Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_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: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:615769 original size:59 final size:57
Alignment explanation
Indices: 615695--615810 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 57
615685 TTTGAAATGG
**
615695 GTGCTATTTCAGGAATTTAATTCTAAAAAAAGGTTTTATTTTGAGAATTTAATTCGAAA
1 GTGCTATTTCAGGAATTTAATTC-AAAAAAA-GTGCTATTTTGAGAATTTAATTCGAAA
** * *
615754 GTGCTATTTTTGGAATTTAATTCGAAAAAAGTGCTATTTTGGGAATTTAATTCGAAA
1 GTGCTATTTCAGGAATTTAATTCAAAAAAAGTGCTATTTTGAGAATTTAATTCGAAA
615811 AAAGGTGCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 24 0.47
58 6 0.12
59 21 0.41
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (57 bp):
GTGCTATTTCAGGAATTTAATTCAAAAAAAGTGCTATTTTGAGAATTTAATTCGAAA
Found at i:615908 original size:10 final size:10
Alignment explanation
Indices: 615895--615921 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
615885 TTGACCAGAA
615895 CTTTGACCGG
1 CTTTGACCGG
615905 CTTTGACCGG
1 CTTTGACCGG
615915 CTTTGAC
1 CTTTGAC
615922 TGGCCATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.30, G:0.26, T:0.33
Consensus pattern (10 bp):
CTTTGACCGG
Found at i:622912 original size:29 final size:29
Alignment explanation
Indices: 622886--623065 Score: 213
Period size: 29 Copynumber: 6.2 Consensus size: 29
622876 ATCGGGTGAC
622886 ATTTTGGGAA-TTAATTCAAAATGGGTGCT
1 ATTTTGGGAATTTAATTCAAAA-GGGTGCT
* *
622915 ATTTTGGAAATTTAATTCGAAAAAGGTGCT
1 ATTTTGGGAATTTAATTC-AAAAGGGTGCT
* *
622945 ATTTTGGGAATTTAATTTGAAAAAGGTGCT
1 ATTTTGGGAATTTAA-TTCAAAAGGGTGCT
*
622975 ATTTTGGGAATTTAATTCAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAGGGTGCT
*
623004 ATTTTGGGAA-TTAATTCGAAAAGGGTGTT
1 ATTTTGGGAATTTAATTC-AAAAGGGTGCT
* * * *
623033 ATTTTGGTAA-TTATTTTAAAAGGGTGTT
1 ATTTTGGGAATTTAATTCAAAAGGGTGCT
623061 ATTTT
1 ATTTT
623066 ATAAAATGGT
Statistics
Matches: 137, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
28 23 0.17
29 55 0.40
30 53 0.39
31 6 0.04
ACGTcount: A:0.32, C:0.04, G:0.22, T:0.41
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCAAAAGGGTGCT
Found at i:622999 original size:59 final size:59
Alignment explanation
Indices: 622886--623044 Score: 232
Period size: 59 Copynumber: 2.7 Consensus size: 59
622876 ATCGGGTGAC
*
622886 ATTTTGGGAATTAA-TTCAAAATGGGTGCTATTTTGGAAATTTAATTCGAAAAAGGTGCT
1 ATTTTGGGAATTAATTTGAAAA-GGGTGCTATTTTGGAAATTTAATTCGAAAAAGGTGCT
* *
622945 ATTTTGGGAATTTAATTTGAAAAAGGTGCTATTTTGGGAATTTAATTC-AAAAAGGTGCT
1 ATTTTGGGAA-TTAATTTGAAAAGGGTGCTATTTTGGAAATTTAATTCGAAAAAGGTGCT
* * *
623004 ATTTTGGGAATTAATTCGAAAAGGGTGTTATTTTGGTAATT
1 ATTTTGGGAATTAATTTGAAAAGGGTGCTATTTTGGAAATT
623045 ATTTTAAAAG
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
58 27 0.30
59 31 0.34
60 27 0.30
61 6 0.07
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.40
Consensus pattern (59 bp):
ATTTTGGGAATTAATTTGAAAAGGGTGCTATTTTGGAAATTTAATTCGAAAAAGGTGCT
Found at i:625021 original size:25 final size:23
Alignment explanation
Indices: 624980--625026 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
624970 ATTTTATAAT
624980 TTTTAAAAGTTTAATAAAAATTA
1 TTTTAAAAGTTTAATAAAAATTA
*
625003 TTTTAAAATGATTTAATAATAATT
1 TTTTAAAA-G-TTTAATAAAAATT
625027 TTAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTTAAAAGTTTAATAAAAATTA
Found at i:626567 original size:35 final size:36
Alignment explanation
Indices: 626444--626586 Score: 120
Period size: 36 Copynumber: 4.1 Consensus size: 36
626434 TGCATGCTAT
* *
626444 TTATGTCACTTAGT--ATAAA-ATAATAATAATAAGA
1 TTATGTCACTTAGTGAATAAACTTATTAATAATAA-A
* *
626478 -TACT-TCATTTAGTGAATAAACTTATTAATAATAAG
1 TTA-TGTCACTTAGTGAATAAACTTATTAATAATAAA
** *
626513 TGGTGTCACTTAGTGAATAAAGTTATTAATAATAAA
1 TTATGTCACTTAGTGAATAAACTTATTAATAATAAA
* * * *
626549 TTAT-TCGCTTAGTGAATAAATTTATAAATTA-AAA
1 TTATGTCACTTAGTGAATAAACTTATTAATAATAAA
626583 TTAT
1 TTAT
626587 ATTCAATTTA
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
33 10 0.11
34 8 0.09
35 29 0.33
36 41 0.47
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.39
Consensus pattern (36 bp):
TTATGTCACTTAGTGAATAAACTTATTAATAATAAA
Found at i:627957 original size:22 final size:23
Alignment explanation
Indices: 627929--627988 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
627919 TGTTTTTATA
627929 TATATTAACTTAAAAATAT-TTT
1 TATATTAACTTAAAAATATATTT
*
627951 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA-AAAATATATTT
*
627975 TATTATTTACTTAA
1 TA-TATTAACTTAA
627989 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 6 0.19
24 5 0.16
25 9 0.28
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATTAACTTAAAAATATATTT
Found at i:628015 original size:24 final size:25
Alignment explanation
Indices: 627990--628035 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
627980 TTTACTTAAT
627990 TTTAAAAA-ATAT-TTTCATGTTCA
1 TTTAAAAATATATATTTCATGTTCA
*
628013 TTTAAAAATATATATTTTATGTT
1 TTTAAAAATATATATTTCATGTT
628036 GAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 4 0.20
25 8 0.40
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTAAAAATATATATTTCATGTTCA
Found at i:629034 original size:2 final size:2
Alignment explanation
Indices: 629027--629067 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
629017 TTAGTTTTAG
629027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
629068 TCACTAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:630792 original size:2 final size:2
Alignment explanation
Indices: 630785--630810 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
630775 TTATCTAAGC
630785 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
630811 TACATTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:631573 original size:156 final size:155
Alignment explanation
Indices: 631085--631616 Score: 672
Period size: 157 Copynumber: 3.4 Consensus size: 155
631075 TGTGGTATAT
* * * * * *
631085 GAGCATGTGGTTTAAATTTAGTAAAAAACAGACTTCAAATAAATGACGAATTGAAGGAATAAAGA
1 GAGCATGTGGCTCAAATTTGGT-AAAAACAGACTTAAAATAAATGACGAATTGAAGAAAT-AAGG
* * * * *
631150 GCTTATGATAATTTAAAGGACTAAATTGAAAAATAAAAACATTGTTAACAAAAAGAGGAATTGAA
64 GATTATGAAAAATTAAAGGACTAAATTGAAAAATAAAAA-ATTATTATCAAAAAGAGGAATTGAA
*
631215 AGTACACATGTATTCTACTATGTTTTAG
128 AGTACACATGTATTCTACTATGGTTTAG
* * *
631243 GAGCATGTGGCTCAAATTTGGTAAAAACAGACTTAAATTAAACGACGAAATGAAGAAATAAGGTG
1 GAGCATGTGGCTCAAATTTGGTAAAAACAGACTTAAAATAAATGACGAATTGAAGAAATAAGG-G
631308 ATTATGAAAAATTAAAGGACTAAATTGAAAAATAAAAAAATTATTATCAAAAAGAGGAATTGAAA
65 ATTATGAAAAATTAAAGGACTAAATTGAAAAAT-AAAAAATTATTATCAAAAAGAGGAATTGAAA
* * *
631373 GTTCATATGTATTCTAATATGGTTTAG
129 GTACACATGTATTCTACTATGGTTTAG
* *
631400 GAGCATGTGACTCAAATTTGGTAAACAACAGGCTTAAAATAAATGACGAATTGAAGAAATAAGGG
1 GAGCATGTGGCTCAAATTTGGTAAA-AACAGACTTAAAATAAATGACGAATTGAAGAAATAAGGG
* * * * *
631465 ATTATGAAAAATTGAATGACTAAATTGAAAAATAAAAATTTATTATCGAAAGGAGGAATTGAAAG
65 ATTATGAAAAATTAAAGGACTAAATTGAAAAATAAAAAATTATTATCAAAAAGAGGAATTGAAAG
* * *
631530 TAAACATGCATTCTACTATGGTTTAA
130 TACACATGTATTCTACTATGGTTTAG
* * * * * *
631556 GAGCATGTGGTTAAAATTTGGTGAAAA-TGAACTTAAAATTAAGGA-GAAATTGAAGAAATAA
1 GAGCATGTGGCTCAAATTTGGTAAAAACAG-ACTTAAAATAAATGACG-AATTGAAGAAATAA
631617 TGAAATCATG
Statistics
Matches: 327, Mismatches: 42, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
154 2 0.01
155 28 0.09
156 73 0.22
157 166 0.51
158 58 0.18
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.27
Consensus pattern (155 bp):
GAGCATGTGGCTCAAATTTGGTAAAAACAGACTTAAAATAAATGACGAATTGAAGAAATAAGGGA
TTATGAAAAATTAAAGGACTAAATTGAAAAATAAAAAATTATTATCAAAAAGAGGAATTGAAAGT
ACACATGTATTCTACTATGGTTTAG
Found at i:632070 original size:21 final size:20
Alignment explanation
Indices: 632055--632155 Score: 107
Period size: 21 Copynumber: 4.9 Consensus size: 20
632045 CGCGATTTAT
632055 TCCAAGTT-CGTTGCGATAG
1 TCCAAGTTCCGTTGCGATAG
*
632074 TCGAAGTTCGCGTTGCGATAG
1 TCCAAGTTC-CGTTGCGATAG
* *
632095 TCGAAGTTCGCGTTGCGAATTAT
1 TCCAAGTTC-CGTTGCG-A-TAG
*
632118 TCCAAATT-CGTTGCGATAG
1 TCCAAGTTCCGTTGCGATAG
632137 TCCAAGTTCGCGTTGCGAT
1 TCCAAGTTC-CGTTGCGAT
632156 TTATTCCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
19 16 0.23
20 1 0.01
21 44 0.63
22 1 0.01
23 8 0.11
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (20 bp):
TCCAAGTTCCGTTGCGATAG
Found at i:632109 original size:42 final size:40
Alignment explanation
Indices: 632055--632171 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 40
632045 CGCGATTTAT
* *
632055 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATAG
1 TCCAAGTTCGCGTTGCGATAGTCCAAATT--CGTTGCGATAG
* *
632095 TCGAAGTTCGCGTTGCGAATTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCGCGTTGCG-A-TAGTCCAAATTCGTTGCGATAG
*
632137 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
1 TCCAAGTTCGCGTTGCGA--TAGTCCAAATTCGTT
632172 CCTACATAGT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
40 7 0.10
41 1 0.01
42 50 0.75
43 1 0.01
44 8 0.12
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (40 bp):
TCCAAGTTCGCGTTGCGATAGTCCAAATTCGTTGCGATAG
Found at i:632171 original size:21 final size:20
Alignment explanation
Indices: 632105--632171 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
632095 TCGAAGTTCG
632105 CGTTGCGAATTATTCCAAATT
1 CGTTGCG-ATTATTCCAAATT
* *
632126 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
632145 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
632168 CGTT
1 CGTT
632172 CCTACATAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 9 0.24
20 1 0.03
21 19 0.50
23 9 0.24
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:632312 original size:6 final size:6
Alignment explanation
Indices: 632296--632325 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
632286 GTCTGTCTCG
632296 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
632326 ATAATACGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:632547 original size:42 final size:42
Alignment explanation
Indices: 632417--632558 Score: 151
Period size: 42 Copynumber: 3.4 Consensus size: 42
632407 CGTTGCGATT
* ** *
632417 TTGGACTATCGCAATGAATTTGGAATAAATCGCAACACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATTACAACGCGAAC
* * * *
632459 TTCGACTATCGCAACGAATTTGTAATAAA-TATCAATGCTAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATTA-CAACGCGAAC
* * *
632501 TTGGACTATCGAAACAAATTTGGAATAAATTACAACGCGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATTACAACGCGAAC
**
632543 TTGGAAAATCGCAACG
1 TTGGACTATCGCAACG
632559 CGAACTTGGA
Statistics
Matches: 79, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
42 77 0.97
43 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATTACAACGCGAAC
Found at i:632557 original size:21 final size:21
Alignment explanation
Indices: 632533--632602 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
632523 GAATAAATTA
632533 CAACGCGAATTTGGAAAATCG
1 CAACGCGAATTTGGAAAATCG
* **
632554 CAACGCGAACTTGGACTATCG
1 CAACGCGAATTTGGAAAATCG
* * *
632575 CAATGCGAATAT-GTAAATCG
1 CAACGCGAATTTGGAAAATCG
*
632595 CAATGCGA
1 CAACGCGA
632603 TAGTCGAAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 13 0.32
21 27 0.68
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (21 bp):
CAACGCGAATTTGGAAAATCG
Found at i:632672 original size:97 final size:98
Alignment explanation
Indices: 632555--632747 Score: 361
Period size: 97 Copynumber: 2.0 Consensus size: 98
632545 GGAAAATCGC
632555 AACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATT
1 AACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATT
632620 GCGAATCTGGAAACTGATTTGCGATA-CGGAAG
66 GCGAATCTGGAAACTGATTTGCGATATCGGAAG
* *
632652 AACGCGAACTTGGACTATCGCAATTCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTT
1 AACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATT
632717 GCGAATCTGGAAACTGATTTGCGATATCGGA
66 GCGAATCTGGAAACTGATTTGCGATATCGGA
632748 GATCGTGTTG
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 89 0.96
98 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (98 bp):
AACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATT
GCGAATCTGGAAACTGATTTGCGATATCGGAAG
Found at i:633377 original size:3 final size:3
Alignment explanation
Indices: 633369--633434 Score: 80
Period size: 3 Copynumber: 21.3 Consensus size: 3
633359 CTAATTTAAC
*
633369 ATT ATT ATT ATT AGTT ATT ATT ATT ATT CTT ATT ATT ATT -TT CATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
*
633415 ATT AAT ATTT ATT ATT ATT A
1 ATT ATT A-TT ATT ATT ATT A
633435 CATATTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 2 0.04
3 46 0.84
4 7 0.13
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:633426 original size:25 final size:27
Alignment explanation
Indices: 633370--633434 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
633360 TAATTTAACA
*
633370 TTATTATTATTAGTTATTATTATTATTC
1 TTATTATTATTA-TTATTATTAATATTC
633398 TTATTATTATT-TTCATTATTAATA-T-
1 TTATTATTATTATT-ATTATTAATATTC
633423 TTATTATTATTA
1 TTATTATTATTA
633435 CATATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 11 0.32
26 3 0.09
27 9 0.26
28 11 0.32
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (27 bp):
TTATTATTATTATTATTATTAATATTC
Found at i:633480 original size:13 final size:12
Alignment explanation
Indices: 633454--633496 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
633444 TGTTACATGC
633454 CCAAAACC-AGG
1 CCAAAACCAAGG
633465 CCAAAACCCAAGG
1 CCAAAA-CCAAGG
*
633478 CCAAAACCAA-C
1 CCAAAACCAAGG
633489 CCAAAACC
1 CCAAAACC
633497 CGATTGCAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 14 0.48
12 6 0.21
13 9 0.31
ACGTcount: A:0.49, C:0.42, G:0.09, T:0.00
Consensus pattern (12 bp):
CCAAAACCAAGG
Found at i:638657 original size:17 final size:19
Alignment explanation
Indices: 638635--638683 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
638625 CGAATCGAAT
638635 ATGGTATCGATACT-C-AA
1 ATGGTATCGATACTACTAA
* *
638652 ATGGTACCGATACTACTAT
1 ATGGTATCGATACTACTAA
638671 ATGGTATCGATAC
1 ATGGTATCGATAC
638684 CCCCTCTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 1 0.04
19 13 0.48
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (19 bp):
ATGGTATCGATACTACTAA
Found at i:639506 original size:24 final size:24
Alignment explanation
Indices: 639456--639507 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
639446 AAAACAGTTC
* ** *
639456 AAAAAAGAGGGAAAAAAGATGTTA
1 AAAAAAGAGAGAAAAAAGACATGA
*
639480 AAAAAAGAGAGAGAAAAGACATGA
1 AAAAAAGAGAGAAAAAAGACATGA
639504 AAAA
1 AAAA
639508 TGGAAAACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.67, C:0.02, G:0.23, T:0.08
Consensus pattern (24 bp):
AAAAAAGAGAGAAAAAAGACATGA
Found at i:639916 original size:16 final size:17
Alignment explanation
Indices: 639895--639937 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
639885 AATGAATGGA
639895 TGTTACAATTGCA-TTT
1 TGTTACAATTGCATTTT
639911 TGTTACAATTGCATTTT
1 TGTTACAATTGCATTTT
*
639928 TGTTCCAATT
1 TGTTACAATT
639938 TGTGATGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (17 bp):
TGTTACAATTGCATTTT
Found at i:641582 original size:23 final size:22
Alignment explanation
Indices: 641535--641583 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
641525 CCAAAGGACG
*
641535 ACAT-GGTTTCACTGAAGAGCC
1 ACATAGGTTTCACCGAAGAGCC
* *
641556 ACATAGGTTTGCACCGAAGTGCT
1 ACATAGGTTT-CACCGAAGAGCC
641579 ACATA
1 ACATA
641584 TAGTCCTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 14 0.61
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
ACATAGGTTTCACCGAAGAGCC
Found at i:641930 original size:164 final size:163
Alignment explanation
Indices: 641625--641952 Score: 590
Period size: 165 Copynumber: 2.0 Consensus size: 163
641615 TCTTGGCATG
641625 CCAACTATACCTCTAATCCTCATACATATACTTTGACTTTTAACCATATAGTTTATTTATCTTTC
1 CCAACTATACCTCTAATCCTCATACATATA-TTTGACTTTTAACCATATAGTTTATTTATCTTTC
641690 TTATTCAAGTATTTCTTATTCATATAAGCACTTTCACATTGAGAATCTTCGTATAACTCATGTTC
65 TTATTCAAGTATTTCTTATTCATATAAGCACTTTCACATTGAGAATCTTCGTATAACTCATGTTC
641755 ACATATCACATATTCATACATATACTCATAATCAT
130 ACATATCACATATTCAT-CATATACTCATAATCAT
641790 CCAACTATACCTCTAATCCTCATACATACT-TTTGACTTTTAACCATATAG-TTATTTATCTTTC
1 CCAACTATACCTCTAATCCTCATACATA-TATTTGACTTTTAACCATATAGTTTATTTATCTTTC
641853 ATTATTCCAAGTATTTCTTATTCATATAAGCACTTTCACATTGAGAATCTTCGTAT-ACTCATGT
65 -TTATT-CAAGTATTTCTTATTCATATAAGCACTTTCACATTGAGAATCTTCGTATAACTCATGT
641917 TCACATATCACATATTCATCATATACTCATAATCAT
128 TCACATATCACATATTCATCATATACTCATAATCAT
641953 TCATCAATTT
Statistics
Matches: 160, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
163 30 0.19
164 52 0.32
165 77 0.48
166 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (163 bp):
CCAACTATACCTCTAATCCTCATACATATATTTGACTTTTAACCATATAGTTTATTTATCTTTCT
TATTCAAGTATTTCTTATTCATATAAGCACTTTCACATTGAGAATCTTCGTATAACTCATGTTCA
CATATCACATATTCATCATATACTCATAATCAT
Found at i:643543 original size:20 final size:19
Alignment explanation
Indices: 643518--643571 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
643508 TTGCCTGAAG
643518 AAAAAATGAAAGAAAATTA
1 AAAAAATGAAAGAAAATTA
643537 TAAAAAATGAAAGAAAATTA
1 -AAAAAATGAAAGAAAATTA
*
643557 AATAAA-GAAAGAAAA
1 AAAAAATGAAAGAAAA
643572 AAGTAAAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 9 0.27
19 5 0.15
20 19 0.58
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (19 bp):
AAAAAATGAAAGAAAATTA
Found at i:643604 original size:18 final size:19
Alignment explanation
Indices: 643583--643623 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
643573 AGTAAAGAGG
643583 AAAG-AAAAGAAGAA-AAAT
1 AAAGAAAAAG-AGAATAAAT
643601 AAAGAAAAAGAGAATAAAT
1 AAAGAAAAAGAGAATAAAT
643620 AAAG
1 AAAG
643624 GGGGTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (19 bp):
AAAGAAAAAGAGAATAAAT
Found at i:643694 original size:45 final size:43
Alignment explanation
Indices: 643620--643703 Score: 98
Period size: 45 Copynumber: 1.9 Consensus size: 43
643610 GAGAATAAAT
* * *
643620 AAAGGGGGTTCAAGATAAAACTCGTAAAGGG-TGTCTTGAAACC
1 AAAGGAGGTTCAAGATAAAACCCGCAAAGGGCTG-CTTGAAACC
*
643663 AAAGGAGGTCTCAAGTTGAAAACCCGCAAAGGGCTGCTTGA
1 AAAGGAGGT-TCAAGAT-AAAACCCGCAAAGGGCTGCTTGA
643704 GAATTGTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
43 8 0.24
44 6 0.18
45 18 0.53
46 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.19
Consensus pattern (43 bp):
AAAGGAGGTTCAAGATAAAACCCGCAAAGGGCTGCTTGAAACC
Found at i:645053 original size:134 final size:134
Alignment explanation
Indices: 644809--645390 Score: 652
Period size: 134 Copynumber: 4.3 Consensus size: 134
644799 AGACAAGAGA
* * * * * *
644809 AACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAATGGAATTAATCAACATCCTCATATCTG
1 AACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATCTG
* * * *
644874 ATTTTCCCCCAAGAAGAAGC-GAGATAGATCCCTCTCTTTCTAGATTTGATATTCCCTAAGT-AG
66 ATTTTCCCTCAAGAAGAAGCAGA-ACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGA-
644937 TAGTGG
129 TAGTGG
* * * *
644943 AACAAGTCTGCTTGGATTCAATATTCCTTGAAGAACAGTGGAATGAATCAGA-ATCCCCAGATCT
1 AACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCA-ACATCCCCAGATCT
** * * * *
645007 GATTTTCCCTCAAGAAGAAGTGGAGCAGATCCCTCTCTTTCAAGATTTAATATTCTCTGAGTGAC
65 GATTTTCCCTCAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGAT
*
645072 AATGG
130 AGTGG
* * * * * *
645077 AACAAGTCTACCTCAATTCAATATTCCCTAAAGAATAGTTGAATGAATCAACATCCCTATATCTG
1 AACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATCTG
* * * *
645142 ATTTTTCCTTAAGAAGAAGCAGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTTAGTGATA
66 ATTTTCCCTCAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGATA
645207 GTGG
131 GTGG
* * * * * **
645211 AATAAGTTTACCTCGATTCAATCTTCCCTGATGAACAGTGGAATGAATCAA-AGTCTCTGGATCT
1 AACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACA-TCCCCAGATCT
* * *
645275 GATTTTCCCTCAAGAAGAAGCATAAC-GAATCCCTTTCTTTCAAGATTTGATATTCCCTGAGTAA
65 GATTTTCCCTCAAGAAGAAGCAGAACAG-ATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGA
* * **
645339 CAATAA
129 TAGTGG
* * *
645345 AACAAGTCTACCTCGATTTAATATTCCCTAAAGAACAATGGAATGA
1 AACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGA
645391 GTTAACGTTT
Statistics
Matches: 374, Mismatches: 68, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
133 3 0.01
134 367 0.98
135 4 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (134 bp):
AACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATCTG
ATTTTCCCTCAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGATA
GTGG
Found at i:645286 original size:268 final size:268
Alignment explanation
Indices: 644808--645390 Score: 753
Period size: 268 Copynumber: 2.2 Consensus size: 268
644798 AAGACAAGAG
* * * *
644808 AAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAATGGAATTAATCAACATCCTCATATCT
1 AAACAAGTCTACCTCGATTCAATATTCCCTAAAGAACAATGGAATGAATCAACATCCTCATATCT
* * *
644873 GATTTTCCCCCAAGAAGAAGCGAGATAGATCCCTCTCTTTCTAGATTTGATATTCCCTAAGTAGT
