices: 486179--486229 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
486169 GTTTATTGGC
486179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486221 -T AT AT -T AT A
1 AT AT AT AT AT A
486230 ATCATTCTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:490617 original size:6 final size:7
Alignment explanation
Indices: 490562--490622 Score: 54
Period size: 7 Copynumber: 8.1 Consensus size: 7
490552 AATCCATGAA
490562 TTTTAAT
1 TTTTAAT
490569 TTAGTTAA-
1 TT--TTAAT
490577 TTTT-AT
1 TTTTAAT
490583 TTTTCATAT
1 TTTT-A-AT
490592 TTTTAAAAT
1 TTTT--AAT
490601 TTTTAAT
1 TTTTAAT
490608 TTTTAAT
1 TTTTAAT
490615 TTTTAAT
1 TTTTAAT
490622 T
1 T
490623 CTAATCTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
5 1 0.02
6 6 0.13
7 20 0.43
8 2 0.04
9 16 0.35
10 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (7 bp):
TTTTAAT
Found at i:494834 original size:10 final size:10
Alignment explanation
Indices: 494819--494843 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
494809 ACAATATTAT
494819 GTAGAGCTAG
1 GTAGAGCTAG
494829 GTAGAGCTAG
1 GTAGAGCTAG
494839 GTAGA
1 GTAGA
494844 CATTAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (10 bp):
GTAGAGCTAG
Found at i:498917 original size:22 final size:21
Alignment explanation
Indices: 498877--498922 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
498867 TTGACTGTTA
* *
498877 ATTTTTTAAAAAAATTAAATT
1 ATTTTTTAAAAAAACTAAAAT
*
498898 ATTTTTTAAAATTAACTAAAAT
1 ATTTTTTAAAA-AAACTAAAAT
498920 ATT
1 ATT
498923 GTCTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTTTTAAAAAAACTAAAAT
Found at i:501110 original size:42 final size:42
Alignment explanation
Indices: 501042--501185 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 42
501032 GACGCTAAAG
** ** * *
501042 ACCTTTAGCGGCATTTTTTTACAAACGCCGCTAAAAACCATG
1 ACCTTTAGCGGCGCTTTCCTACAAACGCCGCTAAAGACCATA
* * *
501084 ACCTTTAGCGGCGCTTTCCTAAAAACGACACTAAAGACCATA
1 ACCTTTAGCGGCGCTTTCCTACAAACGCCGCTAAAGACCATA
*
501126 ACCTTTAGCGGCGCTTTTTCC-GCAAACGCCGCTAAAGACCATA
1 ACCTTTAGCGGCGC--TTTCCTACAAACGCCGCTAAAGACCATA
*
501169 ACCTTTAGCGACGCTTT
1 ACCTTTAGCGGCGCTTT
501186 TCTCGCAAAT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.03
42 47 0.55
43 31 0.36
44 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (42 bp):
ACCTTTAGCGGCGCTTTCCTACAAACGCCGCTAAAGACCATA
Found at i:501167 original size:43 final size:42
Alignment explanation
Indices: 501063--501204 Score: 169
Period size: 43 Copynumber: 3.3 Consensus size: 42
501053 CATTTTTTTA
* * *
501063 CAAACGCCGCTAAAAACCATGACCTTTAGCGGCGC-TTTCCTA
1 CAAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCC-G
* * *
501105 AAAACGACACTAAAGACCATAACCTTTAGCGGCGCTTTTTCCG
1 CAAACGCCGCTAAAGACCATAACCTTTAGCGGCGC-TTTTCCG
*
501148 CAAACGCCGCTAAAGACCATAACCTTTAGCGACGCTTTTCTCG
1 CAAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTC-CG
* *
501191 CAAATGCCGGTAAA
1 CAAACGCCGCTAAA
501205 AATTATAAAC
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
42 35 0.41
43 45 0.53
44 5 0.06
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (42 bp):
CAAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCCG
Found at i:501262 original size:21 final size:20
Alignment explanation
Indices: 501228--501282 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
501218 AAAAAATTAT
501228 TTTATTTTAATTAAATAATA
1 TTTATTTTAATTAAATAATA
* *
501248 TTTATTTTATGTTAAATATTA
1 TTTATTTTA-ATTAAATAATA
501269 TATTATGTTTAATT
1 T-TTAT-TTTAATT
501283 TTTGAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.31
21 10 0.34
22 6 0.21
23 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATTTTAATTAAATAATA
Found at i:501280 original size:18 final size:18
Alignment explanation
Indices: 501244--501277 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
501234 TTAATTAAAT
*
501244 AATATTTATTTTATGTTA
1 AATATTTATATTATGTTA
501262 AATA-TTATATTATGTT
1 AATATTTATATTATGTT
501278 TAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
AATATTTATATTATGTTA
Found at i:501463 original size:43 final size:42
Alignment explanation
Indices: 501327--501506 Score: 202
Period size: 42 Copynumber: 4.2 Consensus size: 42
501317 ATTAAAAAAG
**
501327 CGCCGCTAAAGACCATGACCTTTAGCG-GCATTTTTTTACAAA
1 CGCCGCTAAAGACCATGACCTTTAGCGCGC-TTTTCCTACAAA
* *
501369 CGCCGCTAAAGACCATGATCTTTAGCGGCGC-TTTCCTAAAAA
1 CGCCGCTAAAGACCATGACCTTTAGC-GCGCTTTTCCTACAAA
* * **
501411 CGCCACTAAAGACCATAACCTTTAGCAGCGCTTTTCCCGCAAA
1 CGCCGCTAAAGACCATGACCTTTAGC-GCGCTTTTCCTACAAA
* * *
501454 CGCCGCTAAAGATCATGACCTTTAGCGACGCTTTTCTTGCAAA
1 CGCCGCTAAAGACCATGACCTTTAGCG-CGCTTTTCCTACAAA
*
501497 CGCCGATAAA
1 CGCCGCTAAA
501507 AATTGTAAAC
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
42 61 0.52
43 54 0.46
44 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (42 bp):
CGCCGCTAAAGACCATGACCTTTAGCGCGCTTTTCCTACAAA
Found at i:501464 original size:85 final size:85
Alignment explanation
Indices: 501321--501487 Score: 221
Period size: 85 Copynumber: 2.0 Consensus size: 85
501311 TTTTTAATTA
* * ***
501321 AAAAAGCGCCGCTAAAGACCATGACCTTTAGCGGCATTTTTTTACAAACGCCGCTAAAGACCATG
1 AAAAAGCGCCACTAAAGACCATAACCTTTAGCGGCATTTTCCCACAAACGCCGCTAAAGACCATG
* *
501386 ATCTTTAGCGGCGCTTTCCT
66 ACCTTTAGCGACGCTTTCCT
* *
501406 AAAAA-CGCCACTAAAGACCATAACCTTTAGCAGCGC-TTTTCCCGCAAACGCCGCTAAAGATCA
1 AAAAAGCGCCACTAAAGACCATAACCTTTAGC-G-GCATTTTCCCACAAACGCCGCTAAAGACCA
501469 TGACCTTTAGCGACGCTTT
64 TGACCTTTAGCGACGCTTT
501488 TCTTGCAAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
84 24 0.34
85 45 0.63
86 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (85 bp):
AAAAAGCGCCACTAAAGACCATAACCTTTAGCGGCATTTTCCCACAAACGCCGCTAAAGACCATG
ACCTTTAGCGACGCTTTCCT
Found at i:501565 original size:22 final size:23
Alignment explanation
Indices: 501540--501582 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
501530 TTTATTTTAA
*
501540 TTAAATAATAT-TTATTTTTATG
1 TTAAATAATATATTATGTTTATG
*
501562 TTAAATATTATATTATGTTTA
1 TTAAATAATATATTATGTTTA
501583 ATTTTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (23 bp):
TTAAATAATATATTATGTTTATG
Found at i:501619 original size:302 final size:302
Alignment explanation
Indices: 501041--501617 Score: 1037
Period size: 302 Copynumber: 1.9 Consensus size: 302
501031 CGACGCTAAA
501041 GACCTTTAGCGGCATTTTTTTACAAACGCCGCTAAAAACCATGACCTTTAGCGGCGCTTTCCTAA
1 GACCTTTAGCGGCATTTTTTTACAAACGCCGCTAAAAACCATGACCTTTAGCGGCGCTTTCCTAA
* *
501106 AAACGACACTAAAGACCATAACCTTTAGCGGCGCTTTTTCCGCAAACGCCGCTAAAGACCATAAC
66 AAACGACACTAAAGACCATAACCTTTAGCAGCGCTTTTCCCGCAAACGCCGCTAAAGACCATAAC
* *
501171 CTTTAGCGACGCTTTTCTCGCAAATGCCGGTAAAAATTATAAACTTTAAAAAATTATTTTATTTT
131 CTTTAGCGACGCTTTTCTCGCAAACGCCGATAAAAATTATAAACTTTAAAAAATTATTTTATTTT
501236 AATTAAATAATATTTATTTTATGTTAAATATTATATTATGTTTAATTTTTGAAATTTGAACTTTA
196 AATTAAATAATATTTATTTTATGTTAAATATTATATTATGTTTAATTTTTGAAATTTGAACTTTA
501301 AACTACATATTTTTTAATTAAAAAAGCGCCGCTAAAGACCAT
261 AACTACATATTTTTTAATTAAAAAAGCGCCGCTAAAGACCAT
* *
501343 GACCTTTAGCGGCATTTTTTTACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTCCTAA
1 GACCTTTAGCGGCATTTTTTTACAAACGCCGCTAAAAACCATGACCTTTAGCGGCGCTTTCCTAA
* * *
501408 AAACGCCACTAAAGACCATAACCTTTAGCAGCGCTTTTCCCGCAAACGCCGCTAAAGATCATGAC
66 AAACGACACTAAAGACCATAACCTTTAGCAGCGCTTTTCCCGCAAACGCCGCTAAAGACCATAAC
* *
501473 CTTTAGCGACGCTTTTCTTGCAAACGCCGATAAAAATTGTAAACTTTAAAAAATTATTTTATTTT
131 CTTTAGCGACGCTTTTCTCGCAAACGCCGATAAAAATTATAAACTTTAAAAAATTATTTTATTTT
501538 AATTAAATAATATTTATTTTTATGTTAAATATTATATTATGTTTAATTTTTGAAATTTGAACTTT
196 AATTAAATAATATTTA-TTTTATGTTAAATATTATATTATGTTTAATTTTTGAAATTTGAACTTT
*
501603 AAACTATATATTTTT
260 AAACTACATATTTTT
501618 AAGGATAAAT
