Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009576.1 Corchorus capsularis cultivar CVL-1 contig09597, 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: 104508
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:347 original size:21 final size:20
Alignment explanation
Indices: 307--350 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
297 TTGTTTGGTC
*
307 TGATTATTGATTAATGAAAA
1 TGATTATTGATTAATAAAAA
327 TGATTATTTGATCTAA-AAAAA
1 TGATTA-TTGAT-TAATAAAAA
348 TGA
1 TGA
351 GTGGACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 12 0.57
22 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (20 bp):
TGATTATTGATTAATAAAAA
Found at i:671 original size:163 final size:163
Alignment explanation
Indices: 402--731 Score: 633
Period size: 163 Copynumber: 2.0 Consensus size: 163
392 TTATTAATAA
402 AAAAAAAGTACTAATTATGAACGAAGTGTGTGGCCAAAAAAAAATTATGAACGAAGTGATAATAT
1 AAAAAAAGTACTAATTATGAACGAAGTGTGTGGCCAAAAAAAAATTATGAACGAAGTGATAATAT
*
467 GATAAAAAGATAGAGTGATGTTTTGTTTATCCGTATTCATTATTGCTACACCTTACACAGATTTA
66 GATAAAAAAATAGAGTGATGTTTTGTTTATCCGTATTCATTATTGCTACACCTTACACAGATTTA
*
532 TTTTCTTTTTAATTAAGTTTAGCAATTATGATT
131 TTTTCTTTTTAATTAAGTTTAGCAATTATAATT
565 AAAAAAAGTACTAATTATGAACGAAGTGTGTGGCCAAAAAAAAATTATGAACGAAGTGATAATAT
1 AAAAAAAGTACTAATTATGAACGAAGTGTGTGGCCAAAAAAAAATTATGAACGAAGTGATAATAT
*
630 GATAAAAAAATAGTGTGATGTTTTGTTTATCCGTATTCATTATTGCTACACCTTACACAGATTTA
66 GATAAAAAAATAGAGTGATGTTTTGTTTATCCGTATTCATTATTGCTACACCTTACACAGATTTA
695 TTTTCTTTTTAATTAAGTTTAGCAATTATAATT
131 TTTTCTTTTTAATTAAGTTTAGCAATTATAATT
728 AAAA
1 AAAA
732 GGGATCAAGT
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (163 bp):
AAAAAAAGTACTAATTATGAACGAAGTGTGTGGCCAAAAAAAAATTATGAACGAAGTGATAATAT
GATAAAAAAATAGAGTGATGTTTTGTTTATCCGTATTCATTATTGCTACACCTTACACAGATTTA
TTTTCTTTTTAATTAAGTTTAGCAATTATAATT
Found at i:1435 original size:31 final size:31
Alignment explanation
Indices: 1397--1626 Score: 208
Period size: 31 Copynumber: 7.5 Consensus size: 31
1387 AAAGGCTAAT
*
1397 TGCTCAAATAAGGGCCTAACGTTTGTC-AAAA
1 TGCTCAAATAAGGGCCTAACG-TTATCGAAAA
* * * * **
1428 TGCTCAAATAAGGATCCGATC-TT-T-TAATT
1 TGCTCAAATAAGG-GCCTAACGTTATCGAAAA
1457 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* * * **
1488 TGCTCAAATAAGGGCCCGATC-TT-T-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA
1517 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* *
1548 CGCTCAAATAAGGACCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
* *
1579 CGCTCAAATAAGGACCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
1610 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
1627 GATGTCAATT
Statistics
Matches: 161, Mismatches: 25, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
28 8 0.05
29 30 0.19
30 13 0.08
31 102 0.63
32 8 0.05
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:1494 original size:60 final size:59
Alignment explanation
Indices: 1401--1622 Score: 277
Period size: 60 Copynumber: 3.7 Consensus size: 59
1391 GCTAATTGCT
*
1401 CAAATAAGGGCCTAACGTTTGTC-AAAATGCTCAAATAAGGATCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGA-CCGATCTTTTAATTTGGC
*
1461 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAA-GGACCGATCTTTTAATTTGGC
* * * * ***
1521 CAAATAAGGGCCTAACGTTATCGAAAACGCTCAAATAAGGACCTAACGTTATCGAA-AACGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCGATC-TT-T-TAATTTGGC
*
1582 TCAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGG
1 -CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG
1623 GCCTGATGTC
Statistics
Matches: 144, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
59 10 0.07
60 89 0.62
61 5 0.03
62 40 0.28
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCGATCTTTTAATTTGGC
Found at i:1532 original size:29 final size:29
Alignment explanation
Indices: 1432--1532 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
1422 TCAAAATGCT
**
1432 CAAATAAGGATCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTTAATTTGGC
* * * **
1461 CAAATAAGGG-CCTAACGTTATCGAAAAT-GC
1 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC
1491 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
1521 CAAATAAGGGCC
1 CAAATAAGGGCC
1533 TAACGTTATC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 4 0.07
29 26 0.47
30 6 0.11
31 15 0.27
32 4 0.07
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:1692 original size:31 final size:31
Alignment explanation
Indices: 1656--1756 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 31
1646 CGTGAGACAA
1656 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
** ** **
1687 GCCCTTATTTG-GTCAAATT--CAAATATGGG
1 GCCCTTATTTGAG-CATTTTGGCAAACGTTAG
1716 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
*
1747 GTCCTTATTT
1 GCCCTTATTT
1757 AGCCAAATTA
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
29 21 0.40
30 2 0.04
31 30 0.57
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAG
Found at i:1729 original size:60 final size:60
Alignment explanation
Indices: 1656--1813 Score: 217
Period size: 60 Copynumber: 2.6 Consensus size: 60
1646 CGTGAGACAA
* * * * **
1656 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTCAAATATGGG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCAG
*
1716 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGTCCTTATTTAGCCAAATTAAAAGATCAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCAG
* * * *
1776 ACCTTTATTTGAGCATTTTGACAAACGTTAAGCCCTTA
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTA
1814 CTTGAACAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 86 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCAG
Found at i:13996 original size:19 final size:19
Alignment explanation
Indices: 13962--13998 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13952 TAGCAAAAAA
* *
13962 GAATTTGGATGTTTTGTTT
1 GAATTTGGAGGCTTTGTTT
13981 GAATTTGGAGGCTTTGTT
1 GAATTTGGAGGCTTTGTT
13999 GTTATGTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.03, G:0.30, T:0.51
Consensus pattern (19 bp):
GAATTTGGAGGCTTTGTTT
Found at i:20696 original size:21 final size:21
Alignment explanation
Indices: 20672--20715 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
20662 GGTATCTGGA
20672 TTGCTAAACACCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
* *
20693 TTGCTAAATACCGCCCTCCTT
1 TTGCTAAACACCGCCCCCCTT
20714 TT
1 TT
20716 TACACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.41, G:0.09, T:0.32
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCCTT
Found at i:20997 original size:22 final size:23
Alignment explanation
Indices: 20945--20998 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
20935 AAAATAATTT
*
20945 TTAATTAATTAGTATTTAATTAC
1 TTAATTTATTAGTATTTAATTAC
* *
20968 TTAGTTTATTAGT-TTTAATTAG
1 TTAATTTATTAGTATTTAATTAC
20990 TTAATTTAT
1 TTAATTTAT
20999 GATTAACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
