Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005153.1 Hibiscus syriacus cultivar Beakdansim tig00011619_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: 97788
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4217 original size:44 final size:44
Alignment explanation
Indices: 4120--4218 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
4110 GCGTTTGTAA
*
4120 AAACGCCGCAATATACCATACATTTAGCGACATTTGTATACTAG
1 AAACACCGCAATATACCATACATTTAGCGACATTTGTATACTAG
* * *** *
4164 AAACGCCGCAATATACCATACATTTATCGGTGTTTGTATACTAT
1 AAACACCGCAATATACCATACATTTAGCGACATTTGTATACTAG
*
4208 AAATACCGCAA
1 AAACACCGCAA
4219 ATTCTCAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (44 bp):
AAACACCGCAATATACCATACATTTAGCGACATTTGTATACTAG
Found at i:4402 original size:44 final size:43
Alignment explanation
Indices: 4291--4405 Score: 108
Period size: 43 Copynumber: 2.7 Consensus size: 43
4281 ACATTTATGG
* * *
4291 GAAAAACGCCGCAAAATATCAACACCTACTACGGCGTTCGTAA
1 GAAAAACGCCGCTAAACATCAACACCTACTACAGCGTTCGTAA
* * * * * *
4334 GTAAAACGCCTCTAAATC-TTAACACCTACTGCATCGTTTGTTGAA
1 GAAAAACGCCGCTAAA-CATCAACACCTACTACAGCGTTCG-T-AA
4379 -AAAAACGCCGCTAAACATCAACACCTA
1 GAAAAACGCCGCTAAACATCAACACCTA
4406 TTGCGGCATT
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
43 31 0.55
44 23 0.41
45 2 0.04
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (43 bp):
GAAAAACGCCGCTAAACATCAACACCTACTACAGCGTTCGTAA
Found at i:7603 original size:15 final size:17
Alignment explanation
Indices: 7583--7614 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
7573 TGACTTTGAT
7583 ATATTTT-AAT-GAAAG
1 ATATTTTCAATAGAAAG
7598 ATATTTTCAATAGAAAG
1 ATATTTTCAATAGAAAG
7615 TGGTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (17 bp):
ATATTTTCAATAGAAAG
Found at i:12923 original size:9 final size:9
Alignment explanation
Indices: 12894--12931 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
12884 AGGGTAATTG
12894 AAAATTCAAGA
1 AAAATT-AA-A
12905 AAAATT-AA
1 AAAATTAAA
12913 AAAATTAAA
1 AAAATTAAA
12922 AAAATTAAA
1 AAAATTAAA
12931 A
1 A
12932 TCAAAGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 13 0.50
11 6 0.23
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:12924 original size:17 final size:19
Alignment explanation
Indices: 12894--12931 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
12884 AGGGTAATTG
12894 AAAATTCAAGAAAAATTAA
1 AAAATTCAAGAAAAATTAA
12913 AAAATT-AA-AAAAATTAA
1 AAAATTCAAGAAAAATTAA
12930 AA
1 AA
12932 TCAAAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAATTCAAGAAAAATTAA
Found at i:22914 original size:19 final size:19
Alignment explanation
Indices: 22890--22977 Score: 113
Period size: 19 Copynumber: 4.5 Consensus size: 19
22880 TCTACAGTTG
22890 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
22909 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
22928 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
22949 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
22969 TCGTTGCGA
1 TCGTTGCGA
22978 AAATTCGTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 38 0.66
20 5 0.09
21 5 0.09
22 10 0.17
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:30697 original size:39 final size:39
Alignment explanation
Indices: 30641--31375 Score: 885
Period size: 39 Copynumber: 19.1 Consensus size: 39
30631 TTTAATTTTT
* *
30641 TTTTGTTTTGAGCGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
30680 TTTTGTTTCAAGAGAAACTATTTCAAGCGAGATAAAATT
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
*
30719 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
*
30758 TTTTGTTTCGAGGGAGACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* **
30797 TTTTGTTTCGAGGGAGACTATCTCAAGAAAGATAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
30836 TTCTGTTTCGAGGGAAACTAGCTCAAACAAGATAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* *
30875 TTCTGTTTCGAGGGAAA-TGATCTGAAGCGAGATAAAATC
1 TTTTGTTTCGAGGGAAACT-ATCTCAAGCGAGATAAAATC
*
30914 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * * *
30953 TTATGTTTCGAGGGAAACTATCTTAAGTGAGACAAAACC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* ** *
30992 TTTTATTTCGAGGGAAACTATCTCAAATGAGACAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
*
31031 TTTTGTTTCGAGAGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
*
31070 TTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * *
31109 TTTTGTTTGGAGGGAAATTATCTCAAGCGAGACAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * * *
31148 TTATATTTCAAGGGAAACAAACTCAAGC-------AATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * * *
31180 TTCTATTTCAAGTGAAACTATCTCAAGCGAGATACAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* *
31219 TTTT-TTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
31257 TTTTGTTTCAAGGGAAATTATATCAAGCGAGACAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * * *
31296 TTCTGTTTCAACGGAAACTATCTCAAGAGAGACAAAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
31335 TTTTGTTTCAAGGAAAACTATCTCAAACGAGATACAATC