Statistics
Matches: 262, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
302 200 0.76
303 62 0.24
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.36
Consensus pattern (302 bp):
GACCTTTAGCGGCATTTTTTTACAAACGCCGCTAAAAACCATGACCTTTAGCGGCGCTTTCCTAA
AAACGACACTAAAGACCATAACCTTTAGCAGCGCTTTTCCCGCAAACGCCGCTAAAGACCATAAC
CTTTAGCGACGCTTTTCTCGCAAACGCCGATAAAAATTATAAACTTTAAAAAATTATTTTATTTT
AATTAAATAATATTTATTTTATGTTAAATATTATATTATGTTTAATTTTTGAAATTTGAACTTTA
AACTACATATTTTTTAATTAAAAAAGCGCCGCTAAAGACCAT
Found at i:507647 original size:8 final size:7
Alignment explanation
Indices: 507597--507710 Score: 50
Period size: 7 Copynumber: 15.9 Consensus size: 7
507587 CTCTAACCCC
507597 TAAACCT
1 TAAACCT
* *
507604 TAAATCA
1 TAAACCT
* *
507611 TAAAACA
1 TAAACCT
507618 TAAATCCT
1 TAAA-CCT
*
507626 TAACCCT
1 TAAACCT
507633 T-AACCTT
1 TAAACC-T
507640 TAAACCT
1 TAAACCT
*
507647 TAAACCC
1 TAAACCT
*
507654 TAACCCCT
1 TAA-ACCT
*
507662 CTAAAACT
1 -TAAACCT
*
507670 TAAACCC
1 TAAACCT
*
507677 TAACCCT
1 TAAACCT
* *
507684 TAACCCA
1 TAAACCT
*
507691 TAAACCA
1 TAAACCT
* *
507698 TAATCCA
1 TAAACCT
507705 TAAACC
1 TAAACC
507711 CATAATCCAT
Statistics
Matches: 82, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
6 3 0.04
7 64 0.78
8 12 0.15
9 3 0.04
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACCT
Found at i:507713 original size:15 final size:15
Alignment explanation
Indices: 507678--507738 Score: 97
Period size: 15 Copynumber: 4.1 Consensus size: 15
507668 CTTAAACCCT
* *
507678 AACCCTTAACCCATA
1 AACCCATAATCCATA
507693 AA-CCATAATCCATA
1 AACCCATAATCCATA
507707 AACCCATAATCCATA
1 AACCCATAATCCATA
507722 AACCCATAATCCATA
1 AACCCATAATCCATA
507737 AA
1 AA
507739 TCTTAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.20
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:507720 original size:7 final size:7
Alignment explanation
Indices: 507688--507737 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
507678 AACCCTTAAC
*
507688 CCATAAA
1 CCATAAT
507695 CCATAAT
1 CCATAAT
*
507702 CCATAAAC
1 CCAT-AAT
507710 CCATAAT
1 CCATAAT
*
507717 CCATAAAC
1 CCAT-AAT
507725 CCATAAT
1 CCATAAT
507732 CCATAA
1 CCATAA
507738 ATCTTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 24 0.67
8 12 0.33
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (7 bp):
CCATAAT
Found at i:508225 original size:41 final size:41
Alignment explanation
Indices: 508177--508365 Score: 247
Period size: 41 Copynumber: 4.6 Consensus size: 41
508167 TAATTTTTTT
**
508177 GCGGCGTTTTCCCAAAAGCGCCGCTAAAACCTCGATCTATA
1 GCGGCGTTTTTTCAAAAGCGCCGCTAAAACCTCGATCTATA
**
508218 G-GCGCGTTTTCCCAAAAGCGCCGCTAAAACCTCGATCTATA
1 GCG-GCGTTTTTTCAAAAGCGCCGCTAAAACCTCGATCTATA
* * * * * *
508259 GTGACGTTTTTTCAAAAGCGCCGTTAAAAACT-GAGCAATA
1 GCGGCGTTTTTTCAAAAGCGCCGCTAAAACCTCGATCTATA
* *
508299 GCGGCGTTTTTTAAAAAGCGCCGCTAAAAGCTCGATCTATA
1 GCGGCGTTTTTTCAAAAGCGCCGCTAAAACCTCGATCTATA
508340 GCGGCGTTTTTTCAAAAGCGCCGCTA
1 GCGGCGTTTTTTCAAAAGCGCCGCTA
508366 TTGTTCAGTT
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 34 0.26
41 95 0.73
42 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGTTTTTTCAAAAGCGCCGCTAAAACCTCGATCTATA
Found at i:508389 original size:81 final size:81
Alignment explanation
Indices: 508189--508365 Score: 230
Period size: 81 Copynumber: 2.2 Consensus size: 81
508179 GGCGTTTTCC
* * * ***
508189 CAAAAGCGCCGCTAAAACCTCGATCTATAG-GCGCGTTTTCCCAAAAGCGCCGCTAAAACCTCGA
1 CAAAAGCGCCGCTAAAAACTC-AGCAATAGCG-GCGTTTTTTAAAAAGCGCCGCTAAAACCTCGA
*
508253 TCTATAGTGACGTTTTTT
64 TCTATAGCGACGTTTTTT
* * *
508271 CAAAAGCGCCGTTAAAAACTGAGCAATAGCGGCGTTTTTTAAAAAGCGCCGCTAAAAGCTCGATC
1 CAAAAGCGCCGCTAAAAACTCAGCAATAGCGGCGTTTTTTAAAAAGCGCCGCTAAAACCTCGATC
*
508336 TATAGCGGCGTTTTTT
66 TATAGCGACGTTTTTT
508352 CAAAAGCGCCGCTA
1 CAAAAGCGCCGCTA
508366 TTGTTCAGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 63 0.77
82 19 0.23
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (81 bp):
CAAAAGCGCCGCTAAAAACTCAGCAATAGCGGCGTTTTTTAAAAAGCGCCGCTAAAACCTCGATC
TATAGCGACGTTTTTT
Found at i:508423 original size:41 final size:40
Alignment explanation
Indices: 508338--508487 Score: 126
Period size: 41 Copynumber: 3.7 Consensus size: 40
508328 GCTCGATCTA
** * * *
508338 TAGCGGCGTTTTTTC-AAAAGCGCCGCTATTGTTCAGTTTC
1 TAGCGGCGTTTTGACTAAAAACGCCGCTATTGCTCA-TTTT
*
508378 TAGCGGCGTTTTGACTAAAAACGCCACTATTGCTCTATTTT
1 TAGCGGCGTTTTGACTAAAAACGCCGCTATTGCTC-ATTTT
* * *
508419 TAGCGGTGTTTGGA-TCAAAAACGCTGCTATTGCTCAATTTT
1 TAGCGGCGTTTTGACT-AAAAACGCCGCTATTGCTC-ATTTT
* * * *
508460 TTGTGGCGTTTT-AATGAAAACGCCGCTA
1 TAGCGGCGTTTTGACTAAAAACGCCGCTA
508488 ATGTATAATA
Statistics
Matches: 89, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
40 26 0.29
41 62 0.70
42 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (40 bp):
TAGCGGCGTTTTGACTAAAAACGCCGCTATTGCTCATTTT
Found at i:521818 original size:23 final size:23
Alignment explanation
Indices: 521792--521837 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
521782 ACCAACTGAG
521792 AAAGTGCCTAGCCTGTAGGCTAA
1 AAAGTGCCTAGCCTGTAGGCTAA
521815 AAAGTGCCTAGCCTGTAGGCTAA
1 AAAGTGCCTAGCCTGTAGGCTAA
521838 CATCCTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
AAAGTGCCTAGCCTGTAGGCTAA
Found at i:528872 original size:17 final size:17
Alignment explanation
Indices: 528850--528886 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
528840 GTTTCATTGT
528850 AAACTTAACTAAAATCA
1 AAACTTAACTAAAATCA
* *
528867 AAACTTAATTAAAATTA
1 AAACTTAACTAAAATCA
528884 AAA
1 AAA
528887 GTTTATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (17 bp):
AAACTTAACTAAAATCA
Found at i:533235 original size:46 final size:44
Alignment explanation
Indices: 533131--533238 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
533121 TGTCTTTGAC
** * * *
533131 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
533175 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
533221 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
533239 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:537036 original size:71 final size:71
Alignment explanation
Indices: 536948--537111 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
536938 CGATTTGTCT
536948 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
537013 CTTTCA
66 CTTTCA
537019 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
537084 CTTTCA
66 CTTTCA
537090 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
537112 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:537149 original size:71 final size:70
Alignment explanation
Indices: 536948--537145 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
536938 CGATTTGTCT
* * * *
536948 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
537013 CTTTCA
65 CTTTCA
* * * *
537019 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
537084 CTTTCA
65 CTTTCA
* *
537090 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
537146 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:544613 original size:71 final size:71
Alignment explanation
Indices: 544527--544690 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
544517 CGATTTGTCT
544527 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
544592 CTTTCA
66 CTTTCA
544598 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
544663 CTTTCA
66 CTTTCA
544669 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
544691 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:544728 original size:71 final size:70
Alignment explanation
Indices: 544527--544724 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
544517 CGATTTGTCT
* * * *