TTAATTTATTAGTATTTAATTAC
Found at i:22843 original size:7 final size:7
Alignment explanation
Indices: 22833--22867 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
22823 AAAACTTATA
22833 TATAAAT
1 TATAAAT
22840 TATAAAT
1 TATAAAT
22847 TATAAAT
1 TATAAAT
22854 TA-AAAT
1 TATAAAT
*
22860 TATTAAT
1 TATAAAT
22867 T
1 T
22868 TTCAGAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TATAAAT
Found at i:22852 original size:14 final size:13
Alignment explanation
Indices: 22833--22867 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
22823 AAAACTTATA
22833 TATAAATTATAAAT
1 TATAAATTA-AAAT
22847 TATAAATTAAAAT
1 TATAAATTAAAAT
*
22860 TATTAATT
1 TATAAATT
22868 TTCAGAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATAAATTAAAAT
Found at i:23988 original size:11 final size:11
Alignment explanation
Indices: 23972--24005 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
23962 CCAACAATTG
23972 GAATCAGAGCC
1 GAATCAGAGCC
*
23983 GAATCAGAGGC
1 GAATCAGAGCC
23994 GAATCAGAGCC
1 GAATCAGAGCC
24005 G
1 G
24006 TATAAGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.32, T:0.09
Consensus pattern (11 bp):
GAATCAGAGCC
Found at i:24259 original size:14 final size:14
Alignment explanation
Indices: 24240--24285 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
24230 CTATACAAAT
24240 TCCTATCTAAATAG
1 TCCTATCTAAATAG
24254 TCCTATAC-AAAT--
1 TCCTAT-CTAAATAG
24266 TCCTATCTAAATAG
1 TCCTATCTAAATAG
24280 TCCTAT
1 TCCTAT
24286 ACAAATTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 1 0.04
12 10 0.36
14 16 0.57
15 1 0.04
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (14 bp):
TCCTATCTAAATAG
Found at i:24265 original size:26 final size:26
Alignment explanation
Indices: 24229--24295 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
24219 GCATCGATAA
24229 CCTATACAAATTCCTATCTAAATAGT
1 CCTATACAAATTCCTATCTAAATAGT
24255 CCTATACAAATTCCTATCTAAATAGT
1 CCTATACAAATTCCTATCTAAATAGT
24281 CCTATACAAATTCCT
1 CCTATACAAATTCCT
24296 TTTCACCACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.34
Consensus pattern (26 bp):
CCTATACAAATTCCTATCTAAATAGT
Found at i:24291 original size:14 final size:12
Alignment explanation
Indices: 24229--24295 Score: 66
Period size: 12 Copynumber: 5.2 Consensus size: 12
24219 GCATCGATAA
24229 CCTATACAAATT
1 CCTATACAAATT
24241 CCTAT-CTAAATAGT
1 CCTATAC-AAAT--T
24255 CCTATACAAATT
1 CCTATACAAATT
24267 CCTAT-CTAAATAGT
1 CCTATAC-AAAT--T
24281 CCTATACAAATT
1 CCTATACAAATT
24293 CCT
1 CCT
24296 TTTCACCACC
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.04
12 23 0.49
14 20 0.43
15 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.34
Consensus pattern (12 bp):
CCTATACAAATT
Found at i:24311 original size:42 final size:41
Alignment explanation
Indices: 24264--24350 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 41
24254 TCCTATACAA
* * *
24264 ATTCCTATCTAAATAGTCCTATACAAATTCCTTTTCACCACC
1 ATTCCTATATAAATAATCCTATACAAATT-CTTTTCACCAAC
24306 ATTCCTATATAAATAATCCTATACAAATTCTTTTCACCAAC
1 ATTCCTATATAAATAATCCTATACAAATTCTTTTCACCAAC
24347 ATTC
1 ATTC
24351 TGTCTGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.36
42 27 0.64
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (41 bp):
ATTCCTATATAAATAATCCTATACAAATTCTTTTCACCAAC
Found at i:27052 original size:27 final size:27
Alignment explanation
Indices: 27021--27084 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
