Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008627.1 Hibiscus syriacus cultivar Beakdansim tig00111594_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: 1073793
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 5 of 6
Found at i:855298 original size:18 final size:17
Alignment explanation
Indices: 855275--855308 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
855265 TCACCAAAAT
*
855275 ACCAAGGAAAGGAGATTA
1 ACCAAGCAAAGG-GATTA
855293 ACCAAGCAAAGGGATT
1 ACCAAGCAAAGGGATT
855309 TATTTCAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.15, G:0.26, T:0.12
Consensus pattern (17 bp):
ACCAAGCAAAGGGATTA
Found at i:860755 original size:31 final size:31
Alignment explanation
Indices: 860714--860809 Score: 120
Period size: 31 Copynumber: 3.0 Consensus size: 31
860704 TGTGAAATCA
*
860714 AATACTAGTCAGGATGCATTCAAATAATTCAC
1 AATAC-AGTCAGGATGCATTCAAATAATGCAC
* *
860746 AATACAGTCAGGCTGCATTCATATAATGCAC
1 AATACAGTCAGGATGCATTCAAATAATGCAC
* * *
860777 ATTACAGTCAGGTTTCTATTCAAATAATGCAC
1 AATACAGTCAGGATGC-ATTCAAATAATGCAC
860809 A
1 A
860810 TGAGTGTCAG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 36 0.64
32 20 0.36
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (31 bp):
AATACAGTCAGGATGCATTCAAATAATGCAC
Found at i:863440 original size:15 final size:15
Alignment explanation
Indices: 863420--863456 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
863410 TTATCATGGC
863420 GTATGTTCCAATGTA
1 GTATGTTCCAATGTA
863435 GTATGTTCCAATGTA
1 GTATGTTCCAATGTA
863450 GTA-GTTC
1 GTATGTTC
863457 TAAAATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (15 bp):
GTATGTTCCAATGTA
Found at i:865374 original size:41 final size:40
Alignment explanation
Indices: 865329--865420 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 40
865319 TGAAGGAATG
*
865329 AGTATCGATACTGACCCCTT-GGTATCGATACTAAGGGTTGT
1 AGTATCGATACTAACCCCTTAGGT-T-GATACTAAGGGTTGT
* ** * * *
865370 AGTATAGATACTAACCTTTTATGTTGATATTGAGGGTTGT
1 AGTATCGATACTAACCCCTTAGGTTGATACTAAGGGTTGT
865410 AGTATCGATAC
1 AGTATCGATAC
865421 CAGATGCTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
40 23 0.55
41 17 0.40
42 2 0.05
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (40 bp):
AGTATCGATACTAACCCCTTAGGTTGATACTAAGGGTTGT
Found at i:865494 original size:20 final size:19
Alignment explanation
Indices: 865457--865505 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
865447 CTCGGTCTTA
*
865457 ATACTGAAGGAATGGTATCT
1 ATACTGAA-GAATGGTATCC
*
865477 ATACTGAAGATTGAGTATCC
1 ATACTGAAGAATG-GTATCC
*
865497 ATACCGAAG
1 ATACTGAAG
865506 GCTTGATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (19 bp):
ATACTGAAGAATGGTATCC
Found at i:866184 original size:54 final size:53
Alignment explanation
Indices: 866126--866557 Score: 544
Period size: 54 Copynumber: 8.1 Consensus size: 53
866116 CGTAGTATCG
* * * * * *
866126 ATACGGTCGTTCGTAAATATATTATGAATTTCGTGGTTTGTACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAA-TTCGTGGGTTGCACACTTAGTGCCT
* * * * * * *
866180 ATACGGTAGTTGAACAACATATGATAAATTATGTGTGTTGTACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATT-CGTGGGTTGCACACTTAGTGCCT
* * *
866234 ATACTGTCGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTACCT
1 ATACGGTCGTTCATCAACATATGATGAATT-CGTGGGTTGCACACTTAGTGCCT
** * * *
866288 ATATAGTCGTTCATCAATATATGATGAATTATGTGGGTTGCACACTTAGTGCCA
1 ATACGGTCGTTCATCAACATATGATGAATT-CGTGGGTTGCACACTTAGTGCCT
*
866342 ATACGGTCGTTCATCAATATATGATGAATTCAGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTC-GTGGGTTGCACACTTAGTGCCT
* **
866396 ATACGGTCTTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTTT
1 ATACGGTCGTTCATCAACATATGATGAATTC-GTGGGTTGCACACTTAGTGCCT
*
866450 ATACGGTCGTTCATCAACATATGATGAATTCGTGGCTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCGTGGGTTGCACACTTAGTGCCT
*
866503 ATACGATCGTTCATCAACATATGATGAATTCTGTGGGTTG--CACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTC-GTGGGTTGCACACTTAGTGCCT
866555 ATA
1 ATA
866558 ATACACATAG
Statistics
Matches: 330, Mismatches: 45, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
52 15 0.05
53 51 0.15
54 264 0.80
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (53 bp):
ATACGGTCGTTCATCAACATATGATGAATTCGTGGGTTGCACACTTAGTGCCT
Found at i:875391 original size:165 final size:170
Alignment explanation
Indices: 875120--875454 Score: 601
Period size: 165 Copynumber: 2.0 Consensus size: 170
875110 TTTAAAAAAG
875120 AAAGAACAAATTTAAACAATTTTTGTTTTCATAATTGTGCAAAAGTACACTTTATTTAATTATAA
1 AAAGAACAAATTTAAACAATTTTTGTTTTCATAATTGTGCAAAAGTACACTTTATTTAATTATAA
*
875185 TTTAAAAAATAAACAATTTATTACTTAAAAATTAATTTTGATAC-ATTAAATATTGACTACAAAA
66 TTTAAAAAATAAACAAATTATTACTTAAAAATTAATTTTGATACAATTAAATATTGACTACAAAA
875249 AACTTAAATAAAT-AA-TTATTAC-T-TATTTATGCAATT
131 AACTTAAATAAATAAATTTATTACTTATATTTATGCAATT
875285 AAAGAACAAATTTAAACAATTTTTGTTTTCATAATTGTGCAAAAGTACACTTTATTTAATTATAA
1 AAAGAACAAATTTAAACAATTTTTGTTTTCATAATTGTGCAAAAGTACACTTTATTTAATTATAA
*
875350 TTT-TAAAATAAACAAATTATTACTTAAAAATTAATTTTTGATACAATTAAATATTGACTACAAA
66 TTTAAAAAATAAACAAATTATTACTTAAAAATTAA-TTTTGATACAATTAAATATTGACTACAAA
875414 AAACTTAAATAAATAAATTTATTACTTATATTTATGCAATT
130 AAACTTAAATAAATAAATTTATTACTTATATTTATGCAATT
875455 CTTGTCGATG
Statistics
Matches: 162, Mismatches: 2, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
164 29 0.18
165 77 0.48
166 33 0.20
167 2 0.01
168 7 0.04
169 1 0.01
170 13 0.08
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (170 bp):
AAAGAACAAATTTAAACAATTTTTGTTTTCATAATTGTGCAAAAGTACACTTTATTTAATTATAA
TTTAAAAAATAAACAAATTATTACTTAAAAATTAATTTTGATACAATTAAATATTGACTACAAAA
AACTTAAATAAATAAATTTATTACTTATATTTATGCAATT
Found at i:884569 original size:21 final size:20
Alignment explanation
Indices: 884537--884576 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
884527 ATTCTCAATT
*
884537 CCTCCTCTTCAATCCCTAAC
1 CCTCCTCCTCAATCCCTAAC
884557 CCTCGCTCCTCAATCCCTAA
1 CCTC-CTCCTCAATCCCTAA
884577 ATCTTCCTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.50, G:0.03, T:0.28
Consensus pattern (20 bp):
CCTCCTCCTCAATCCCTAAC
Found at i:888575 original size:83 final size:83
Alignment explanation
Indices: 888436--888604 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
888426 GATTCTCATT
888436 AATGTTTCATTATGTCACAAATTTTCAATTGTTCACAATGTGAAATCCCTATAAATGTCATGTAA
1 AATGTTTCATTATGTCACAAATTTTCAATTGTTCACAATGTGAAATCCCTATAAATGTCATGTAA
888501 ACCTACTAGGTTAAACAC
66 ACCTACTAGGTTAAACAC
888519 AATGTTTCATTATGTCACAAATTTTCAATTGTTCACAATGTGAAATCCCTATAAATGTCATGTAA
1 AATGTTTCATTATGTCACAAATTTTCAATTGTTCACAATGTGAAATCCCTATAAATGTCATGTAA
888584 ACCTACTAGGTTAAACAC
66 ACCTACTAGGTTAAACAC
888602 AAT
1 AAT
888605 TGAAAACAAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (83 bp):
AATGTTTCATTATGTCACAAATTTTCAATTGTTCACAATGTGAAATCCCTATAAATGTCATGTAA
ACCTACTAGGTTAAACAC
Found at i:890364 original size:58 final size:58
Alignment explanation
Indices: 890235--890410 Score: 196
Period size: 58 Copynumber: 3.0 Consensus size: 58
890225 ACAAAATATC
* * ** *
890235 AAGG-AAATAAATTATTGAATTTATTTCATTGTTAGAATCTTGCATTGATTCTAGCTTGGT
1 AAGGAAAATAAATTATTGAATTTATTTCCTTG--AGAATCTTG-AATGATTCTAATTTTGT
* * *
890295 -AGAAAAATAAATTGTTAAATTTATTTCCTTGAGAATCTTGAATGATTCTAATTTTGT
1 AAGGAAAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAATTTTGT
* ** *
890352 AAGGAAAATAAATAATTGAATTTATTTGTTTGAAAATCTTGAATGATTCT-ATTTTGT
1 AAGGAAAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAATTTTGT
890409 AA
1 AA
890411 AAGTAAATAA
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
57 22 0.22
58 51 0.52
59 2 0.02
60 24 0.24
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43
Consensus pattern (58 bp):
AAGGAAAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAATTTTGT
Found at i:890447 original size:57 final size:59
Alignment explanation
Indices: 890299--890451 Score: 176
Period size: 58 Copynumber: 2.6 Consensus size: 59
890289 CTTGGTAGAA
*
890299 AAATAAATTGTTAAATTTATTTCCTTGAGAATCTTGAATGATTCTAATTTTGTAAGGAAAAT
1 AAAT-AATTGTT-AATTTATTTTCTTGAGAATCTTGAATGATTCTAATTTTGTAA-GAAAAT
* *
890361 AAATAATTG--AATTTATTTGT-TTGAAAATCTTGAATGATTCT-ATTTTGT-A-AAAGT
1 AAATAATTGTTAATTTATTT-TCTTGAGAATCTTGAATGATTCTAATTTTGTAAGAAAAT
890415 AAATAATTGGTTAATTTATTTTCTT-AGGAATCTTGAA
1 AAATAATT-GTTAATTTATTTTCTTGA-GAATCTTGAA
890452 GGATCTTGTT
Statistics
Matches: 81, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
54 12 0.15
55 1 0.01
56 3 0.04
57 27 0.33
58 29 0.36
61 5 0.06
62 4 0.05
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (59 bp):
AAATAATTGTTAATTTATTTTCTTGAGAATCTTGAATGATTCTAATTTTGTAAGAAAAT
Found at i:890546 original size:39 final size:38
Alignment explanation
Indices: 890463--890946 Score: 247
Period size: 39 Copynumber: 12.2 Consensus size: 38
890453 GATCTTGTTA
*
890463 TGTAAAAGGAAAAAAATCG--GAATTTATTTTCTTATTT
1 TGTAAAAGGAAATAAATCGTTGAATTTATTTTC-TATTT
* * *
890500 TAT-AAAGGAAATAAATTGTTGGATTTAGTTTTCTATTT
1 TGTAAAAGGAAATAAATCGTTGAATTTA-TTTTCTATTT
* *
890538 TGTAAAAGGAAATAAATCGAAACAATCATTGGATTTATTTTCCTAGTT
1 TGTAAAAGGAAATAAATCG---------TTGAATTTATTTT-CTATTT
* * *
890586 TATAAAAGG-AATGAAA-GGGTGAATTTATTTTCCTTATTT
1 TGTAAAAGGAAAT-AAATCGTTGAATTTATTTT-C-TATTT
* * *
890625 TCTAAAAGG-AATAAATCGTTGGATTTTATATTCTATTT
1 TGTAAAAGGAAATAAATCGTT-GAATTTATTTTCTATTT
* *
890663 TGT--AAGGAAATAAAACGTTGAATTTATTGTCTATTT
1 TGTAAAAGGAAATAAATCGTTGAATTTATTTTCTATTT
* *
890699 TGTAAAA-GAAATAAATCATTTAATTTATTTTTCTAAGAATCTT
1 TGTAAAAGGAAATAAATCGTTGAATTTA-TTTTCT----AT-TT
* *** ** * * **
890742 ATATGATTCTGG-TTTGTAATCGTAGAATTTATTTTTCCTGGTT
1 -TGT-A-AAAGGAAAT-AAATCGTTGAATTTA-TTTT-CTATTT
* *
890785 TGTAAACGGAAATAAATCGTTGGATTTATTTTCCTATTT
1 TGTAAAAGGAAATAAATCGTTGAATTTATTTT-CTATTT
* * *
890824 TGTAGAAGGAAAT-AATCGTAG-ATTTATTTTTTGATTT
1 TGTAAAAGGAAATAAATCGTTGAATTTATTTTCT-ATTT
* * * *
890861 TGTAAAATGAAATAAATCATAGAATTTATTTTCTTTGCTT
1 TGTAAAAGGAAATAAATCGTTGAATTTATTTTCTAT--TT
*
890901 TGTAAAAGGAAATAAATCGTTGGAA-TTATTTTCCTAATT
1 TGTAAAAGGAAATAAATCGTT-GAATTTATTTT-CTATTT
890940 TGTAAAA
1 TGTAAAA
890947 AATTATTGGA