1 TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
31374 TT
1 TT
31376 CTTTAAAAAC
Statistics
Matches: 611, Mismatches: 75, Indels: 20
0.87 0.11 0.03
Matches are distributed among these distances:
32 28 0.05
38 36 0.06
39 546 0.89
40 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (39 bp):
TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
Found at i:31187 original size:32 final size:32
Alignment explanation
Indices: 31144--31207 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
31134 AGCGAGACAA
31144 AATCTTATATTTCAAGGGAAACAAACTCAAGC
1 AATCTTATATTTCAAGGGAAACAAACTCAAGC
* * * *
31176 AATCTTCTATTTCAAGTGAAACTATCTCAAGC
1 AATCTTATATTTCAAGGGAAACAAACTCAAGC
31208 GAGATACAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (32 bp):
AATCTTATATTTCAAGGGAAACAAACTCAAGC
Found at i:31473 original size:76 final size:76
Alignment explanation
Indices: 31380--31709 Score: 355
Period size: 76 Copynumber: 4.3 Consensus size: 76
31370 AATCTTCTTT
* * **
31380 AAAAACAATCTTGAGTGAAATGAAA-AGTCTTCTTTCGAGTAAAAACTGTGTCAAGCGAGACAAA
1 AAAAACAATCTTGAGTGAAAT-AAATCGTCTTGTTTCGAGTAAAAACTGTCCCAAGCGAGACAAA
*
31444 TCTTGTTTTATA-
65 TCTTATTTTA-AG
* * * * *
31456 AAAAACAATATTAAGTGAAATAAATCTTCTTGTTTTGAGTAAAAATTGTCCCAAGCGAGACAAAT
1 AAAAACAATCTTGAGTGAAATAAATCGTCTTGTTTCGAGTAAAAACTGTCCCAAGCGAGACAAAT
*
31521 CTTTTTTTTTAAG
66 C--TTATTTTAAG
* * *
31534 AAAAACAATCTTGAGTGAAATAAATCTTCTTGTTTTGAGTAAAAACTGTCCCAAACGAGACAAAT
1 AAAAACAATCTTGAGTGAAATAAATCGTCTTGTTTCGAGTAAAAACTGTCCCAAGCGAGACAAAT
*
31599 CTTCTTTTAAG
66 CTTATTTTAAG
* * * * * * *
31610 AAAAACAATCTTGAGTCAAATGAAT-GTCTTATTTCAAAT-AAAACTGTCTCAAGTGAGACAAAG
1 AAAAACAATCTTGAGTGAAATAAATCGTCTTGTTTCGAGTAAAAACTGTCCCAAGCGAGACAAA-
31673 TC-TATTTTAAG
65 TCTTATTTTAAG
** *
31684 AAAAACAATCTCAAGTGAGATAAATC
1 AAAAACAATCTTGAGTGAAATAAATC
31710 CCCTGTATTA
Statistics
Matches: 217, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
74 48 0.22
75 14 0.06
76 85 0.39
77 1 0.00
78 69 0.32
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (76 bp):
AAAAACAATCTTGAGTGAAATAAATCGTCTTGTTTCGAGTAAAAACTGTCCCAAGCGAGACAAAT
CTTATTTTAAG
Found at i:31521 original size:40 final size:40
Alignment explanation
Indices: 31477--31604 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 40
31467 TAAGTGAAAT
*
31477 AAATCTTCTTGTTTTGAGTAAAAATTGTCCCAAGCGAGAC
1 AAATCTTCTTGTTTTGAGTAAAAACTGTCCCAAGCGAGAC
* * ** *** * * *
31517 AAATCTT-TTTTTTTAAG-AAAAACAATCTTGAGTGAAAT
1 AAATCTTCTTGTTTTGAGTAAAAACTGTCCCAAGCGAGAC
*
31555 AAATCTTCTTGTTTTGAGTAAAAACTGTCCCAAACGAGAC
1 AAATCTTCTTGTTTTGAGTAAAAACTGTCCCAAGCGAGAC
31595 AAATCTTCTT
1 AAATCTTCTT
31605 TTAAGAAAAA
Statistics
Matches: 64, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
38 19 0.30
39 16 0.25
40 29 0.45
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (40 bp):
AAATCTTCTTGTTTTGAGTAAAAACTGTCCCAAGCGAGAC
Found at i:45651 original size:19 final size:20
Alignment explanation
Indices: 45623--45661 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
45613 TTTTTTATGT
*
45623 TTTTTTCTCCT-ATTTTTTC
1 TTTTTCCTCCTCATTTTTTC
45642 TTTTTCCTCCTCATTTTTTC
1 TTTTTCCTCCTCATTTTTTC
45662 AGTCTGGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTCCTCCTCATTTTTTC
Found at i:50523 original size:25 final size:25
Alignment explanation
Indices: 50495--50543 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
50485 TAGGCCAATT
50495 AATAAACGCATGAATCACAAGAAAA
1 AATAAACGCATGAATCACAAGAAAA
50520 AATAAACGCATGAATCACAAGAAA
1 AATAAACGCATGAATCACAAGAAA
50544 TACATAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (25 bp):
AATAAACGCATGAATCACAAGAAAA
Found at i:53115 original size:37 final size:38
Alignment explanation
Indices: 53074--53151 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
53064 AATAAAATTA
*
53074 TTTTAA-T-AAAATTAAATGTAAGTGTTTAATGTGTTCT
1 TTTTAAGTCAAAA-TAAATGAAAGTGTTTAATGTGTTCT
**
53111 TTTTAAGTCTTAATAAATGAAAGTGTTTAATGTGTTCT
1 TTTTAAGTCAAAATAAATGAAAGTGTTTAATGTGTTCT
53149 TTT
1 TTT
53152 ATTTTATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 6 0.17
38 28 0.78
39 2 0.06
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.50
Consensus pattern (38 bp):
TTTTAAGTCAAAATAAATGAAAGTGTTTAATGTGTTCT
Found at i:56147 original size:35 final size:35
Alignment explanation
Indices: 56084--56183 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
56074 TTTCGTCCTA
*
56084 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
56121 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
56156 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
56184 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:56665 original size:2 final size:2
Alignment explanation
Indices: 56660--56705 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
56650 TAAAGTTATC
56660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
56702 AT AT
1 AT AT
56706 TTATTATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56730 original size:25 final size:24
Alignment explanation