544527 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
544592 CTTTCA
65 CTTTCA
* * * *
544598 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
544663 CTTTCA
65 CTTTCA
* *
544669 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
544725 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:547132 original size:46 final size:47
Alignment explanation
Indices: 546993--547132 Score: 151
Period size: 46 Copynumber: 2.9 Consensus size: 47
546983 ATGTGCTTCT
*
546993 GTATAAGACCATAGCAGGGCTATGGCATCGGTACAATGTGATTCGTGCTCCC
1 GTATAAGACCATAGCAGGGCTATGGCATCGGT---ATGTGA-T-GTGATCCC
*
547045 TTATAAGACCATAGCTA-GGCTATGGCATCGGTATG-GTATGTGAT-CC
1 GTATAAGACCATAGC-AGGGCTATGGCATCGGTATGTG-ATGTGATCCC
* * *
547091 GTGTAAGACCATAGCAGGGCTATGGCTTCGGTGTGTGATGTG
1 GTATAAGACCATAGCAGGGCTATGGCATCGGTATGTGATGTG
547133 TAACAATGTG
Statistics
Matches: 78, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
45 1 0.01
46 36 0.46
47 5 0.06
48 2 0.03
49 4 0.05
52 29 0.37
53 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (47 bp):
GTATAAGACCATAGCAGGGCTATGGCATCGGTATGTGATGTGATCCC
Found at i:548999 original size:42 final size:41
Alignment explanation
Indices: 548941--549025 Score: 136
Period size: 40 Copynumber: 2.0 Consensus size: 41
548931 TCGCCGCGGA
548941 TTATTATAAACCGGGTTAAGTCCCAGAGAGGCATTCGTGCCGG
1 TTATTATAAACCGGGTTAAGTCCC-GA-AGGCATTCGTGCCGG
*
548984 TTATTAT-AACCGGGTTAAGTCCCGAAGGCATTCGTGCTGG
1 TTATTATAAACCGGGTTAAGTCCCGAAGGCATTCGTGCCGG
549024 TT
1 TT
549026 GTTACATCCG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 16 0.39
41 2 0.05
42 16 0.39
43 7 0.17
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (41 bp):
TTATTATAAACCGGGTTAAGTCCCGAAGGCATTCGTGCCGG
Found at i:550609 original size:46 final size:46
Alignment explanation
Indices: 550542--550717 Score: 164
Period size: 46 Copynumber: 3.8 Consensus size: 46
550532 TATTTGGGCA
*
550542 TCCGAACTCGTTGAATTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
550588 TCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
* * * *
550633 CATCCGAACTCGTTGAGTTGAGTCTGGGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * * *
550681 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGG
550718 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 1 0.01
46 59 0.56
47 26 0.25
48 1 0.01
50 4 0.04
51 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:550697 original size:93 final size:93
Alignment explanation
Indices: 550538--550709 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
550528 AGGATATTTG
* * *
550538 GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAG
550603 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * * *
550631 GGCATCCGAACTCGTTGAGTTGAGTCTGGGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAG
550696 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
550710 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:551596 original size:14 final size:14
Alignment explanation
Indices: 551577--551605 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
551567 ACTTTGGAAA
551577 TTCACCATAAATTT
1 TTCACCATAAATTT
551591 TTCACCATAAATTT
1 TTCACCATAAATTT
551605 T
1 T
551606 AAAAGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (14 bp):
TTCACCATAAATTT
Found at i:553703 original size:15 final size:15
Alignment explanation
Indices: 553683--553751 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
553673 GTATCTTGGG
553683 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
553698 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
553713 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
553728 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
553743 TTTCTTTAT
1 TTTCTTTAT
553752 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:553752 original size:30 final size:30
Alignment explanation
Indices: 553674--553761 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
553664 CATAGTATCG
* * * *
553674 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
553704 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
553734 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
553762 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:556186 original size:46 final size:46
Alignment explanation
Indices: 556133--556308 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
556123 TATTTGGGCA
556133 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
556179 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
556224 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
556272 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
556309 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:556288 original size:93 final size:93
Alignment explanation
Indices: 556129--556300 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
556119 AGGATATTTG
* *
556129 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
556194 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
556222 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
556287 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
556301 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:561303 original size:35 final size:35
Alignment explanation
Indices: 561259--561424 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
561249 TCCTCATTGA
** *
561259 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
561294 AATGCCATACCTACATTT-TTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
561333 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
561368 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
561403 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
561425 CTTTTCCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
34 12 0.10
35 75 0.65
38 2 0.02
39 18 0.16
40 9 0.08
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:561344 original size:74 final size:73
Alignment explanation
Indices: 561254--561424 Score: 217
Period size: 74 Copynumber: 2.4 Consensus size: 73
561244 GGTTTTCCTC
** * * **
561254 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTT-TTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
561317 TCAGTATGG
65 TCAGTATGG
*
561326 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
561391 CTCAGTATGG
64 CTCAGTATGG
561401 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
561425 CTTTTCCATG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
70 21 0.24
72 1 0.01
73 9 0.10
74 44 0.50
75 13 0.15
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:568045 original size:40 final size:40
Alignment explanation
Indices: 567990--568124 Score: 207
Period size: 40 Copynumber: 3.4 Consensus size: 40
567980 TATGTGCATA
567990 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
568030 GCATTCGTGCTGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* * **
568070 GCATTCGTGCGGGTTATTATAACTGAGTTAAGTCCTAAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
568110 GCATTTGTGCTGGTT
1 GCATTCGTGCGGGTT
568125 GTTACATCCG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:570278 original size:20 final size:20
Alignment explanation
Indices: 570253--570290 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
570243 GCCTTACGGG
*
570253 CAGGCCACGCGGGCATGTCC
1 CAGGCCACACGGGCATGTCC
570273 CAGGCCACACGGGCATGT
1 CAGGCCACACGGGCATGT
570291 GCCCCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.37, G:0.34, T:0.11
Consensus pattern (20 bp):
CAGGCCACACGGGCATGTCC
Found at i:571460 original size:18 final size:19
Alignment explanation
Indices: 571422--571462 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
571412 GAAATTTTAG
571422 TTTCTCCTCAAAAGTTTTT
1 TTTCTCCTCAAAAGTTTTT
