Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014724.1 Kokia drynarioides strain JFW-HI SEQ_129763, 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: 148167
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:11690 original size:27 final size:25
Alignment explanation
Indices: 11632--11692 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
11622 CATATCTTGG
11632 AATTTG-TATTTAAATTTTTTTATC
1 AATTTGATATTTAAATTTTTTTATC
** *
11656 AAAGTGATATTTAAATTATTTTTTCTC
1 AATTTGATATTTAAA-T-TTTTTTATC
11683 AATTTGATAT
1 AATTTGATAT
11693 CTCTATAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 8 0.28
26 1 0.03
27 16 0.55
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (25 bp):
AATTTGATATTTAAATTTTTTTATC
Found at i:12660 original size:21 final size:20
Alignment explanation
Indices: 12631--12672 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
12621 AATAATATAT
* *
12631 TAATTAATAATATTATTATTA
1 TAATAAATAATAATATT-TTA
12652 TAATAAATAATAATATTTTA
1 TAATAAATAATAATATTTTA
12672 T
1 T
12673 TATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAATAATAATATTTTA
Found at i:12687 original size:29 final size:24
Alignment explanation
Indices: 12626--12675 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
12616 TTTCAAATAA
* *
12626 TATATTAATTAATAATATTATTAT
1 TATAATAAATAATAATATTATTAT
12650 TATAATAAATAATAATATT-TTAT
1 TATAATAAATAATAATATTATTAT
12673 TAT
1 TAT
12676 TTATATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATAATAAATAATAATATTATTAT
Found at i:13047 original size:61 final size:58
Alignment explanation
Indices: 12952--13166 Score: 170
Period size: 61 Copynumber: 3.6 Consensus size: 58
12942 CAACACCCCT
* * * * *
12952 TTTTTGTCAGATAAAAAA--T-ACAATTTTTTTGTGTTGGTCATACAATGGCAGACACTCA
1 TTTTT-TCAGATAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGC-GACAC-CC
* *
13010 TATTTTTCTGATAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGTAATGGCCGACACCCCC
1 T-TTTTTCAGATAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGG-CGACA--CCC
* * * * *
13072 TTTTCTCGGATAAAAAAATT--ACATTTTTGGGTGTTGGCCATGCAATGGTCGACACCCC
1 TTTTTTCAGATAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGG-CGACA-CCC
* * *
13130 CTTATTCAGATAAAAAAATTTCAAATTTTTTTGGTGT
1 TTTTTTCAGAT-AAAAAATTTCAAAATTTTTTGGTGT
13167 CGACCACCTA
Statistics
Matches: 125, Mismatches: 22, Indels: 17
0.76 0.13 0.10
Matches are distributed among these distances:
58 23 0.18
59 42 0.34
60 1 0.01
61 55 0.44
62 3 0.02
63 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (58 bp):
TTTTTTCAGATAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCGACACCC
Found at i:13068 original size:120 final size:120
Alignment explanation
Indices: 12944--13166 Score: 265
Period size: 120 Copynumber: 1.9 Consensus size: 120
12934 AAAATTTGCA
* * ** *
12944 ACACCCCTTTTTTGTCAGAT-AAAAAA-TACAATTTTTTTGTGTTGGTCATACAATGG-CAGACA
1 ACACCCC-CTTTTCTCAGATAAAAAAATTAC-ATTTTTGGGTGTTGGCCATACAATGGTC-GACA
* * *
13006 CTCATATTTTTCTGAT-AAAAAATTTCAAAATTTTTTGGTGTTGGCCATGTAATGGCCG
63 C-CACATTATTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGTAATGGCCG
* * *
13064 ACACCCCCTTTTCTCGGATAAAAAAATTACATTTTTGGGTGTTGGCCATGCAATGGTCGACACCC
1 ACACCCCCTTTTCTCAGATAAAAAAATTACATTTTTGGGTGTTGGCCATACAATGGTCGACACCA
* *
13129 CCTTATTCAGATAAAAAAATTTCAAATTTTTTTGGTGT
66 CATTATTCAGATAAAAAAATTTCAAAATTTTTTGGTGT
13167 CGACCACCTA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
119 18 0.21
120 64 0.74
121 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (120 bp):
ACACCCCCTTTTCTCAGATAAAAAAATTACATTTTTGGGTGTTGGCCATACAATGGTCGACACCA
CATTATTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGTAATGGCCG
Found at i:13148 original size:58 final size:59
Alignment explanation
Indices: 13035--13149 Score: 178
Period size: 59 Copynumber: 2.0 Consensus size: 59
13025 AAATTTCAAA
* * * *
13035 ATTTTTTGGTGTTGGCCATGTAATGGCCGACACCCCCTTTTCTCGGATAAAAAAATTAC
1 ATTTTTGGGTGTTGGCCATGCAATGGCCGACACCCCCTTATCTCAGATAAAAAAATTAC
*
13094 ATTTTTGGGTGTTGGCCATGCAATGGTCGACACCCCCTTAT-TCAGATAAAAAAATT
1 ATTTTTGGGTGTTGGCCATGCAATGGCCGACACCCCCTTATCTCAGATAAAAAAATT
13150 TCAAATTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 14 0.27
59 37 0.73
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (59 bp):
ATTTTTGGGTGTTGGCCATGCAATGGCCGACACCCCCTTATCTCAGATAAAAAAATTAC
Found at i:13321 original size:61 final size:62