Indices: 56701--56779 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
56691 TATATACTAT
56701 TATATTTATTATTTTACTATTAACG
1 TATA-TTATTATTTTACTATTAACG
* * * * **
56726 TATATAAATATTTTTCTCTT-TTG
1 TATATTATTATTTTACTATTAACG
56749 CTACTATTATTATTTTACTATTAACG
1 -TA-TATTATTATTTTACTATTAACG
56775 TATAT
1 TATAT
56780 AAATATGTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 7
0.67 0.21 0.12
Matches are distributed among these distances:
23 1 0.03
24 17 0.44
25 20 0.51
26 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.56
Consensus pattern (24 bp):
TATATTATTATTTTACTATTAACG
Found at i:56759 original size:49 final size:50
Alignment explanation
Indices: 56706--56812 Score: 198
Period size: 49 Copynumber: 2.1 Consensus size: 50
56696 ACTATTATAT
56706 TTATTATTTTACTATTAACGTATATAAATA-TTTTTCTCTTTTGCTACTA
1 TTATTATTTTACTATTAACGTATATAAATAGTTTTTCTCTTTTGCTACTA
56755 TTATTATTTTACTATTAACGTATATAAATATGTTTTTCTCTTTTGCTACTA
1 TTATTATTTTACTATTAACGTATATAAATA-GTTTTTCTCTTTTGCTACTA
56806 TTATTAT
1 TTATTAT
56813 CATTATATGT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
49 30 0.54
51 26 0.46
ACGTcount: A:0.28, C:0.11, G:0.05, T:0.56
Consensus pattern (50 bp):
TTATTATTTTACTATTAACGTATATAAATAGTTTTTCTCTTTTGCTACTA
Found at i:56960 original size:16 final size:16
Alignment explanation
Indices: 56939--56972 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56929 CATGTATTTA
56939 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
56955 TATTATTTTACTTTAT
1 TATTATATTACATTAT
56971 TA
1 TA
56973 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:56977 original size:21 final size:22
Alignment explanation
Indices: 56953--57002 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
56943 ATATTACATT
*
56953 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
*
56974 ATTATT-TTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
56995 TTTATTAT
1 ATTATTAT
57003 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.46
21 12 0.50
22 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:57001 original size:9 final size:9
Alignment explanation
Indices: 56988--57021 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
56978 TTTTTTTCGT
*
56988 TATTATATT
1 TATTATATA
56997 TATTATATA
1 TATTATATA
57006 TA-TATATA
1 TATTATATA
57014 TATTATAT
1 TATTATAT
57022 CATAATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:60357 original size:18 final size:18
Alignment explanation
Indices: 60334--60373 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
60324 GGGCAAAAAG
60334 AAAAAA-GAAAAGAAGCAA
1 AAAAAAGGAAAA-AAGCAA
*
60352 AAAAAAGGAAAAAAGGAA
1 AAAAAAGGAAAAAAGCAA
60370 AAAA
1 AAAA
60374 CACAAGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAGGAAAAAAGCAA
Found at i:60386 original size:15 final size:14
Alignment explanation
Indices: 60368--60401 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
60358 GGAAAAAAGG
60368 AAAAAACACAAGAAC
1 AAAAAACA-AAGAAC
*
60383 AAAAAAGAAAGAAC
1 AAAAAACAAAGAAC
60397 AAAAA
1 AAAAA
60402 TAAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAGAAC
Found at i:61049 original size:22 final size:22
Alignment explanation
Indices: 61021--61071 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
61011 CCCCATCAAT
61021 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
61043 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
61065 CCTTTGA
1 CCTTTGA
61072 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:61981 original size:36 final size:36
Alignment explanation
Indices: 61935--62035 Score: 157
Period size: 37 Copynumber: 2.8 Consensus size: 36
61925 TCACCATTGC
61935 CTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGT
1 CTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGT
* *
61971 CTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTT
1 CTCTCTTGAGACAGTTTCCCTTGAAAC-AAACTTTGT
* *
62008 CTCCCTTGAGACAGTTTCTCTTGAAACA
1 CTCTCTTGAGACAGTTTCCCTTGAAACA
62036 TAAACATTGA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 28 0.47
37 32 0.53
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.37
Consensus pattern (36 bp):
CTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGT
Found at i:62125 original size:102 final size:102
Alignment explanation
Indices: 61949--62406 Score: 772
Period size: 102 Copynumber: 4.5 Consensus size: 102
61939 CTTGAGACAG
** * * *
61949 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
62014 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *** *
62051 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCATCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
62116 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
62153 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
62218 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
62255 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAAAAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
62320 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
** *
62357 TTTCCCTTGAAATGAATTTCATCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