*
571441 TTTCTCTTCAAAAGTTTTT
1 TTTCTCCTCAAAAGTTTTT
571460 TTT
1 TTT
571463 TTTCCCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTCTCCTCAAAAGTTTTT
Found at i:571481 original size:22 final size:22
Alignment explanation
Indices: 571436--571482 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
571426 TCCTCAAAAG
* *
571436 TTTTTTTTCTCTTCAAAAGTTT
1 TTTTTTTTCCCTTCAAAAGATT
571458 TTTTTTTTCCCTT-AAAAGCATT
1 TTTTTTTTCCCTTCAAAAG-ATT
571480 TTT
1 TTT
571483 GAGAAGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.19, C:0.15, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTTTTTCCCTTCAAAAGATT
Found at i:572555 original size:3 final size:3
Alignment explanation
Indices: 572547--572605 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
572537 CGAGCGAGAC
* * ** * * *
572547 GAA GAA GAA GAA GAT GAC GTT GAA GAT GAA GAA GAG GAA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
572595 GAA GAA GAA GA
1 GAA GAA GAA GA
572606 GCCGAGGCTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.54, C:0.02, G:0.37, T:0.07
Consensus pattern (3 bp):
GAA
Found at i:572571 original size:21 final size:21
Alignment explanation
Indices: 572547--572602 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
572537 CGAGCGAGAC
* * **
572547 GAAGAAGAAGAAGATGACGTT
1 GAAGAAGAAGAAGAGGAAGAG
*
572568 GAAGATGAAGAAGAGGAAGAG
1 GAAGAAGAAGAAGAGGAAGAG
572589 GAAGAAGAAGAAGA
1 GAAGAAGAAGAAGA
572603 AGAGCCGAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.54, C:0.02, G:0.38, T:0.07
Consensus pattern (21 bp):
GAAGAAGAAGAAGAGGAAGAG
Found at i:576269 original size:44 final size:43
Alignment explanation
Indices: 576206--576292 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 43
576196 TCCTAATTGG
*
576206 GAAAATAGTTCCCTTATTCTAATAAACTTATTAAAACATAAAAA
1 GAAAATAGTTCCCTTATTCTAATAAAC-TACTAAAACATAAAAA
* *
576250 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAA
576293 TATTTCTAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 14 0.35
44 26 0.65
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (43 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAA
Found at i:580992 original size:44 final size:43
Alignment explanation
Indices: 580929--581015 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 43
580919 TCCTAATTGG
580929 GAAAATAGTTCCCTTATTCT-TATAAACTTACTAAAACATAAAAA
1 GAAAATAGTTCCCTTATTCTAT-TAAAC-TACTAAAACATAAAAA
*
580973 GAAAATAGTTCCCTTATTCTATTAAACTACTAAAAGATAAAAA
1 GAAAATAGTTCCCTTATTCTATTAAACTACTAAAACATAAAAA
581016 TATTTCTAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 15 0.37
44 25 0.61
45 1 0.02
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (43 bp):
GAAAATAGTTCCCTTATTCTATTAAACTACTAAAACATAAAAA
Found at i:586250 original size:19 final size:20
Alignment explanation
Indices: 586215--586257 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
586205 GTATATAATT
*
586215 TTTTATAATATTTTTTTAAC
1 TTTTATAATATTATTTTAAC
586235 TTTTAT-ATATTATTTTAAC
1 TTTTATAATATTATTTTAAC
586254 TTTT
1 TTTT
586258 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATAATATTATTTTAAC
Found at i:586258 original size:20 final size:21
Alignment explanation
Indices: 586214--586267 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
586204 AGTATATAAT
*
586214 TTTTTATAATATTTTTTTAAC
1 TTTTTATAATATTATTTTAAC
586235 -TTTTAT-ATATTATTTTAAC
1 TTTTTATAATATTATTTTAAC
*
586254 TTTTTAAAAT-TTAT
1 TTTTTATAATATTAT
586268 AATTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 12 0.41
20 15 0.52
21 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATAATATTATTTTAAC
Found at i:586342 original size:17 final size:17
Alignment explanation
Indices: 586318--586353 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
586308 AAAAATTATA
586318 TATTATATATAAT-TTT
1 TATTATATATAATATTT
586334 TATTAATATATAATATTT
1 TATT-ATATATAATATTT
586352 TA
1 TA
586354 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 9 0.50
18 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATATATAATATTT
Found at i:586480 original size:20 final size:22
Alignment explanation
Indices: 586437--586483 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
586427 AAGTCAAAAG
586437 TATTTTTAAATATTATAATTTT
1 TATTTTTAAATATTATAATTTT
*
586459 TATTTTTAAAT-TTA-ATTTTT
1 TATTTTTAAATATTATAATTTT
586479 TATTT
1 TATTT
586484 AAATAAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 3 0.12
22 11 0.46
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTTAAATATTATAATTTT
Found at i:597244 original size:20 final size:20
Alignment explanation
Indices: 597219--597260 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
597209 TCTAACGGGA
597219 GTTGGG-TTTTTCTTTTTTGG
1 GTTGGGCTTTTT-TTTTTTGG
597239 GTTGGGCCTTTTTTTTTTTGG
1 GTTGGG-CTTTTTTTTTTTGG
597260 G
1 G
597261 GGGGGGGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 9 0.45
22 5 0.25
ACGTcount: A:0.00, C:0.07, G:0.31, T:0.62
Consensus pattern (20 bp):
GTTGGGCTTTTTTTTTTTGG
Found at i:602155 original size:16 final size:16
Alignment explanation
Indices: 602134--602164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
602124 AAATTTAGTG
602134 TTAATTGTGAATTTAT
1 TTAATTGTGAATTTAT
*
602150 TTAATTTTGAATTTA
1 TTAATTGTGAATTTA
602165 ATTTGTCAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (16 bp):
TTAATTGTGAATTTAT
Found at i:602437 original size:9 final size:9
Alignment explanation
Indices: 602423--602448 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
602413 ATATTTACAT
602423 ATTTCATCA
1 ATTTCATCA
602432 ATTTCATCA
1 ATTTCATCA
602441 ATTTCATC
1 ATTTCATC
602449 CTAATGGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (9 bp):
ATTTCATCA
Found at i:603991 original size:23 final size:24
Alignment explanation
Indices: 603960--604008 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
603950 ACACATTTAA
603960 TTTAA-TTTTCA-ATATATTATATT
1 TTTAATTTTTCACATATATTA-ATT
* *
603983 TTTACTTTTTCACTTATATTAATT
1 TTTAATTTTTCACATATATTAATT
604007 TT
1 TT
604009 GAAAAGTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
24 11 0.50
25 7 0.32
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAATTTTTCACATATATTAATT
Found at i:607801 original size:24 final size:22
Alignment explanation
Indices: 607766--607819 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
607756 CGTCAACCAC
*
607766 ACTAATTTTTAATAATAAAAATAG
1 ACTAATTTTTAAT--TAAAAAAAG
607790 A-TAATTCTTTAATTAAAAAAAG
1 ACTAATT-TTTAATTAAAAAAAG
607812 ACTAATTT
1 ACTAATTT
607820 ACTCACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (22 bp):
ACTAATTTTTAATTAAAAAAAG
Found at i:608755 original size:29 final size:29
Alignment explanation
Indices: 608720--608777 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
608710 TTATTGGGAG
608720 TGGATCAAATTAG-CCACTATATTATTAAA
1 TGGATCAAATTAGTCC-CTATATTATTAAA
*
608749 TGGATCAATTTAGTCCCTATATTATTAAA
1 TGGATCAAATTAGTCCCTATATTATTAAA
608778 AAGAATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (29 bp):
TGGATCAAATTAGTCCCTATATTATTAAA
Found at i:615257 original size:31 final size:31
Alignment explanation
Indices: 615222--615281 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
615212 TGTAATTTGA
* *
615222 TCAATTTTAGTTTTTATA-TTTTTCGAATTGG
1 TCAATTTTAGTCTCTATACTTTTT-GAATTGG
615253 TCAATTTTAGTCTCTATACTTTTTGAATT
1 TCAATTTTAGTCTCTATACTTTTTGAATT
615282 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (31 bp):
TCAATTTTAGTCTCTATACTTTTTGAATTGG
Found at i:616676 original size:18 final size:18
Alignment explanation
Indices: 616649--616683 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
616639 CCCTTCGTTT
*
616649 AAAAATTCGAAAATAAAA
1 AAAAAATCGAAAATAAAA