27011 AATAACACAT
*
27021 CAAAGTCCCTAATATTACTAATAAAAA
1 CAAAGTCCCTAAAATTACTAATAAAAA
27048 CAAAGTCCCTAAAATTACTAATAAAAA
1 CAAAGTCCCTAAAATTACTAATAAAAA
27075 CAAAGTCCCT
1 CAAAGTCCCT
27085 TCAAACATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.50, C:0.22, G:0.05, T:0.23
Consensus pattern (27 bp):
CAAAGTCCCTAAAATTACTAATAAAAA
Found at i:27547 original size:27 final size:24
Alignment explanation
Indices: 27516--27567 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 24
27506 ATGTCTTTTT
27516 ATAAAGTTCTACAGTAACTATTTTTCA
1 ATAAAG-T-TACA-TAACTATTTTTCA
*
27543 ATAAAGTTATATAACTATTTTTCA
1 ATAAAGTTACATAACTATTTTTCA
27567 A
1 A
27568 AAAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 14 0.58
25 3 0.12
26 1 0.04
27 6 0.25
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (24 bp):
ATAAAGTTACATAACTATTTTTCA
Found at i:30883 original size:42 final size:42
Alignment explanation
Indices: 30797--30884 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
30787 ACTTATACGA
* *
30797 ATTCCTATATAAATAATCCTATACAGATTCCTTTTCACGTCC
1 ATTCCTATATAAATAATCCTATACAAATTCCTTTTCACGACC
30839 ATTCCTATATAAATAATCCT-TAACAAATTCCTTTTCAAC-ACC
1 ATTCCTATATAAATAATCCTAT-ACAAATTCCTTTTC-ACGACC
30881 ATTC
1 ATTC
30885 TGTTTGTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 1 0.02
42 39 0.93
43 2 0.05
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (42 bp):
ATTCCTATATAAATAATCCTATACAAATTCCTTTTCACGACC
Found at i:37815 original size:17 final size:17
Alignment explanation
Indices: 37793--37826 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
37783 GGATCATCAT
37793 GGAAAATCG-TGAGAAAA
1 GGAAAAT-GATGAGAAAA
37810 GGAAAATGATGAGAAAA
1 GGAAAATGATGAGAAAA
37827 AGAATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (17 bp):
GGAAAATGATGAGAAAA
Found at i:38356 original size:42 final size:42
Alignment explanation
Indices: 38288--38369 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
38278 ATCAAAGAAA
*
38288 TAACAATGGGCAAGTCTAAAAGAAGACAGATCTGGAGAATAT
1 TAACAAGGGGCAAGTCTAAAAGAAGACAGATCTGGAGAATAT
*
38330 TAACAAGGGGCAAAGTCT-AAATAAGACAGATCTGGAGAAT
1 TAACAAGGGGC-AAGTCTAAAAGAAGACAGATCTGGAGAAT
38370 TGAGTGTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 31 0.84
43 6 0.16
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.18
Consensus pattern (42 bp):
TAACAAGGGGCAAGTCTAAAAGAAGACAGATCTGGAGAATAT
Found at i:41237 original size:15 final size:15
Alignment explanation
Indices: 41219--41250 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41209 AATTGTTTAC
*
41219 TTTTGCTCTGTTTTT
1 TTTTCCTCTGTTTTT
41234 TTTTCCTCTGTTTTT
1 TTTTCCTCTGTTTTT
41249 TT
1 TT
41251 CACTTTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (15 bp):
TTTTCCTCTGTTTTT
Found at i:42167 original size:6 final size:6
Alignment explanation
Indices: 42156--42182 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42146 AACCCAGTTA
42156 AATTAG AATTAG AATTAG AATTAG AAT
1 AATTAG AATTAG AATTAG AATTAG AAT
42183 AGATAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
AATTAG
Found at i:48901 original size:2 final size:2
Alignment explanation
Indices: 48894--48921 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48884 GGTACACCAA
48894 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
48922 TATGCTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51114 original size:32 final size:33
Alignment explanation