Alignment explanation
Indices: 13186--13332 Score: 224
Period size: 62 Copynumber: 2.4 Consensus size: 62
13176 ATTCTCGGAT
* * *
13186 AAAAAAATTTCAATTTTTTTTATCCGAGAAAAGGGGGTATCGACCATTGCATGGCCGACACC
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGAGGGTATCGACCATTGCATGGCCGACACC
* * * *
13248 AAAAAAATTTGAAATTTTTTTATCCGAGAACAGAGGGTGTCGGCCATTGCATGGCTGACA-C
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGAGGGTATCGACCATTGCATGGCCGACACC
13309 AAAAAAATTTGAAATTTTTTTATC
1 AAAAAAATTTGAAATTTTTTTATC
13333 TGAAAATGGC
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
61 25 0.32
62 53 0.68
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (62 bp):
AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGAGGGTATCGACCATTGCATGGCCGACACC
Found at i:13410 original size:99 final size:98
Alignment explanation
Indices: 13236--13431 Score: 227
Period size: 99 Copynumber: 2.0 Consensus size: 98
13226 CGACCATTGC
* * **
13236 ATGGCCGACACCAAAAAAATTTGAAATTTTTTTATCCGAGAACAGAGGGTGTCGGCCATTGCATG
1 ATGGCCGACACCAAAAAAA-TTGAAATTTTTTTATCAGAAAACAGAGGGTGTCCACCATTGCATG
**
13301 GCTGACACAAAAAAATTTGAAATTTTTTTATCTGAAA
65 GCCAACACAAAAAAA-TTG-AA-TTTTTTATCTGAAA
* * * *
13338 ATGGCCGACACC-CAAAAA-TGCAATTTTTTTATCAGATAAATAGA-GGTGTCCACCATTGTATG
1 ATGGCCGACACCAAAAAAATTGAAATTTTTTTATCAGA-AAACAGAGGGTGTCCACCATTGCATG
*
13400 GCCAACACAAAAAAATTGTATTTTTTATCTGA
65 GCCAACACAAAAAAATTGAATTTTTTATCTGA
13432 CAAAAAAGGG
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
96 12 0.15
97 1 0.01
98 3 0.04
99 44 0.54
100 5 0.06
101 5 0.06
102 12 0.15
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (98 bp):
ATGGCCGACACCAAAAAAATTGAAATTTTTTTATCAGAAAACAGAGGGTGTCCACCATTGCATGG
CCAACACAAAAAAATTGAATTTTTTATCTGAAA
Found at i:14729 original size:17 final size:19
Alignment explanation
Indices: 14702--14740 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
14692 GATATGGGAC
*
14702 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
14720 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
14738 AAA
1 AAA
14741 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:19698 original size:29 final size:28
Alignment explanation
Indices: 19665--19733 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
19655 ATGTTTTCAA
*
19665 ATAATATATTAATTAATAATATTATTA-TT
1 ATAATATAATAA-TAAT-ATATTATTATTT
*
19694 ATAATA-AATAATAATATTTTATTATTT
1 ATAATATAATAATAATATATTATTATTT
*
19721 ATATTATAA-AATA
1 ATAATATAATAATA
19734 TAAAGAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 8 0.23
27 15 0.43
28 6 0.17
29 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
ATAATATAATAATAATATATTATTATTT
Found at i:19703 original size:21 final size:20
Alignment explanation
Indices: 19674--19715 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
19664 AATAATATAT
* *
19674 TAATTAATAATATTATTATTA
1 TAATAAATAATAATATT-TTA
19695 TAATAAATAATAATATTTTA
1 TAATAAATAATAATATTTTA
19715 T
1 T
19716 TATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAATAATAATATTTTA
Found at i:19705 original size:24 final size:23
Alignment explanation
Indices: 19669--19718 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
19659 TTTCAAATAA
* *
19669 TATATTAATTAATAATATTATTAT
1 TATAATAAATAATAATATT-TTAT
19693 TATAATAAATAATAATATTTTAT
1 TATAATAAATAATAATATTTTAT
19716 TAT
1 TAT
19719 TTATATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATAATAAATAATAATATTTTAT
Found at i:20793 original size:17 final size:19
Alignment explanation
Indices: 20766--20804 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
20756 GAAATGGGAC
*
20766 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
20784 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
20802 AAA
1 AAA
20805 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:26419 original size:68 final size:68
Alignment explanation
Indices: 26266--26505 Score: 272
Period size: 68 Copynumber: 3.5 Consensus size: 68
26256 AGTTCGCCAA
* * *
26266 GACAATAAACATGGGATCATGTTGTGTAAGACCATAGTTGGGCTT-TGGA-AACATAT-AAGTCC
1 GACAGTAAACATGAGATCATATTGTGTAAGACCATAGTTGGG-TTAT-GACAACATATGAAGTCC
*
26328 GCTAG
64 GTTAG
* ** *
26333 GACAGTAAACATGGGATCATATTGTGTAAGACCATAACTGGGTTATGACAACATATGAAGTCCAT
1 GACAGTAAACATGAGATCATATTGTGTAAGACCATAGTTGGGTTATGACAACATATGAAGTCCGT
26398 TAG
66 TAG
* * * * * * *
26401 GACAGTAAATATGAGATCATGTTATGTAAGACCATAGTTGAGTTATAACAACATATGAAGGCTGT