*
616667 AAAAAATCGATAATAAA
1 AAAAAATCGAAAATAAA
616684 GTCAAATATT
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:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAAAATCGAAAATAAAA
Found at i:619680 original size:17 final size:17
Alignment explanation
Indices: 619660--619693 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
619650 ACTAAAATTT
*
619660 TAAAATTAAATATTAAA
1 TAAAACTAAATATTAAA
*
619677 TAAAACTAAATTTTAAA
1 TAAAACTAAATATTAAA
619694 AGTTTAAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAACTAAATATTAAA
Found at i:621343 original size:31 final size:31
Alignment explanation
Indices: 621305--621375 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
621295 AATGAAATCC
*
621305 AAGTTCAAGGGCAAAATTGGATCTAATTGCT
1 AAGTTCAAGGGCAAAATTGGACCTAATTGCT
621336 AAGTTCAAGGGCAAAATTGGACCTAATTGCT
1 AAGTTCAAGGGCAAAATTGGACCTAATTGCT
621367 AAGTTCAAG
1 AAGTTCAAG
621376 TACTAAATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (31 bp):
AAGTTCAAGGGCAAAATTGGACCTAATTGCT
Found at i:621384 original size:31 final size:31
Alignment explanation
Indices: 621305--621386 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
621295 AATGAAATCC
* *
621305 AAGTTCAAGGGCAAAATTGGATCTAATTGCT
1 AAGTTCAAGGACAAAATTGGACCTAATTGCT
*
621336 AAGTTCAAGGGCAAAATTGGACCTAATTGCT
1 AAGTTCAAGGACAAAATTGGACCTAATTGCT
* *
621367 AAGTTCAAGTACTAAATTGG
1 AAGTTCAAGGACAAAATTGG
621387 TCCAAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (31 bp):
AAGTTCAAGGACAAAATTGGACCTAATTGCT
Found at i:633487 original size:17 final size:17
Alignment explanation
Indices: 633465--633511 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
633455 TTGAAAACCT
633465 CAAAATTAATATTTTTA
1 CAAAATTAATATTTTTA
*
633482 CAAAATT--TATTTTAA
1 CAAAATTAATATTTTTA
*
633497 CAATATTAAT-TTTTT
1 CAAAATTAATATTTTT
633512 CTTAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 13 0.52
16 4 0.16
17 8 0.32
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
CAAAATTAATATTTTTA
Found at i:634035 original size:7 final size:7
Alignment explanation
Indices: 634023--634051 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
634013 GGTATGAACC
634023 CTTTCGA
1 CTTTCGA
634030 CTTTCGA
1 CTTTCGA
634037 CTTTCGA
1 CTTTCGA
634044 CTTTCGA
1 CTTTCGA
634051 C
1 C
634052 ACCTCAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.41
Consensus pattern (7 bp):
CTTTCGA
Found at i:635084 original size:43 final size:43
Alignment explanation
Indices: 635023--635106 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
635013 AAAAATATGT
*
635023 ACCTACTATACAAGCATAAAACATATTTAGAATATAGGAATCA
1 ACCTACTATACAAGCATAAAACATATTTAGAATATACGAATCA
635066 ACCTACTATACAAGCATAAAACATATTTAGAATATACGAAT
1 ACCTACTATACAAGCATAAAACATATTTAGAATATACGAAT
635107 TAAATTGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.26
Consensus pattern (43 bp):
ACCTACTATACAAGCATAAAACATATTTAGAATATACGAATCA
Found at i:642347 original size:2 final size:2
Alignment explanation
Indices: 642340--642369 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
642330 ATGCTCAATT
642340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
642370 GAGGATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:645030 original size:19 final size:19
Alignment explanation
Indices: 645006--645051 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
644996 TATAAGGGCA
645006 GCCATGGCCGACATGAAAG
1 GCCATGGCCGACATGAAAG
645025 GCCATGGCCGACATGAAAG
1 GCCATGGCCGACATGAAAG
*
645044 ACCATGGC
1 GCCATGGC
645052 GTGTCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.11
Consensus pattern (19 bp):
GCCATGGCCGACATGAAAG
Found at i:648927 original size:2 final size:2
Alignment explanation
Indices: 648920--648952 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
648910 AGAAGAGCTA
648920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
648953 GACAAAAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:649417 original size:32 final size:32
Alignment explanation
Indices: 649379--649443 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
649369 TGTTTTTCAT
649379 ATATTACCTCCAAATAAAAGCCCAATTAATTC
1 ATATTACCTCCAAATAAAAGCCCAATTAATTC
* *
649411 ATATTACCTCCAAATCAAAGCCGAATTAATTC
1 ATATTACCTCCAAATAAAAGCCCAATTAATTC
649443 A
1 A
649444 CAGAAAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.28
Consensus pattern (32 bp):
ATATTACCTCCAAATAAAAGCCCAATTAATTC
Found at i:652436 original size:45 final size:45
Alignment explanation
Indices: 652386--652481 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
652376 TTAAAAATAT
652386 ATAAAACCATAAAAAATTGTAATATGCAGAGAATCTATTTTTTTA
1 ATAAAACCATAAAAAATTGTAATATGCAGAGAATCTATTTTTTTA
*
652431 ATAAAACCATAAAAATTTGTAATATGCAGAGAATCTATTTTTTTA
1 ATAAAACCATAAAAAATTGTAATATGCAGAGAATCTATTTTTTTA
652476 ATAAAA
1 ATAAAA
652482 AAATTTGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (45 bp):
ATAAAACCATAAAAAATTGTAATATGCAGAGAATCTATTTTTTTA
Found at i:656387 original size:47 final size:47
Alignment explanation
Indices: 656331--656441 Score: 150
Period size: 47 Copynumber: 2.4 Consensus size: 47
656321 TTTTAGGTTA
* **
656331 AAATCAATTCAAGTTCACATTCTCAAGATTTGCATTGAATCGGATTC
1 AAATCAATTCAAGTTCACATTCTCAAAATTCACATTGAATCGGATTC
** * * *
656378 TGATCAATTCAAGCTCACATTCTTAAAATTCACGTTGAATCGGATTC
1 AAATCAATTCAAGTTCACATTCTCAAAATTCACATTGAATCGGATTC
656425 AAATCAATTCAAGTTCA
1 AAATCAATTCAAGTTCA
656442 GTTGTTGAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (47 bp):
AAATCAATTCAAGTTCACATTCTCAAAATTCACATTGAATCGGATTC
Found at i:659306 original size:33 final size:33
Alignment explanation
Indices: 659268--659335 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
659258 TCATATAAAT
659268 TTTTAGTTGAATTTTGTGTTAGAATCAATTTAA
1 TTTTAGTTGAATTTTGTGTTAGAATCAATTTAA
659301 TTTTAGTTGAATTTTGTGTTAGAATCAATTTAA
1 TTTTAGTTGAATTTTGTGTTAGAATCAATTTAA
659334 TT
1 TT
659336 AAGAAAATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (33 bp):
TTTTAGTTGAATTTTGTGTTAGAATCAATTTAA
Found at i:659322 original size:16 final size:16
Alignment explanation
Indices: 659270--659322 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
659260 ATATAAATTT
659270 TTAGTTGAATTTTGTG
1 TTAGTTGAATTTTGTG
* * ** *
659286 TTAGAATCAATTTAATT
1 TTAG-TTGAATTTTGTG
659303 TTAGTTGAATTTTGTG
1 TTAGTTGAATTTTGTG
659319 TTAG
1 TTAG
659323 AATCAATTTA
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (16 bp):
TTAGTTGAATTTTGTG
Found at i:666259 original size:22 final size:23
Alignment explanation
Indices: 666234--666277 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
666224 ATTTTTAGAG
* *
666234 ACGA-AATTAAAATTTAATTTTT
1 ACGATAATAAAAATATAATTTTT
666256 ACGATAATAAAAATATAATTTT
1 ACGATAATAAAAATATAATTTT
666278 ATCATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (23 bp):
ACGATAATAAAAATATAATTTTT
Found at i:669763 original size:3 final size:3
Alignment explanation
Indices: 669755--669786 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
669745 TTCCAAACCT
669755 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
669787 TATGGTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:677243 original size:20 final size:19
Alignment explanation
Indices: 677196--677243 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
677186 ATATAATCTT
677196 TATTATGTT-TTATTTTCA
1 TATTATGTTATTATTTTCA
* *
677214 TATTAT-TTATTGTTTTTA
1 TATTATGTTATTATTTTCA
677232 TATATATGTTAT
1 TAT-TATGTTAT
677244 GTATATCACG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 3 0.12
20 4 0.16
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (19 bp):
TATTATGTTATTATTTTCA
Found at i:678738 original size:29 final size:30