66 GATTTTCCCCCAAGAAGAAGCGAGACAGATCCATCTCTTTCAAGATTTGATATTCCCTAAGTAGT
* * * *
644938 AGTGGAACAAGTCTGCTTGGATTCAATATTCCTTGAAGAACAGTGGAATGAATCAGAATCCCCAG
131 AGTGGAACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAGAATCCCCAG
** * *
645003 ATCTGATTTTCCCTCAAGAAGAAGTGGAGC-AGATCCCTCTCTTTCAAGATTTAATATTCTCTGA
196 ATCTGATTTTCCCTCAAGAAGAAGCAGAACGA-ATCCCTCTCTTTCAAGATTTAATATTCCCTGA
* *
645067 GTGACAATG
260 GTAACAATA
* * * * *
645076 GAACAAGTCTACCTCAATTCAATATTCCCTAAAGAATAGTTGAATGAATCAACATCC-CTATATC
1 AAACAAGTCTACCTCGATTCAATATTCCCTAAAGAACAATGGAATGAATCAACATCCTC-ATATC
* ** *
645140 TGATTTTTCCTTAAGAAGAAGC-AGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTTAGT-
65 TGATTTTCCCCCAAGAAGAAGCGAG-ACAGATCCATCTCTTTCAAGATTTGATATTCCCTAAGTA
* * * * *
645203 GATAGTGGAATAAGTTTACCTCGATTCAATCTTCCCTGATGAACAGTGGAATGAATCA-AAGTCT
129 G-TAGTGGAACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAGAA-TCC
** * * *
645267 CTGGATCTGATTTTCCCTCAAGAAGAAGCATAACGAATCCCTTTCTTTCAAGATTTGATATTCCC
192 CCAGATCTGATTTTCCCTCAAGAAGAAGCAGAACGAATCCCTCTCTTTCAAGATTTAATATTCCC
645332 TGAGTAACAATA
257 TGAGTAACAATA
*
645344 AAACAAGTCTACCTCGATTTAATATTCCCTAAAGAACAATGGAATGA
1 AAACAAGTCTACCTCGATTCAATATTCCCTAAAGAACAATGGAATGA
645391 GTTAACGTTT
Statistics
Matches: 268, Mismatches: 42, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
267 6 0.02
268 261 0.97
269 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (268 bp):
AAACAAGTCTACCTCGATTCAATATTCCCTAAAGAACAATGGAATGAATCAACATCCTCATATCT
GATTTTCCCCCAAGAAGAAGCGAGACAGATCCATCTCTTTCAAGATTTGATATTCCCTAAGTAGT
AGTGGAACAAGTCTACCTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAGAATCCCCAG
ATCTGATTTTCCCTCAAGAAGAAGCAGAACGAATCCCTCTCTTTCAAGATTTAATATTCCCTGAG
TAACAATA
Found at i:645571 original size:3 final size:3
Alignment explanation
Indices: 645563--645616 Score: 65
Period size: 3 Copynumber: 17.3 Consensus size: 3
645553 CAAATTTAAC
*
645563 ATT ATT ATT AGTT ATT ATT ATT ATT ATT -TT CATT ATT AAT ATTT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A-TT ATT
645610 ATT ATT A
1 ATT ATT A
645617 CATATTTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
2 2 0.04
3 36 0.80
4 7 0.16
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:646597 original size:7 final size:7
Alignment explanation
Indices: 646580--646611 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
646570 CTCTTTTAGA
646580 GAAAGAAT
1 GAAA-AAT
646588 GAAAAAT
1 GAAAAAT
646595 GAAAAAT
1 GAAAAAT
646602 GAAAAAT
1 GAAAAAT
646609 GAA
1 GAA
646612 GAGGATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (7 bp):
GAAAAAT
Found at i:647824 original size:14 final size:14
Alignment explanation
Indices: 647805--647831 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
647795 TTTTTATCTT
647805 TTAAAATTATTTTC
1 TTAAAATTATTTTC
647819 TTAAAATTATTTT
1 TTAAAATTATTTT
647832 AAAGGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTC
Found at i:658504 original size:16 final size:17
Alignment explanation
Indices: 658477--658512 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
658467 GATATGAAAA
658477 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
658494 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
658510 AAA
1 AAA
658513 ACGTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:660558 original size:17 final size:18
Alignment explanation
Indices: 660536--660571 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
660526 ATTTATTTCA
*
660536 TTTCATT-CTTATTTTAT
1 TTTCATTACTTATATTAT
660553 TTTCATTACTTATATTAT
1 TTTCATTACTTATATTAT
660571 T
1 T
660572 ATCCCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCATTACTTATATTAT
Found at i:660855 original size:17 final size:17
Alignment explanation
Indices: 660833--660906 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
660823 AATTGGAGTG
660833 CAAAAAGAAAGAAAAGA
1 CAAAAAGAAAGAAAAGA
660850 CAAAAAG-AAGAAAA-A
1 CAAAAAGAAAGAAAAGA
*
660865 TCAGAAAAG-AATAAAAGA
1 -CA-AAAAGAAAGAAAAGA
**
660883 -AAAGAA-AAAGAAAATT
1 CAAA-AAGAAAGAAAAGA
660899 CAAAAAGA
1 CAAAAAGA
660907 GAAAGCAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
15 3 0.07
16 20 0.43
17 22 0.48
18 1 0.02
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.05
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGA
Found at i:660863 original size:25 final size:24
Alignment explanation
Indices: 660835--660910 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 24
660825 TTGGAGTGCA
660835 AAAAGAAAGAAAAGACAAAAAGAAG
1 AAAA-AAAGAAAAGACAAAAAGAAG
*
660860 AAAAATCAGAAAAGA-ATAAAAGAA-
1 AAAAA-AAGAAAAGACA-AAAAGAAG
**
660884 AAGAAAAAGAAAATTCAAAAAG-AG
1 AA-AAAAAGAAAAGACAAAAAGAAG
660908 AAA
1 AAA
660911 GCAAGCCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
23 2 0.05
24 17 0.40
25 23 0.55
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (24 bp):
AAAAAAAGAAAAGACAAAAAGAAG
Found at i:664171 original size:19 final size:19
Alignment explanation
Indices: 664147--664216 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
664137 CGGCCAAGAG
664147 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
664166 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
* * *
664185 CATGTATTTTTATCAAAAAT
1 CATGTATCTTCAT-TAAAAT
*
664205 CATGTATTTTCA
1 CATGTATCTTCA
664217 AAGGGGTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 30 0.65
20 16 0.35
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:664649 original size:17 final size:17
Alignment explanation
Indices: 664627--664659 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
664617 CTATCCTTTA
664627 TTTATTTCA-TTTCATTC
1 TTTATTT-ATTTTCATTC
664644 TTTATTTATTTTCATT
1 TTTATTTATTTTCATT
664660 ACTTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTATTTTCATTC
Found at i:671265 original size:14 final size:14
Alignment explanation
Indices: 671248--671274 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
671238 GAATGCACAT
671248 AAACGAACATAAAC
1 AAACGAACATAAAC
671262 AAACGAACATAAA
1 AAACGAACATAAA
671275 TTAAAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.19, G:0.07, T:0.07
Consensus pattern (14 bp):
AAACGAACATAAAC
Found at i:673695 original size:8 final size:7
Alignment explanation
Indices: 673675--673736 Score: 56
Period size: 8 Copynumber: 8.4 Consensus size: 7
673665 ACAAAAATAT
673675 TTTATTA
1 TTTATTA
673682 TATTATATA
1 T-TTAT-TA
673691 TTTATTTA
1 TTTA-TTA
673699 TTTATTA
1 TTTATTA
673706 -TTATTA
1 TTTATTA
673712 -TTATTA
1 TTTATTA
*
673718 TATTTTTA
1 T-TTATTA
673726 TTTTATTA
1 -TTTATTA
673734 TTT
1 TTT
673737 TTCCAGGCCC
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 12 0.26
7 7 0.15
8 23 0.49
9 5 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTATTA
Found at i:673708 original size:3 final size:3
Alignment explanation
Indices: 673672--673735 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
673662 TCTACAAAAA
673672 TAT T-T TAT TA- TAT TAT ATATT TATT TATT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT -TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT
*
673718 TAT TTT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
673736 TTTCCAGGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
2 8 0.15
3 32 0.60
4 12 0.23
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:673735 original size:25 final size:26
Alignment explanation
Indices: 673672--673735 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
673662 TCTACAAAAA
673672 TATTTTATTA-TATTATATATTTATT
1 TATTTTATTATTATTATATATTTATT
673697 TA-TTTATTATTATTAT-TATTATATTTT
1 TATTTTATTATTATTATATATT-TA--TT
673724 TATTTTATTATT
1 TATTTTATTATT
673736 TTTCCAGGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
24 11 0.32
25 10 0.29
27 4 0.12
28 9 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TATTTTATTATTATTATATATTTATT
Found at i:674151 original size:11 final size:11
Alignment explanation
Indices: 674127--674279 Score: 50
Period size: 10 Copynumber: 13.5 Consensus size: 11
674117 TGACTTATTC
674127 TTTTTATTTCAT
1 TTTTTATTT-AT
674139 TTTTTATTTAT
1 TTTTTATTTAT
674150 TTACTTTATATATAT
1 TT--TTTAT-T-TAT
*
674165 TTTTCATTT-T
1 TTTTTATTTAT
** *
674175 CTCCTAATTTTCAT
1 -TTTTTA-TTT-AT
674189 TTTTT-TTTAT
1 TTTTTATTTAT
* *
674199 TTCTT-TTTAC
1 TTTTTATTTAT
*
674209 ATTTT-TTTAT
1 TTTTTATTTAT
*
674219 ATATTTATTTAT
1 -TTTTTATTTAT
*
674231 TTTTT-TTCA-
1 TTTTTATTTAT
674240 TTTTTATTAATAT
1 TTTTTATT--TAT
* *
674253 TATTATATTAAT
1 T-TTTTATTTAT
674265 TTTTTA-TTAT
1 TTTTTATTTAT
674275 TTTTT
1 TTTTT
674280 TCTCATGTTT
Statistics
Matches: 105, Mismatches: 21, Indels: 32
0.66 0.13 0.20
Matches are distributed among these distances:
9 5 0.05
10 31 0.30
11 22 0.21
12 22 0.21
13 12 0.11
14 8 0.08
15 5 0.05
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:674200 original size:10 final size:10
Alignment explanation
Indices: 674182--674244 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
674172 TTTCTCCTAA
674182 TTTTCATTTT
1 TTTTCATTTT
*
674192 TTTTTATTTCT
1 TTTTCATTT-T
674203 TTTTACATTTT
1 TTTT-CATTTT
674214 TTTAT-ATATTT
1 TTT-TCAT-TTT
*
674225 ATTT-ATTTT
1 TTTTCATTTT
674234 TTTTCATTTT
1 TTTTCATTTT
674244 T
1 T
674245 ATTAATATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
9 6 0.14
10 19 0.43
11 14 0.32
12 5 0.11
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:674205 original size:20 final size:20
Alignment explanation
Indices: 674182--674244 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 20
674172 TTTCTCCTAA
674182 TTTTCATTTTTTTTTATTTCT
1 TTTTCATTTTTTTTTATTT-T
*
674203 TTTTACATTTTTTTATATATTT
1 TTTT-CATTTTTTTTTAT-TTT
* *
674225 ATTT-ATTTTTTTTCATTTT
1 TTTTCATTTTTTTTTATTTT
674244 T
1 T
674245 ATTAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 4 0.11
22 16 0.46
23 2 0.06
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCATTTTTTTTTATTTT
Found at i:674245 original size:20 final size:20
Alignment explanation
Indices: 674187--674293 Score: 58
Period size: 22 Copynumber: 5.0 Consensus size: 20
674177 CCTAATTTTC
*
674187 ATTTTTTTTTATTTCTT-TTT
1 ATTTTTTTTCATTT-TTATTT
*
674207 ACATTTTTTTAT-ATATTTATTT
1 --ATTTTTTT-TCATTTTTATTT
674229 ATTTTTTTTCATTTTTATTAAT
1 ATTTTTTTTCATTTTTATT--T
* *
674251 ATTATTATATTAATTTTT-TATT
1 ATT-TT-TTTTCATTTTTAT-TT
*
674273 ATTTTTTTCTCATGTTTATTT
1 ATTTTTTT-TCATTTTTATTT
674294 TTACAATCTA
Statistics
Matches: 68, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
19 1 0.01
20 18 0.26
21 12 0.18