Statistics
Matches: 343, Mismatches: 63, Indels: 80
0.71 0.13 0.16
Matches are distributed among these distances:
36 35 0.10
37 53 0.15
38 58 0.17
39 76 0.22
40 50 0.15
41 7 0.02
42 4 0.01
43 4 0.01
44 2 0.01
45 1 0.00
46 1 0.00
47 25 0.07
48 27 0.08
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (38 bp):
TGTAAAAGGAAATAAATCGTTGAATTTATTTTCTATTT
Found at i:890676 original size:37 final size:37
Alignment explanation
Indices: 890605--890727 Score: 117
Period size: 37 Copynumber: 3.3 Consensus size: 37
890595 AATGAAAGGG
* *
890605 TGAATTTATTTTCCTTATTTTCTAAAAGG-AATAAATCGT
1 TGAATTTATTGT-C-TATTTTGT-AAAGGAAATAAATCGT
* *
890644 TGGATTTTATAT-TCTATTTTGT-AAGGAAATAAAACGT
1 T-GAATTTAT-TGTCTATTTTGTAAAGGAAATAAATCGT
* *
890681 TGAATTTATTGTCTATTTTGTAAAAGAAATAAATCAT
1 TGAATTTATTGTCTATTTTGTAAAGGAAATAAATCGT
*
890718 TTAATTTATT
1 TGAATTTATT
890728 TTTCTAAGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
35 1 0.01
36 21 0.30
37 31 0.44
38 7 0.10
39 2 0.03
40 8 0.11
41 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (37 bp):
TGAATTTATTGTCTATTTTGTAAAGGAAATAAATCGT
Found at i:890689 original size:36 final size:38
Alignment explanation
Indices: 890606--890713 Score: 107
Period size: 36 Copynumber: 2.8 Consensus size: 38
890596 ATGAAAGGGT
* * *
890606 GAATTTATTTTCCTTATTTTCTAAAAGG-AATAAATCGTTG
1 GAATTTATTGT-C-TATTTTGT-AAAGGAAATAAAACGTTG
*
890646 GATTTTATAT-TCTATTTTGT-AAGGAAATAAAACGTT-
1 GAATTTAT-TGTCTATTTTGTAAAGGAAATAAAACGTTG
*
890682 GAATTTATTGTCTATTTTGTAAAAGAAATAAA
1 GAATTTATTGTCTATTTTGTAAAGGAAATAAA
890714 TCATTTAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
35 1 0.02
36 21 0.36
37 20 0.34
38 7 0.12
39 1 0.02
40 8 0.14
41 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (38 bp):
GAATTTATTGTCTATTTTGTAAAGGAAATAAAACGTTG
Found at i:890814 original size:40 final size:39
Alignment explanation
Indices: 890759--890946 Score: 175
Period size: 40 Copynumber: 4.8 Consensus size: 39
890749 TCTGGTTTGT
* * * *
890759 AATCGTAGAATTTATTTTTCCTGGTTTGTAAACGGAAATA
1 AATCGTTGGATTTA-TTTTCCTGTTTTGTAAAAGGAAATA
* *
890799 AATCGTTGGATTTATTTTCCTATTTTGTAGAAGGAAAT-
1 AATCGTTGGATTTATTTTCCTGTTTTGTAAAAGGAAATA
* * *
890837 AATCG-TAGATTTATTTT-TTGATTTTGTAAAATGAAATA
1 AATCGTTGGATTTATTTTCCTG-TTTTGTAAAAGGAAATA
* * * * *
890875 AATCATAGAATTTATTTTCTTTGCTTTGTAAAAGGAAATA
1 AATCGTTGGATTTATTTTC-CTGTTTTGTAAAAGGAAATA
* **
890915 AATCGTTGGAATTATTTTCCTAATTTGTAAAA
1 AATCGTTGGATTTATTTTCCTGTTTTGTAAAA
890947 AATTATTGGA
Statistics
Matches: 119, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
36 1 0.01
37 25 0.21
38 9 0.08
39 39 0.33
40 42 0.35
41 3 0.03
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (39 bp):
AATCGTTGGATTTATTTTCCTGTTTTGTAAAAGGAAATA
Found at i:891006 original size:4 final size:4
Alignment explanation
Indices: 890997--891021 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
890987 ATTCTATTTT
890997 GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
891022 GAATTGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:891804 original size:38 final size:38
Alignment explanation
Indices: 891693--892008 Score: 158
Period size: 39 Copynumber: 8.1 Consensus size: 38
891683 CACCTCAAAT
* *
891693 TTTCTTATTTTCTAAAAGGAAATAAATCGTTGGATTTA
1 TTTCTTATTTTATAAAAGGAAATAAATCGTTGAATTTA
* *
891731 TTT-TCTATTTTGT-AAAGGAAATAAAACGTTGAATTTA
1 TTTCT-TATTTTATAAAAGGAAATAAATCGTTGAATTTA
* * *
891768 TTTCTTATTTTATAAAAAGAAATAAATCATTTAATTTA
1 TTTCTTATTTTATAAAAGGAAATAAATCGTTGAATTTA
* *** ** * * *
891806 TTTTCTAAGAATCTTATATGATTCTGG-TTTGTAATCGTAGAATTTT
1 -TTTCT---TAT-TT-TAT-A-AAAGGAAAT-AAATCGTTGAATTTA
* ** * * *
891852 TTTCCTGGTTTGTAAACGGAAA-AAATCGTTGGATTTA
1 TTTCTTATTTTATAAAAGGAAATAAATCGTTGAATTTA
* * *
891889 TTTTCCTATTTTGTAGAAGGAAATAAATCGTT-AGATTTA
1 -TTTCTTATTTTATAAAAGGAAATAAATCGTTGA-ATTTA
* * * * *
891928 TTTTTTGATTTTGTAAAATGAAATAAATCATAGAATTTA
1 TTTCTT-ATTTTATAAAAGGAAATAAATCGTTGAATTTA
** *
891967 TTTTCTTGCTTTGTAAAAGGAAATAAATCGTTGGAA-TTA
1 -TTTCTTATTTTATAAAAGGAAATAAATCGTT-GAATTTA
892006 TTT
1 TTT
892009 TCCTAATTTT
Statistics
Matches: 207, Mismatches: 51, Indels: 40
0.69 0.17 0.13
Matches are distributed among these distances:
37 44 0.21
38 58 0.28
39 68 0.33
40 11 0.05
41 2 0.01
42 2 0.01
43 2 0.01
44 3 0.01
45 6 0.03
46 11 0.05
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (38 bp):
TTTCTTATTTTATAAAAGGAAATAAATCGTTGAATTTA
Found at i:891917 original size:39 final size:39
Alignment explanation
Indices: 891838--892024 Score: 191
Period size: 39 Copynumber: 4.8 Consensus size: 39
891828 TCTGGTTTGT
* * ** *
891838 AATCGTAGAATTT-TTTTCCTGGTTTGTAAACGGAAA-A
1 AATCGTTGGATTTATTTTCCTATTTTGTAAAAGGAAATA
*
891875 AATCGTTGGATTTATTTTCCTATTTTGTAGAAGGAAATA
1 AATCGTTGGATTTATTTTCCTATTTTGTAAAAGGAAATA
* * *
891914 AATCGTTAGATTTATTTT-TTGATTTTGTAAAATGAAATA
1 AATCGTTGGATTTATTTTCCT-ATTTTGTAAAAGGAAATA
* * * * **
891953 AATCATAGAATTTATTTTCTTGCTTTGTAAAAGGAAATA
1 AATCGTTGGATTTATTTTCCTATTTTGTAAAAGGAAATA
*
891992 AATCGTTGGAATTATTTTCCTAATTTTGTAAAA
1 AATCGTTGGATTTATTTTCCT-ATTTTGTAAAA
892025 AAATTATTGG
Statistics
Matches: 121, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
37 11 0.09
38 20 0.17
39 79 0.65
40 11 0.09
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.43
Consensus pattern (39 bp):
AATCGTTGGATTTATTTTCCTATTTTGTAAAAGGAAATA
Found at i:892042 original size:78 final size:77
Alignment explanation
Indices: 891884--892052 Score: 189
Period size: 78 Copynumber: 2.2 Consensus size: 77
891874 AAATCGTTGG
* ** * * * *
891884 ATTTATTTTCCTATTTTGTAGAAGGAAATAAATCGTTAGATTTATTTTTTGATTTTGTAAAATGA
1 ATTTATTTTCTTGCTTTGTAAAAGGAAATAAATCGTTAGAATTATTTTCTAATTTTGTAAAA-GA
*
891949 AATAAATCATAGA
65 AATAAATAATAGA
*
891962 ATTTATTTTCTTGCTTTGTAAAAGGAAATAAATCGTTGGAATTATTTTCCTAATTTTGTAAAA-A
1 ATTTATTTTCTTGCTTTGTAAAAGGAAATAAATCGTTAGAATTATTTT-CTAATTTTGTAAAAGA
* *
892026 AATTATTGGAAT-GA
65 AATAAAT--AATAGA
892040 ATTTATTTTCTTG
1 ATTTATTTTCTTG
892053 GGAATCAAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
77 6 0.08
78 57 0.74
79 14 0.18
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (77 bp):
ATTTATTTTCTTGCTTTGTAAAAGGAAATAAATCGTTAGAATTATTTTCTAATTTTGTAAAAGAA
ATAAATAATAGA
Found at i:897853 original size:54 final size:55
Alignment explanation
Indices: 897795--897903 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 55
897785 TCCAAAAAAA
897795 TTGTTAAGCATCAGTGGAAACTCATATATGTTGATAAAAATACTATGA-GCCATC
1 TTGTTAAGCATCAGTGGAAACTCATATATGTTGATAAAAATACTATGAGGCCATC
897849 TTGTTAAGCATCAGTGGAAACTCATATATGTTGATAAAAATACTATGAGGCCATC
1 TTGTTAAGCATCAGTGGAAACTCATATATGTTGATAAAAATACTATGAGGCCATC
897904 ATCCTTTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 48 0.89
55 6 0.11
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (55 bp):
TTGTTAAGCATCAGTGGAAACTCATATATGTTGATAAAAATACTATGAGGCCATC
Found at i:898834 original size:21 final size:20
Alignment explanation
Indices: 898748--898946 Score: 114
Period size: 21 Copynumber: 9.8 Consensus size: 20
898738 AAATGACCAA
**
898748 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
898767 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
898787 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
898807 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
898828 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
898849 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
898869 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* **
898890 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
898910 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
898931 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
898947 ACACATAAAT
Statistics
Matches: 134, Mismatches: 39, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
19 16 0.12
20 56 0.42
21 62 0.46
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:898896 original size:20 final size:20
Alignment explanation
Indices: 898871--899025 Score: 105
Period size: 20 Copynumber: 7.7 Consensus size: 20
898861 GCGATTTTCC
898871 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
** * * *
898891 AAAATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATAT-G
898912 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
* *
898932 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATG
* **
898951 ATAAATCGCAACGCGTATCCG
1 A-AAATCGCAACGCGAATATG
* * * **
898972 TAAATCGCAACGTGTATCCG
1 AAAATCGCAACGCGAATATG
* * **
898992 TAAATCGCAACGCGTATGGG
1 AAAATCGCAACGCGAATATG
*
899012 TAAATCGCAACGCG
1 AAAATCGCAACGCG
899026 TATCCGTATA
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 95 0.86
21 15 0.14
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:898908 original size:41 final size:41
Alignment explanation
Indices: 898829--898940 Score: 174
Period size: 41 Copynumber: 2.7 Consensus size: 41
898819 GCGATTCTTG
*
898829 AAAATCGCAATGCG-ATA-GTACAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATG-A-AAA-TCGCATTGCGATTTTCC
898871 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
898912 AAAATCGCAACGCGAATATGAAAATCGCA
1 AAAATCGCAACGCGAATATGAAAATCGCA
898941 ACGCGAACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
41 46 0.69
42 16 0.24
43 4 0.06
44 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
Found at i:899005 original size:60 final size:60
Alignment explanation
Indices: 898913--899107 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
898903 CGATTTTCCA
* ** * *
898913 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * ***
898973 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* ** *
899033 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCACAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
899094 AAAATCGCAACGCG
1 -AAATCGCAACGCG
899108 ATATTTAAAG
Statistics
Matches: 113, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
60 82 0.73
61 19 0.17
62 12 0.11
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:899026 original size:20 final size:20
Alignment explanation
Indices: 898913--899107 Score: 214