Alignment explanation
Indices: 678705--678762 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
678695 ATGCTTTAGC
*
678705 GTGCAATTGTATACATG-AATTTTGATTTT
1 GTGCAATTCTATACATGAAATTTTGATTTT
*
678734 GTGCAATTCTATAGATGAAATTTTGATTT
1 GTGCAATTCTATACATGAAATTTTGATTT
678763 GATCTAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (30 bp):
GTGCAATTCTATACATGAAATTTTGATTTT
Found at i:678990 original size:29 final size:30
Alignment explanation
Indices: 678957--679015 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
678947 TCACGGGTAT
*
678957 AATTGCAC-CAAATTAAAGTTTATGTATAC
1 AATTGCACACAAATTAAAGTTCATGTATAC
*
678986 AATTGCACATTAAATTAAAGTTCATGTATA
1 AATTGCACA-CAAATTAAAGTTCATGTATA
679016 ATTTTAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (30 bp):
AATTGCACACAAATTAAAGTTCATGTATAC
Found at i:679018 original size:29 final size:27
Alignment explanation
Indices: 678953--679018 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 27
678943 AGTTTCACGG
*
678953 GTATAATTGCACCAAATTAAAGTTTAT
1 GTATAATTGCACCAAATTAAAGTTCAT
*
678980 GTATACAATTGCACATTAAATTAAAGTTCAT
1 GTAT--AATTGCAC--CAAATTAAAGTTCAT
679011 GTATAATT
1 GTATAATT
679019 TTAAGATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 4 0.12
29 12 0.36
31 17 0.52
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (27 bp):
GTATAATTGCACCAAATTAAAGTTCAT
Found at i:682394 original size:28 final size:28
Alignment explanation
Indices: 682325--682425 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
682315 GACAAGATTG
* * * *
682325 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
682355 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
682383 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
682412 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
682426 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:687578 original size:15 final size:16
Alignment explanation
Indices: 687554--687585 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
687544 AAATTCTTTT
687554 TATATAAATTCTAAAA
1 TATATAAATTCTAAAA
687570 TATAT-AATTCTAAAA
1 TATATAAATTCTAAAA
687585 T
1 T
687586 TCTCAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAAATTCTAAAA
Found at i:688470 original size:13 final size:13
Alignment explanation
Indices: 688452--688476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
688442 CCACCGTGCG
688452 CGGTGGCCGGCGA
1 CGGTGGCCGGCGA
688465 CGGTGGCCGGCG
1 CGGTGGCCGGCG
688477 GCGGCGGATG
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:0.04, C:0.32, G:0.56, T:0.08
Consensus pattern (13 bp):
CGGTGGCCGGCGA
Found at i:689479 original size:11 final size:11
Alignment explanation
Indices: 689463--689495 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
689453 TTTTTAATAC
689463 TATATTATGTA
1 TATATTATGTA
*
689474 TATATTATATA
1 TATATTATGTA
689485 TATA-TATGTA
1 TATATTATGTA
689495 T
1 T
689496 GTATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (11 bp):
TATATTATGTA
Found at i:689573 original size:29 final size:30
Alignment explanation
Indices: 689414--689570 Score: 73
Period size: 29 Copynumber: 5.3 Consensus size: 30
689404 ATTTTGTAAC
689414 ATTAT-TATTATTATTTCTAATGTGTATGT
1 ATTATATATTATTATTTCTAATGTGTATGT
* *
689443 ATTATATA-TA-T-TTT-TAATACTATAT-T
1 ATTATATATTATTATTTCTAAT-GTGTATGT
* * *
689469 ATGTATATATTA-TATATAT-ATATGTATGT
1 AT-TATATATTATTATTTCTAATGTGTATGT
* ** *
689498 ATATATTTATGAAGTATTATTAATAAT-TGTTTTGT
1 AT-TA--TAT--ATTATTATTTCTAATGTG-TATGT
**
689533 AACAT-TATTATTATTTCTAATGTGTATGT
1 ATTATATATTATTATTTCTAATGTGTATGT
689562 ATTATATAT
1 ATTATATAT
689571 ATTTTTAATA
Statistics
Matches: 94, Mismatches: 18, Indels: 31
0.66 0.13 0.22
Matches are distributed among these distances:
26 7 0.07
27 13 0.14
28 8 0.09
29 35 0.37
30 8 0.09
31 4 0.04
32 1 0.01
33 3 0.03
34 8 0.09
35 7 0.07
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (30 bp):
ATTATATATTATTATTTCTAATGTGTATGT
Found at i:689598 original size:119 final size:120
Alignment explanation
Indices: 689357--689626 Score: 470
Period size: 119 Copynumber: 2.2 Consensus size: 120
689347 ATTTTTAACA
689357 TATATATATATATGTATGTATATATTTATGAAGTATTATTAATAATTATTTTGTAACATTATTAT
1 TATATATATATATGTATGTATATATTTATGAAGTATTATTAATAATTATTTTGTAAC--TATTAT
689422 TATTATTTCTAATGTGTATGTATTATATATATTTTTAATACTATATTATGTATATAT
64 TATTATTTCTAATGTGTATGTATTATATATATTTTTAATACTATATTATGTATATAT
*
689479 TATATATATATATGTATGTATATATTTATGAAGTATTATTAATAATTGTTTTGTAAC-ATTATTA
1 TATATATATATATGTATGTATATATTTATGAAGTATTATTAATAATTATTTTGTAACTATTATTA
689543 TTATTTCTAATGTGTATGTATTATATATATTTTTAATACTATATTATGTATATAT
66 TTATTTCTAATGTGTATGTATTATATATATTTTTAATACTATATTATGTATATAT
* *
689598 TATATTATATATATATATTTATTATATTT
1 TATA-TATATATATGTATGTA-TATATTT
689627 TTATGTATAT
Statistics
Matches: 143, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
119 66 0.46
120 14 0.10
121 7 0.05
122 56 0.39
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (120 bp):
TATATATATATATGTATGTATATATTTATGAAGTATTATTAATAATTATTTTGTAACTATTATTA
TTATTTCTAATGTGTATGTATTATATATATTTTTAATACTATATTATGTATATAT
Found at i:689631 original size:41 final size:39
Alignment explanation
Indices: 689442--689639 Score: 126
Period size: 41 Copynumber: 5.0 Consensus size: 39
689432 AATGTGTATG
689442 TATTATATATATTTTTAATACTATATTATGTATATATTA
1 TATTATATATATTTTTAATACTATATTATGTATATATTA
*
689481 TA-TATATATATGTATGT-ATA-TAT-TTATG-A-AGTATTA
1 TATTATATATAT-T-TTTAATACTATATTATGTATA-TATTA
* * * * * * *
689517 T-TAATA-ATTGTTTTGTAACATTATTATTATTTCTAATGTGTA
1 TATTATATA-TATTTT-TAATACTA-TATTATGTAT-ATAT-TA
689559 TGTATTATATATATTTTTAATACTATATTATGTATATATTA
1 --TATTATATATATTTTTAATACTATATTATGTATATATTA
* *
689600 TATTATATATATATATTTATTA-TATTTTTATGTATATATT
1 TATTATATATAT-T-TTTAATACTA-TATTATGTATATATT
689640 TTAATATCAC
Statistics
Matches: 121, Mismatches: 17, Indels: 40
0.68 0.10 0.22
Matches are distributed among these distances:
34 1 0.01
35 4 0.03
36 14 0.12
37 7 0.06
38 13 0.11
39 22 0.18
40 5 0.04
41 24 0.20
42 6 0.05
43 8 0.07
44 7 0.06
45 9 0.07
46 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (39 bp):
TATTATATATATTTTTAATACTATATTATGTATATATTA
Found at i:689639 original size:23 final size:22
Alignment explanation
Indices: 689564--689640 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
689554 GTGTATGTAT
*
689564 TATATATATTT-TTAATACTATA
1 TATATATATTTATT-ATATTATA
* *
689586 T-TATGTATATATTATATTATA
1 TATATATATTTATTATATTATA
*
689607 TATATATATTTATTATATTTTTA
1 TATATATATTTATTATA-TTATA
*
689630 TGTATATATTT
1 TATATATATTT
689641 TAATATCACA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 15 0.33
22 16 0.36
23 14 0.31
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (22 bp):
TATATATATTTATTATATTATA
Found at i:689822 original size:3 final size:3
Alignment explanation
Indices: 689816--689865 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
689806 TAAATTCATA
* * *
689816 TAT TAT TAT CAT TAT T-T TCT ATGT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
689860 TAT TAT
1 TAT TAT
689866 CATTGTCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:691307 original size:3 final size:3
Alignment explanation
Indices: 691299--691363 Score: 103
Period size: 3 Copynumber: 21.0 Consensus size: 3
691289 TGTATTTTCA
691299 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
691348 TAT ATAT TTT TAT TAT
1 TAT -TAT TAT TAT TAT
691364 ATGCATATAC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:702136 original size:72 final size:72
Alignment explanation
Indices: 702017--702187 Score: 186
Period size: 72 Copynumber: 2.3 Consensus size: 72
702007 GTTTCATAAT
* * * * * * *
702017 TCAACTCATATTGCGGGAGGTAAGTTGAGCCTCAGGACACGCTGAGGTAATTTT-GA-TCTCCGT