62407 TAAACATTGA
Statistics
Matches: 333, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 333 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:62220 original size:37 final size:37
Alignment explanation
Indices: 62153--62239 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
62143 ATTGGAAACA
** * *
62153 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
62189 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
62226 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
62240 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:62396 original size:65 final size:65
Alignment explanation
Indices: 62313--62471 Score: 291
Period size: 65 Copynumber: 2.4 Consensus size: 65
62303 AAAAATTTTG
*
62313 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
* *
62378 TCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG
1 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
62443 TCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACA
62472 AAATTTTGTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 90 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (65 bp):
TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
Found at i:63237 original size:160 final size:160
Alignment explanation
Indices: 62973--63309 Score: 602
Period size: 160 Copynumber: 2.1 Consensus size: 160
62963 CAACACAAGT
*
62973 TCAACTTCACAACGAAGGGACGACTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1 TCAACTTCACAACGAAGAGACGACTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
63038 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
66 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
*
63103 GACTGTCAACAAACAATTTCGGAGCCAATC
131 GACTGTCAACAAACAATTTCGGAGCCAAAC
*
63133 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1 TCAACTTCACAACGAAGAGACGACTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
* *
63198 ACTTTACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
66 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
* *
63263 GACTGTCGACAAGCAATTTCGGAGCCAAAC
131 GACTGTCAACAAACAATTTCGGAGCCAAAC
*
63293 TCAACTTCACAGCGAAG
1 TCAACTTCACAACGAAG
63310 GATATTGGAC
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
160 169 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (160 bp):
TCAACTTCACAACGAAGAGACGACTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
GACTGTCAACAAACAATTTCGGAGCCAAAC
Found at i:63462 original size:106 final size:104
Alignment explanation
Indices: 63133--63634 Score: 513
Period size: 106 Copynumber: 4.9 Consensus size: 104
63123 GGAGCCAATC
* * * * * *
63133 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATA-ATTTCCCAGTTTCAGGGCCAATTTT
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA-ACATTT-TCAATTTCAGAGCCAATTTC
* * * * *
63197 AACTTTACAGCGAAGGATATTGGACCCAAGACAGCACAAGC
64 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * * * **
63238 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCGAC--A-A---GCAATTTCGGAGCCAAACTCAA
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACATTTTCAATTTCAGAGCCAATTTCAA
63297 CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
66 CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
*
63336 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTC
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACA-TTTTC-AATTTCAGAGCCAATTTC
* *
63401 AACTCCGCAGCGAAGGATATTGGACTCGAGACAACACAAGT
64 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * * *
63442 TCAACTTCACAATGAAGGGACGGTTGATTGTCAAC-AAGA-TTTC--GTTCAGAGTCAATTTCAT
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACATTTTCAATTTCAGAGCCAATTTCAA
* * *
63503 CTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGC
66 CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * * * * *
63542 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAATAATTTCCCAGTTCCAGAACCAATTTC
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-CATTT-TCAATTTCAGAGCCAATTTC
*
63607 AACTTCACAGCGGAGGATATTGGACTCG
64 AACTTCACAGCGAAGGATATTGGACTCG
63635 GAACAATATT
Statistics
Matches: 328, Mismatches: 55, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
98 79 0.24
100 80 0.24
101 3 0.01
102 3 0.01
103 6 0.02
104 1 0.00
105 33 0.10
106 123 0.38
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (104 bp):
TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACATTTTCAATTTCAGAGCCAATTTCAA
CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
Found at i:63548 original size:206 final size:201
Alignment explanation
Indices: 63132--63634 Score: 612
Period size: 206 Copynumber: 2.5 Consensus size: 201
63122 CGGAGCCAAT
* * *
63132 CTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTT
1 CTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAA-AATTTCCCAGTTTCAGAGCCAATTTC
* * * * * *
63197 AACTTTACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGC
65 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGC
* *
63262 TGACTGTCGACAAGCAATTTCGGAGCCAAACTCAACTTCACAGCGAAGGATATTGGACTCGAGAC