22 23 0.34
23 4 0.06
24 10 0.15
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (20 bp):
ATTTTTTTTCATTTTTATTT
Found at i:674258 original size:28 final size:32
Alignment explanation
Indices: 674194--674261 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 32
674184 TTCATTTTTT
674194 TTTATTTCTTTTTACATTTTTTTATATATTTA
1 TTTATTTCTTTTTACATTTTTTTATATATTTA
674226 TTTATTT-TTTTT-CATTTTTATTA-ATA-TTA
1 TTTATTTCTTTTTACATTTTT-TTATATATTTA
674255 TTATATT
1 TT-TATT
674262 AATTTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 5 0.15
30 14 0.41
31 8 0.24
32 7 0.21
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (32 bp):
TTTATTTCTTTTTACATTTTTTTATATATTTA
Found at i:674277 original size:34 final size:30
Alignment explanation
Indices: 674197--674280 Score: 89
Period size: 34 Copynumber: 2.6 Consensus size: 30
674187 ATTTTTTTTT
*
674197 ATTTCTTTTTACATTTTTTTATATATTTATTT
1 ATTT-TTTTT-CATTTTTTTATATATTTATTA
674229 ATTTTTTTTCATTTTTATTAATATTATTATATTA
1 ATTTTTTTTCATTTTT-TT-ATA-TATT-TATTA
674263 ATTTTTTATT-ATTTTTTT
1 ATTTTTT-TTCATTTTTTT
674281 CTCATGTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
30 7 0.15
31 7 0.15
32 7 0.15
33 6 0.13
34 17 0.37
35 2 0.04
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (30 bp):
ATTTTTTTTCATTTTTTTATATATTTATTA
Found at i:678181 original size:110 final size:110
Alignment explanation
Indices: 677981--678620 Score: 894
Period size: 110 Copynumber: 5.9 Consensus size: 110
677971 GATGGTGGTT
* * * * *
677981 GCTCAACTTCACAGCGAAGGGGCGACTGACGGTCAACAAAAAAATTTTCATTTTTATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
678046 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
678091 GCTCAACTTCACATCGAAGGGGCGAATAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
678156 AATTTCAACTTCACAACGAAAGATATTGCACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * * *
678201 GTTCAACTTCACAGTGAAGGGGCGGCTGACTGTTAACAAACAACTTTTCAGTTTCATTCAGAGTT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
678266 AATTTCAATTTCACAACGAATGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
678311 GCTTAACTTTACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
678376 AATTTTAACTTCACAGCGAAGGATATTGGACTAGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
678421 GTTCAACTTCAAAGAGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
678486 AATTTCAACTTCACAGTGAAGGATATTGGAATCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * * *
678531 GCTCAACTTCACAGCAAAGGGGCGTCTGGCTGTCAACAAATAAC-TTT-ATGATT--TT-AGAGT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCA-GTTTCATTCAGAGT
* * *
678591 CAATTTTAACTTCACGGTGAAGGATATTGG
65 CAATTTCAACTTCACAGCGAAGGATATTGG
678621 CCTTGAAACA
Statistics
Matches: 474, Mismatches: 55, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
106 33 0.07
107 2 0.00
108 1 0.00
109 6 0.01
110 432 0.91
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:678983 original size:84 final size:83
Alignment explanation
Indices: 678745--679507 Score: 704
Period size: 84 Copynumber: 9.2 Consensus size: 83
678735 TCGTGCCCAA
* * * *
678745 CAAAGGCCTTCGAGTTCAACTACGCTCGGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCT
* * **
678810 ATAAGGGTTATCTGCCAAC
66 AGAAGGGTTATATG-TGAC
* * * * * * ** * * *
678829 CGAAGACCCTCAAGTTCGATTACACTCATCTTTGAAGGCACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
678894 TAGAAGGGTTATATGTGAC
65 TAGAAGGGTTATATGTGAC
* *
678913 CAAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * **
678978 GAGAAGGGTTATCTGCCAAC
65 TAGAAGGGTTATATG-TGAC
* * * *
678998 CAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCT
* *
679063 AGAA---TGACTATCTG-C
66 AGAAGGGTTA-TATGTGAC
* * * * * * * * *
679078 CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGAACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
*
679143 TAGAAGGGTTATCTGTGAC
65 TAGAAGGGTTATATGTGAC
* * *
679162 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAACATAACTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * *
679227 GAGAAGGGTTATCT-TCCAAC
65 TAGAAGGGTTATATGT--GAC
* *
679247 CAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCT
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCT
*
679312 AGAAGGG-T-TATCTG-C
66 AGAAGGGTTATATGTGAC
* * * * * * * *
679327 CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC-GACATAACTCAAGG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAG-CATAACTTAAGT
* * *
679391 CTAGAAGGGTTATTTGTCAA
64 CTAGAAGGGTTATATGTGAC
* * * * * * *
679411 CAAAGACCTTCGAGTTCGACTCCACTCAACTCAAAGGCACCATCATTTGCAGCATAGCTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTTAAGTC
* *
679476 AAGAAGGGCTATA--TG-C
65 TAGAAGGGTTATATGTGAC
679492 CAAAGACCTTCGAGTT
1 CAAAGACCTTCGAGTT
679508 TGATTCCATT
Statistics
Matches: 550, Mismatches: 109, Indels: 43
0.78 0.16 0.06
Matches are distributed among these distances:
80 55 0.10
81 82 0.15
82 6 0.01
83 17 0.03
84 294 0.53
85 96 0.17
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (83 bp):
CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCT
AGAAGGGTTATATGTGAC
Found at i:679193 original size:249 final size:249
Alignment explanation
Indices: 678741--679494 Score: 1100
Period size: 249 Copynumber: 3.0 Consensus size: 249
678731 GGAATCGTGC
* * * *
678741 CCAA-CAAAGGCCTTCGAGTTCAACTACGCTCGGCTCCAAGGCACATCATTTGCAGCATAACTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTA
* * * * *
678805 AGTCAATAAGGGTTATCTGCCAACCGAAGACCCTCAAGTTCGATTACACTCATCTTTGAAGGCAC
66 AGTCAAGAAGGGTTATCTGCC-A---AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
*
678870 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAAGACCTTCGAATTCGACT
127 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAAGACCTTCGAGTTCGACT
678935 ACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
192 ACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
* *
678993 CCAACCAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCACATCATTTGTAGCATAGCTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTA
* * ** *
679058 AGTCGAGAATGACTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGAACATCA
66 AGTCAAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
*
679123 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGC
131 TTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAAGACCTTCGAGTTCGACTACGC
* * *
679188 TCAGCTCCAAGGCATATCATTTACAACATAACTTAAGTCGAGAAGGGTTATCTT
196 TCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
*
679242 CCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTA
*
679307 AGTCTAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
66 AGTCAAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
* * * * *
679372 TTTAC-GACATAACTCAAGGCTAGAAGGGTTATTTGTCAAC-AAAGACCTTCGAGTTCGACTCCA
131 TTTACAG-CATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAAGACCTTCGAGTTCGACTACG
* * * * * * * * *
679435 CTCAACTCAAAGGCACCATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATATG
195 CTCAGCTCCAAGGCA-TATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
679491 CCAA
1 CCAA
679495 AGACCTTCGA
Statistics
Matches: 453, Mismatches: 46, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
248 35 0.08
249 343 0.76
252 5 0.01
253 70 0.15
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (249 bp):
CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTA
AGTCAAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
TTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
Found at i:679483 original size:165 final size:164
Alignment explanation
Indices: 678742--679512 Score: 761
Period size: 165 Copynumber: 4.6 Consensus size: 164
678732 GAATCGTGCC
* * *
678742 CAACAAAGGCCTTCGAGTTCAACTACGCTCGGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
1 CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
* * * * **
678807 TCAATAAGGGTTATCTGCCAACCGAAGACCCTCAAGTTCGATTACACTCATCTTTGAAGGCACAT
66 TCAAGAAGGGTTATCTGCC-A---AAGACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCACAT
* *
678872 CATTTAC-AGCATAACTCAAGGCTAGAAGGGTTATATGT
126 CATTTACGAGCATAACTCAAGGCGAGAAGGGTTATTTGT
* * * *
678910 GACCAAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAA
1 CAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
* *
678975 GTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGA-TCAGCTCCAAGGCACA
65 GTCAAGAAGGGTTATCTG----CCAAAGACCTTCGAGTTCGATTAC-ACTCAGCTCCAAGGCACA
* * * * ** *
679039 TCATTT--GTAGCATAGCTTAAGTCGAGAATGACTATCTG-
125 TCATTTACG-AGCATAACTCAAGGCGAGAAGGGTTATTTGT
* * * * * * * *
679077 C--CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGAACATCATTTACAGCATAACTCAA
1 CAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAA
* * * * *
679140 GGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
65 GTCAAGAAGGGTTATC--TG-CC-AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACAT
* * * *
679205 CATTTAC-AACATAACTTAAGTCGAGAAGGGTTATCTT-C
126 CATTTACGAGCATAACTCAAGGCGAGAAGGGTTAT-TTGT
* *
679243 CAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAA
1 CAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
* * * *
679308 GTCTAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
65 GTCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCAT
*
679373 TTACGA-CATAACTCAAGGCTAGAAGGGTTATTTGT
129 TTACGAGCATAACTCAAGGCGAGAAGGGTTATTTGT
* * * * * *
679408 CAACAAAGACCTTCGAGTTCGACTCCACTCAACTCAAAGGCACCATCATTTGCAGCATAGCTCAA
1 CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTTAA
* * * *
679473 GGCAAGAAGGGCTATATGCCAAAGACCTTCGAGTTTGATT
65 GTCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATT
679513 CCATTTAACT
Statistics
Matches: 502, Mismatches: 77, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
164 90 0.18
165 203 0.40
166 5 0.01
167 2 0.00
168 79 0.16
169 119 0.24
170 1 0.00
172 1 0.00
173 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (164 bp):
CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
TCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTT
ACGAGCATAACTCAAGGCGAGAAGGGTTATTTGT
Found at i:679875 original size:12 final size:12
Alignment explanation
Indices: 679858--679918 Score: 56
Period size: 11 Copynumber: 5.1 Consensus size: 12
679848 AACATTTTAT
679858 TATATTATATTA
1 TATATTATATTA
679870 TATATT-TATTA
1 TATATTATATTA
679881 T-TATTATTATTA
1 TATATTA-TATTA
679893 TTATTATTATATT-
1 -TA-TATTATATTA
* *
679906 TTTATTTTATTA
1 TATATTATATTA
679918 T
1 T
679919 TTTTGTAGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 4 0.10