Indices: 51055--51120 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
51045 GTCTTAGTGG
51055 ATTCCTAATAGAGTTGGAAAAATAGAAGTTCAA
1 ATTCCTAATAGAGTTGGAAAAATAGAAGTTCAA
51088 ATTCCTAATAGAGTTGG-AAAATAGAAGTTCAA
1 ATTCCTAATAGAGTTGGAAAAATAGAAGTTCAA
51120 A
1 A
51121 GTGCAAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.48
33 17 0.52
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (33 bp):
ATTCCTAATAGAGTTGGAAAAATAGAAGTTCAA
Found at i:58635 original size:11 final size:11
Alignment explanation
Indices: 58621--58658 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
58611 ATTCATAACA
58621 AATTTATAATT
1 AATTTATAATT
58632 AATTTATAATT
1 AATTTATAATT
58643 -ATTTGATAATT
1 AATTT-ATAATT
*
58654 TATTT
1 AATTT
58659 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:58837 original size:8 final size:8
Alignment explanation
Indices: 58826--58854 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
58816 TTATTTTAGG
58826 TTTTTTAT
1 TTTTTTAT
58834 TTTTTTA-
1 TTTTTTAT
58841 TTTTTTAT
1 TTTTTTAT
58849 TTTTTT
1 TTTTTT
58855 TTATCTAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:58853 original size:15 final size:15
Alignment explanation
Indices: 58826--58854 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58816 TTATTTTAGG
58826 TTTTTTATTTTTTTA
1 TTTTTTATTTTTTTA
58841 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
58855 TTATCTAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTATTTTTTTA
Found at i:62507 original size:433 final size:432
Alignment explanation
Indices: 61699--62687 Score: 1049
Period size: 433 Copynumber: 2.3 Consensus size: 432
61689 TGATATTTTT
* * * * * * * *
61699 TTCTATTTGTCCGATTAAGGTTATTCAAGTATCTATTAAAAGGTAATTTTATGACCTA-AAATCT
1 TTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGGCAATTTCATAATCTACAACT-T
* * * ** * * * *
61763 TCATT--AAGAACTCGAAAGTC-AATTTTAATTTTTTGATTCTAAAAAAATGCTTCCGAAATTTT
65 TCATTGAAAG-ACTCAAAAG-CAAATTTTTATATTTCAATTCAAAAAAAATGCTTCCTAAATGTG
* * * ** *** * * * *
61825 GTAGTTTTGGTTGCCGGT-TAATTTAATATTGTATAGTTTTTTG-TCCACATGTCCAATTGAAGC
128 GTCGTTTCGATTGTTGGTCT-ATTTAATACCATATA-ATTTTCGATCCACATGACCAATTAAAGC
* * * * * * *
61888 TATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGATTTCTATGAAGGACCCGAAAGCTAA
191 TATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGATTTCTATGAAGAACCCAAAAGATAA
* * *
61953 ATTTGATCTACGAGTTTCGTTAAGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACA
256 ATTTGATCTACGAGTTTCATGAAGGTTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATTAACA
* *
62018 AACATTTTCTTATTTGGATTATTGATCAAATGACCCTCATACTTTTATACTTTATACTACTTAGT
321 AACATTTTCTTATTTGAATTATTGATCAAATCACCCTCATACTTTTATACTTTATACTACTT--T
* *
62083 CCTTTACAAATTCTATCTTA-A-T-CGCTT-TATTTTTTTTAA-TCTTTG
384 CCTTTACAAATTCTATCTTATATTACACTTAT-TTTTTTTTAATTCTTTA
* * * * *
62128 TTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGCAATTTCATAATCTACATA-TT
1 TTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGGCAATTTCATAATCTACA-ACTT
* *
62192 TCA-TGAAGGATTCAAAAGCAAATTTTTATGCATGTTTCAATTC-AAAAAAATGCTTCCTAAATG
65 TCATTGAAAGACTCAAAAGCAAATTTTTAT--A--TTTCAATTCAAAAAAAATGCTTCCTAAATG
* *
62255 TGGTCGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACATGAGCAATTAAAGT
126 TGGTCGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACATGACCAATTAAAGC
* *
62320 TATTCAAGTGTTGGTTAAAAAGGTTACTGTATAATCTACGACTTTC-ATGAAGAACCCAAAAGAT
191 TATTCAAGTGTCGGTT-AAAAGGTTACTGCATAATCTACGA-TTTCTATGAAGAACCCAAAAGAT