130 TGACTGTCAACAAG-AATTTCGGAGCCAAACTCAACTTCACAGCGAAGGATATTAGACTCGAGAC
63327 AACACAAG
194 AACACAAG
* * * *
63335 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTT
1 CTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-A-TTTCCCAGTTTCAGAGCCAATTT
* * * *
63400 CAACTCCGCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGG
64 CAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGG
* * * ** *
63465 TTGATTGTCAACAAG-ATTTCGTTCAGAGTCAATTTCATCTTCACAGCGAAGGATATTAGACTCG
129 CTGACTGTCAACAAGAATTTCG----GAGCCAAACTCAACTTCACAGCGAAGGATATTAGACTCG
*
63529 AGACAGCACAAG
190 AGACAACACAAG
* * ** * *
63541 CTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAATAATTTCCCAGTTCCAGAACCAATTT
1 CTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AA-AATTTCCCAGTTTCAGAGCCAATTT
*
63606 CAACTTCACAGCGGAGGATATTGGACTCG
64 CAACTTCACAGCGAAGGATATTGGACTCG
63635 GAACAATATT
Statistics
Matches: 253, Mismatches: 39, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
202 7 0.03
203 37 0.15
204 85 0.34
206 120 0.47
207 3 0.01
208 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (201 bp):
CTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAATTTCCCAGTTTCAGAGCCAATTTCA
ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCT
GACTGTCAACAAGAATTTCGGAGCCAAACTCAACTTCACAGCGAAGGATATTAGACTCGAGACAA
CACAAG
Found at i:64158 original size:35 final size:35
Alignment explanation
Indices: 64095--64194 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
64085 TTTCGTCCTA
*
64095 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
64132 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
64167 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
64195 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:64765 original size:51 final size:51
Alignment explanation
Indices: 64710--64820 Score: 213
Period size: 51 Copynumber: 2.2 Consensus size: 51
64700 CTATTATATT
64710 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
*
64761 TATTATTATTTTACTATTAACGTATATAAATATGTTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
64812 TATTATTAT
1 TATTATTAT
64821 CATTATATGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.56
Consensus pattern (51 bp):
TATTATTATTTTACTATTAACGTATATAAATATATTTTTCTCTTTTGCTAC
Found at i:64970 original size:16 final size:16
Alignment explanation
Indices: 64949--64982 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
64939 CATGTATTTA
64949 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
64965 TATTATTTTACTTTAT
1 TATTATATTACATTAT
64981 TA
1 TA
64983 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:64987 original size:21 final size:22
Alignment explanation
Indices: 64963--65012 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
64953 ATATTACATT
*
64963 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
*
64984 ATTATT-TTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
65005 TTTATTAT
1 ATTATTAT
65013 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.46
21 12 0.50
22 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:80092 original size:18 final size:17
Alignment explanation
Indices: 80059--80092 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
80049 TCAATTGAAA
*
80059 AAAAAATCCATGATAAT
1 AAAAAATCCATAATAAT
80076 AAAAAATCCATCAATAA
1 AAAAAATCCAT-AATAA
80093 AATGAATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAAATCCATAATAAT
Found at i:81540 original size:166 final size:164
Alignment explanation
Indices: 81261--81587 Score: 465
Period size: 166 Copynumber: 2.0 Consensus size: 164
81251 TATGAAAAGA
* * *
81261 TTGTAAATATGTTACCTGGAATTCTAGCTACTGAAACTTATCTCAAAATCAACCAATGGTTAATT
1 TTGTAAATATGATACCTGAAATTCTAGCTACTGAAACTTATCTCAAAATCAACCAACGGTTAATT
* * * * * *
81326 TTCCCTTTTCCTAGATTTAGAGCTTTTCCCCAATTCCTTTTCTAAATTAAATCAAGAATATGAAT
66 TTCCCTTTCCCTAGATTTAGAGCTTTCCCCCAATTCCTTTTATAAATTAAAGCAAGAAGATAAAT
*
81391 TATTAACCTATATAGGGGTTAGATTAGAGTTATGG
131 TATTAACCTAT-TAGGGCTTAGATTAGAGTTATGG
* * * *
81426 TTGTAAATGTGATACCTGTAAATTCTAGCTATTGAGACTTATCTTAAAATCAACCAACGGTTAAT
1 TTGTAAATATGATACCTG-AAATTCTAGCTACTGAAACTTATCTCAAAATCAACCAACGGTTAAT
** * *
81491 TTTTTCTTTCCCTAGCTTTAGAGCTTTCCCCCACTTCCTTTTATAAATTAAAGCAAGAAGATAAA
65 TTTCCCTTTCCCTAGATTTAGAGCTTTCCCCCAATTCCTTTTATAAATTAAAGCAAGAAGATAAA
*
81556 TTATTAACCTATTAGGGCTTATATTAGAGTTA
130 TTATTAACCTATTAGGGCTTAGATTAGAGTTA
81588 AGAACACTCT
Statistics
Matches: 142, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
165 34 0.24
166 108 0.76
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (164 bp):
TTGTAAATATGATACCTGAAATTCTAGCTACTGAAACTTATCTCAAAATCAACCAACGGTTAATT
TTCCCTTTCCCTAGATTTAGAGCTTTCCCCCAATTCCTTTTATAAATTAAAGCAAGAAGATAAAT
TATTAACCTATTAGGGCTTAGATTAGAGTTATGG
Found at i:83245 original size:51 final size:51
Alignment explanation
Indices: 83176--83288 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 51
83166 TGAAAAATAA
* * * * *
83176 AAAATAATAATAACCTAAAGATGATGTAGT-AATTATATCTTAATTTCTAAT
1 AAAATAATAATAAACTAAAGATAATATAGTAAAATA-ATCTTAATTCCTAAT