11 14 0.34
12 13 0.32
13 1 0.02
14 4 0.10
15 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATATTATATTA
Found at i:679883 original size:3 final size:3
Alignment explanation
Indices: 679854--679919 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
679844 CAAAAACATT
679854 TTA TTA -TA TTA -TA TTA TATA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA
*
679899 TTA -TA TTT TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
679920 TTTGTAGGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.15
3 42 0.76
4 4 0.07
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:681500 original size:16 final size:17
Alignment explanation
Indices: 681474--681507 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
681464 AAAATAAGAA
681474 ATCTAAAAATTATAAAC
1 ATCTAAAAATTATAAAC
*
681491 ATCT-AAAATTATTAAC
1 ATCTAAAAATTATAAAC
681507 A
1 A
681508 ACATTACCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (17 bp):
ATCTAAAAATTATAAAC
Found at i:683489 original size:135 final size:137
Alignment explanation
Indices: 682954--683513 Score: 485
Period size: 138 Copynumber: 4.1 Consensus size: 137
682944 CCATAAAGGA
* * * **
682954 GAGGACCAAATT-AAATATTCTACTAAATTAAAGGACTAAGGTGAAATTAAACCTAAGATAAATG
1 GAGGACCAAATTAAAAT-TTCTCCTAAATTAAAGTACTAAAGTGAAATTAAACCTAAGATGGA-G
* ** ** * ** ** * *
683018 -TTCTAATATT-AAACCTAACCAATTTTTGCTAATTATTAAATCGAATAACCAAAATGGAACCTC
64 ACTCTAATATTGAAACCTAATTAATTTTAAC-AATTATTGAATCGAATAATTAATTTAGAACATC
* * *
683081 GGGCAAAAGT
128 AGACAAAAGC
* * * *
683091 GATGACCAAATCAGAAA-TTCTCCTAAATTAAAGTACTAAACTGATATTAAACCTAAGATGGAGA
1 GAGGACCAAATTA-AAATTTCTCCTAAATTAAAGTACTAAAGTGAAATTAAACCTAAGATGGAGA
* * * * *
683155 CTCTAAAAATGAAACCTAATCAATTTTAACAAATTATTTG-ATTGAATAATTAATTTAGAACACC
65 CTCTAATATTGAAACCTAATTAATTTTAAC-AATTA-TTGAATCGAATAATTAATTTAGAACATC
683219 A-AGCAAAAGC
128 AGA-CAAAAGC
* * * * * * *
683229 GAGGACTAAATTTAAATTTCTCTTAAATTAAGGGACTAAAGTGTAATTAAACCTAAGATGGAGGC
1 GAGGACCAAATTAAAATTTCTCCTAAATTAAAGTACTAAAGTGAAATTAAACCTAAGATGGAGAC
* ** *
683294 TCTAATATTAAAATATAATTAATTTTAACCAATTATTGAATCG-ATAATTAATTT-GAAACATTA
66 TCTAATATTGAAACCTAATTAATTTTAA-CAATTATTGAATCGAATAATTAATTTAG-AACATCA
*
683357 GACAAAA-T
129 GACAAAAGC
* * * *
683365 GAGGACCAAGTTAAAATTTCTCCTAAATTAAATTATTAAAGTGAAATT-AACCTAAGATAGAGAC
1 GAGGACCAAATTAAAATTTCTCCTAAATTAAAGTACTAAAGTGAAATTAAACCTAAGATGGAGAC
* * * *
683429 TCTAATATTGAAACCCAATTAATTTTATCATTTTATTGAATCGAATAA-TCATTTAGAACATCAG
66 TCTAATATTGAAACCTAATTAATTTTAACA-ATTATTGAATCGAATAATTAATTTAGAACATCAG
683493 ACATAAAGAC
130 ACA-AAAG-C
*
683503 AAGGACCAAAT
1 GAGGACCAAAT
683514 CGAATATTCA
Statistics
Matches: 335, Mismatches: 71, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
134 2 0.01
135 63 0.19
136 49 0.15
137 82 0.24
138 133 0.40
139 6 0.02
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (137 bp):
GAGGACCAAATTAAAATTTCTCCTAAATTAAAGTACTAAAGTGAAATTAAACCTAAGATGGAGAC
TCTAATATTGAAACCTAATTAATTTTAACAATTATTGAATCGAATAATTAATTTAGAACATCAGA
CAAAAGC
Found at i:693251 original size:22 final size:21
Alignment explanation
Indices: 693226--693266 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
693216 TTAAATTTTC
*
693226 TATTATTTTATTATAAATATAA
1 TATTATTTTAATA-AAATATAA
*
693248 TATTTTTTTAATAAAATAT
1 TATTATTTTAATAAAATAT
693267 CACTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATTTTAATAAAATATAA
Found at i:693425 original size:16 final size:16
Alignment explanation
Indices: 693406--693445 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
693396 ATTTGGTTCA
* * *
693406 GGTTTCTTTCGGTTTT
1 GGTTGCTTTCAGTTTG
693422 GGTTGCTTTCAGTTTG
1 GGTTGCTTTCAGTTTG
693438 GGTTGCTT
1 GGTTGCTT
693446 AGGCTCAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.03, C:0.12, G:0.30, T:0.55
Consensus pattern (16 bp):
GGTTGCTTTCAGTTTG
Found at i:693491 original size:16 final size:16
Alignment explanation
Indices: 693465--693504 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
693455 TTAATTTTGG
*
693465 TTTCTGTTCAGGTTAA
1 TTTCGGTTCAGGTTAA
* *
693481 TTTTGGTTCAGGTTGA
1 TTTCGGTTCAGGTTAA
693497 TTTCGGTT
1 TTTCGGTT
693505 TCGCGAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.12, C:0.10, G:0.25, T:0.53
Consensus pattern (16 bp):
TTTCGGTTCAGGTTAA
Found at i:694869 original size:118 final size:117
Alignment explanation
Indices: 694692--694928 Score: 298
Period size: 118 Copynumber: 2.0 Consensus size: 117
694682 TATAGACGAA
* * * * *
694692 TTATTCTCATTATGAACTCTTATTGAAAAGGTTGATTCATCTCCTTCTGTGATGGATTTGAGCT-
1 TTATTCTCATTATAAACTCTTATTGAAAAGGTCGATCCACCTCCTTCTATGATGGATTTGAG-TA
* * * * * *
694756 AAATGTCGAA-CAAGTTCTTTTCATTATGAACTTCTTTTCTCTTTTTGGATGAG
65 AAAGGTCGAAGCAA-TTCTTCTCATTATGAACTTATTCTCCCTCTTTGGATGAG
* *
694809 TTATTCTCATTATAAACTCTCTATTGCAAATGTCGATCCACCTCCTTCTATGATGGATTTGAGTA
1 TTATTCTCATTATAAACTCT-TATTGAAAAGGTCGATCCACCTCCTTCTATGATGGATTTGAGTA
* *
694874 AAAGGTTGAAGCAATTCTTCTCATTATTAACTTATTCTCCCTCTTTGGATGAG
65 AAAGGTCGAAGCAATTCTTCTCATTATGAACTTATTCTCCCTCTTTGGATGAG
694927 TT
1 TT
694929 TTTATACGTG
Statistics
Matches: 102, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
117 20 0.20
118 79 0.77
119 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (117 bp):
TTATTCTCATTATAAACTCTTATTGAAAAGGTCGATCCACCTCCTTCTATGATGGATTTGAGTAA
AAGGTCGAAGCAATTCTTCTCATTATGAACTTATTCTCCCTCTTTGGATGAG
Found at i:696038 original size:19 final size:19
Alignment explanation
Indices: 696014--696066 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
696004 AATGACCAAC
696014 AAAATCGCAATGCGAAATA
1 AAAATCGCAATGCGAAATA
696033 AAAATCGCAATGCGAAATA
1 AAAATCGCAATGCGAAATA
*
696052 AAAATCGCAACGCGA
1 AAAATCGCAATGCGA
696067 TATCCAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATA
Found at i:696118 original size:21 final size:20
Alignment explanation
Indices: 696094--696226 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 20
696084 TAGTTCCTAG
696094 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
* *
696114 GAATCGTAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
696135 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTAT-GAA
*
696157 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
696177 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
696197 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
696217 TATCGCAACG
1 AATCGCAACG
696227 AGTATCCGTA
Statistics
Matches: 85, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.54
21 33 0.39
22 3 0.04
23 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:696182 original size:20 final size:20
Alignment explanation
Indices: 696157--696391 Score: 125
Period size: 20 Copynumber: 11.7 Consensus size: 20
696147 GATTTTCCAT
*
696157 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
696177 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
696197 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
696217 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
696238 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
696258 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
696278 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
696298 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * * *
696318 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
696338 AATCGCAACGAC-AATACATAA
1 AATCGCAACG-CGAATAC-GAA
* * *
696359 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
696379 AATCACAACGCGA
1 AATCGCAACGCGA
696392 TTTTTAAAGC
Statistics
Matches: 165, Mismatches: 42, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.01
20 128 0.78
21 35 0.21
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:696261 original size:81 final size:80
Alignment explanation
Indices: 696157--696388 Score: 236
Period size: 81 Copynumber: 2.9 Consensus size: 80
696147 GATTTTCCAT
* ** * * *
696157 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT-A-AAT
* *
696220 CGCAACGAGTATCCGTAA
64 CGCAACGAGAATACGT-A
* * * ** *
696238 AATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAAATCGTAACGCGTATCCGTAAATCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCG
696303 CAACGAGAATACGTA
66 CAACGAGAATACGTA
* * *
696318 AATCGCAATGTGTATCCGTAAATCGCAACGACAATACATA-AAATCGCAACGCGTATCCGTAAAT
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATAAATCGCAACGCGTATCCGTAAAT
*
696382 CACAACG
64 CGCAACG
696389 CGATTTTTAA
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
80 28 0.23
81 88 0.72
82 6 0.05
83 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCG
CAACGAGAATACGTA
Found at i:696290 original size:40 final size:41
Alignment explanation
Indices: 696222--696388 Score: 239
Period size: 40 Copynumber: 4.1 Consensus size: 41
696212 CTGACTATCG
* *
696222 CAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCA
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCA
* *
696263 CAACGAGAATACGT-AAATCGTAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCA
* * *
696303 CAACGAGAATACGT-AAATCGCAATGTGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCA
* *
696343 CAACGACAATACATAAAATCGCAACGCGTATCCGTAAATCA
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCA
696384 CAACG
1 CAACG
696389 CGATTTTTAA
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 73 0.65
41 40 0.35
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCA
Found at i:696338 original size:60 final size:61
Alignment explanation
Indices: 696218--696388 Score: 182
Period size: 60 Copynumber: 2.8 Consensus size: 61
696208 GATTCTGACT
* * *
696218 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAAAATCGCAACGAGAATACGTAAATCACAACGAGAATACGTAA
* * * * * * *
696279 ATCGTAACGCGTATCCGT-AAATCGCAACGAGAATACGTAAATCGCAATGTGTATCCGTAA
1 ATCGCAACGAGTATCCGTAAAATCGCAACGAGAATACGTAAATCACAACGAGAATACGTAA
** * * * * *
696339 ATCGCAACGACAATACATAAAATCGCAACGCGTATCCGTAAATCACAACG
1 ATCGCAACGAGTATCCGTAAAATCGCAACGAGAATACGTAAATCACAACG
696389 CGATTTTTAA
Statistics
Matches: 88, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
60 46 0.52
61 42 0.48
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (61 bp):
ATCGCAACGAGTATCCGTAAAATCGCAACGAGAATACGTAAATCACAACGAGAATACGTAA
Found at i:696975 original size:20 final size:20
Alignment explanation
Indices: 696950--697040 Score: 114
Period size: 20 Copynumber: 4.5 Consensus size: 20
696940 TTCTAAACTT
*
696950 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
696970 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