* * *
62384 -AATTTGATCTATGAGTTTCATGAAGGGTTCAATAGGAAATTTTTATGTTTTAAGATCTCCATTA
254 AAATTTGATCTACGAGTTTCATGAA-GGTTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATTA
* * *
62448 ACAAATATTTTCTTATTTGAATTAATT-ATCAAATCACCCTCATACTTTTCTATTTTATACTACT
318 ACAAACATTTTCTTATTTGAATT-ATTGATCAAATCACCCTCATACTTTTATACTTTATACTACT
*
62512 TTCCTTTACAAATTCTATTTTATTTGATTTAACACTTATTTTTTTTTAATTTTCTTTA
382 TTCCTTTACAAATTCTATCTTA--T-A-TT-ACACTTATTTTTTTTTAA--TTCTTTA
* * *
62570 TTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGGTAATTTTATGATCTACAACTTT
1 TTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGGCAATTTCATAATCTACAACTTT
*
62635 CATTGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAAAATGCTT
66 CATTGAAAGACTCAAAAGCAAATTTTTATATTTCAATTC-AAAAAAAATGCTT
62688 TTGAAATTTT
Statistics
Matches: 463, Mismatches: 66, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
428 2 0.00
429 69 0.15
430 4 0.01
431 26 0.06
432 95 0.21
433 135 0.29
434 7 0.02
435 1 0.00
437 1 0.00
439 23 0.05
440 1 0.00
441 14 0.03
442 62 0.13
443 23 0.05
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (432 bp):
TTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGGCAATTTCATAATCTACAACTTT
CATTGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAAATGCTTCCTAAATGTGGTC
GTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACATGACCAATTAAAGCTATTC
AAGTGTCGGTTAAAAGGTTACTGCATAATCTACGATTTCTATGAAGAACCCAAAAGATAAATTTG
ATCTACGAGTTTCATGAAGGTTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATTAACAAACAT
TTTCTTATTTGAATTATTGATCAAATCACCCTCATACTTTTATACTTTATACTACTTTCCTTTAC
AAATTCTATCTTATATTACACTTATTTTTTTTTAATTCTTTA
Found at i:64002 original size:11 final size:11
Alignment explanation
Indices: 63959--63996 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
63949 TTTTTATATA
*
63959 AAATAAATTAT
1 AAATTAATTAT
63970 CAAA-TAATTAT
1 -AAATTAATTAT
63981 AAATTAATTAT
1 AAATTAATTAT
63992 AAATT
1 AAATT
63997 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:64289 original size:59 final size:58
Alignment explanation
Indices: 64198--64318 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 58
64188 ATTTCTCTCA
* *
64198 TTCATATTTTTTTTTCTCCATATTTTATTGTCTTTCTATTCTCTTGTCTTTTCCATAC
1 TTCATATTTTTTCTTCTCCATATTTTATTGTCTCTCTATTCTCTTGTCTTTTCCATAC
64256 TTCATATTTTCTTCTTCTCCATATTTTATTGTCTCTCTATTCTCTTGTCTTTTCCATAC
1 TTCATATTTT-TTCTTCTCCATATTTTATTGTCTCTCTATTCTCTTGTCTTTTCCATAC
64315 TTCA
1 TTCA
64319 ATTCTACTCC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 10 0.17
59 50 0.83
ACGTcount: A:0.14, C:0.23, G:0.03, T:0.60
Consensus pattern (58 bp):
TTCATATTTTTTCTTCTCCATATTTTATTGTCTCTCTATTCTCTTGTCTTTTCCATAC
Found at i:64444 original size:65 final size:65
Alignment explanation
Indices: 64340--64468 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 65
64330 TTGCTTTGTT
64340 TTGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTATTAGAAGAATTTATAAAATA
1 TTGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTATTAGAAGAATTTATAAAATA
* *
64405 TTGTTATCATTTCACAACAAAATTTCATTTTTTAACTGAATTTTCTTAGAAGAATTTATAAAAT
1 TTGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTATTAGAAGAATTTATAAAAT
64469 TTCATTTCTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (65 bp):
TTGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTATTAGAAGAATTTATAAAATA
Found at i:64481 original size:41 final size:41
Alignment explanation