**
83227 AAAATAATAATAAACTAAAGATAATATTTTAAAATCAATCTTAATTCCTAAT
1 AAAATAATAATAAACTAAAGATAATATAGTAAAAT-AATCTTAATTCCTAAT
83279 AAAATAATAA
1 AAAATAATAA
83289 ATCTAATCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 25 0.47
52 27 0.51
53 1 0.02
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (51 bp):
AAAATAATAATAAACTAAAGATAATATAGTAAAATAATCTTAATTCCTAAT
Found at i:87850 original size:52 final size:51
Alignment explanation
Indices: 87754--87866 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
87744 CTAGTAAATA
* * *
87754 AAAATAATAATAAACTAAAGATAATATTGTGATCCTATCCTAATTTCTAAT
1 AAAATAATAATAAACCAAAGACAATATTGTGAACCTATCCTAATTTCTAAT
* * * *
87805 AAAATAATAATAAACCAAAGACAATGTTTTTAACTCTATCTTAATTTCTAAT
1 AAAATAATAATAAACCAAAGACAATATTGTGAAC-CTATCCTAATTTCTAAT
87857 AAAATAATAA
1 AAAATAATAA
87867 ATCTAATCCT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 28 0.52
52 26 0.48
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.35
Consensus pattern (51 bp):
AAAATAATAATAAACCAAAGACAATATTGTGAACCTATCCTAATTTCTAAT
Found at i:88365 original size:9 final size:9
Alignment explanation
Indices: 88344--88376 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
88334 TATGCAGTTT
88344 TGTTGTT-A
1 TGTTGTTCA
88352 TGTTGTTCA
1 TGTTGTTCA
88361 TGTTGTTCA
1 TGTTGTTCA
88370 TGTTGTT
1 TGTTGTT
88377 TTTCTTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.09, C:0.06, G:0.24, T:0.61
Consensus pattern (9 bp):
TGTTGTTCA
Found at i:89028 original size:60 final size:59
Alignment explanation
Indices: 88963--89149 Score: 189
Period size: 60 Copynumber: 3.1 Consensus size: 59
88953 ATGCATCATA
88963 CATCCTTAATA-TATGATTCTCATTTTAAATTAGTCCCTAAACTTTTAAATATTTCAATTT
1 CATCCTTAA-ACTATGATT-TCATTTTAAATTAGTCCCTAAACTTTTAAATATTTCAATTT
* * * *
89023 CATCCTTAAACTATGACTATCATTTTAAATTAGT-CCTCAAAGTTTTAAACATTTCATTTT
1 CATCCTTAAACTATGA-TTTCATTTTAAATTAGTCCCT-AAACTTTTAAATATTTCAATTT
** * * * * * *
89083 CATCCCCAAACTATAATGTTCATTCTAAATTAGTCCCCAAAATTTTTGAATATTTTAATTT
1 CATCCTTAAACTATGAT-TTCATTTTAAATTAGT-CCCTAAACTTTTAAATATTTCAATTT
*
89144 TATCCT
1 CATCCT
89150 AAATTATACG
Statistics
Matches: 104, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
59 5 0.05
60 75 0.72
61 22 0.21
62 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (59 bp):
CATCCTTAAACTATGATTTCATTTTAAATTAGTCCCTAAACTTTTAAATATTTCAATTT
Found at i:92658 original size:3 final size:3
Alignment explanation
Indices: 92650--92698 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
92640 GGCCCGTTTG
** *
92650 TAA TAA TAA TTT TAA TAA TAA TAA -AA AAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
92697 TA
1 TA
92699 GAAAATGGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:92691 original size:26 final size:26
Alignment explanation
Indices: 92651--92703 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
92641 GCCCGTTTGT
**
92651 AATAATAATTTTAATAATAATAAAAA
1 AATAATAATAATAATAATAATAAAAA
*
92677 AATAATAATAATAATAATAATAGAAA
1 AATAATAATAATAATAATAATAAAAA
92703 A
1 A
92704 TGGGAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
AATAATAATAATAATAATAATAAAAA
Found at i:93255 original size:116 final size:114
Alignment explanation
Indices: 93050--94239 Score: 845
Period size: 113 Copynumber: 10.6 Consensus size: 114
93040 AGAGTTATGT
*
93050 AAAAGGTTGAACAAGA-TCTTCTCATTGTGAA--CTTC-TTCTTCTTCAGAT--GAGTTCTTCTC
1 AAAAGGTTGAACAA-ATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTC
* * ** *
93109 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGC
65 ATTATGAACTTACTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
93159 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGA-GAGTTCTTCT
* * *
93224 CATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
64 CATTATGAACT-TACTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
* * * * *
93275 AAAAGGTTGAAAAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAAAT--GAGTTCTTCTA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTC
* * * * * *** **
93338 ATTAAGAATTTTCTCTGGGAAAGTTGATGTTGATCTATCTTCTTCTGTGATAGAATT-ATGC
65 ATTATGAACTTACTCT-GGAAA----A-GCTGATC---CATC--AAATGAT-GAATTCAAAC
* ** *
93399 AAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGAT--GAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTC
* * * *
93461 ----T--A--TA---TGGTAATGTTGATCCAT-AGAATGATGAATTCAAGC
65 ATTATGAACTTACTCTGGAAAAGCTGATCCATCA-AATGATGAATTCAAAC
* * *
93500 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTT-ATTCTTTCTTCAGAT--GAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTC-TTCTTCAGATGAGAGTTCTTCT
* * * * ** * *
93562 CGTTATGAACTCGAC-CTGGTAATGCTGATCCATTGAATCATGAATTCAAGC
64 CATTATGAACT-TACTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
* * *
93613 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT--GAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTC
* * *
93676 ----T--A--TA---TGGAAATGTTGATCCAT-AGAATGATGAATTCAAGC
65 ATTATGAACTTACTCTGGAAAAGCTGATCCATCA-AATGATGAATTCAAAC
* *