696990 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
697011 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
697030 AAAATCGCAAC
1 AAAATCGCAAC
697041 GAGATAATCG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
19 16 0.26
20 30 0.48
21 16 0.26
ACGTcount: A:0.51, C:0.20, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:697029 original size:40 final size:40
Alignment explanation
Indices: 696950--697044 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
696940 TTCTAAACTT
696950 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACACGAAAATG
** *
696990 ACTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAATCGCAACACGAAAATG
697030 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
697045 TAATCGCAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 29 0.60
41 19 0.40
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.12
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATG
Found at i:697138 original size:20 final size:19
Alignment explanation
Indices: 697067--697146 Score: 106
Period size: 20 Copynumber: 4.1 Consensus size: 19
697057 GAAACCAAAA
*
697067 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
697086 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
697105 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
697125 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
697145 TC
1 TC
697147 AACCAAACGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
19 19 0.36
20 33 0.62
21 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:699193 original size:21 final size:21
Alignment explanation
Indices: 699169--699235 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
699159 TCATTCCTCG
699169 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
699190 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
699211 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
699232 AGAG
1 AGAG
699236 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:699193 original size:42 final size:42
Alignment explanation
Indices: 699117--699235 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
699107 GACTCGCCTG
* * * * * * *
699117 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
699159 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
699201 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
699236 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:700608 original size:14 final size:14
Alignment explanation
Indices: 700589--700624 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
700579 ATTGTTTAAT
700589 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
700603 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
700617 TGATTTGT
1 TGATTTGT
700625 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:700753 original size:19 final size:19
Alignment explanation
Indices: 700731--700789 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
700721 AAAAATGACT
700731 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
700750 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
700764 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
700783 ATCGCAA
1 ATCGCAA
700790 CGACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:700773 original size:33 final size:33
Alignment explanation
Indices: 700731--700810 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
700721 AAAAATGACT
* *
700731 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
700764 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
700797 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
700811 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:700862 original size:33 final size:33
Alignment explanation
Indices: 700820--700913 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
700810 ACTAAATTCG
*
700820 CGTTGCGATTTTTATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
* *
700853 CGTTGCGATTTTAATTTCACATTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
* *
700886 CGTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTAATTTCGCATTGCGAT
700914 AGTCATTTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
Found at i:700966 original size:19 final size:19
Alignment explanation
Indices: 700816--700967 Score: 82
Period size: 19 Copynumber: 8.7 Consensus size: 19
700806 CGAAACTAAA
* *
700816 TTCGCGTTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
*
700835 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
* *
700851 CTCG--TTGCGATTTTAAT
1 TTCGCATTGCGATTTTCAT
*
700868 TTCACATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
700884 CTCG--TTACGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
700901 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
700920 TTCCGCGTTGCGATTTTCA-
1 TT-CGCATTGCGATTTTCAT
*
700939 --CG--TTACGATTTTCAT
1 TTCGCATTGCGATTTTCAT
700954 TTCGCATTGCGATT
1 TTCGCATTGCGATT
700968 CTCTCGTTGC
Statistics
Matches: 96, Mismatches: 21, Indels: 32
0.64 0.14 0.21
Matches are distributed among these distances:
14 22 0.23
16 13 0.14
17 12 0.12
19 36 0.38
20 13 0.14
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:700989 original size:33 final size:34
Alignment explanation
Indices: 700907--701000 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
700897 TCATTTCGCA
*
700907 TTGCGATAGTCATTTCCGCGTTGCGATTTTCACG
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTCACG
* ** * *
700941 TTACGATTTTCATTT-CGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTCACG
*
700974 TTGCGATAGTAATTTCCGCGTTGCGAT
1 TTGCGATAGTCATTTCCGCGTTGCGAT
701001 AGACATTAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 26 0.54
34 22 0.46
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCGTTGCGATTCTCACG
Found at i:701046 original size:20 final size:20
Alignment explanation
Indices: 700973--701046 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
700963 CGATTCTCTC
* *
700973 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
700993 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
701013 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
701034 GTTGCGATAGTCA
1 GTTGCGATAGTCA
701047 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:703556 original size:24 final size:24
Alignment explanation
Indices: 703529--703575 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
703519 CAAAATCCGA
703529 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
703553 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
703576 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:703584 original size:24 final size:24
Alignment explanation
Indices: 703533--703584 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
703523 ATCCGAGTAT
** *
703533 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
703557 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
703581 TGAC
1 TGAC
703585 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:704457 original size:20 final size:20
Alignment explanation
Indices: 704441--704641 Score: 181
Period size: 20 Copynumber: 9.9 Consensus size: 20
704431 TGATTTATAG
*
704441 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
704461 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
704481 ATTCGCATTGCGATTTACGG
1 ATTCGCATTGCGATTTACGT
* * *
704501 ATACGCATTACAATTTACGT
1 ATTCGCATTGCGATTTACGT
*
704521 ATTCTCATTGCGATTTACAG-
1 ATTCGCATTGCGATTTAC-GT
* * *
704541 ATACGCGTTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
704561 ATTCTCGTTGCGATTTACGG
1 ATTCGCATTGCGATTTACGT
* *
704581 ATACGCGTTGCGATTTTACGT
1 ATTCGCATTGCGA-TTTACGT
** * *
704602 ATT-GTTGTTGCAATTTACGG
1 ATTCG-CATTGCGATTTACGT
*
704622 ATACGCATTGCGATGTTACG
1 ATTCGCATTGCGAT-TTACG
704642 GATACTCGTT
Statistics
Matches: 146, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.01
20 124 0.85
21 21 0.14
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:704476 original size:40 final size:40
Alignment explanation
Indices: 704441--704641 Score: 249
Period size: 40 Copynumber: 5.0 Consensus size: 40
704431 TGATTTATAG
* * *
704441 ATTCACATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCTCATTGCGATTTACGGATACGCATTGCGATTTACGT
* * *
704481 ATTCGCATTGCGATTTACGGATACGCATTACAATTTACGT
1 ATTCTCATTGCGATTTACGGATACGCATTGCGATTTACGT
* * *
704521 ATTCTCATTGCGATTTACAGATACGCGTTGCAATTTACGT
1 ATTCTCATTGCGATTTACGGATACGCATTGCGATTTACGT
* *
704561 ATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 ATTCTCATTGCGATTTACGGATACGCATTGCGA-TTTACGT
* ** *
704602 ATTGTTGTTGCAATTTACGGATACGCATTGCGATGTTACG
1 ATTCTCATTGCGATTTACGGATACGCATTGCGAT-TTACG
704642 GATACTCGTT
Statistics
Matches: 143, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 102 0.71
41 41 0.29
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (40 bp):
ATTCTCATTGCGATTTACGGATACGCATTGCGATTTACGT
Found at i:704688 original size:20 final size:20
Alignment explanation
Indices: 704659--704717 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
704649 GTTGTGATAG
*
704659 TCATAATCGCGTTGCGATTT
1 TCATATTCGCGTTGCGATTT
*
704679 AT-ATGTTCGCGTTGCGATTT
1 -TCATATTCGCGTTGCGATTT
*
704699 TCATATTCGCGTTACGATT
1 TCATATTCGCGTTGCGATT
704718 ATGGAAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (20 bp):
TCATATTCGCGTTGCGATTT
Found at i:713478 original size:10 final size:9
Alignment explanation
Indices: 713458--713489 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
713448 GTCTCTATAG
713458 TTTT-ATTT
1 TTTTAATTT
713466 TTTTAATTT
1 TTTTAATTT
713475 TTTTAATTT
1 TTTTAATTT
713484 TTTTAA
1 TTTTAA
713490 AGCATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTAATTT
Found at i:721370 original size:20 final size:21
Alignment explanation
Indices: 721343--721402 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
721333 TCCAGAACCC
721343 CATGGGGGTATCGATTCCCCT
1 CATGGGGGTATCGATTCCCCT
* * *
721364 -GTGGGGGGAATCGGTT-CCCT
1 CAT-GGGGGTATCGATTCCCCT
*
721384 CATGGGGGTATTGATTCCC
1 CATGGGGGTATCGATTCCC
721403 TCTGCACCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.28
Consensus pattern (21 bp):
CATGGGGGTATCGATTCCCCT
Found at i:725248 original size:22 final size:21
Alignment explanation
Indices: 725206--725245 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
725196 GAGTTTATTT
*
725206 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
725227 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
725246 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:729058 original size:16 final size:17