Indices: 64423--64509 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
64413 ATTTCACAAC
*
64423 AAAATTTCATTTTTTAACTGAATTTTCTTAGAAGAATTTAT
1 AAAATTTCATTTCTTAACTGAATTTTCTTAGAAGAATTTAT
64464 AAAATTTCATTTCTTAACTGAATTTTCTTAGAAGAATTTAT
1 AAAATTTCATTTCTTAACTGAATTTTCTTAGAAGAATTTAT
64505 AAAAT
1 AAAAT
64510 AAAACAGTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (41 bp):
AAAATTTCATTTCTTAACTGAATTTTCTTAGAAGAATTTAT
Found at i:68599 original size:4 final size:4
Alignment explanation
Indices: 68590--68630 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
68580 TCTTCACTCC
**
68590 CTTT CTTT CTTT CTTT CTTT CTTT CAAT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
68631 CTTTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:77553 original size:99 final size:99
Alignment explanation
Indices: 77382--77572 Score: 292
Period size: 99 Copynumber: 1.9 Consensus size: 99
77372 GACCTTGACA
* * * *
77382 AAATCGGCCTTCTTATTCCTGTTGGAAGACCGATATAATGACAATATTTTGGCCATTATCGGTTT
1 AAATCGACCTTCTTATTCCTCTTGGAACACCGATATAATGACAATATGTTGGCCATTATCGGTTT
* * *
77447 GTAAGAGTTGGGTGAGGCCTGGGCTTGCGGGGAG
66 GTAAGAGTTAGGTAAGGCCTGGACTTGCGGGGAG
* *
77481 AAATCGACCTTCTTATTCCTCTTGGAACACCGGTATAATGGCAATATGTTGGCCATTATCGGTTT
1 AAATCGACCTTCTTATTCCTCTTGGAACACCGATATAATGACAATATGTTGGCCATTATCGGTTT
*
77546 GTAAGAGTTAGGTAAGGCTTGGACTTG
66 GTAAGAGTTAGGTAAGGCCTGGACTTG
77573 GGGAGGGGGG
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 82 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (99 bp):
AAATCGACCTTCTTATTCCTCTTGGAACACCGATATAATGACAATATGTTGGCCATTATCGGTTT
GTAAGAGTTAGGTAAGGCCTGGACTTGCGGGGAG
Found at i:77956 original size:2 final size:2
Alignment explanation
Indices: 77949--77978 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
77939 TATTTTCACG
77949 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
77979 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77983 original size:2 final size:2
Alignment explanation
Indices: 77978--78050 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
77968 TATATATATA
77978 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
78020 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
78051 ATAAGAAACC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:78470 original size:11 final size:11
Alignment explanation
Indices: 78443--78490 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
78433 GAAGTTCGTG
78443 TTTGAAGACTTA
1 TTTGAAGA-TTA
*
78455 TTTGAAGATAA
1 TTTGAAGATTA
78466 TTTGAAGATTA
1 TTTGAAGATTA
78477 -TTGAAGAATTA
1 TTTGAAG-ATTA
78488 TTT
1 TTT
78491 CAAGGAGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 6 0.19
11 16 0.50
12 10 0.31
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:83087 original size:78 final size:80
Alignment explanation
Indices: 82922--83088 Score: 250
Period size: 78 Copynumber: 2.1 Consensus size: 80
82912 TTTCTAGCCT
82922 GCTGGATTTATGTTGGTGGTGCTGCTTAGTTTGATTAGGATTTGTTCTGTTGGTTTTAAGTCTTA
1 GCTGGATTTATGTTGGT-GTGCTGCTTAGTTTGATTAGGATTTGTTCTGTTGGTTTTAAGTCTTA
82987 GGTATTGAAGGTTTTG
65 GGTATTGAAGGTTTTG
** * *
83003 ATTGGATTTATGTT-GT-TGCTGCTTGGTTTGATTGGGATTTGATT-TGTTGGTTTTAAGTCTTA
1 GCTGGATTTATGTTGGTGTGCTGCTTAGTTTGATTAGGATTTG-TTCTGTTGGTTTTAAGTCTTA
*
83065 GGTGTTGAAGGTTTTG
65 GGTATTGAAGGTTTTG
83081 GCTGGATT
1 GCTGGATT
83089 AGTGCATGAC
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
78 62 0.79
79 2 0.03
80 2 0.03
81 12 0.15