Period size: 20 Copynumber: 9.7 Consensus size: 20
898903 CGATTTTCCA
* ** *
898913 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
898933 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
898953 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
898973 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
898993 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
899013 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
899033 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
899053 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
*
899073 AAAATCACAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
899094 AAAATCGCAACGCG
1 -AAATCGCAACGCG
899108 ATATTTAAAG
Statistics
Matches: 147, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.01
20 115 0.78
21 29 0.20
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:899527 original size:33 final size:33
Alignment explanation
Indices: 899488--899558 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
899478 TTCACTTAGA
* *
899488 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
899521 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
899554 TTTCA
1 TTTCA
899559 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:899682 original size:20 final size:20
Alignment explanation
Indices: 899636--899713 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
899626 TTTGCAGAAG
*
899636 AGTCGCAACGAGATAAATGAA
1 AGTCGCAACGAGA-GAATGAA
* *
899657 AATCGCAACGAGAGAATGAC
1 AGTCGCAACGAGAGAATGAA
*
899677 TGTCGCAACGAGAGAAATGAA
1 AGTCGCAACGAGAG-AATGAA
899698 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
899714 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
19 3 0.06
20 28 0.57
21 18 0.37
ACGTcount: A:0.45, C:0.17, G:0.27, T:0.12
Consensus pattern (20 bp):
AGTCGCAACGAGAGAATGAA
Found at i:899695 original size:41 final size:40
Alignment explanation
Indices: 899637--899713 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
899627 TTGCAGAAGA
* *
899637 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATG-AAAGCGCAACGAGAGAATGACT
899678 GTCGCAACGAGAGAAATGAAAGCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAGCGCAACGAGAGAAT
899714 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 17 0.50
41 17 0.50
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (40 bp):
GTCGCAACGAGAGAAATGAAAGCGCAACGAGAGAATGACT
Found at i:899719 original size:14 final size:14
Alignment explanation
Indices: 899700--899752 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
899690 GAAATGAAAG
899700 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
899714 CGCAACGCGAATGAAAAT
1 CGCAA--CG-A-GAGAAT
*
899732 CGCAATGAGAGAAT
1 CGCAACGAGAGAAT
899746 CGCAACG
1 CGCAACG
899753 CGAACCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.52
15 1 0.03
16 3 0.10
17 1 0.03
18 10 0.32
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:899742 original size:32 final size:32
Alignment explanation
Indices: 899692--899767 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
899682 CAACGAGAGA
*
899692 AATG-AAAGCGCAACGAGAGAATCGCAACGCG
1 AATGAAAATCGCAACGAGAGAATCGCAACGCG
*
899723 AATGAAAATCGCAATGAGAGAATCGCAACGCG
1 AATGAAAATCGCAACGAGAGAATCGCAACGCG
**
899755 AACCAAAATCGCA
1 AATGAAAATCGCA
899768 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 4 0.10
32 36 0.90
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (32 bp):
AATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:899790 original size:19 final size:18
Alignment explanation
Indices: 899763--899880 Score: 80
Period size: 14 Copynumber: 7.1 Consensus size: 18
899753 CGAACCAAAA
*
899763 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
899782 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
899796 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
899815 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
899829 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
899847 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
899862 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
899880 T
1 T
899881 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.39
16 8 0.10
17 8 0.10
18 1 0.01
19 30 0.39
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:899804 original size:14 final size:14
Alignment explanation
Indices: 899785--899874 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
899775 TTTCATTTCG
899785 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
899799 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
899818 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
899832 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
899849 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
899865 CGTTGCGATT
1 CGTTGCGATT
899875 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:899810 original size:33 final size:33
Alignment explanation
Indices: 899768--899882 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
899758 CAAAATCGCA
899768 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
899801 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
899834 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
899867 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
899883 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:901877 original size:92 final size:92
Alignment explanation
Indices: 901520--901893 Score: 657
Period size: 91 Copynumber: 4.1 Consensus size: 92
901510 TAGATTGCTT
* *
901520 AGTAAATTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
901585 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
901612 AGTAAATTTGTTCGGTTGCTGCCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TG-AATAGT
1 AGTAAA-TTGTTCGGTTGCTG-CCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
*
901674 ATTTGTCTTTGTTTTGTCTTTTGGTTTAA
64 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
901703 AGTAAATTGTTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTAT
1 AGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
901767 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
901794 AGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
901859 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
901886 AGTAAATT
1 AGTAAATT
901894 TATCCATTCA
Statistics
Matches: 268, Mismatches: 8, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
88 26 0.10
89 4 0.01
90 16 0.06
91 97 0.36
92 81 0.30
93 12 0.04
94 32 0.12
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (92 bp):
AGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:901977 original size:19 final size:19
Alignment explanation
Indices: 901937--902065 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
901927 TAGTTTACTT
* *
901937 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
901957 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* **
901976 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
901995 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
902009 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
902028 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
902042 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
902061 TCGCA
1 TCGCA
902066 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 44 0.50
20 13 0.15
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:902021 original size:33 final size:32
Alignment explanation
Indices: 901973--902065 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
901963 CGCGAAACCA
* **
901973 AAATCACAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
902005 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
902038 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
902066 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:902063 original size:52 final size:52
Alignment explanation
Indices: 901937--902065 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
901927 TAGTTTACTT
**
901937 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCACAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCACAACGCGAAA
* * * *
901989 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCACAACG-CGAA-A
*
902042 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
902066 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCACAACGCGAAA
Found at i:902083 original size:19 final size:19
Alignment explanation
Indices: 902061--902193 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
902051 GAAACCAAAA
*
902061 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
902080 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
902096 T--CG-TGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
902112 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
902128 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
**
902144 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
902163 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
902183 TCGTGTTGCGA
1 TCGCGTTGCGA
902194 AAGTAAACTA
Statistics
Matches: 92, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
13 5 0.05
14 9 0.10
15 6 0.07
16 10 0.11
17 6 0.07
18 9 0.10
19 35 0.38
20 12 0.13
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:902108 original size:32 final size:33
Alignment explanation
Indices: 902066--902156 Score: 150
Period size: 32 Copynumber: 2.8 Consensus size: 33
902056 CAAAATCGCA
*
902066 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
902099 -TGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
902131 TTGCGA-TTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
902157 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 49 0.91
33 5 0.09
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:904127 original size:13 final size:13
Alignment explanation
Indices: 904084--904118 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
904074 GATTGTTTAA
904084 TTGATTTGTAAAG
1 TTGATTTGTAAAG
*
904097 ATGATTTGTAAAG
1 TTGATTTGTAAAG
904110 TTGATTTGT
1 TTGATTTGT
904119 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (13 bp):