1 GACAGTAAACATGAGATCATATTGTGTAAGACCATAGTTGGGTTATGACAACATATGAAGTCCGT
26466 CT-G
66 -TAG
* *
26469 GACACTAAACATGAGATCATATTGTGTAACACCATAG
1 GACAGTAAACATGAGATCATATTGTGTAAGACCATAG
26506 CTACATATGA
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
66 4 0.03
67 46 0.31
68 96 0.65
69 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (68 bp):
GACAGTAAACATGAGATCATATTGTGTAAGACCATAGTTGGGTTATGACAACATATGAAGTCCGT
TAG
Found at i:34701 original size:3 final size:3
Alignment explanation
Indices: 34695--34722 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34685 TTGTTGCTGT
34695 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
34723 TTTATGCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:36787 original size:18 final size:18
Alignment explanation
Indices: 36765--36806 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
36755 TTTTTAATTA
36765 AAAAAATATATAAAAT-TTC
1 AAAAAA-AT-TAAAATATTC
*
36784 AAAAAAATTCAAATATTC
1 AAAAAAATTAAAATATTC
36802 AAAAA
1 AAAAA
36807 GAATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAAATTAAAATATTC
Found at i:38418 original size:20 final size:20
Alignment explanation
Indices: 38393--38433 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38383 GACATTTAAA
*
38393 CCTAGATGAGTAACTCAATC
1 CCTAGATAAGTAACTCAATC
* *
38413 CCTAGATAAGTGACTCGATC
1 CCTAGATAAGTAACTCAATC
38433 C
1 C
38434 ATGATCAGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (20 bp):
CCTAGATAAGTAACTCAATC
Found at i:39369 original size:18 final size:19
Alignment explanation
Indices: 39321--39370 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
39311 AGTTTCATTA
* *
39321 ATTTAGAAATGAATTTTTT
1 ATTTATAAATTAATTTTTT
* *
39340 ATTTTTACATTAATTTTTT
1 ATTTATAAATTAATTTTTT
39359 -TTTATAAATTAA
1 ATTTATAAATTAA
39371 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTATAAATTAATTTTTT
Found at i:41197 original size:61 final size:60
Alignment explanation
Indices: 41111--41233 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 60
41101 GAAAAAAAAA
* **
41111 TTTGGTGTTGGCCATTGCATAGTCGACACCCCTTTTTAATCTGATAAAAAAATCAATTTT
1 TTTGGTGTTGACCATTGCATAGTCGACACCCCTTTTTAATCAAATAAAAAAATCAATTTT
* ** *
41171 TTTGTGTGTTGACCA-TGCAATGGTCGACACCCCTTTTTTGTCAAATAAAAAATTCAATTTT
1 TTTG-GTGTTGACCATTGC-ATAGTCGACACCCCTTTTTAATCAAATAAAAAAATCAATTTT
41232 TT
1 TT
41234 GCACAAGACA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 7 0.13
61 47 0.87
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (60 bp):
TTTGGTGTTGACCATTGCATAGTCGACACCCCTTTTTAATCAAATAAAAAAATCAATTTT
Found at i:42570 original size:11 final size:12
Alignment explanation
Indices: 42530--42578 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
42520 TATTTGTGTA
42530 AAAATTAATTTG
1 AAAATTAATTTG
42542 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
42556 TTGAAATTAATTTG
1 --AAAATTAATTTG
42570 AAAATTAAT
1 AAAATTAAT
42579 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:42899 original size:162 final size:164
Alignment explanation
Indices: 42682--43067 Score: 553
Period size: 168 Copynumber: 2.3 Consensus size: 164
42672 ATTTAAAATT
* * *
42682 AATTTAACATTATTTAAATAAAAAAATTTATTATAATATT-TCAATTTATATCAAATATTGTGTT
1 AATTTAA-A-TATTTAAAT-AAAAAA-TTATTATTATATTAT-AATTTTTATCAAATAATGTGTT
* * *
42746 CATTTGATAATACATTATTTATCAAATTTTCATATTTAAATTACAAATTATTATTATATT-A-TT
61 CATTTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTATTATTATATTAATTT
42809 ATCAAATAATATATTGATTTGATAATACATTATTTACTA
126 ATCAAATAATATATTGATTTGATAATACATTATTTACTA
*
42848 AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTCATTT
*
42913 GACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTGTTATTATATTACAATTTTTA
66 GACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTATTATTATATT--AA--TTTA
* * *
42978 TCAAATAATGTGTTGATTTGATAATACATTATTTATTA
127 TCAAATAATATATTGATTTGATAATACATTATTTACTA
* *
43016 ATTTTAAATATTTAAATAAAAATTTATTATTATATTATAATTTTTATCAAAT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAAT
43068 TTTAAAATTA
Statistics
Matches: 200, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
162 87 0.44
163 7 0.04
164 9 0.05
165 2 0.01
166 7 0.04
168 88 0.44
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (164 bp):
AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTCATTT
GACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTATTATTATATTAATTTATCAA
ATAATATATTGATTTGATAATACATTATTTACTA
Found at i:42923 original size:84 final size:83
Alignment explanation
Indices: 42682--43067 Score: 489
Period size: 84 Copynumber: 4.6 Consensus size: 83
42672 ATTTAAAATT
* * *
42682 AATTTAACATTATTTAAATAAAAAAATTTATTATAATATT-TCAATTTATATCAAATATTGTGTT
1 AATTTAA-A-TATTTAAAT-AAAAAA-TTATTATTATATTAT-AATTTTTATCAAATAATGTGTT
*
42746 CATTTGATAATACATTATTTATCA
61 GATTTGATAATACATTATTTAT-A
** * * * *
42770 AATTTTCATATTTAAATTACAAATTATTATTATA-T-T-A---TTATCAAATAATATATTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTT
42829 GATAATACATTATTTACTA
66 GATAATACATTATTTA-TA
42848 AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTT
*
42913 GACAATACATTATTTATCA
66 GATAATACATTATTTAT-A
** * *
42932 AATTTTCATATTTAAATAAAAAATTGTTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTT
42997 GATAATACATTATTTATTA
66 GATAATACATTATTTA-TA
* *
43016 ATTTTAAATATTTAAATAAAAATTTATTATTATATTATAATTTTTATCAAAT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAAT
43068 TTTAAAATTA
Statistics
Matches: 261, Mismatches: 28, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
78 64 0.25
79 2 0.01
80 1 0.00
81 2 0.01
83 3 0.01
84 169 0.65
85 5 0.02
86 9 0.03
87 1 0.00
88 5 0.02
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (83 bp):
AATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTT
GATAATACATTATTTATA
Found at i:43045 original size:168 final size:161
Alignment explanation
Indices: 42679--43067 Score: 546
Period size: 162 Copynumber: 2.3 Consensus size: 161
42669 TACATTTAAA
* * *
42679 ATTAATTTAACATTATTTAAATAAAAAAATTTATTATAATATT-TCAATTTATATCAAATATTGT
1 ATTAATTTAA-A-TATTTAAAT--AAAAATTTATTATTATATTAT-AATTTTTATCAAATAATGT
* * *
42743 GTTCATTTGATAATACATTATTTATCAAATTTTCATATTTAAATTACAAATTATTATTATATTAT
61 GTTCATTTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTATTATTATATTAT
42808 TATCAAATAATATATTGATTTGATAATACATTATTT
126 TATCAAATAATATATTGATTTGATAATACATTATTT
* * *
42844 ACTAAATTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTG
1 A-TTAATTTAAATATTTAAATAAAAATTTATTATTATATTATAATTTTTATCAAATAATGTGTTC
*
42909 ATTTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTGTTATTATATTACAATT
65 ATTTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTATTATTATATT---A--
* *
42974 TTTATCAAATAATGTGTTGATTTGATAATACATTATTT
125 -TTATCAAATAATATATTGATTTGATAATACATTATTT
43012 ATTAATTTTAAATATTTAAATAAAAATTTATTATTATATTATAATTTTTATCAAAT
1 ATTAA-TTTAAATATTTAAATAAAAATTTATTATTATATTATAATTTTTATCAAAT
43068 TTTAAAATTA
Statistics
Matches: 201, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
162 92 0.46
163 1 0.00
164 9 0.04
165 3 0.01
166 8 0.04
167 3 0.01
168 85 0.42
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (161 bp):
ATTAATTTAAATATTTAAATAAAAATTTATTATTATATTATAATTTTTATCAAATAATGTGTTCA
TTTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTATTATTATATTATTATCA
AATAATATATTGATTTGATAATACATTATTT
Found at i:43188 original size:22 final size:23
Alignment explanation
Indices: 43160--43218 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
43150 TAGACCACCC
*
43160 AAATTCCAACTCACCTAAATC-G
1 AAATTCCAACTCACCTAAAACTG
* *
43182 AAATTCCAGCTCA-GTAAAACTG
1 AAATTCCAACTCACCTAAAACTG
43204 AAATTCCAACTCACC
1 AAATTCCAACTCACC
43219 AACACCTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
AAATTCCAACTCACCTAAAACTG
Found at i:44371 original size:30 final size:30
Alignment explanation
Indices: 44337--44417 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
44327 TCCATTTACT
* * * *
44337 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
44367 TTTTAAATTTAATTTCTAATTTCCTATATA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
*
44397 TTTT-AATTTTATTTCCTAATT
1 TTTTAAATTTAATTT-CTAATT
44418 CTTGTATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 9 0.20
30 36 0.80
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTATATA
Found at i:44425 original size:29 final size:29
Alignment explanation
Indices: 44337--44440 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 29
44327 TCCATTTACT
* * * * *
44337 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTT-AATTTTATTTCTAATTTCCTATATA
*
44367 TTTTAAATTTAATTTCTAATTTCCTATATA
1 TTTT-AATTTTATTTCTAATTTCCTATATA
* *
44397 TTTTAATTTTATTTCCTAA-TTCTTGTATA
1 TTTTAATTTTATTT-CTAATTTCCTATATA
*
44426 TTCTAATTATTATTT