ACGTcount: A:0.14, C:0.05, G:0.31, T:0.49
Consensus pattern (80 bp):
GCTGGATTTATGTTGGTGTGCTGCTTAGTTTGATTAGGATTTGTTCTGTTGGTTTTAAGTCTTAG
GTATTGAAGGTTTTG
Found at i:89313 original size:7 final size:8
Alignment explanation
Indices: 89282--89344 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 8
89272 AGTAGTCATG
89282 AGTTTGAA
1 AGTTTGAA
89290 AGTTTG-A
1 AGTTTGAA
*
89297 AGGTTGAA
1 AGTTTGAA
89305 AGTTT-AA
1 AGTTTGAA
* *
89312 AGATTGAG
1 AGTTTGAA
*
89320 AGAATTGAAA
1 AG-TTTG-AA
89330 AGTTTGAA
1 AGTTTGAA
89338 A-TTTGAA
1 AGTTTGAA
89345 GGAAAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
7 18 0.40
8 17 0.38
9 7 0.16
10 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.33
Consensus pattern (8 bp):
AGTTTGAA
Found at i:89318 original size:15 final size:15
Alignment explanation
Indices: 89285--89318 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
89275 AGTCATGAGT
* *
89285 TTGAAAGTTTGAAGG
1 TTGAAAGTTTAAAGA
89300 TTGAAAGTTTAAAGA
1 TTGAAAGTTTAAAGA
89315 TTGA
1 TTGA
89319 GAGAATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (15 bp):
TTGAAAGTTTAAAGA
Found at i:91126 original size:24 final size:21
Alignment explanation
Indices: 91074--91113 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
91064 GACTGAAGGG
91074 GCTTCATCACAAAGCAGCAGA
1 GCTTCATCACAAAGCAGCAGA
* *
91095 GCTGCATCACAAAGTAGCA
1 GCTTCATCACAAAGCAGCA
91114 TGCAGCTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.15
Consensus pattern (21 bp):
GCTTCATCACAAAGCAGCAGA
Found at i:97148 original size:105 final size:102
Alignment explanation
Indices: 96853--97151 Score: 287
Period size: 102 Copynumber: 2.9 Consensus size: 102
96843 GATCGAGTTG
* * * * * * * * *
96853 CCATCGCCGCTTTTTGCCGCTGGGAAGGACCCC-AAATCGCCACCGCCTCCAAATCCAGCTCCTC
1 CCATCGCTGCCTTTTGCAGCAGGGAA-GACCCCAAAATCGCCCCCGTCTCCGAAGCCAGCTCCTT
* * * * * **
96917 CAAAAAATCAACATATGATCGAGCTGCCTATAAAACGAA
65 CAACACATCAAGATGTGATCGAGCTGCCCATGCAAC-AA
* * ** * *
96956 -GATCACCACCTTTTGCAGCTGGGAAGACCCCAAAATCGCCGCCGTCTCCGAAGCCAGCTCCTTC
1 CCATCGCTGCCTTTTGCAGCAGGGAAGACCCCAAAATCGCCCCCGTCTCCGAAGCCAGCTCCTTC
97020 AACACATCAAGATGTGATCGAGCTGCCCATGCAACAA
66 AACACATCAAGATGTGATCGAGCTGCCCATGCAACAA
* * *
97057 CCATCGCTGCCTTTTGCAGCAGGGAAGACCCCAATATTGCCACCACGGTCTCCGAATCCAGCTCC
1 CCATCGCTGCCTTTTGCAGCAGGGAAGACCCCAAAATCGCC-CC-C-GTCTCCGAAGCCAGCTCC
* * *
97122 TTCAACACGTCAGGATTTGATCGAGCTGCC
63 TTCAACACATCAAGATGTGATCGAGCTGCC
97152 TAATTTACAA
Statistics
Matches: 162, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
101 8 0.05
102 108 0.67
103 1 0.01
104 1 0.01
105 44 0.27
ACGTcount: A:0.27, C:0.35, G:0.19, T:0.19
Consensus pattern (102 bp):
CCATCGCTGCCTTTTGCAGCAGGGAAGACCCCAAAATCGCCCCCGTCTCCGAAGCCAGCTCCTTC
AACACATCAAGATGTGATCGAGCTGCCCATGCAACAA
Found at i:98484 original size:2 final size:2
Alignment explanation
Indices: 98477--98503 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
98467 AGACATTGAT
98477 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
98504 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:103199 original size:20 final size:20
Alignment explanation
Indices: 103174--103214 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
103164 GCCCCACATC
103174 AACCTTTTTTACCATTCATA
1 AACCTTTTTTACCATTCATA
103194 AACCTTTTTTACCATTCATA
1 AACCTTTTTTACCATTCATA
103214 A
1 A
103215 GTTGATAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (20 bp):
AACCTTTTTTACCATTCATA
Done.