TTGATTTGTAAAG
Found at i:904246 original size:19 final size:19
Alignment explanation
Indices: 904222--904320 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
904212 AAAATTGACT
904222 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
904241 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
904260 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
904274 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
904293 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
904312 ATCGCAATG
1 ATCGCAATG
904321 GGAGATCGCA
Statistics
Matches: 72, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 50 0.69
20 6 0.08
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:904300 original size:52 final size:51
Alignment explanation
Indices: 904222--904336 Score: 187
Period size: 52 Copynumber: 2.2 Consensus size: 51
904212 AAAATTGACT
904222 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAG
* *
904273 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAATGGGAG
1 -ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAG
904325 ATCGCAATGCGA
1 ATCGCAATGCGA
904337 TTTTAATTTC
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 12 0.20
52 42 0.70
53 6 0.10
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (51 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAG
Found at i:904427 original size:50 final size:50
Alignment explanation
Indices: 904326--904489 Score: 235
Period size: 50 Copynumber: 3.2 Consensus size: 50
904316 CAATGGGAGA
* *
904326 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCG--TCTCTCGTTGCGATTTTCATT
904378 TCGCATTGCCGATTTTCATTTCGCATTGCG-CTCTCGTTGCGATTTTCA-T
1 TCGCATTG-CGATTTTCATTTCGCATTGCGTCTCTCGTTGCGATTTTCATT
904427 TCGCATTGCGATTTTCATTTCGCA-TGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCG--TCTCTCGTTGCGATTTTCATT
904478 TCCGCATTGCGA
1 T-CGCATTGCGA
904490 AATGTAATGG
Statistics
Matches: 104, Mismatches: 2, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
47 4 0.04
48 16 0.15
49 9 0.09
50 36 0.35
51 2 0.02
52 17 0.16
53 20 0.19
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (50 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGTCTCTCGTTGCGATTTTCATT
Found at i:904489 original size:20 final size:19
Alignment explanation
Indices: 904326--904489 Score: 125
Period size: 20 Copynumber: 9.6 Consensus size: 19
904316 CAATGGGAGA
* *
904326 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
904345 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
904361 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
904378 TCGCATTGCCGATTTTCATT
1 TCGCATTG-CGATTTTCATT
*
904398 TCGCATTGCG-----C-TC
1 TCGCATTGCGATTTTCATT
904411 TCG--TTGCGATTTTCA-T
1 TCGCATTGCGATTTTCATT
904427 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
904446 TCGCA-TGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
904461 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
904478 TCCGCATTGCGA
1 T-CGCATTGCGA
904490 AATGTAATGG
Statistics
Matches: 115, Mismatches: 8, Indels: 43
0.69 0.05 0.26
Matches are distributed among these distances:
11 5 0.04
13 4 0.03
14 12 0.10
15 4 0.03
16 17 0.15
17 8 0.07
18 19 0.17
19 21 0.18
20 25 0.22
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:904572 original size:19 final size:19
Alignment explanation
Indices: 904548--904643 Score: 125
Period size: 19 Copynumber: 5.4 Consensus size: 19
904538 AAAATTGACT
904548 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
904567 ATCGCAATGCG-AATGAAA
1 ATCGCAATGCGAAATGAAA
*
904585 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
904599 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
904618 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
904637 ATCGCAA
1 ATCGCAA
904644 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 4 0.06
18 15 0.22
19 33 0.48
20 6 0.09
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:904624 original size:51 final size:52
Alignment explanation
Indices: 904548--904662 Score: 207
Period size: 51 Copynumber: 2.2 Consensus size: 52
904538 AAAATTGACT
904548 ATCGCAATGCGAAATGAAAATCGCAATGC-G-AATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGA
904599 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
904651 ATCGCAATGCGA
1 ATCGCAATGCGA
904663 TTTTCATCGC
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
51 29 0.47
52 29 0.47
53 4 0.06
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
Found at i:907193 original size:24 final size:24
Alignment explanation
Indices: 907159--907205 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
907149 CTGAAACATC
907159 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
907183 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
907206 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:907915 original size:20 final size:20
Alignment explanation
Indices: 907887--908136 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
907877 AAATTTCAGT
* *
907887 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
907907 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
907927 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
907947 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
907967 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
* *
907987 GTTGTGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
908007 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
908027 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
908047 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
908067 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
908087 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
908107 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
908127 GTTGCGATTT
1 GTTGCGATTT
908137 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:908153 original size:21 final size:21
Alignment explanation
Indices: 908123--908205 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
908113 ATTTTCATAT
*
908123 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
908144 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
908165 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
908186 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
908206 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:908196 original size:42 final size:43
Alignment explanation
Indices: 908103--908201 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
908093 ATTTATGTGT
* *
908103 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
908144 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
908186 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
908202 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:909587 original size:16 final size:16
Alignment explanation
Indices: 909568--909601 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
909558 ATTAATGTGC
909568 AAGGATCATAATGATG
1 AAGGATCATAATGATG
*
909584 AAGGATCATAATTATG
1 AAGGATCATAATGATG
909600 AA
1 AA
909602 TTTAATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (16 bp):
AAGGATCATAATGATG
Found at i:916031 original size:23 final size:22
Alignment explanation
Indices: 916004--916079 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
915994 TACAGTAGAG
916004 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
* * * *
916026 TTGCATCGGTGTACCTTCATGG-
1 -TGCATCGATGCACATTCAAGGA
* *
916048 TGAATCGATGCACTTTCAAGGGA
1 TGCATCGATGCACATTCAA-GGA
916071 TGCATCGAT
1 TGCATCGAT
916080 ACACTAACTA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 14 0.34
22 2 0.05
23 25 0.61
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:920260 original size:18 final size:19
Alignment explanation
Indices: 920223--920261 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
920213 CGAGTCCTTC
920223 TCCTTCGGTTCATTTTTGAA
1 TCCTTCGGTTCA-TTTTGAA
*
920243 TCCTTCGTTTCA-TTTGAA
1 TCCTTCGGTTCATTTTGAA
920261 T
1 T
920262 TTTCTTCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.15, C:0.21, G:0.13, T:0.51
Consensus pattern (19 bp):
TCCTTCGGTTCATTTTGAA
Found at i:929474 original size:21 final size:21
Alignment explanation
Indices: 929448--929511 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
929438 TTTTGGTGCA
*
929448 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
929469 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
929490 GAATGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATCCCCCCCA
929512 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:932251 original size:22 final size:21
Alignment explanation
Indices: 932215--932269 Score: 101
Period size: 22 Copynumber: 2.6 Consensus size: 21
932205 CTCGGAGGGA
932215 ACCGATTCCCCCATAGGGGGT
1 ACCGATTCCCCCATAGGGGGT
932236 ACCGATTCTCCCCATAGGGGGT
1 ACCGATTC-CCCCATAGGGGGT
932258 ACCGATTCCCCC
1 ACCGATTCCCCC
932270 TTGTTCAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 12 0.36
22 21 0.64
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.20
Consensus pattern (21 bp):
ACCGATTCCCCCATAGGGGGT
Found at i:936036 original size:15 final size:15
Alignment explanation
Indices: 936016--936048 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
936006 ATAAGATAAG
*
936016 GATGCTAATTAAATA
1 GATGCTAATTAAAGA
936031 GATGCTAATTAAAGA
1 GATGCTAATTAAAGA
936046 GAT
1 GAT
936049 AGATGAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (15 bp):
GATGCTAATTAAAGA
Found at i:936118 original size:15 final size:15
Alignment explanation
Indices: 936098--936127 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
936088 TTAAATGTGA
936098 TATTTCCCATTAACT
1 TATTTCCCATTAACT
936113 TATTTCCCATTAACT
1 TATTTCCCATTAACT
936128 ATAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTTCCCATTAACT
Found at i:936314 original size:31 final size:30
Alignment explanation
Indices: 936279--936345 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
936269 TTTTTCTTTT
*
936279 ATAATATAAAAATAAGTTAAAAATAAAATAA
1 ATAATATAAAAATAA-TTAAAAATAAAACAA
***
936310 ATAATATTTTAATAATTAAAAATAAAACAA
1 ATAATATAAAAATAATTAAAAATAAAACAA