1 TTTTAATT-TTATTT
44441 TTTGAAAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 24 0.38
30 40 0.62
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTTAATTTTATTTCTAATTTCCTATATA
Found at i:45457 original size:62 final size:61
Alignment explanation
Indices: 45247--45488 Score: 228
Period size: 62 Copynumber: 4.0 Consensus size: 61
45237 AGGGAAAGTT
* * * * **
45247 GGTGTCGACCATTATATGGCCAACACTAAAAAAATTT-AATTTTTTACCAAATAAAAAGGG
1 GGTGTCGACCATTACATGACCAACACCAAAAAAATTTGAATTTTTTATCTGATAAAAAGGG
** **
45307 GGTGTCGGTCATGGCATGACCAACA-CAAAAAAATTTGAATTTTTTATCTGATAAAAA-GG
1 GGTGTCGACCATTACATGACCAACACCAAAAAAATTTGAATTTTTTATCTGATAAAAAGGG
* * * * *
45366 GATGTCCACTA-TGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAGGG
1 GGTGTCGACCATTACATGACCAACACCAAAAAAATTTG-AA-TTTTTTATCTGATAAAAAGGG
* * *
45427 GGTGTCGGCCATTACATGGA-CAACACCAAAAAATTTTGAAATTTTTTTATTTGA-AAAAAGGG
1 GGTGTCGACCATTACAT-GACCAACACCAAAAAAATTTG-AA-TTTTTTATCTGATAAAAAGGG
45489 ATGGCCAACA
Statistics
Matches: 152, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
58 12 0.08
59 29 0.19
60 43 0.28
61 21 0.14
62 45 0.30
63 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (61 bp):
GGTGTCGACCATTACATGACCAACACCAAAAAAATTTGAATTTTTTATCTGATAAAAAGGG
Found at i:45458 original size:61 final size:62
Alignment explanation
Indices: 45299--45488 Score: 239
Period size: 62 Copynumber: 3.1 Consensus size: 62
45289 TTTACCAAAT
* * *
45299 AAAAAGGGGGTGTCGGTCATGGCATGACCAACA-CAAAAAAATTTG-AA-TTTTTTATCTGA
1 AAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTGA
* ** *
45358 TAAAAA-GGGATGTCCACTA-TGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTGA
1 -AAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTGA
* *
45419 AAAAAGGGGGTGTCGGCCATTACATGGA-CAACACCAAAAAATTTTGAAATTTTTTTATTTGA
1 AAAAAGGGGGTGTCGGCCATTGCAT-GACCAACACCAAAAAATTTTGAAATTTTTTTATCTGA
45481 AAAAAGGG
1 AAAAAGGG
45489 ATGGCCAACA
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
58 12 0.11
59 19 0.17
60 12 0.11
61 21 0.19
62 45 0.41
63 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (62 bp):
AAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTGA
Found at i:45566 original size:167 final size:164
Alignment explanation
Indices: 45326--45640 Score: 420
Period size: 167 Copynumber: 1.9 Consensus size: 164
45316 CATGGCATGA
*
45326 CCAACACAAAAAAATTTGAATTTTTTATCTGATAAAAAGGGATGTCCACTATGCATGACCAACAC
1 CCAACACAAAAAAATTTGAATTTTTTATCTGATAAAAAGGGATGTCCACCATGCATGACCAACAC
* ** *
45391 CAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGGGGGTGTCGGCCATTACATGGACAACACCAA
66 CAAAAAATTTTGAAAATTTTTTATCTGAAAAAAAAGGGTGTCGACCATTACATGGACAACACCAA
45456 AAAATTTTGAAATTTTTTTATTTGAAAAAAGGGATGG
131 AAAA-TTTG--ATTTTTTTATTTGAAAAAAGGGATGG
** * * * *
45493 CCAACACCCAAAAATTTGATTTTTTTAT-TAGATAAATAGGGGTGT-CAGCCATTGCATGGCCAA
1 CCAACACAAAAAAATTTGAATTTTTTATCT-GATAAAAAGGGATGTCCA-CCA-TGCATGACCAA
* * *
45556 CACC-AAAAATTTTGAAAATTTTTTATCTGAAAAAAAAGGGTGTCGATCATTTCATGGCCAACAC
63 CACCAAAAAATTTTGAAAATTTTTTATCTGAAAAAAAAGGGTGTCGACCATTACATGGACAACAC
*
45620 CTAAAAATTTGATTTTTTTAT
128 CAAAAAATTTGATTTTTTTAT
45641 CAGATAAATA
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
164 10 0.08
166 7 0.05
167 99 0.76
168 14 0.11
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (164 bp):
CCAACACAAAAAAATTTGAATTTTTTATCTGATAAAAAGGGATGTCCACCATGCATGACCAACAC
CAAAAAATTTTGAAAATTTTTTATCTGAAAAAAAAGGGTGTCGACCATTACATGGACAACACCAA
AAAATTTGATTTTTTTATTTGAAAAAAGGGATGG
Found at i:45591 original size:106 final size:108
Alignment explanation
Indices: 45384--45590 Score: 289
Period size: 106 Copynumber: 1.9 Consensus size: 108
45374 CTATGCATGA
*
45384 CCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGGGGGTGTCGGCCATTACATGGACA
1 CCAACACCAAAAAATTTTG-AATTTTTTTATCTGAAAAAAGGGGGTGTCAGCCATTACATGGACA
* *
45449 ACACCAAAAAATTTTGAAATTTTTTTATTTGAAAAAAGGGATGG
65 ACACCAAAAAATTTTGAAAATTTTTTATCTGAAAAAAGGGATGG
* * * *
45493 CCAACACCCAAAAA-TTTG-ATTTTTTTAT-TAGATAAATA-GGGGTGTCAGCCATTGCATGGCC
1 CCAACACCAAAAAATTTTGAATTTTTTTATCT-GA-AAAAAGGGGGTGTCAGCCATTACATGGAC
45554 AACACC-AAAAATTTTGAAAATTTTTTATCTGAAAAAA
64 AACACCAAAAAATTTTGAAAATTTTTTATCTGAAAAAA
45591 AAGGGTGTCG
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
105 30 0.34
106 38 0.43
107 4 0.04
108 4 0.04
109 13 0.15
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (108 bp):