1 TCAACTCATATTGCGAGAGGTGAGTGGAGCCTCAGGACACACCGAGGT-ATTTTAAATTCTAC--
*
702080 TTTC-GAAAA
63 TTTCAAAAAA
* *
702089 TCAACTCATATTGCGAGAGGTGAGTGGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCTACTT
1 TCAACTCATATTGCGAGAGGTGAGTGGAGCCTCAGGACACACCGAGGTATTTT-AAATTCTACTT
702154 TCAAAAAAA
65 TC-AAAAAA
702163 TCAACTCATATTGCGAGAGGTGAGT
1 TCAACTCATATTGCGAGAGGTGAGT
702188 TGAGTCTTGG
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
71 5 0.06
72 45 0.54
73 1 0.01
74 33 0.39
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAGGTGAGTGGAGCCTCAGGACACACCGAGGTATTTTAAATTCTACTTT
CAAAAAA
Found at i:702176 original size:74 final size:74
Alignment explanation
Indices: 702085--702354 Score: 283
Period size: 74 Copynumber: 3.5 Consensus size: 74
702075 TCCGTTTTCG
*
702085 AAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
702150 ACTTTCAAA
66 ACTTTCAAA
** * * * * *
702159 AAAATCAACTCATATTGCGAGAGGTGAGTTGAG--TCTTGGCTCACGTGTTGAGTCACTTTCAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACAC-CG-AG-GT-ATTTTCAAA
* * *
702222 TTCTATTTTTATATCTGCTTTT
62 TTCTACTTTCA-A--------A
*
702244 TAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTC
1 AAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTC
702309 TACTTTCAAA
65 TACTTTCAAA
*
702319 AGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
702355 TGGCTCACAT
Statistics
Matches: 156, Mismatches: 24, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
72 8 0.05
73 1 0.01
74 56 0.36
75 13 0.08
76 16 0.10
77 1 0.01
83 1 0.01
84 16 0.10
85 14 0.09
86 21 0.13
87 1 0.01
88 8 0.05
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
ACTTTCAAA
Found at i:702272 original size:160 final size:161
Alignment explanation
Indices: 702086--702519 Score: 649
Period size: 160 Copynumber: 2.7 Consensus size: 161
702076 CCGTTTTCGA
*
702086 AAATCAACTCAT-ATTGCGAGAGGTGAGTGGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
1 AAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
* *
702150 ACTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTTGGCTCACGTGTTGAGTCAC
66 ACTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGTTGAGTCAC
702215 TTTCAATTTCTATTTTTATATCTG-CTTTTT
131 TTTCAATTTCTATTTTTATATCTGTCTTTTT
702245 AAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
1 AAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
*
702310 ACTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGTTGAGTCAC
66 ACTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGTTGAGTCAC
* * *
702375 TTTCAATTTCTGTTTTTATGTCTGTTTTTTTTTTTT
131 TTTCAATTTCTATTTTTATATCTG-----TCTTTTT
* * *
702411 AAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC-AATTGT
1 AAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
** *** * *
702475 TGTTTGTCAAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCT
66 ACTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
702520 CAGTGCACAC
Statistics
Matches: 250, Mismatches: 18, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
159 12 0.05
160 135 0.54
165 42 0.17
166 61 0.24
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (161 bp):
AAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCT
ACTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGTTGAGTCAC
TTTCAATTTCTATTTTTATATCTGTCTTTTT
Found at i:702671 original size:95 final size:95
Alignment explanation
Indices: 702483--702658 Score: 232
Period size: 95 Copynumber: 1.9 Consensus size: 95
702473 GTTGTTTGTC
* * *
702483 AAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGTGCACACTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGTGAACACTGAGGTATTGTCAACTTT
* *
702548 TGCTTTCCAATTTCTGCCTTTCAAAAAAAA
66 CGCTTTCCAATTTATGCCTTTCAAAAAAAA
* *
702578 AAAAATCAACTCATATTGCGAA-AGGTGAGTTGAGCCTCAG-GAAACGCTGAGGTATTGTCAACT
1 AAAAATCAACTCATACTGC-AAGAGGTGAGTTGAGCCTCAGTG-AACACTGAGGTATTGTCAACT
*
702641 TTCG-TTTCTTAATTTATG
64 TTCGCTTTC-CAATTTATG
702659 TTTTTTCCAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
94 5 0.07
95 63 0.90
96 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
AAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGTGAACACTGAGGTATTGTCAACTTT
CGCTTTCCAATTTATGCCTTTCAAAAAAAA
Found at i:702877 original size:88 final size:90
Alignment explanation
Indices: 702578--702882 Score: 266
Period size: 89 Copynumber: 3.4 Consensus size: 90
702568 TCAAAAAAAA
* *
702578 AAAAATCAACTCATATTGCGAA-AGGTGAGTTGAGCCTCAGGA--A-ACGCTGAGGTATTGTCAA
1 AAAAATCAACTCATATTGC-AAGAGGTGAGTTGAGCCTCAGGATCACACGCCGAGGTATTTTCAA
* * *** * *
702639 CT-TTCGTTTCTTAATTTATGTTTTTTCC
65 -TAATCTTTTGGCAAATTATG-CTTTT-C
* * * *
702667 AAAAATTAATTCATATTGCTAGAGGTGAATTGAGCCTCAGGATCACACGCCGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGATCACACGCCGAGGTATTTTCAA-
* ** *
702732 TAATGTTTTTTCAATTTATGCTTTTC
65 TAATCTTTTGGCAAATTATGCTTTTC
* * * * *
702758 AAGAATCAACTCATCTTACAAGAGGTGAGTTGAGCCTC-GGGTCACATGCCGAGGTATTTTCAA-
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGATCACACGCCGAGGTATTTTCAAT
*
702821 AATCTGTTTGGCAAATTCTG-TTTTC
66 AATCT-TTTGGCAAATTATGCTTTTC
* * *
702846 AAAAATCAACTCATTTTGCGAGAAGTGAGTTGAGCCT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
702883 TTGCTCACGT
Statistics
Matches: 178, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
88 42 0.24
89 46 0.26
90 23 0.13
91 33 0.19
92 21 0.12
93 13 0.07
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (90 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGATCACACGCCGAGGTATTTTCAAT
AATCTTTTGGCAAATTATGCTTTTC
Found at i:702904 original size:88 final size:89
Alignment explanation
Indices: 702661--702969 Score: 218
Period size: 88 Copynumber: 3.4 Consensus size: 89
702651 AATTTATGTT
* * * * * * * *
702661 TTTTCCAAAAATTAATTCATATTGCTAGAGGTGAATTGAGCCTCAGGATCACACGCCGAGGTA-T
1 TTTT-CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGCTCACATGCCGAGCTATT
* *
702725 TTTCAATTAATGTTTTTTC-AAT-T-TATG
64 TTTCAA--AAT-CTGTTTCAAATGTCTA-G
* * * * * * *
702752 CTTTTCAAGAATCAACTCATCTTACAAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA-TT
1 -TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGCCGAGCTATTT
702816 TTCAAAATCTGTTTGGCAAAT-TCT-G
65 TTCAAAATCTGTTT--CAAATGTCTAG
* ** * *
702841 TTTTCAAAAATCAACTCATTTTGCGAGAAGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTT
1 TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGCCGAGCTATTTT
** **
702906 TCAATTTCTGTTTTTAATGTCTAG
66 TCAAAATCTGTTTCAAATGTCTAG
* * * *
702930 TTTTTAAAAGTCAATTCATATTGCGAGAAATGAGTTGAGC
1 TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
702970 TCAGGATCAC
Statistics
Matches: 179, Mismatches: 31, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
87 7 0.04
88 56 0.31
89 52 0.29
90 27 0.15
91 33 0.18
92 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (89 bp):
TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGCCGAGCTATTTT
TCAAAATCTGTTTCAAATGTCTAG
Found at i:704496 original size:3 final size:3
Alignment explanation
Indices: 704488--704542 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
704478 TGTATTTTCA
* *
704488 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TTT TAT ATAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT
704535 TAT T-T TAT
1 TAT TAT TAT
704543 GCATATACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 37 0.82
4 6 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:705928 original size:8 final size:8
Alignment explanation
Indices: 705915--705939 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
705905 ATCAAACTTC
705915 AGTTTTCA
1 AGTTTTCA
705923 AGTTTTCA
1 AGTTTTCA
705931 AGTTTTCA
1 AGTTTTCA
705939 A
1 A