93715 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTTCTTCAGAT--GAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTC-TTCTTCAGATGAGAGTTCTTCT
* * * * ** * *
93777 CATTATGAACTCGAC-CTGGTAATGATGATCCATTGAATCATGAATTCAAGC
64 CATTATGAACT-TACTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
* * *
93828 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT--GAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTC
* ** * * * * * * *
93891 ATTATGAACTCAAACTGGAAATGTTGATCCACCGAGTGATGAATTTAAGC
65 ATTATGAACTTACTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
* * * *
93941 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAAT--GAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTC
* * * ** * *
94004 ATTATGAACTCGAC-CTGGTAATGCTGATCCATTGAATCATGAATTCAAGC
65 ATTATGAACT-TACTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
* *
94054 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGAT--GAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTC
** * * ** *
94117 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC
65 ATTATGAACTTACTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
* * *
94167 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT--GAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTC
94230 ATTATGAACT
65 ATTATGAACT
94240 CTTACTGGAA
Statistics
Matches: 921, Mismatches: 103, Indels: 110
0.81 0.09 0.10
Matches are distributed among these distances:
100 7 0.01
101 45 0.05
102 107 0.12
103 2 0.00
104 1 0.00
106 9 0.01
107 1 0.00
108 3 0.00
109 29 0.03
111 6 0.01
112 8 0.01
113 517 0.56
114 9 0.01
115 1 0.00
116 97 0.11
117 3 0.00
119 7 0.01
122 3 0.00
123 16 0.02
124 45 0.05
125 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (114 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGAGTTCTTCTCA
TTATGAACTTACTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
Found at i:93712 original size:215 final size:218
Alignment explanation
Indices: 93397--94240 Score: 1272
Period size: 226 Copynumber: 3.8 Consensus size: 218
93387 ATAGAATTAT
* * *
93397 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
93461 -TAT-A-TGGTAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
66 ATATAATTGGAAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
* * *
93523 ATTATGAACTTCTTATTCTTTCTTCAGATGAGTTCTTCTCGTTATGAACTCGACCTGGTAATGCT
131 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCT
93588 GATCCATTGAATCATGAATTCAA
196 GATCCATTGAATCATGAATTCAA
93611 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
93676 -TAT-A-TGGAAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
66 ATATAATTGGAAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
* *
93738 ATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGAT
131 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCT
93803 GATCCATTGAATCATGAATTCAA
196 GATCCATTGAATCATGAATTCAA
93826 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * *
93891 ATTATGAACTCAAACTGGAAATGTTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAG
66 A-TAT-AA-T-----TGGAAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAG
*
93956 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTG
123 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
94021 GTAATGCTGATCCATTGAATCATGAATTCAA
188 GTAATGCTGATCCATTGAATCATGAATTCAA
* * *
94052 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * **
94117 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCA-AGTGATGGATTTGAGCAAAAAGTTGAACAA
66 A-TAT-AA-----T-TGGAAATGTTGATCCAT-AGAATGATGAATTCAAGCAAAAAGTTGAACAA
94181 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
122 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
94241 TTACTGGAAA
Statistics
Matches: 588, Mismatches: 25, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
214 43 0.07
215 229 0.39
217 3 0.01
219 1 0.00
226 311 0.53
230 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (218 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATATAATTGGAAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCT
GATCCATTGAATCATGAATTCAA
Found at i:93887 original size:113 final size:113
Alignment explanation
Indices: 93680--94270 Score: 862
Period size: 113 Copynumber: 5.2 Consensus size: 113
93670 CTTCTCTATA
* *
93680 TGGAAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
1 TGGAAATGCTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
*
93745 ACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
66 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
* * *
93793 TGGTAATGATGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
1 TGGAAATGCTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
* *
93858 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAAC
66 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
* ** * *
93906 TGGAAATGTTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
1 TGGAAATGCTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
*
93971 ACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACC
66 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