936340 A-AATAT
1 ATAATAT
936346 TTCCGCCGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.16
30 15 0.47
31 12 0.38
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (30 bp):
ATAATATAAAAATAATTAAAAATAAAACAA
Found at i:936331 original size:30 final size:30
Alignment explanation
Indices: 936289--936347 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
936279 ATAATATAAA
*
936289 AATAAGTTAAAAATAAAATAAATAATATTTT
1 AATAAGTTAAAAATAAAACAAA-AATATTTT
936320 AATAA-TTAAAAATAAAACAAAAATATTT
1 AATAAGTTAAAAATAAAACAAAAATATTT
936348 CCGCCGCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.26
30 15 0.56
31 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (30 bp):
AATAAGTTAAAAATAAAACAAAAATATTTT
Found at i:937585 original size:10 final size:10
Alignment explanation
Indices: 937570--937615 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
937560 TTATTTTTTC
*
937570 TAAAAATAAA
1 TAAAAATTAA
937580 TAAAAATGTAA
1 TAAAAAT-TAA
*
937591 TAAAAATGAA
1 TAAAAATTAA
*
937601 TAAAATTTAA
1 TAAAAATTAA
937611 TAAAA
1 TAAAA
937616 GTATAATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:937592 original size:11 final size:11
Alignment explanation
Indices: 937578--937615 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
937568 TCTAAAAATA
937578 AATAAAAATGT
1 AATAAAAATGT
937589 AATAAAAATG-
1 AATAAAAATGT
*
937599 AAT-AAAATTT
1 AATAAAAATGT
937609 AATAAAA
1 AATAAAA
937616 GTATAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 5 0.21
10 6 0.25
11 13 0.54
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (11 bp):
AATAAAAATGT
Found at i:937605 original size:20 final size:21
Alignment explanation
Indices: 937570--937615 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
937560 TTATTTTTTC
937570 TAAAAATAAATAAAAATGTAA
1 TAAAAATAAATAAAAATGTAA
* *
937591 TAAAAATGAAT-AAAATTTAA
1 TAAAAATAAATAAAAATGTAA
937611 TAAAA
1 TAAAA
937616 GTATAATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
TAAAAATAAATAAAAATGTAA
Found at i:938244 original size:20 final size:20
Alignment explanation
Indices: 938221--938276 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
938211 TTTACATTAT
938221 ATTTTTATTGAATTTTA-TTC
1 ATTTTTATT-AATTTTATTTC
* *
938241 ATTTTTAATTCATTTTATTTT
1 ATTTTT-ATTAATTTTATTTC
*
938262 ATTTTTATTTATTTT
1 ATTTTTATTAATTTT
938277 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTTTATTAATTTTATTTC
Found at i:938251 original size:11 final size:10
Alignment explanation
Indices: 938221--938277 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
938211 TTTACATTAT
*
938221 ATTTTTATTG
1 ATTTTTATTC
*
938231 AATTTTATTC
1 ATTTTTATTC
938241 ATTTTTAATTC
1 ATTTTT-ATTC
*
938252 A-TTTTATTTT
1 ATTTTTA-TTC
*
938262 ATTTTTATTT
1 ATTTTTATTC
938272 ATTTTT
1 ATTTTT
938278 TAAAAAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 1 0.03
10 29 0.73
11 10 0.25
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:941551 original size:18 final size:18
Alignment explanation
Indices: 941528--941562 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
941518 TTCCATCCGG
*
941528 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
941546 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
941563 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:942891 original size:18 final size:18
Alignment explanation
Indices: 942884--942932 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
942874 GTAAACGGGT
942884 CGGGTCGGGTCGGGTAAA
1 CGGGTCGGGTCGGGTAAA
*
942902 CGGGTTGGGTCGGGTAAA
1 CGGGTCGGGTCGGGTAAA
942920 CGGGTCGGGTCGG
1 CGGGTCGGGTCGG
942933 ATTGTGACCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.12, C:0.16, G:0.53, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTAAA
Found at i:942898 original size:23 final size:23
Alignment explanation
Indices: 942868--942932 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
942858 CGGGTCAACA
942868 GGTCGGGTAAACGGGTCGGGTCG
1 GGTCGGGTAAACGGGTCGGGTCG
942891 GGTCGGGTAAACGGGT----T-G
1 GGTCGGGTAAACGGGTCGGGTCG
942909 GGTCGGGTAAACGGGTCGGGTCG
1 GGTCGGGTAAACGGGTCGGGTCG
942932 G
1 G
942933 ATTGTGACCG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
18 17 0.46
19 1 0.03
22 1 0.03
23 18 0.49
ACGTcount: A:0.14, C:0.15, G:0.52, T:0.18
Consensus pattern (23 bp):
GGTCGGGTAAACGGGTCGGGTCG
Found at i:942929 original size:13 final size:13
Alignment explanation
Indices: 942858--942911 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
942848 CGACGGTCAA
* *
942858 CGGGTCAACAGGT
1 CGGGTAAACGGGT
942871 CGGGTAAACGGGT
1 CGGGTAAACGGGT
942884 CGGGT---CGGGT
1 CGGGTAAACGGGT
942894 CGGGTAAACGGGT
1 CGGGTAAACGGGT
*
942907 TGGGT
1 CGGGT
942912 CGGGTAAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 10 0.29
13 25 0.71
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:944351 original size:20 final size:20
Alignment explanation
Indices: 944328--944374 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
944318 GTTTCCAATT
*
944328 TCGCAATGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
944348 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
944368 TCGCAAC
1 TCGCAAC
944375 ACAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:944391 original size:20 final size:20
Alignment explanation
Indices: 944368--944653 Score: 261
Period size: 20 Copynumber: 14.3 Consensus size: 20
944358 AATTTGTAAA
944368 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
944388 TCGCAATGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
944408 TCGCAATACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
944428 TCGCGACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
944448 TCGCAACAC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
944468 TCGCAACAC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
944488 TCGCAACGC-GAATTTGT-AAA-
1 TCGCAACACAGAA---GTCAAAT
944508 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
944528 TCGCAATGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
944548 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
944568 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
944588 TCGCAACGCCA-ATTTGT-AAA-
1 TCGCAAC-ACAGA--AGTCAAAT
*
944608 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
944628 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
944648 TCGCAA
1 TCGCAA
944654 TGCGGAATTT
Statistics
Matches: 227, Mismatches: 21, Indels: 36
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.02
19 15 0.07
20 190 0.84
21 13 0.06
22 5 0.02
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:944391 original size:60 final size:61
Alignment explanation
Indices: 944327--944675 Score: 328
Period size: 60 Copynumber: 5.8 Consensus size: 61
944317 AGTTTCCAAT
* * *
944327 TTCGCAATGCGAATATGT-AAA-TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-ATA-GTCAAATTCGCAACGCGAA-TAGTCAAATTCGCAACACAAAAGTCAAA
* ** * *
944387 TTCGCAATGCGATAGTCAAATTCGCAATAC-AAAAGTCAAATTCGCGACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAA
* * * **
944447 TTCGCAACACGATAGTCAAATTCGCAACACG-ATAGTCAAATTCGCAACGCGAATTTGT-AAA
1 TTCGCAACGCGATAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACAC-AA-AAGTCAAA
* *
944508 -TCGCAACACAGA-AGTCAAATTCGCAATGCG-ATAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGC-GATAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAA
* *
944567 TTCGCAACGCGATAGTCAAATTCGCAACGCCAATTTGT-AAA-TCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACGCGAA-TAGTCAAATTCGCAACACAAAAGTCAAA
* * * * * *
944627 TTCGCAACACAAAAGTCAAATTCGCAATGCGGAAT-TTCAAATTCACAAC
1 TTCGCAACGCGATAGTCAAATTCGCAACGC-GAATAGTCAAATTCGCAAC
944676 GCGAAACACA
Statistics
Matches: 243, Mismatches: 30, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
58 6 0.02
59 19 0.08
60 194 0.80
61 19 0.08
62 5 0.02
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (61 bp):
TTCGCAACGCGATAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:947006 original size:42 final size:41
Alignment explanation
Indices: 946959--947058 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
946949 GTTAGGGAAG
* *
946959 TTACGTGATGAGGTCGGTGCTTTGCGTCATGAGG-TCGGTACT
1 TTACGTGATGAGGT-GGTGCATGGCGTCATGAGGTTCGGT-CT
* ** *
947001 TTACGTGAAGATAATGGTGCATGGCGTGATGAGGTTCGGTCT
1 TTACGTGATGA-GGTGGTGCATGGCGTCATGAGGTTCGGTCT
*
947043 TTACGTGGTGAGGTGG
1 TTACGTGATGAGGTGG
947059 ATTTTTTATG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 3 0.07
42 37 0.80
43 6 0.13
ACGTcount: A:0.17, C:0.13, G:0.38, T:0.32
Consensus pattern (41 bp):
TTACGTGATGAGGTGGTGCATGGCGTCATGAGGTTCGGTCT
Found at i:947462 original size:21 final size:21
Alignment explanation
Indices: 947439--947534 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
947429 GGCATCTTCT
* *
947439 ATCGTTCAAGAGGTCCCTCTT
1 ATCGTTCAAGAGGCCCCTCTC
* * *
947460 ATC-ATCGAAGAAGCCCCTCCC
1 ATCGTTC-AAGAGGCCCCTCTC
* * *
947481 ACCATTCAAGAGG-CCCTGTC
1 ATCGTTCAAGAGGCCCCTCTC
*
947501 ATCGTTCAAGAGGCCCCTGTC
1 ATCGTTCAAGAGGCCCCTCTC
947522 ATCGTTCAAGAGG
1 ATCGTTCAAGAGG
947535 TCCCGCCTAC
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
20 18 0.30
21 40 0.67
22 2 0.03
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCTC
Found at i:947508 original size:20 final size:21
Alignment explanation
Indices: 947485--947534 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
947475 CCTCCCACCA
947485 TTCAAGAGG-CCCTGTCATCG
1 TTCAAGAGGCCCCTGTCATCG
947505 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTGTCATCG
947526 TTCAAGAGG
1 TTCAAGAGG
947535 TCCCGCCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (21 bp):
TTCAAGAGGCCCCTGTCATCG
Found at i:949431 original size:18 final size:18
Alignment explanation
Indices: 949408--949443 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
949398 AATTCGGTTG
*
949408 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
949426 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
949444 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:950419 original size:18 final size:18
Alignment explanation