705940 TAAATCGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (8 bp):
AGTTTTCA
Found at i:707905 original size:84 final size:84
Alignment explanation
Indices: 707728--707906 Score: 304
Period size: 84 Copynumber: 2.1 Consensus size: 84
707718 AATTCAATAG
* *
707728 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAATGAATTTAAACTAACGAAACAGA
1 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
707793 GATCTCCTCGAGTTCTTAT
66 GATCTCCTCGAGTTCTTAT
* *
707812 AATCAATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTATACTAACCAAACAGA
1 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
*
707877 GATCTCCTCGCGTTCTTAT
66 GATCTCCTCGAGTTCTTAT
*
707896 AATTGATTATT
1 AATCGATTATT
707907 GCATTTTGTC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (84 bp):
AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
GATCTCCTCGAGTTCTTAT
Found at i:718776 original size:41 final size:39
Alignment explanation
Indices: 718730--718817 Score: 126
Period size: 37 Copynumber: 2.3 Consensus size: 39
718720 TAAAAAGTAT
* *
718730 TTATATTAAAAAACACTACCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACAC-A-AATAAATATAATAAATATTTTA
718771 TTATATT--AAAACACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACAAATAAATATAATAAATATTTTA
718808 TTATATTAAA
1 TTATATTAAA
718818 TTTAATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
37 27 0.63
38 1 0.02
39 8 0.19
41 7 0.16
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAAACACAAATAAATATAATAAATATTTTA
Found at i:720108 original size:90 final size:85
Alignment explanation
Indices: 719937--720138 Score: 233
Period size: 90 Copynumber: 2.3 Consensus size: 85
719927 TTTAAGAGTG
* * * *
719937 CAAAAAGTCCTCAAGCTTTTTAAAAAAAGCAATTAAGTCTTCCTTTTATTGCACTCAATTAAGCA
1 CAAAAAGCCCTCAAACTTTTTCAAAAAAGCAATTAAGCCTTCCTTTTATTGCACTCAATTAAGCA
720002 CTTGAACTTTCAAAATGTAT
66 CTTGAACTTTCAAAATGTAT
* * *
720022 CAAAAAAGCCCTCAAACCTTTTCAAAAAAGCAATTAAGCCCTTACTTTTTTCTTTGCACTCAATT
1 C-AAAAAGCCCTCAAACTTTTTCAAAAAAGCAATTAAG-CCTT-C-CTTTT-ATTGCACTCAATT
** * * *
720087 GGGTATTTGAATTTTCAAAATGTAT
61 AAGCACTTGAACTTTCAAAATGTAT
720112 CAAAAAGACCCTCAAACTTTTTTCAAA
1 CAAAAAG-CCCTCAAAC-TTTTTCAAA
720139 CAAAAGCCTC
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
85 1 0.01
86 32 0.33
87 3 0.03
88 1 0.01
89 10 0.10
90 42 0.43
91 8 0.08
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (85 bp):
CAAAAAGCCCTCAAACTTTTTCAAAAAAGCAATTAAGCCTTCCTTTTATTGCACTCAATTAAGCA
CTTGAACTTTCAAAATGTAT
Found at i:720269 original size:10 final size:9
Alignment explanation
Indices: 720234--720320 Score: 52
Period size: 9 Copynumber: 9.1 Consensus size: 9
720224 ATAAAATATT
*
720234 AAATATTAA
1 AAATATAAA
720243 AAAT-TAAA
1 AAATATAAA
720251 AAATATAAA
1 AAATATAAA
*
720260 AAATCGTAAAA
1 AAAT-AT-AAA
720271 ATATATATAAA
1 A-A-ATATAAA
*
720282 AAATTTGTAAA
1 AAA--TATAAA
*
720293 AAAT-TATA
1 AAATATAAA
*
720301 AAATATATAG
1 AAATATA-AA
720311 AAATATAAA
1 AAATATAAA
720320 A
1 A
720321 TTTTATAAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
8 14 0.23
9 18 0.30
10 9 0.15
11 16 0.26
12 2 0.03
13 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (9 bp):
AAATATAAA
Found at i:720281 original size:22 final size:22
Alignment explanation
Indices: 720248--720303 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
720238 ATTAAAAATT
720248 AAAAA-ATATAAAAAA-TCGTA
1 AAAAATATATAAAAAATTCGTA
*
720268 AAAATATATATAAAAAATTTGTA
1 AAAA-ATATATAAAAAATTCGTA
720291 AAAAAT-TATAAAA
1 AAAAATATATAAAA
720304 TATATAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.12
21 8 0.25
22 12 0.38
23 8 0.25
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATATATAAAAAATTCGTA
Found at i:720451 original size:18 final size:19
Alignment explanation
Indices: 720410--720452 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
720400 AAAAGAAACA
720410 TTTTATATTTTTTCTATAC
1 TTTTATATTTTTTCTATAC
*
720429 TTTTAT-TTATTTT-TATTC
1 TTTTATATT-TTTTCTATAC
720447 TTTTAT
1 TTTTAT
720453 CAATTTCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATATTTTTTCTATAC
Found at i:720554 original size:17 final size:17
Alignment explanation
Indices: 720534--720622 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 17
720524 TTTTTTTATG
720534 ATTTTTATAAAATTTTA
1 ATTTTTATAAAATTTTA
* ***
720551 ATTTTTTTATTTTTTTA
1 ATTTTTATAAAATTTTA
720568 CGATTTTTATAAAAAATTTCTA
1 --ATTTTTAT--AAAATTT-TA
*
720590 ATTTTTA-ATAATTTTTA
1 ATTTTTATA-AAATTTTA
720607 ATTTTTATTAAAATTT
1 ATTTTTA-TAAAATTT
720623 CATAGTTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
17 23 0.43
18 10 0.19
19 8 0.15
20 7 0.13
21 4 0.07
22 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (17 bp):
ATTTTTATAAAATTTTA
Found at i:720561 original size:36 final size:38
Alignment explanation
Indices: 720521--720595 Score: 118
Period size: 36 Copynumber: 2.0 Consensus size: 38
720511 ATAGGAGTCG
*
720521 TTATTTTTTTATGATTTTTAT-AAAATTT-TAATTTTT
1 TTATTTTTTTACGATTTTTATAAAAATTTCTAATTTTT
720557 TTATTTTTTTACGATTTTTATAAAAAATTTCTAATTTTT
1 TTATTTTTTTACGATTTTTAT-AAAAATTTCTAATTTTT
720596 AATAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 20 0.57
38 7 0.20
39 8 0.23
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (38 bp):
TTATTTTTTTACGATTTTTATAAAAATTTCTAATTTTT
Found at i:720595 original size:37 final size:35
Alignment explanation
Indices: 720521--720622 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 35
720511 ATAGGAGTCG
*
720521 TTATTTTTTTATGATTTTTATAAAATTTTAATTTTT
1 TTATTTTTTTACGATTTTTATAAAATTTTAA-TTTT
720557 TTATTTTTTTACGATTTTTATAAAAAATTTCTAATTTT
1 TTATTTTTTTACGATTTTTAT--AAAATTT-TAATTTT
* *
720595 TAATAATTTTTA--ATTTTTATTAAAATTT
1 TTAT-TTTTTTACGATTTTTA-TAAAATTT
720623 CATAGTTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
36 27 0.47
37 7 0.12
38 15 0.26
39 9 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (35 bp):
TTATTTTTTTACGATTTTTATAAAATTTTAATTTT
Found at i:721537 original size:34 final size:34
Alignment explanation
Indices: 721499--721564 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
721489 TTTGGGCGGC
721499 AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
1 AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
**
721533 AAAGATTGGGCATGTTTCAGTGTTAGGGTTTG
1 AAAGATTGGGCATACTTCAGTGTTAGGGTTTG
721565 ATATAAGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.08, G:0.33, T:0.36
Consensus pattern (34 bp):
AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
Found at i:721698 original size:89 final size:89
Alignment explanation
Indices: 721547--721722 Score: 334
Period size: 89 Copynumber: 2.0 Consensus size: 89
721537 ATTGGGCATG
*
721547 TTTCAGTGTTAGGGTTTGATATAAGTCTGGAAAATCTCATAATTATAAATGTTTAATATTAGTAA
1 TTTCAGTGTTAGGGTTTGATATAAGTCTGAAAAATCTCATAATTATAAATGTTTAATATTAGTAA
*
721612 ATAATTAACACAATTATTGATATA
66 ATAATTAACACAATTATCGATATA
721636 TTTCAGTGTTAGGGTTTGATATAAGTCTGAAAAATCTCATAATTATAAATGTTTAATATTAGTAA
1 TTTCAGTGTTAGGGTTTGATATAAGTCTGAAAAATCTCATAATTATAAATGTTTAATATTAGTAA
721701 ATAATTAACACAATTATCGATA
66 ATAATTAACACAATTATCGATA
721723 AAGATTAGGC
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (89 bp):
TTTCAGTGTTAGGGTTTGATATAAGTCTGAAAAATCTCATAATTATAAATGTTTAATATTAGTAA
ATAATTAACACAATTATCGATATA
Found at i:724050 original size:47 final size:47
Alignment explanation
Indices: 723941--724051 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
723931 CCGGGATAAG
* * *
723941 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
723988 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
724035 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
724052 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Done.