CCAACACCAAAAAATTTTGAATTTTTTTATCTGAAAAAAGGGGGTGTCAGCCATTACATGGACAA
CACCAAAAAATTTTGAAAATTTTTTATCTGAAAAAAGGGATGG
Found at i:45631 original size:61 final size:59
Alignment explanation
Indices: 45489--45640 Score: 159
Period size: 61 Copynumber: 2.5 Consensus size: 59
45479 GAAAAAAGGG
* * * *
45489 ATGGCCAACACCCAAAAATTTG-ATTTTTTTATTAGATAAATAGGGGTGTCAGCCATTGC
1 ATGGCCAACA-CCAAAAATTTGAAATTTTTTATTAGAAAAAAAAGGGTGTCAGCCATTGC
* *
45548 ATGGCCAACACCAAAAATTTTGAAAATTTTTTATCT-GAAAAAAAAGGGTGTC-GATCATTTC
1 ATGGCCAACACCAAAAA-TTTG-AAATTTTTTAT-TAGAAAAAAAAGGGTGTCAG-CCATTGC
*
45609 ATGGCCAACACCTAAAAATTTG-ATTTTTTTAT
1 ATGGCCAACACC-AAAAATTTGAAATTTTTTAT
45641 CAGATAAATA
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
58 7 0.09
59 23 0.29
60 1 0.01
61 43 0.54
62 6 0.08
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (59 bp):
ATGGCCAACACCAAAAATTTGAAATTTTTTATTAGAAAAAAAAGGGTGTCAGCCATTGC
Found at i:45719 original size:93 final size:92
Alignment explanation
Indices: 45560--45828 Score: 355
Period size: 93 Copynumber: 2.9 Consensus size: 92
45550 GGCCAACACC
* *
45560 AAAAATTTTGAAAATTTTTTATCTGAAAAAAA-AGGGTGTCGATCATTTCATGGCCAACACCTAA
1 AAAAATTTTG-AAATTTTTTATCTGAAAAAAAGA-GGTGTCGACCATTGCATGGCCAACACCTAA
45624 AAATTTGATTTTTTTATCAGATAAATAAG
64 AAATTTGATTTTTTTATCAGATAAATAAG
* * *
45653 AAAAATTTTGAAATTTTTTAATTTGAAAAAAAGAGGTGTCGGCCATTGCATGGCCAATATCC-AA
1 AAAAATTTTGAAATTTTTT-ATCTGAAAAAAAGAGGTGTCGACCATTGCATGGCCAACA-CCTAA
*
45717 AAATTTGATTTTTTTATCAGATAAATAGG
64 AAATTTGATTTTTTTATCAGATAAATAAG
* * * **
45746 AAAAATTTTGAAATTTTTTATCTG-AAAAAGGGGGTGTCGACCATTGCATGGTCAACACAAAAAA
1 AAAAATTTTGAAATTTTTTATCTGAAAAAAAGAGGTGTCGACCATTGCATGGCCAACACCTAAAA
45810 ATTTTGAAATTTTTTTATC
66 A-TTTG--ATTTTTTTATC
45829 TGAAAAAATG
Statistics
Matches: 156, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
90 1 0.01
91 33 0.21
92 17 0.11
93 91 0.58
94 14 0.09
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (92 bp):
AAAAATTTTGAAATTTTTTATCTGAAAAAAAGAGGTGTCGACCATTGCATGGCCAACACCTAAAA
ATTTGATTTTTTTATCAGATAAATAAG
Found at i:45855 original size:62 final size:61
Alignment explanation
Indices: 45746--45949 Score: 290
Period size: 62 Copynumber: 3.4 Consensus size: 61
45736 GATAAATAGG
* * * * *
45746 AAAAATTTTGAAA-TTTTTTATCTGAAAAAGGGGGTGTCGACCATTGCATGGTCAACACAA
1 AAAAATTTTGAAATTTTTTTATCTGAAAAAAGGGATGTCAACCATTGCATGGCCAACACCA
45806 AAAAATTTTGAAATTTTTTTATCTGAAAAAATGGGATGTCAACCATTGCATGGCCAACACCA
1 AAAAATTTTGAAATTTTTTTATCTGAAAAAA-GGGATGTCAACCATTGCATGGCCAACACCA
** *
45868 AAAAATTTTGAAATTTTTTTATCTGAAAAAAGGGAATGTCAGTCATTGCATGGCCAACACCC
1 AAAAATTTTGAAATTTTTTTATCTGAAAAAAGGG-ATGTCAACCATTGCATGGCCAACACCA
45930 AAAAA-TTTG--ATTTTTTTATC
1 AAAAATTTTGAAATTTTTTTATC
45950 AGATAAATAG
Statistics
Matches: 133, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
59 11 0.08
60 13 0.10
61 23 0.17
62 86 0.65
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (61 bp):
AAAAATTTTGAAATTTTTTTATCTGAAAAAAGGGATGTCAACCATTGCATGGCCAACACCA
Found at i:45922 original size:215 final size:217
Alignment explanation
Indices: 45653--46053 Score: 594
Period size: 215 Copynumber: 1.9 Consensus size: 217
45643 GATAAATAAG
* * * *
45653 AAAAATTTTGAAATTTTTTAATTTGAAAAAAAGAGGTGTCGGCCATTGCATGGCCAATATCCAAA
1 AAAAATTTTGAAATTTTTTAATCTGAAAAAAAGAGGTGTCAGCCATTGCATGGCCAACACCCAAA
*
45718 AATTTGATTTTTTTATCAGATAAATAGGAAAAATTTTGAA-ATTTTTTATCTG-AAAAAGGGGGT
66 AATTTGATTTTTTTATCAGATAAATAGGAAAAATTTTGAATATTTTTTATCTGAAAAAAGGGGAT
** * *
45781 GTCGACCATTGCATGGTCAACACAAAAAAATTTTGAAATTTTTTTATCTGAAAAAATGGGATGTC
131 GTCGACCATTGCATGCCCAACACAAAAAAAATTTGAAATTCTTTTATCTGAAAAAATGGGATGTC
45846 AACCATTGCATGGCCAACACCA
196 AACCATTGCATGGCCAACACCA
* *
45868 AAAAATTTTGAAATTTTTTTATCTG-AAAAAAG-GGAATGTCAGTCATTGCATGGCCAACACCCA
1 AAAAATTTTGAAATTTTTTAATCTGAAAAAAAGAGG--TGTCAGCCATTGCATGGCCAACACCCA
* * * *
45931 AAAATTTGATTTTTTTATCAGATAAATAGGAAAAGTTTTGAATTTTTTTTATTTGAAAAAATGGG
64 AAAATTTGATTTTTTTATCAGATAAATAGGAAAAATTTTGAATATTTTTTATCTGAAAAAAGGGG
* * *
45996 ATGTTGATCATTGCATGCCCAACACAAAAAAAATTTGAAATTCTTTTATTTGAAAAAA
129 ATGTCGACCATTGCATGCCCAACACAAAAAAAATTTGAAATTCTTTTATCTGAAAAAA
46054 GGGGGTGTTG
Statistics
Matches: 164, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
213 2 0.01
214 7 0.04
215 87 0.53
216 10 0.06
217 58 0.35
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (217 bp):