Indices: 950396--950432 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
950386 CGAAATTTAT
*
950396 ATTGAAATTTAAACTCAA
1 ATTGAAATTGAAACTCAA
*
950414 ATTGAAATTGAAATTCAA
1 ATTGAAATTGAAACTCAA
950432 A
1 A
950433 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (18 bp):
ATTGAAATTGAAACTCAA
Found at i:950956 original size:20 final size:20
Alignment explanation
Indices: 950931--950972 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
950921 TTGTGATTTT
*
950931 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
950951 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
950971 GC
1 GC
950973 AACACTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:951299 original size:18 final size:18
Alignment explanation
Indices: 951276--951311 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
951266 AAGCCGGTTG
951276 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
951294 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
951312 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:953747 original size:12 final size:12
Alignment explanation
Indices: 953726--953759 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
953716 GGTCGTGGGT
*
953726 TTTGAGATTGTG
1 TTTGATATTGTG
953738 TTTGATATTGTG
1 TTTGATATTGTG
*
953750 TTTGGTATTG
1 TTTGATATTG
953760 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:954390 original size:14 final size:15
Alignment explanation
Indices: 954354--954391 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
954344 TAAATCATTG
954354 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
954369 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
954384 AAAAATTA
1 AAAAATTA
954392 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:954637 original size:21 final size:18
Alignment explanation
Indices: 954579--954637 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
954569 GCGAATTCAA
*
954579 AAATCTAGTTGCAAATTTG
1 AAAT-TAGTTGCGAATTTG
* *
954598 AAATTAGTTGTGAAATTG
1 AAATTAGTTGCGAATTTG
954616 AAATTCCACGTTGCGAATTTG
1 AAATT--A-GTTGCGAATTTG
954637 A
1 A
954638 CTTCTGTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 16 0.50
19 4 0.12
20 1 0.03
21 11 0.34
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (18 bp):
AAATTAGTTGCGAATTTG
Found at i:954775 original size:20 final size:19
Alignment explanation
Indices: 954726--954779 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
954716 CGATTTACAT
954726 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
954745 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
954765 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
954780 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:955917 original size:36 final size:36
Alignment explanation
Indices: 955872--955944 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
955862 ATACTTATAC
* * *
955872 TGTATTGTAATGTAATGTAGGAGTTAATGTTTCTAA
1 TGTAATGTAATGTAATATAGGAGTTAATGCTTCTAA
*
955908 TGTAATGTAATGTAATATATGAGTTAATGCTTCTAA
1 TGTAATGTAATGTAATATAGGAGTTAATGCTTCTAA
955944 T
1 T
955945 ATAGGAGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (36 bp):
TGTAATGTAATGTAATATAGGAGTTAATGCTTCTAA
Found at i:969212 original size:20 final size:20
Alignment explanation
Indices: 969183--969221 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
969173 ATTCCACCAC
*
969183 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
969203 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
969222 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:983208 original size:67 final size:67
Alignment explanation
Indices: 983100--983233 Score: 196
Period size: 67 Copynumber: 2.0 Consensus size: 67
983090 GGTATGAAGG
* * * * *
983100 CTCTGGCAGGTTCACTCGCTGTTGGTAATTCCTTGTATAGGTTCAACATCGACTGGTAATTCCTT
1 CTCTGACAGGTTCACTCGCTGCTGGTAATTCCTTGAATAGGTTCAACACCGACTGATAATTCCTT
983165 AT
66 AT
* * *
983167 CTCTGACAGGTTCAGTCGCTGCTGGTAATTCTTTGAATAGGTTTAACACCGACTGATAATTCCTT
1 CTCTGACAGGTTCACTCGCTGCTGGTAATTCCTTGAATAGGTTCAACACCGACTGATAATTCCTT
983232 AT
66 AT
983234 AGACCTAAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (67 bp):
CTCTGACAGGTTCACTCGCTGCTGGTAATTCCTTGAATAGGTTCAACACCGACTGATAATTCCTT
AT
Found at i:988628 original size:7 final size:7
Alignment explanation
Indices: 988618--988683 Score: 59
Period size: 7 Copynumber: 9.7 Consensus size: 7
988608 AAAAAATAGA
988618 AAAAAGG
1 AAAAAGG
*
988625 AAAAGAGA
1 AAAA-AGG
988633 ATAAAAGG
1 A-AAAAGG
988641 --AAA-G
1 AAAAAGG
988645 AAAAAGG
1 AAAAAGG
988652 AAAAAGG
1 AAAAAGG
988659 AAAAA-G
1 AAAAAGG
*
988665 AAAAAAG
1 AAAAAGG
*
988672 AAAAACG
1 AAAAAGG
988679 AAAAA
1 AAAAA
988684 ATTAATAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 9 0.18
7 29 0.58
8 5 0.10
9 3 0.06
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (7 bp):
AAAAAGG
Found at i:988638 original size:16 final size:15
Alignment explanation
Indices: 988610--988684 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 15
988600 GTCTGATGAA
*
988610 AAAATAGAAAAAAGG
1 AAAAGAGAAAAAAGG
988625 AAAAGAGAATAAAAGG
1 AAAAGAGAA-AAAAGG
* *
988641 AAAGAAAAAGGAAAAAGG
1 --A-AAAGAGAAAAAAGG
988659 AAAA-AGAAAAAA-G
1 AAAAGAGAAAAAAGG
988672 AAAA-ACGAAAAAA
1 AAAAGA-GAAAAAA
988685 TTAATAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
13 6 0.12
14 14 0.27
15 11 0.22
16 7 0.14
18 7 0.14
19 6 0.12
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (15 bp):
AAAAGAGAAAAAAGG
Found at i:988664 original size:20 final size:20
Alignment explanation
Indices: 988641--988683 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
988631 GAATAAAAGG
* *
988641 AAAGAAAAAGGAAAAAGGAA
1 AAAGAAAAAAGAAAAACGAA
988661 AAAGAAAAAAGAAAAACGAA
1 AAAGAAAAAAGAAAAACGAA
988681 AAA
1 AAA
988684 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAGAAAAACGAA
Found at i:995628 original size:29 final size:29
Alignment explanation
Indices: 995596--995661 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
995586 AAATCCATCA
995596 GCAAAACAAAAATAAATACATGATTAAAT
1 GCAAAACAAAAATAAATACATGATTAAAT
*
995625 GCAAAACAACAATAAATACATGATTAAAT
1 GCAAAACAAAAATAAATACATGATTAAAT
*
995654 ACAAAACA
1 GCAAAACA
995662 TTTAGAGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.62, C:0.14, G:0.06, T:0.18
Consensus pattern (29 bp):
GCAAAACAAAAATAAATACATGATTAAAT
Found at i:997423 original size:2 final size:2
Alignment explanation
Indices: 997416--997458 Score: 50
Period size: 2 Copynumber: 19.5 Consensus size: 2
997406 TTATTGTATG
997416 AT AT AT AT AT AGT AT AT AGT AT AT AT AT AGT AT AT AGT AT AT A
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT A-T AT AT A-T AT AT A
997459 GTTGCTTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 29 0.78
3 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (2 bp):
AT
Found at i:997433 original size:7 final size:7
Alignment explanation
Indices: 997416--997460 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
997406 TTATTGTATG
997416 ATATA-T
1 ATATAGT
997422 ATATAGT
1 ATATAGT
997429 ATATAG-
1 ATATAGT
997435 -TATA-T
1 ATATAGT
997440 ATATAGT
1 ATATAGT
997447 ATATAGT
1 ATATAGT
997454 ATATAGT
1 ATATAGT
997461 TGCTTGTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.11
6 9 0.26
7 22 0.63
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (7 bp):
ATATAGT
Found at i:997440 original size:18 final size:18
Alignment explanation
Indices: 997417--997458 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
997407 TATTGTATGA
997417 TATATATATAGTATATAG
1 TATATATATAGTATATAG
997435 TATATATATAGTATATAG
1 TATATATATAGTATATAG
997453 TATATA
1 TATATA
997459 GTTGCTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (18 bp):
TATATATATAGTATATAG
Found at i:999309 original size:31 final size:33
Alignment explanation
Indices: 999240--999309 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 33
999230 TTCTATAGTT
* *
999240 ATTAATTAAATCCAGTTTAGGTTCCTTAATTAG
1 ATTAATTAAATCAAGTTTAGGTTCCTTAATTAA
999273 A--AATTAAAT-AAGTTTA-GTATCCTTAA-TAA
1 ATTAATTAAATCAAGTTTAGGT-TCCTTAATTAA
999302 ATTAATTA
1 ATTAATTA
999310 GAAACACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
29 5 0.16
30 13 0.41
31 13 0.41
33 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (33 bp):
ATTAATTAAATCAAGTTTAGGTTCCTTAATTAA
Found at i:1003001 original size:20 final size:22
Alignment explanation
Indices: 1002971--1003011 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1002961 CTTACATTAT
1002971 TTTTCTTTCTTTTT-CTTTTTC
1 TTTTCTTTCTTTTTACTTTTTC
1002992 TTTT-TTTCTTTTTACTTTTT
1 TTTTCTTTCTTTTTACTTTTT
1003012 TGAAACAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTCTTTCTTTTTACTTTTTC
Found at i:1003011 original size:16 final size:15
Alignment explanation
Indices: 1002970--1003012 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 15
1002960 TCTTACATTA
1002970 TTTTTCTTTCTTTTTC
1 TTTTTCTTT-TTTTTC
1002986 TTTTTC-TTTTTTTC
1 TTTTTCTTTTTTTTC
1003000 TTTTTACTTTTTT
1 TTTTT-CTTTTTT
1003013 GAAACAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.44
15 3 0.12
16 11 0.44
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTCTTTTTTTTC
Found at i:1003485 original size:91 final size:90
Alignment explanation
Indices: 1003367--1003731 Score: 397
Period size: 91 Copynumber: 4.0 Consensus size: 90
1003357 TGATGAATTA
* * * * * *
1003367 CCAAGCTTGAAAAAGTTCTTCTTATTATGAACTTCTTTTCCCTTGTCGGATGAGTTATTCTCATT
1 CCAAGATTGAACAAGTTATTCTCATTATGAACTT-TTTTCCCTCGTCGGATGAGTTCTTCTCATT
*
1003432 ATGAACTCTACACTGGAAATATTGAT
65 ATGAACTCTCCACTGGAAATATTGAT
* ** * ** *
1003458 CCAAGGTCAAACAAGTTATTCTCATTATGAACTTTTTTCCCTCGTTGGACAAGTTTTTCTCATTA
1 CCAAGATTGAACAAGTTATTCTCATTATGAACTTTTTTCCCTCGTCGGATGAGTTCTTCTCATTA
* * *
1003523 TGAACTCTCCACTGGGAATGTTGAG
66 TGAACTCTCCACTGGAAATATTGAT
* * * * * *
1003548 CCATGTTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
1 CCAAGATTGAACAAGTTATTCTCATTATGAACTT-TTTTCCCTCGTCGGATGAGTTCTTCTCATT
*
1003613 ATGAACTCTCCACTGGAAACATTGAT
65 ATGAACTCTCCACTGGAAATATTGAT
* * * * * *
1003639 CAAATATTGAACAAGTTATTCTCATTATGAACTTTTTCTCCTTCATCGAATGAGTTCCTCTCATT