Alignment explanation
Indices: 729030--729061 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
729020 ATCGCCGACA
729030 AAATTTAACTATTCACG
1 AAATTTAACTATTCACG
729047 AAATTT-ACTATTCAC
1 AAATTTAACTATTCAC
729062 ATGAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTAACTATTCACG
Found at i:730622 original size:2 final size:2
Alignment explanation
Indices: 730615--730654 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
730605 ATTATTTATC
730615 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
730655 TATTGATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:734291 original size:37 final size:37
Alignment explanation
Indices: 734239--734312 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
734229 GGTATTGTTA
* *
734239 GATTATCGGTATTTTGGACTAAAATGTCTTTAAATTT
1 GATTACCGGTATTTTGAACTAAAATGTCTTTAAATTT
*
734276 GATTACCGGTGTTTTGAACTAAAATGTCTTTAAATTT
1 GATTACCGGTATTTTGAACTAAAATGTCTTTAAATTT
734313 ATTTTTTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (37 bp):
GATTACCGGTATTTTGAACTAAAATGTCTTTAAATTT
Found at i:734414 original size:36 final size:36
Alignment explanation
Indices: 734365--734449 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 36
734355 TATCAAATTT
*
734365 TTTTATATTTTTAA-TTTTGTAAAAAATATATATAA-A
1 TTTTATA-ATTTAATTTTTGTAAAAAATATATA-AATA
* *
734401 TTTTATGAATTTAATTTTTTTTTAAAAATATATAAATA
1 TTTTAT-AATTTAA-TTTTTGTAAAAAATATATAAATA
734439 TTTTATAATTT
1 TTTTATAATTT
734450 GTTAAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 11 0.26
37 8 0.19
38 23 0.55
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (36 bp):
TTTTATAATTTAATTTTTGTAAAAAATATATAAATA
Found at i:737716 original size:18 final size:18
Alignment explanation
Indices: 737693--737764 Score: 135
Period size: 18 Copynumber: 4.0 Consensus size: 18
737683 ACATATCACA
737693 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
737711 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
737729 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
*
737747 TATGTCCCCAAGGACCAC
1 TATGTCCCGAAGGACCAC
737765 ATAGACCCTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.28, C:0.35, G:0.21, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:738228 original size:11 final size:10
Alignment explanation
Indices: 738186--738240 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
738176 TTTATTCACT
738186 CATATCATTAA
1 CATATCA-TAA
*
738197 CATAT-GTAA
1 CATATCATAA
738206 CA-ATCAATAA
1 CATATC-ATAA
738216 CATATACATAA
1 CATAT-CATAA
738227 CATATCA-AA
1 CATATCATAA
738236 CATAT
1 CATAT
738241 GCTCATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 2 0.05
9 12 0.32
10 7 0.18
11 16 0.42
12 1 0.03
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (10 bp):
CATATCATAA
Found at i:740173 original size:20 final size:20
Alignment explanation
Indices: 740129--740301 Score: 195
Period size: 20 Copynumber: 8.6 Consensus size: 20
740119 GATTCTGACT
*
740129 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
740150 ATCGCAACGCGTATCCATAA
1 ATCGCAACGCGTATCCGTAA
* * *
740170 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
740190 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
740210 ATCGCAACGAGAATACATAA
1 ATCGCAACGCGTATCCGTAA
*
740230 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
740250 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
740271 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
740291 ATCGCAACGCG
1 ATCGCAACGCG
740302 ATTTTTAAAG
Statistics
Matches: 124, Mismatches: 25, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
20 91 0.73
21 33 0.27
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:740191 original size:81 final size:80
Alignment explanation
Indices: 740088--740299 Score: 266
Period size: 81 Copynumber: 2.6 Consensus size: 80
740078 GATTTTTCAT
* * ** * * * *
740088 AATCGCAACGCGAACATATAAATCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATCCGTAAAA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACAT-AAA
740151 TCGCAACGCGTATCCATA
63 TCGCAACGCGTATCCATA
740169 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACATAAATCG
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACATAAATCG
* *
740234 CAATGCGTATCCGTA
66 CAACGCGTATCCATA
* *
740249 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACG
1 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAAATCGCAACG
740300 CGATTTTTAA
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
80 37 0.32
81 77 0.66
82 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (80 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACATAAATCG
CAACGCGTATCCATA
Found at i:740203 original size:40 final size:41
Alignment explanation
Indices: 740129--740299 Score: 265
Period size: 40 Copynumber: 4.2 Consensus size: 41
740119 GATTCTGACT
* * *
740129 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
740170 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
740210 ATCGCAACGAGAATACAT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
740250 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
740291 ATCGCAACG
1 ATCGCAACG
740300 CGATTTTTAA
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 73 0.61
41 46 0.39
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:740888 original size:20 final size:19
Alignment explanation
Indices: 740863--740934 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
740853 TTCTAAACTT
740863 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
740883 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
740903 ACTATCGCAATGAGAGAAATG
1 AAAATCGCAA-CAGA-AAATG
740924 AAAATCGCAAC
1 AAAATCGCAAC
740935 GAGATAATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:740983 original size:19 final size:19
Alignment explanation
Indices: 740961--741067 Score: 72
Period size: 19 Copynumber: 6.1 Consensus size: 19
740951 GAAACCAAAA
*
740961 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
740980 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
740994 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
741013 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
741027 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
741046 TCCGCGTTACGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
741066 TC
1 TC
741068 AACCAAAAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
14 20 0.30
16 4 0.06
17 5 0.08
19 22 0.33
20 15 0.23
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:741008 original size:33 final size:33
Alignment explanation
Indices: 740966--741059 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
740956 CAAAATCGCA
740966 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
740999 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
741032 TTGCGATAGTCATTTCCGCGTTACGATT
1 TTGCGATTTTCATTT-CGCGTTGCGATT
741060 TTCATTTCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 44 0.80
34 11 0.20
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:743148 original size:21 final size:21
Alignment explanation
Indices: 743090--743149 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
743080 TCGAGAGTAA
743090 CCTCCCACCGTTCAAGAGGTC
1 CCTCCCACCGTTCAAGAGGTC
* ** * *
743111 ACTGTCATCGTTGAAGAGGTC
1 CCTCCCACCGTTCAAGAGGTC
*
743132 CCTCCCACCATTCAAGAG
1 CCTCCCACCGTTCAAGAG
743150 CCCGATTCAC
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (21 bp):
CCTCCCACCGTTCAAGAGGTC
Found at i:744520 original size:14 final size:14
Alignment explanation
Indices: 744501--744550 Score: 91
Period size: 14 Copynumber: 3.6 Consensus size: 14
744491 ATTGTTTAAT
744501 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
744515 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
744529 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
744543 TGATTTGT
1 TGATTTGT
744551 TTAATTGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:744679 original size:19 final size:19
Alignment explanation
Indices: 744657--744715 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
744647 AAAAATGACT
744657 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
744676 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
744690 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
744709 ATCGCAA
1 ATCGCAA
744716 CGACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:744699 original size:33 final size:33
Alignment explanation
Indices: 744657--744736 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
744647 AAAAATGACT
* *
744657 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
744690 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
744723 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
744737 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:744764 original size:19 final size:19
Alignment explanation
Indices: 744742--744893 Score: 109
Period size: 19 Copynumber: 8.7 Consensus size: 19
744732 CGAAACTAAA
744742 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
744761 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
744776 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
744794 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
744809 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
744827 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
744846 TTCTGCGTTGCGATTTTCA-
1 TTC-GCGTTGCGATTTTCAT
744865 ----CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
744880 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
744894 CTCTCGTTGC
Statistics
Matches: 100, Mismatches: 17, Indels: 32
0.67 0.11 0.21
Matches are distributed among these distances:
14 31 0.31
16 6 0.06
17 6 0.06
19 45 0.45
20 12 0.12
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:744788 original size:33 final size:33
Alignment explanation
Indices: 744746--744839 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
744736 ACTAAATTCG
744746 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
744779 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
744812 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
744840 AGTCATTTCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:744868 original size:14 final size:14
Alignment explanation
Indices: 744851--744878 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
744841 GTCATTTCTG
744851 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
744865 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