AAAAATTTTGAAATTTTTTAATCTGAAAAAAAGAGGTGTCAGCCATTGCATGGCCAACACCCAAA
AATTTGATTTTTTTATCAGATAAATAGGAAAAATTTTGAATATTTTTTATCTGAAAAAAGGGGAT
GTCGACCATTGCATGCCCAACACAAAAAAAATTTGAAATTCTTTTATCTGAAAAAATGGGATGTC
AACCATTGCATGGCCAACACCA
Found at i:46085 original size:108 final size:108
Alignment explanation
Indices: 45967--46168 Score: 250
Period size: 107 Copynumber: 1.9 Consensus size: 108
45957 TAGGAAAAGT
* *
45967 TTTGAATTTTTTTTATTTGAA-AAAAT-GGGATGT-TGATCATTGCATGCCCAACACAAAAAAAA
1 TTTGAATTTTTTTTA-TT-AACAAAATAGGGATGTCGGCT-ATTGCATGCCCAACAC-AAAAAAA
* * *
46029 TTTGAAATTCTTTTATTTGAAAAAAGGGGGTGTTGGCCAAGCAAAAA
62 TTTAAAATTCTTTTATCTGAAAAAAAGGGGTGTTGGCCAAGCAAAAA
* * **
46076 TTTG-ATTTTTTTTATTAACTAAATAGGGGTGTCGGCTATTGCATGGTCAACACAAAAAAATTTA
1 TTTGAATTTTTTTTATTAACAAAATAGGGATGTCGGCTATTGCATGCCCAACACAAAAAAATTTA
*
46140 AAATTTTTTTATCTGAAAAAAAGGGGTGT
66 AAATTCTTTTATCTGAAAAAAAGGGGTGT
46169 CGGTCATTGC
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
106 2 0.03
107 42 0.52
108 30 0.38
109 6 0.08
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (108 bp):
TTTGAATTTTTTTTATTAACAAAATAGGGATGTCGGCTATTGCATGCCCAACACAAAAAAATTTA
AAATTCTTTTATCTGAAAAAAAGGGGTGTTGGCCAAGCAAAAA
Found at i:46290 original size:262 final size:263
Alignment explanation
Indices: 45850--46330 Score: 738
Period size: 263 Copynumber: 1.8 Consensus size: 263
45840 GATGTCAACC
* *
45850 ATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGGGAATGTCAGTCATT
1 ATTGCATGGCCAACACCAAAAAAATTTAAAATTTTTTTATCTGAAAAAAGGGAATGTCAGTCATT
*
45915 GCATGGCCAACACCCAAAAATTTGATTTTTTTATCAGATAAATAGGAAAAGTTTTGAATTTTTTT
66 GCATGGCCAACACCCAAAAATTTGATTTTTTTATCAGATAAATAGGAAAAGTTTTGAAATTTTTT
* * * *
45980 TATTTGAAAAAATGGGATGTTGATCATTGCATGCCCAACACAAAAAAAATTTGAAATTCTTTTAT
131 TATCTGAAAAAATGGGATGTCGACCATTGCATGCCCAACACAAAAAAAAATTGAAATTCTTTTAT
* *
46045 TTGAAAAAAGGGGGTGTTGGCCAAGCAAAAATTTGATTTTTTTTATTAACTAAATAGGGGTGTCG
196 TTGAAAAAAGGGGCTGTTAGCCAAGCAAAAATTTGATTTTTTTTATTAACTAAATAGGGGTGTCG
46110 GCT
261 GCT
* * *
46113 ATTGCATGGTCAACA-CAAAAAAATTTAAAATTTTTTTATCTGAAAAAAAGGG-GTGTCGGTCAT
1 ATTGCATGGCCAACACCAAAAAAATTTAAAATTTTTTTATCTG-AAAAAAGGGAATGTCAGTCAT
*
46176 TGCATGGCCAACACTCAAAAATTTGATTTTTTTTATCAGATAAATAGG-AAAGTTTTTGAAATTT
65 TGCATGGCCAACACCCAAAAATTTGA-TTTTTTTATCAGATAAATAGGAAAAG-TTTTGAAATTT
* *
46240 TTTTATCTGAAAAAAT-GGAGTGTCGGCCATTGCATAG-CCAACACAAAAAAAAATTGAAATTTT
128 TTTTATCTGAAAAAATGGGA-TGTCGACCATTGCAT-GCCCAACACAAAAAAAAATTGAAATTCT
*
46303 TTTATTTGATAAAAGGGGCTGTTAGCCA
191 TTTATTTGAAAAAAGGGGCTGTTAGCCA
46331 TTGCATAAGC
Statistics
Matches: 197, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
262 66 0.34
263 130 0.66
264 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (263 bp):
ATTGCATGGCCAACACCAAAAAAATTTAAAATTTTTTTATCTGAAAAAAGGGAATGTCAGTCATT
GCATGGCCAACACCCAAAAATTTGATTTTTTTATCAGATAAATAGGAAAAGTTTTGAAATTTTTT
TATCTGAAAAAATGGGATGTCGACCATTGCATGCCCAACACAAAAAAAAATTGAAATTCTTTTAT
TTGAAAAAAGGGGCTGTTAGCCAAGCAAAAATTTGATTTTTTTTATTAACTAAATAGGGGTGTCG
GCT
Found at i:46301 original size:62 final size:62
Alignment explanation
Indices: 46231--46352 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
46221 AGGAAAGTTT
*
46231 TTGAAATTTTTTTATCTGAAAAAATGGAG-TGTCGGCCATTGCAT-AGCCAACACAAAAAAAAA
1 TTGAAATTTTTTTATCTGAAAAAA-GGAGCTGTCAGCCATTGCATAAG-CAACACAAAAAAAAA
* * * *
46293 TTGAAATTTTTTTATTTGATAAAAGGGGCTGTTAGCCATTGCATAAGCAACACAAAAAAA
1 TTGAAATTTTTTTATCTGAAAAAAGGAGCTGTCAGCCATTGCATAAGCAACACAAAAAAA
46353 TTTGATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
61 3 0.06
62 48 0.91
63 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (62 bp):
TTGAAATTTTTTTATCTGAAAAAAGGAGCTGTCAGCCATTGCATAAGCAACACAAAAAAAAA
Found at i:50612 original size:17 final size:18
Alignment explanation
Indices: 50592--50639 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
50582 AATTCACATA
50592 AAATAACAGTTCATATG-
1 AAATAACAGTTCATATGC
*
50609 AAATAATAGTTC--ATGC
1 AAATAACAGTTCATATGC
50625 ATAATAACAGTTCAT
1 A-AATAACAGTTCAT
50640 TCAATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 1 0.04
17 21 0.84
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (18 bp):
AAATAACAGTTCATATGC
Found at i:50631 original size:34 final size:34
Alignment explanation
Indices: 50593--50661 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
50583 ATTCACATAA
* *
50593 AATAACAGTTCATATGAA-ATAATAGTTCATGCAT