1 CCAAGATTGAACAAGTTATTCTCATTATGAACTTTTT-TCCCTCGTCGGATGAGTTCTTCTCATT
* * * *
1003704 ATGAACTCTCTATTTGAAATGTTGAT
65 ATGAACTCTCCACTGGAAATATTGAT
1003730 CC
1 CC
1003732 CTTAAGTGAG
Statistics
Matches: 225, Mismatches: 47, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
90 77 0.34
91 148 0.66
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (90 bp):
CCAAGATTGAACAAGTTATTCTCATTATGAACTTTTTTCCCTCGTCGGATGAGTTCTTCTCATTA
TGAACTCTCCACTGGAAATATTGAT
Found at i:1004181 original size:36 final size:36
Alignment explanation
Indices: 1004140--1004882 Score: 629
Period size: 36 Copynumber: 21.1 Consensus size: 36
1004130 TTTGAAGATA
* *
1004140 AAGAGAGATAAAATTTGTTTCGAGGGAAACTGTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* * *
1004176 TAGAGAGACAAAACTTTATTTCAAGAGAAACTGTCTC
1 AAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTC
* * * *
1004213 AAGGGAGACAAAAACTTGTTTTAAGAGAAACTGTCTC
1 AAGAGAGAC-AAAATTTGTTTCAAGGGAAACTGTCTC
* * * *
1004250 AAGGGAGCCAAAACTTGTTTCAAGAGAAACTGTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
*
1004286 AAGAAAGACAAAATTTGTTTCAAGGGAAACTGTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* * **
1004322 AAGAGAGACAAAAATCGTTTCAAGGGAAA-AAT-TC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* ** *
1004356 -------ACAAAGTTTATGTTTCAAAAGAAACCGTCTC
1 AAGAGAGACAAA-ATT-TGTTTCAAGGGAAACTGTCTC
*
1004387 AA-AGGAGACAAAATTTGTTTCAAGGGAAAATGTCTC
1 AAGA-GAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* * * *
1004423 AAGGGAGACAAAACTTGTTTCAAGAGAAAATGTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* * *
1004459 AAGGGAGACAAAACTTGTTTCAAGAGAAACTGTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* * * * * *
1004495 AAGGGATACAAAACTTGTTTCAAGAGAAAATGTTTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* * *
1004531 AAGGGAGACAAAACTTGTTTCAAGGGAAACAGTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* * *
1004567 AAGGGAGACAAACTTTGTTTCAAGGGAAACATAT-TC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAAC-TGTCTC
* * *
1004603 -A-A-AG----ATTTTGTATTTCAAGAGAAACTGTCTT
1 AAGAGAGACAAAATTTG--TTTCAAGGGAAACTGTCTC
* * * ** *
1004634 AAGGGAGACAAAACTTGTTTCAAGGGTAACAATCTA
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* * *
1004670 AACAGAGACAAACTTTGTTTCAAGGGAAACATAT-TC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAAC-TGTCTC
** *
1004706 -A-A-AG---ATTTTGTGTTTCAAGAGAAACTGTCTC
1 AAGAGAGACAAAATT-TGTTTCAAGGGAAACTGTCTC
*
1004737 AAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
** * *
1004773 AAGAGAGACAAAATTCATTTCAAGGGAAACGGTCTT
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
* *
1004809 AAGAGAGACAAAATTTGTTTCAAGTGAAACGGTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
1004845 AAGAGAGACAAAATTTGTTTCAAGGGAAAC-GTTCTC
1 AAGAGAGACAAAATTTGTTTCAAGGGAAACTG-TCTC
1004881 AA
1 AA
1004883 AGTTTACGTT
Statistics
Matches: 584, Mismatches: 88, Indels: 70
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.01
28 1 0.00
29 16 0.03
30 8 0.01
31 31 0.05
32 2 0.00
33 4 0.01
34 7 0.01
35 4 0.01
36 430 0.74
37 63 0.11
38 13 0.02
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTC
Found at i:1004479 original size:137 final size:137
Alignment explanation
Indices: 1004229--1004487 Score: 365
Period size: 137 Copynumber: 1.9 Consensus size: 137
1004219 GACAAAAACT
* * * * * *
1004229 TGTTTTAAGAGAAACTGTCTCAAGGGAGCCAAAACTTGTTTCAAGAGAAACTGTCTCAAGAAAGA
1 TGTTTCAAAAGAAACCGTCTCAAAGGAGACAAAACTTGTTTCAAGAGAAAATGTCTCAAGAAAGA
* * * *
1004294 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAATCGTTTCAAGGGAAAAATTCACA
66 CAAAACTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAATCGTTTCAAGAGAAAAATTCACA
1004359 AAGTTTA
131 AAGTTTA
* * **
1004366 TGTTTCAAAAGAAACCGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAAATGTCTCAAGGGAGA
1 TGTTTCAAAAGAAACCGTCTCAAAGGAGACAAAACTTGTTTCAAGAGAAAATGTCTCAAGAAAGA
* * *
1004431 CAAAACTTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAACTTGTTTCAAGAGAAA
66 CAAAACTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAATCGTTTCAAGAGAAA
1004488 CTGTCTCAAG
Statistics
Matches: 105, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
137 105 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (137 bp):
TGTTTCAAAAGAAACCGTCTCAAAGGAGACAAAACTTGTTTCAAGAGAAAATGTCTCAAGAAAGA
CAAAACTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAATCGTTTCAAGAGAAAAATTCACA
AAGTTTA
Found at i:1004555 original size:209 final size:211
Alignment explanation
Indices: 1004180--1004559 Score: 602
Period size: 209 Copynumber: 1.8 Consensus size: 211
1004170 TGTCTCTAGA
* * *
1004180 GAGACAAAACTTTATTTCAAGAGAAACTGTCTCAAGGGAGACAAAAACTTGTTTTAAGAGAAACT
1 GAGACAAAACTTTATTTCAAGAGAAAATGTCTCAAGGGAGACAAAAACTTGTTTCAAGAGAAAAT
* *
1004245 GTCTCAAGGGAGCCAAAACTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAG
66 GTCTCAAGGGAGACAAAACTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTTGTTTCAAG
* *
1004310 GGAAACTGTCTCAAGAGAGACAAAAATCGTTTCAAGGGAAAAATTCACAAAGTTTATGTTTCAAA
131 AGAAAATGTCTCAAGAGAGACAAAAATCGTTTCAAGGGAAAAATTCACAAAGTTTATGTTTCAAA
1004375 AGAAACCGTCTCAAAG
196 AGAAACCGTCTCAAAG
* *
1004391 GAGACAAAA-TTTGTTTCAAGGGAAAATGTCTCAAGGGAGAC-AAAACTTGTTTCAAGAGAAAAT
1 GAGACAAAACTTTATTTCAAGAGAAAATGTCTCAAGGGAGACAAAAACTTGTTTCAAGAGAAAAT
** *
1004454 GTCTCAAGGGAGACAAAACTTGTTTCAAGAGAAACTGTCTCAAGGGATACAAAACTTGTTTCAAG
66 GTCTCAAGGGAGACAAAACTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTTGTTTCAAG
* * * *
1004519 AGAAAATGTTTCAAGGGAGACAAAACTTGTTTCAAGGGAAA
131 AGAAAATGTCTCAAGAGAGACAAAAATCGTTTCAAGGGAAA
1004560 CAGTCTCAAG
Statistics
Matches: 153, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
209 115 0.75
210 29 0.19
211 9 0.06
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (211 bp):
GAGACAAAACTTTATTTCAAGAGAAAATGTCTCAAGGGAGACAAAAACTTGTTTCAAGAGAAAAT
GTCTCAAGGGAGACAAAACTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTTGTTTCAAG
AGAAAATGTCTCAAGAGAGACAAAAATCGTTTCAAGGGAAAAATTCACAAAGTTTATGTTTCAAA
AGAAACCGTCTCAAAG
Found at i:1004678 original size:103 final size:103
Alignment explanation
Indices: 1004404--1004802 Score: 459
Period size: 103 Copynumber: 3.8 Consensus size: 103
1004394 ACAAAATTTG
* * * * *
1004404 TTTCAAGGGAAAATGTCTCAAGGGAGACAAAACTTGTTTCAAGAGAAA-ATGTCTCAAGGGAGAC
1 TTTCAAGAGAAACTGTCTTAAGGGAGACAAAACTTGTTTCAAGGGAAACA-GTCTCAAGAGAGAC
* * * *
1004468 AAAAC-TTGTTTCAAGAGAAAC-TGTCTCAAGGGATACAAAACTTG--
65 -AAACTTTGTTTCAAGGGAAACATAT-TCAA-AGAT------TTTGTA
* *
1004512 TTTCAAGAGAAAATGT-TTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAGTCTCAAGGGAGAC
1 TTTCAAGAGAAACTGTCTT-AAGGGAGACAAAACTTGTTTCAAGGGAAACAGTCTCAAGAGAGAC
1004576 AAACTTTGTTTCAAGGGAAACATATTCAAAGATTTTGTA
65 AAACTTTGTTTCAAGGGAAACATATTCAAAGATTTTGTA
* * * *
1004615 TTTCAAGAGAAACTGTCTTAAGGGAGACAAAACTTGTTTCAAGGGTAACAATCTAAACAGAGACA
1 TTTCAAGAGAAACTGTCTTAAGGGAGACAAAACTTGTTTCAAGGGAAACAGTCTCAAGAGAGACA
*
1004680 AACTTTGTTTCAAGGGAAACATATTCAAAGATTTTGTG
66 AACTTTGTTTCAAGGGAAACATATTCAAAGATTTTGTA
* * *
1004718 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTTCAAGAGAAACTGTCTTAAGGGAGACAAAACTTGTTTCAAGGGAAACAGTCTCAAGAGAGACA
* **
1004783 AAATTCATTTCAAGGGAAAC
66 AACTTTGTTTCAAGGGAAAC
1004803 GGTCTTAAGA
Statistics
Matches: 260, Mismatches: 24, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
101 3 0.01
103 168 0.65
104 2 0.01
107 8 0.03
108 76 0.29
109 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (103 bp):
TTTCAAGAGAAACTGTCTTAAGGGAGACAAAACTTGTTTCAAGGGAAACAGTCTCAAGAGAGACA
AACTTTGTTTCAAGGGAAACATATTCAAAGATTTTGTA
Found at i:1010040 original size:15 final size:17
Alignment explanation
Indices: 1010020--1010054 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
1010010 CTTACATTGC
1010020 TTTCTTTTT-CTTTT-T
1 TTTCTTTTTCCTTTTCT
1010035 TTTCTTTTTCCTTTTCT
1 TTTCTTTTTCCTTTTCT
1010052 TTT
1 TTT
1010055 TGCTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTCTTTTTCCTTTTCT
Found at i:1010063 original size:21 final size:21
Alignment explanation
Indices: 1010020--1010063 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1010010 CTTACATTGC
* *
1010020 TTTCTTTTTCTTTTTTTTCTT
1 TTTCCTTTTCTTTTTCTTCTT
1010041 TTTCCTTTTCTTTTTGCTT-TT
1 TTTCCTTTTCTTTTT-CTTCTT
1010062 TT
1 TT
1010064 GAAACAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTCCTTTTCTTTTTCTTCTT
Found at i:1016171 original size:14 final size:14
Alignment explanation
Indices: 1016154--1016190 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1016144 AGAAGAAAAG
1016154 AAAAAGAAAAAACT-
1 AAAAAGAAAAAA-TA
1016168 AAAAAG-AAAAATA
1 AAAAAGAAAAAATA
1016181 AAAAAGAAAA
1 AAAAAGAAAA
1016191 GAAAAGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.05
13 11 0.52
14 9 0.43
ACGTcount: A:0.84, C:0.03, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAAAGAAAAAATA
Found at i:1016184 original size:13 final size:13
Alignment explanation
Indices: 1016143--1016190 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
1016133 ATTATGCTTG
*
1016143 AAGAAGAAAAGAAA
1 AAGAA-AAAACAAA
1016157 AAGAAAAAACTAAA
1 AAGAAAAAAC-AAA
1016171 AAGAAAAATA-AAA
1 AAGAAAAA-ACAAA
1016184 AAGAAAA
1 AAGAAAA
1016191 GAAAAGGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 14 0.45
14 16 0.52
15 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (13 bp):
AAGAAAAAACAAA
Found at i:1016900 original size:16 final size:15
Alignment explanation
Indices: 1016879--1016908 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1016869 AAAAGTGCCA
1016879 AGAAAAGAAGGAATGG
1 AGAAAAGAA-GAATGG
1016895 AGAAAAGAAGAATG
1 AGAAAAGAAGAATG
1016909 AAAAAAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (15 bp):
AGAAAAGAAGAATGG
Found at i:1018630 original size:20 final size:20
Alignment explanation
Indices: 1018602--1018640 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1018592 AATACCCAAA
*
1018602 TAAAGAGTCCATTTGCATTT
1 TAAAGAGTCCATTTACATTT
*
1018622 TAAATAGTCCATTTACATT
1 TAAAGAGTCCATTTACATT
1018641 GTTTTTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
TAAAGAGTCCATTTACATTT