744879 TTTCGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:744870 original size:53 final size:52
Alignment explanation
Indices: 744781--744892 Score: 170
Period size: 53 Copynumber: 2.1 Consensus size: 52
744771 GATTCCCTCG
** *
744781 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATAGTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
* *
744833 TTGCGATAGTCATTTCTGCGTTGCGATTTTCACGTTGCGATTTTCATTTCGCA
1 TTGCGATAGTCATTTC-GCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
744886 TTGCGAT
1 TTGCGAT
744893 TCTCTCGTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 14 0.26
53 40 0.74
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (52 bp):
TTGCGATAGTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
Found at i:744902 original size:33 final size:34
Alignment explanation
Indices: 744833--744915 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 34
744823 TCATTTCGCA
* *
744833 TTGCGATAGTCATTTCTGCGTTGCGATTTTCACG
1 TTGCGATAGTCATTTCTGCATTGCGATTCTCACG
** *
744867 TTGCGATTTTCATTTC-GCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCTGCATTGCGATTCTCACG
*
744900 TTGCGATAGTAATTTC
1 TTGCGATAGTCATTTC
744916 CGCGTTGGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 27 0.66
34 14 0.34
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATAGTCATTTCTGCATTGCGATTCTCACG
Found at i:744915 original size:86 final size:85
Alignment explanation
Indices: 744742--744933 Score: 258
Period size: 86 Copynumber: 2.2 Consensus size: 85
744732 CGAAACTAAA
** *
744742 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTCGCGTTGCGATAGTCATTTCGCATTGCGATTCCCACGTTGCGATTTTCATTTCGCATTGCGAT
** *
744807 TCTCTCGTTGCGATTTTCAT
66 TCTCTCGTTGCGATAGTAAT
* * **
744827 TTCGCATTGCGATAGTCATTTCTGCGTTGCGATTTTCACGTTGCGATTTTCATTTCGCATTGCGA
1 TTCGCGTTGCGATAGTCATTTC-GCATTGCGATTCCCACGTTGCGATTTTCATTTCGCATTGCGA
744892 TTCTCTCGTTGCGATAGTAAT
65 TTCTCTCGTTGCGATAGTAAT
* *
744913 TTCCGCGTTGGGATAGACATT
1 TT-CGCGTTGCGATAGTCATT
744934 AAGATGATTG
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 19 0.21
86 58 0.63
87 15 0.16
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (85 bp):
TTCGCGTTGCGATAGTCATTTCGCATTGCGATTCCCACGTTGCGATTTTCATTTCGCATTGCGAT
TCTCTCGTTGCGATAGTAAT
Found at i:744922 original size:53 final size:52
Alignment explanation
Indices: 744812--744922 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 52
744802 GCGATTCTCT
* * * *
744812 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCTGCGTTGCGATTTTCA
1 CGTTGCGATTTTCATTTCGCATTGCGATA-TCATCTCTGCGTAGCAATTTCCA
* *
744865 CGTTGCGATTTTCATTTCGCATTGCGAT-TC-TCTCGTTGCGATAGTAATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGATATCATCTC--TGCG-TAGCAATTTCCA
744918 CGTTG
1 CGTTG
744923 GGATAGACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
50 3 0.06
51 2 0.04
52 4 0.08
53 40 0.82
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (52 bp):
CGTTGCGATTTTCATTTCGCATTGCGATATCATCTCTGCGTAGCAATTTCCA
Found at i:747477 original size:24 final size:24
Alignment explanation
Indices: 747450--747496 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
747440 ATCATTAAAA
747450 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
747474 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
747497 TTTCGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:747510 original size:24 final size:24
Alignment explanation
Indices: 747450--747510 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
747440 ATCATTAAAA
* *
747450 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAATACTGACCAAGATCAAAG
** * *
747474 TCCGGGTATTGACCAAGATCAAAT
1 TCCGAATACTGACCAAGATCAAAG
*
747498 TTCGAATACTGAC
1 TCCGAATACTGAC
747511 TAGTACTCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (24 bp):
TCCGAATACTGACCAAGATCAAAG
Found at i:748379 original size:20 final size:19
Alignment explanation
Indices: 748354--748645 Score: 221
Period size: 20 Copynumber: 14.5 Consensus size: 19
748344 GTCAGAATCT
748354 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTAC-GATTCG
*
748374 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACG-ATTCG
*
748394 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACG-ATTCG
* * *
748414 CATTGCGATTTATGGATACG
1 CGTTGCGATTTA-CGATTCG
* *
748434 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCG
*
748454 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTAC-GATTCG
*
748474 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCG
*
748494 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCG
748514 CGTTGCGATTTTACGTATT-G
1 CGTTGCGA-TTTACG-ATTCG
*
748534 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTAC-GATTCG
* *
748555 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTAC-GATTCG
* * *
748576 CGTTGTGATAGT-CAGAATCG
1 CGTTGCGAT-TTAC-GATTCG
*
748596 CGTTGCGATTTA-TATGTTCG
1 CGTTGCGATTTACGA--TTCG
* *
748616 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTAC-GATTCG
748636 CGTTGCGATT
1 CGTTGCGATT
748646 CTGGAAAATC
Statistics
Matches: 227, Mismatches: 27, Indels: 36
0.78 0.09 0.12
Matches are distributed among these distances:
18 1 0.00
19 4 0.02
20 181 0.80
21 39 0.17
22 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTACGATTCG
Found at i:748413 original size:40 final size:40
Alignment explanation
Indices: 748354--748645 Score: 295
Period size: 40 Copynumber: 7.2 Consensus size: 40
748344 GTCAGAATCT
* * *
748354 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCGCGTTGCGATTTACGGATACG
* * *
748394 CATTGCGATTTACGTATTCGCATTGCGATTTATGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
* * *
748434 CATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
*
748474 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
748514 CGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCG-CGTTGCGATTTACGGATACG
* * * * * *
748555 CGTTGCGATTTTACGGATACTCGTTGTGATAGT-CAGA-ATCG
1 CGTTGCGA-TTTACGTATTCGCGTTGCGAT-TTACGGATA-CG
** * * ** *
748596 CGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
748636 CGTTGCGATT
1 CGTTGCGATT
748646 CTGGAAAATC
Statistics
Matches: 217, Mismatches: 27, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
39 2 0.01
40 146 0.67
41 68 0.31
42 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
Found at i:748436 original size:60 final size:60
Alignment explanation
Indices: 748354--748565 Score: 257
Period size: 60 Copynumber: 3.5 Consensus size: 60
748344 GTCAGAATCT
* * *
748354 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTATTCG
* * * *
748414 CATTGCGATTTATGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTAC-GTATTCG
* * * * * *
748474 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-G
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGA-TTTACGTATTCG
*
748534 TCGTTGCGATTTACGGATACGCGTTGCGATTT
1 -CGTTGCGATTTACGGATACGCATTGCGATTT
748566 TACGGATACT
Statistics
Matches: 128, Mismatches: 20, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
60 92 0.72
61 36 0.28
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTATTCG
Found at i:750381 original size:13 final size:14
Alignment explanation
Indices: 750358--750400 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
750348 CATCCAAAAA
750358 TTATAAAATAATTT
1 TTATAAAATAATTT
750372 TTAT-AAATAATTTT
1 TTATAAAATAA-TTT
750386 TTAATAAATATAATT
1 TT-ATAAA-ATAATT
750401 CATTTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.24
14 9 0.36
15 2 0.08
16 4 0.16
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTATAAAATAATTT
Found at i:750432 original size:13 final size:14
Alignment explanation
Indices: 750397--750433 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
750387 TAATAAATAT
750397 AATTCATTTTTCAA
1 AATTCATTTTTCAA
*
750411 AATTTATTTTTCAA
1 AATTCATTTTTCAA
750425 AA-TCATTTT
1 AATTCATTTT
750434 CAATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTCATTTTTCAA
Found at i:753918 original size:144 final size:146
Alignment explanation
Indices: 753573--754050 Score: 359
Period size: 145 Copynumber: 3.3 Consensus size: 146
753563 GACCATCATG
* * * * * *
753573 AACAACATACTGAAAA-TTCAAGACGATCGGATGGTGGACGGA-GATGGATCGAAGAAAA-TAAG
1 AACAACATACT-AAAATTTTAGGACGATCGGACGGTGGAC-GACGATAGATCAAAGAAAACAAAG
* * ** * * * * **
753635 CAGGAC-AGTTTTTGGCCTCTTTCCGATGATCGGGA-TCACCGATCAACATTCCGAACGGTCAAA
64 CCGAACGA-TTTTTGGCCTCTCGCCGACGATCGAGACT-TCCGATCAACATTCCAAACAATCAAA
** *
753698 AGTT-T-CAAGAGACCAGCACA
127 AGTTGTGC--GAGGTCAACACA
* * * *
753718 AACAACATACTAAAAATTTAGGACGATCGGATGGTGGACGACGATAGATCAAAGAAAA-TAAGCT
1 AACAACATACTAAAATTTTAGGACGATCGGACGGTGGACGACGATAGATCAAAGAAAACAAAGCC
* * * * * * * *
753782 GAACGGTTTTTGGCTTTTTGTCGACGATCGGGA--TCTCGATCAACATTCCAAATAATGAAAAGT
66 GAACGATTTTTGGCCTCTCGCCGACGATCGAGACTTC-CGATCAACATTCCAAACAATCAAAAGT
* *
753845 TGTGTC-ATGTCAACACG
130 TGTG-CGAGGTCAACACA
* ** * ** *
753862 AACAACATAATAAAATTTTAGGACGATCGGACGGTGGACGGTGGT-GAATCGGAGAAAACAAATC
1 AACAACATACTAAAATTTTAGGACGATCGGACGGTGGACGACGATAG-ATCAAAGAAAACAAAGC
* * * *
753926 CGGATGATTTTTGGCCTCTCGCCGGCGATCGAGACTTCCGATCAACATTCCGAACAATCAAAAGT
65 CGAACGATTTTTGGCCTCTCGCCGACGATCGAGACTTCCGATCAACATTCCAAACAATCAAAAGT
753991 TGTGCGAGGTCAACACA
130 TGTGCGAGGTCAACACA
* * *
754008 AACAACATACTAAAATTTCAGGTCAATCGGACGGTGGCACGAC
1 AACAACATACTAAAATTTTAGGACGATCGGACGGTGG-ACGAC
754051 AGCGCAACAA
Statistics
Matches: 266, Mismatches: 54, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
143 2 0.01
144 83 0.31
145 105 0.39
146 70 0.26
147 6 0.02
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (146 bp):
AACAACATACTAAAATTTTAGGACGATCGGACGGTGGACGACGATAGATCAAAGAAAACAAAGCC
GAACGATTTTTGGCCTCTCGCCGACGATCGAGACTTCCGATCAACATTCCAAACAATCAAAAGTT
GTGCGAGGTCAACACA
Found at i:754242 original size:29 final size:29
Alignment explanation
Indices: 754210--754327 Score: 85
Period size: 30 Copynumber: 4.0 Consensus size: 29
754200 GTTATTTTAT
754210 TTTAGTCACTTAAGTTTATGTTTTTGCTA
1 TTTAGTCACTTAAGTTTATGTTTTTGCTA
* * * * * *
754239 TTTATGTAATTTAAATATCTGTTTTAGCTA
1 TTTA-GTCACTTAAGTTTATGTTTTTGCTA
* ** * *
754269 TTTTAGCCTTTTAAGTTTATGTTTTTACCA
1 -TTTAGTCACTTAAGTTTATGTTTTTGCTA
* *
754299 TTTAATC-CTTTAAGTTCATGTTTTTGCTA
1 TTTAGTCAC-TTAAGTTTATGTTTTTGCTA
754328 GATTTATTAT
Statistics
Matches: 65, Mismatches: 21, Indels: 6
0.71 0.23 0.07
Matches are distributed among these distances:
29 26 0.40
30 35 0.54
31 4 0.06
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (29 bp):
TTTAGTCACTTAAGTTTATGTTTTTGCTA
Done.