* * * *
94019 TGGTAATGCTGATCCATTGAATCATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
1 TGGAAATGCTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
* ****
94084 ACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTC
66 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
* * * **
94132 TGGAAAAGCTGATCCA-TCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
1 TGGAAATGCTGATCCATTGAA-TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
*
94196 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTA-C
65 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-GACC
* * *
94245 TGGAAATGTTGTTCCATTAAATGATG
1 TGGAAATGCTGATCCATTGAATGATG
94271 GATTTTAATC
Statistics
Matches: 427, Mismatches: 48, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
112 3 0.01
113 420 0.98
114 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
TGGAAATGCTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
Found at i:95129 original size:114 final size:114
Alignment explanation
Indices: 94963--95414 Score: 717
Period size: 114 Copynumber: 4.0 Consensus size: 114
94953 GATCATGCAG
* * * * * * * * * *
94963 TTCATCTTTCAATTCCAATGATGGGTTCTGTGGTTCCTACCGAACCAGATCAGATGACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
* * *
95028 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAT
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAT
*
95077 TTCATCTTTCAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
*
95142 ACACTTCCAGAAGATGGTATTGGGTCTTCGTATTCCTACTATGAGCAAAT
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGC-AAT
*
95192 TT-ATCTTTCAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
*
95256 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAT
*
95305 TTCATCTTTTAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
*
95370 ACACTTCCAGAAGATGCTATTGGGTTTTCGTATTCCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAG
95415 AAAGTAAAAC
Statistics
Matches: 316, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
113 4 0.01
114 307 0.97
115 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAT
Found at i:96119 original size:7 final size:7
Alignment explanation
Indices: 96107--96186 Score: 98
Period size: 7 Copynumber: 12.0 Consensus size: 7
96097 TCTTGACCCC
96107 CTTTTTT
1 CTTTTTT
96114 CTTTTTT
1 CTTTTTT
96121 CTTTTCTT
1 CTTTT-TT
96129 -TTTTTT
1 CTTTTTT
*
96135 TTTTTTT
1 CTTTTTT
96142 CTTTTTT
1 CTTTTTT
96149 CTTTTTT
1 CTTTTTT
96156 C-TTTTT
1 CTTTTTT
96162 C-TTTTT
1 CTTTTTT
96168 C--TTTT
1 CTTTTTT
*
96173 CTTTCTT
1 CTTTTTT
96180 CTTTTTT
1 CTTTTTT
96187 TGTTCTTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
5 5 0.08
6 14 0.21
7 45 0.68
8 2 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:96146 original size:35 final size:38
Alignment explanation
Indices: 96107--96186 Score: 130
Period size: 35 Copynumber: 2.2 Consensus size: 38
96097 TCTTGACCCC
*
96107 CTTTTTTCTTTTTTC-TTTTCTTTTT-TTTT-TTTTTT
1 CTTTTTTCTTTTTTCTTTTTCTTTTTCTTTTCTTTCTT
96142 CTTTTTTCTTTTTTCTTTTTCTTTTTCTTTTCTTTCTT
1 CTTTTTTCTTTTTTCTTTTTCTTTTTCTTTTCTTTCTT
96180 CTTTTTT
1 CTTTTTT
96187 TGTTCTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 15 0.37
36 10 0.24
37 4 0.10
38 12 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (38 bp):
CTTTTTTCTTTTTTCTTTTTCTTTTTCTTTTCTTTCTT
Found at i:96168 original size:42 final size:42
Alignment explanation
Indices: 96107--96196 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 42
96097 TCTTGACCCC
* * *
96107 CTTTTTTCTTTTTTCTTTTCTTTT-TTTTTTTTTTTCTTTTTT
1 CTTTTTTCTTTTTTCTTTTCTTTTCTTTCTTCTTTT-TTTGTT
96149 CTTTTTTC-TTTTTCTTTTTCTTTTCTTTCTTCTTTTTTTGTT
1 CTTTTTTCTTTTTTC-TTTTCTTTTCTTTCTTCTTTTTTTGTT
96191 CTTTTT
1 CTTTTT
96197 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 6 0.14
42 28 0.65
43 9 0.21
ACGTcount: A:0.00, C:0.14, G:0.01, T:0.84
Consensus pattern (42 bp):
CTTTTTTCTTTTTTCTTTTCTTTTCTTTCTTCTTTTTTTGTT
Found at i:96193 original size:35 final size:33
Alignment explanation
Indices: 96109--96199 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 33
96099 TTGACCCCCT
*
96109 TTTTTCTTTTTTCTTTTCTTTTT-TTTTTTTTTTC
1 TTTTTC-TTTTT-TTTTCTTTTTCTTTTTCTTTTC
*
96143 -TTTT-TTCTTTTTTCTTTTTCTTTTTCTTTTC
1 TTTTTCTTTTTTTTTCTTTTTCTTTTTCTTTTC
96174 TTTCTTCTTTTTTTGTTCTTTTTCTT
1 TTT-TTCTTTTTTT-TTCTTTTTCTT
96200 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
30 10 0.20
31 14 0.29
32 2 0.04
33 6 0.12
34 6 0.12
35 11 0.22
ACGTcount: A:0.00, C:0.14, G:0.01, T:0.85
Consensus pattern (33 bp):
TTTTTCTTTTTTTTTCTTTTTCTTTTTCTTTTC
Found at i:96196 original size:1 final size:1
Alignment explanation
Indices: 96108--96187 Score: 61
Period size: 1 Copynumber: 80.0 Consensus size: 1
96098 CTTGACCCCC
* * * * * * * *
96108 TTTTTTCTTTTTTCTTTTCTTTTTTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTCTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
96173 CTTTCTTCTTTTTTT
1 TTTTTTTTTTTTTTT
96188 GTTCTTTTTC
Statistics
Matches: 57, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Done.