Found at i:1021042 original size:96 final size:96
Alignment explanation
Indices: 1020931--1021118 Score: 236
Period size: 96 Copynumber: 2.0 Consensus size: 96
1020921 CGATATCATT
* * * * *
1020931 GTAAGGGTGTCGATA-CAAAACAATTATCAAATCTAATTTCGGTATTGGTACC-GTAAGGGGGTA
1 GTAAGGGTATCGATACCAAAA-AA-TATCAAAGCTAATTTCGGTATCGATACCAGAAAGGGGGTA
**
1020994 TCGCTACCATAGTATATTAGTATCAATACCATG
64 TCGCTACCATAGTATAGAAGTATCAATACCATG
** * *
1021027 GTAAGGGTATCGATACCAGGAAATATCGAAGCTAATTTTGGTATCGATACCAGAAAGGGGGTATC
1 GTAAGGGTATCGATACCAAAAAATATCAAAGCTAATTTCGGTATCGATACCAGAAAGGGGGTATC
*
1021092 GGTACCATAGTATAGAAGTATCAATAC
66 GCTACCATAGTATAGAAGTATCAATAC
1021119 TAGGGTAGTA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
95 23 0.29
96 52 0.67
97 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (96 bp):
GTAAGGGTATCGATACCAAAAAATATCAAAGCTAATTTCGGTATCGATACCAGAAAGGGGGTATC
GCTACCATAGTATAGAAGTATCAATACCATG
Found at i:1021137 original size:96 final size:95
Alignment explanation
Indices: 1020963--1021138 Score: 228
Period size: 96 Copynumber: 1.8 Consensus size: 95
1020953 ATTATCAAAT
* * * ** *
1020963 CTAATTTCGGTATTGGTACCGTAAGGGGGTATCGCTACCATAGTATATTAGTATCAATACCATGG
1 CTAATTTCGGTATCGATACCGAAAGGGGGTATCGCTACCATAGTATAGAAGTATCAATACCAGGG
* *
1021028 TAAGGGTATCGATACCAGGAAATATCGAAG
66 TAAGAGTACCGATACCAGGAAATATCGAAG
* * *
1021058 CTAATTTTGGTATCGATACCAGAAAGGGGGTATCGGTACCATAGTATAGAAGTATCAATACTAGG
1 CTAATTTCGGTATCGATACC-GAAAGGGGGTATCGCTACCATAGTATAGAAGTATCAATACCAGG
1021123 GT-AGTAGTACCGATAC
65 GTAAG-AGTACCGATAC
1021139 TATAGAGCCT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
95 19 0.28
96 49 0.72
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (95 bp):
CTAATTTCGGTATCGATACCGAAAGGGGGTATCGCTACCATAGTATAGAAGTATCAATACCAGGG
TAAGAGTACCGATACCAGGAAATATCGAAG
Found at i:1021568 original size:46 final size:46
Alignment explanation
Indices: 1021460--1021698 Score: 390
Period size: 46 Copynumber: 5.2 Consensus size: 46
1021450 GATGATTATG
* * *
1021460 ATAACTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGAT-AC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
* *
1021505 ATAATTAAAATGCATGAAATGATGTATTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
1021551 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
* * *
1021597 ATAAATAAAATGCATGAAAGGATGGATTAAGACATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
*
1021643 ATAATTAAAATGCATAAAAGGATGCATTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
1021689 ATAATTAAAA
1 ATAATTAAAA
1021699 ATGTATAAAT
Statistics
Matches: 179, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 39 0.22
46 140 0.78
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (46 bp):
ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
Found at i:1021618 original size:26 final size:25
Alignment explanation
Indices: 1021460--1021698 Score: 143
Period size: 20 Copynumber: 10.4 Consensus size: 25
1021450 GATGATTATG
1021460 ATAACTAAAATGCATGAAAGGATG-C
1 ATAA-TAAAATGCATGAAAGGATGCC
* * *
1021485 AT--T--AAGGCATAAAAGGAT-AC
1 ATAATAAAATGCATGAAAGGATGCC
*
1021505 ATAATTAAAATGCATGAAATGATG--
1 ATAA-TAAAATGCATGAAAGGATGCC
* *
1021529 -T-AT-TAAGGCATGAAAGGATGCC
1 ATAATAAAATGCATGAAAGGATGCC
1021551 ATAATTAAAATGCATGAAAGGATG-C
1 ATAA-TAAAATGCATGAAAGGATGCC
*
1021576 AT--T--AAGGCATGAAAGGATGCC
1 ATAATAAAATGCATGAAAGGATGCC
*
1021597 ATAAATAAAATGCATGAAAGGATG-G
1 AT-AATAAAATGCATGAAAGGATGCC
*
1021622 AT--TAAGA--CATGAAAGGATGCC
1 ATAATAAAATGCATGAAAGGATGCC
*
1021643 ATAATTAAAATGCATAAAAGGATG-C
1 ATAA-TAAAATGCATGAAAGGATGCC
*
1021668 AT--T--AAGGCATGAAAGGATGCC
1 ATAATAAAATGCATGAAAGGATGCC
1021689 ATAATTAAAA
1 ATAA-TAAAA
1021699 ATGTATAAAT
Statistics
Matches: 164, Mismatches: 19, Indels: 61
0.67 0.08 0.25
Matches are distributed among these distances:
20 71 0.43
21 9 0.05
22 8 0.05
23 3 0.02
24 7 0.04
25 23 0.14
26 43 0.26
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (25 bp):
ATAATAAAATGCATGAAAGGATGCC
Found at i:1027984 original size:95 final size:96
Alignment explanation
Indices: 1027801--1027998 Score: 244
Period size: 95 Copynumber: 2.1 Consensus size: 96
1027791 CCGTTGAGGC
* * *
1027801 AGTATCG-AACCATTGTAAGGGTATCGATACCAAGCAAACATCGAATCTAATTTCGGTATCGATA
1 AGTATCGAAACCATGGTAAGGGTATCGATACCAAGCAAACATCAAATCTAATTTCGATATCGATA
* **
1027865 CCATAAGGGGGTATCGGTATCATAGTATATT
66 CCATAAGGGGGTATCGGTACCATAGTATAAA
* * *
1027896 AGTATCGAAACCATGGTAAGGGTATCGATA-CTAGGAAACATCAAAGT-TAATTTTGATATCGAT
1 AGTATCGAAACCATGGTAAGGGTATCGATACCAAGCAAACATCAAA-TCTAATTTCGATATCGAT
*
1027959 ACTGGA-AAGGGGGTATCGG-ACCATAGTATAAA
65 AC--CATAAGGGGGTATCGGTACCATAGTATAAA
1027991 AGTATCGA
1 AGTATCGA
1027999 TACTAGGGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
95 53 0.60
96 35 0.39
97 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (96 bp):
AGTATCGAAACCATGGTAAGGGTATCGATACCAAGCAAACATCAAATCTAATTTCGATATCGATA
CCATAAGGGGGTATCGGTACCATAGTATAAA
Found at i:1028415 original size:46 final size:46
Alignment explanation
Indices: 1028341--1028618 Score: 411
Period size: 46 Copynumber: 6.1 Consensus size: 46
1028331 GTTGATTATG
* * * *
1028341 ATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGATGTC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
* *
1028387 ATAATTAAAATGCATGAAAAGATTCATTAAGGCATG-AA--A-GCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
1028429 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
* * *
1028475 AAAACTAAAATGCATGAAAGGATGCCTTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
*
1028521 ATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
* * *
1028567 ATAATTAAAATGCAAGAAATGATGCATTAATGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
1028613 ATAATT
1 ATAATT
1028619 TAAGTGTATA
Statistics
Matches: 212, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
42 36 0.17
43 3 0.01
45 3 0.01
46 170 0.80
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (46 bp):
ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
Found at i:1028416 original size:22 final size:22
Alignment explanation
Indices: 1028390--1028458 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1028380 GGATGTCATA
1028390 ATTAAAATGCATGAAAAGATTC
1 ATTAAAATGCATGAAAAGATTC
* *
1028412 ATT--AAGGCATG-AAAGCCA-TA
1 ATTAAAATGCATGAAAAG--ATTC
* *
1028432 ATTAAAATGCATGAAAGGATGC
1 ATTAAAATGCATGAAAAGATTC
1028454 ATTAA
1 ATTAA
1028459 GGCATGAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 2 0.06
22 15 0.43
23 3 0.09
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (22 bp):
ATTAAAATGCATGAAAAGATTC
Found at i:1028469 original size:20 final size:20
Alignment explanation
Indices: 1028349--1028611 Score: 141
Period size: 20 Copynumber: 11.8 Consensus size: 20
1028339 TGATAACTAA
*
1028349 AATGCATGAAATGATGCATT
1 AATGCATGAAAGGATGCATT
* *
1028369 AAGGCATAAAAGGATGTCATAATT
1 AATGCATGAAAGGATG-C---ATT
* *
1028393 AAAATGCATGAAAAGATTCATT
1 --AATGCATGAAAGGATGCATT
* * *
1028415 AAGGCATGAAAGCCAT-AATT
1 AATGCATGAAAG-GATGCATT
1028435 AAAATGCATGAAAGGATGCATT
1 --AATGCATGAAAGGATGCATT
* *
1028457 AAGGCATGAAAGGATGCCAAAACTAA
1 AATGCATGAAAGGATG-C---A-T-T
*
1028483 AATGCATGAAAGGATGCCTT
1 AATGCATGAAAGGATGCATT
*
1028503 AAGGCATGAAAGGATGCCATAACT
1 AATGCATGAAAGGATG-CAT---T
1028527 AAAATGCATGAAAGGATGCATT
1 --AATGCATGAAAGGATGCATT
*
1028549 AAGGCATGAAAGGATGCCATAATT
1 AATGCATGAAAGGATG-C---ATT
* *
1028573 AAAATGCAAGAAATGATGCATT
1 --AATGCATGAAAGGATGCATT
1028595 AATGCATGAAAGGATGC
1 AATGCATGAAAGGATGC
1028612 CATAATTTAA
Statistics
Matches: 187, Mismatches: 28, Indels: 56
0.69 0.10 0.21
Matches are distributed among these distances:
20 86 0.46
21 10 0.05
22 21 0.11
24 8 0.04
25 7 0.04
26 55 0.29
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AATGCATGAAAGGATGCATT
Found at i:1029216 original size:19 final size:19
Alignment explanation
Indices: 1029179--1029217 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1029169 TTACAAAATA
* * *
1029179 TTAATTAGTCTTTATATTT
1 TTAATTAATCCTTAGATTT
1029198 TTAATTAATCCTTAGATTT
1 TTAATTAATCCTTAGATTT
1029217 T
1 T
1029218 AGGTTCTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (19 bp):
TTAATTAATCCTTAGATTT
Found at i:1029297 original size:18 final size:17
Alignment explanation
Indices: 1029274--1029307 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1029264 AGAAATTAAA
1029274 TAAGTTTAGTATACCTTT
1 TAAGTTTAGTAT-CCTTT
1029292 TAAGTTTAGTATCCTT
1 TAAGTTTAGTATCCTT
1029308 AATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (17 bp):
TAAGTTTAGTATCCTTT
Found at i:1030315 original size:20 final size:20
Alignment explanation
Indices: 1030277--1030315 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1030267 TTTTCATGGG
**
1030277 GGATCGATCCTTTTGAAAAA
1 GGATCGATCCTTTACAAAAA
*
1030297 GGATCGATTCTTTACAAAA
1 GGATCGATCCTTTACAAAA
1030316 TAGAAACTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (20 bp):
GGATCGATCCTTTACAAAAA
Found at i:1031693 original size:2 final size:2
Alignment explanation
Indices: 1031686--1031732 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1031676 TTCACATTCA
1031686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1031728 AT AT A
1 AT AT A
1031733 GATTTTTCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1036356 original size:18 final size:19
Alignment explanation
Indices: 1036323--1036364 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1036313 TTCACATATC
*
1036323 AAAATATAATTATTTTATT
1 AAAATATAAATATTTTATT
1036342 AAAATA-AAATATTTTATT
1 AAAATATAAATATTTTATT
1036360 AAAAT
1 AAAAT
1036365 TATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATATAAATATTTTATT
Found at i:1036362 original size:13 final size:14
Alignment explanation
Indices: 1036330--1036373 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 14
1036320 ATCAAAATAT
1036330 AATTATTTTATTAA
1 AATTATTTTATTAA
1036344 AATAAAATATTTTATTAA
1 AAT----TATTTTATTAA
1036362 AATTATTTTATT
1 AATTATTTTATT
1036374 TTAGTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 12 0.46
18 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATTTTATTAA
Done.