1 AATAACAGTTCAT-TCAATATAATAATTCATGCAT
*
50627 AATAACAGTTCATTCAATATAATAATTCATTCAT
1 AATAACAGTTCATTCAATATAATAATTCATGCAT
50661 A
1 A
50662 TCACATCGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 3 0.10
34 28 0.90
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (34 bp):
AATAACAGTTCATTCAATATAATAATTCATGCAT
Found at i:50648 original size:17 final size:17
Alignment explanation
Indices: 50594--50659 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
50584 TTCACATAAA
*
50594 ATAACAGTTCATATGAA-
1 ATAACAGTTCAT-TCAAT
* *
50611 ATAATAGTTCATGC-AT
1 ATAACAGTTCATTCAAT
50627 AATAACAGTTCATTCAAT
1 -ATAACAGTTCATTCAAT
* *
50645 ATAATAATTCATTCA
1 ATAACAGTTCATTCA
50660 TATCACATCG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
15 1 0.03
17 36 0.92
18 2 0.05
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.35
Consensus pattern (17 bp):
ATAACAGTTCATTCAAT
Found at i:52023 original size:55 final size:55
Alignment explanation
Indices: 51962--52070 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
51952 ATGCTCCTCT
* * **
51962 CGAACTAAAATATCCTTATGCTCTAACCGAGACGTAAGCAGTCCAAAGCTCTACC
1 CGAACTAAAATAGCCTTACGCTCTAACCGAGACGTAAGCAAACCAAAGCTCTACC
* * * *
52017 CGAACTATATTAGCTTTACGCTCTAATCGAGACGTAAGCAAACCAAAGCTCTAC
1 CGAACTAAAATAGCCTTACGCTCTAACCGAGACGTAAGCAAACCAAAGCTCTAC
52071 TCGAGCTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.23
Consensus pattern (55 bp):
CGAACTAAAATAGCCTTACGCTCTAACCGAGACGTAAGCAAACCAAAGCTCTACC
Found at i:53737 original size:18 final size:18
Alignment explanation
Indices: 53711--53771 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
53701 CATATTTTGG
* *
53711 CAAAGTAGTACAATTTAC
1 CAAATTAGTACAATTCAC
*
53729 CAAATTAGTACAGTTCAC
1 CAAATTAGTACAATTCAC
* *
53747 CATATTAATACAGA-TCAC
1 CAAATTAGTACA-ATTCAC
53765 CAAATTA
1 CAAATTA
53772 ACACAATTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (18 bp):
CAAATTAGTACAATTCAC
Found at i:53772 original size:18 final size:18
Alignment explanation
Indices: 53727--53772 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
53717 AGTACAATTT
* *
53727 ACCAAATTAGTACAGTTC
1 ACCAAATTAATACAGATC
*
53745 ACCATATTAATACAGATC
1 ACCAAATTAATACAGATC
53763 ACCAAATTAA
1 ACCAAATTAA
53773 CACAATTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (18 bp):
ACCAAATTAATACAGATC
Found at i:56805 original size:11 final size:11
Alignment explanation
Indices: 56772--56837 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
56762 TAATTTTATA
*
56772 TTTAAAA-AAA
1 TTTAAAATAAT
*
56782 TTTAAATTAAT
1 TTTAAAATAAT
*
56793 TTTGAAATAAT
1 TTTAAAATAAT
*
56804 TTAAAAAATAAT
1 TT-TAAAATAAT
56816 TTT--AATAAT
1 TTTAAAATAAT
*
56825 TTTAAAATCAT
1 TTTAAAATAAT
56836 TT
1 TT
56838 GCTGACGTAG
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
9 9 0.20
10 6 0.14
11 20 0.45
12 9 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
TTTAAAATAAT
Found at i:56822 original size:21 final size:22
Alignment explanation
Indices: 56789--56831 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
56779 AAATTTAAAT
56789 TAATTTTGAAATAATTTAAAAAA
1 TAATTTT-AAATAATTTAAAAAA
*
56812 TAATTTT-AATAATTTTAAAA
1 TAATTTTAAATAATTTAAAAA
56832 TCATTTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAATTTTAAATAATTTAAAAAA
Found at i:56825 original size:32 final size:28
Alignment explanation
Indices: 56755--56830 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 28
56745 GATGATGATG
56755 ATTTTAATAATTTT--ATATTTAAAAAA
1 ATTTTAATAATTTTAAATATTTAAAAAA
*
56781 ATTTAAATTAATTTTGAAATAATTTAAAAAATA
1 ATTTTAA-TAATTTT-AAAT-ATTT-AAAAA-A
56814 ATTTTAATAATTTTAAA
1 ATTTTAATAATTTTAAA
56831 ATCATTTGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
26 6 0.15
27 7 0.17
30 2 0.05
31 7 0.17
32 12 0.29
33 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
ATTTTAATAATTTTAAATATTTAAAAAA
Found at i:62522 original size:2 final size:2
Alignment explanation
Indices: 62515--62552 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
62505 ATTCAATAAA
62515 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
62553 TTACTTTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67786 original size:57 final size:56
Alignment explanation
Indices: 67679--67790 Score: 161
Period size: 57 Copynumber: 2.0 Consensus size: 56
67669 GCCCAGCAAA
* *
67679 AGAATATCGCTCTCCCCGAGCCAGAATCAGAGTATCACTCTTTCCAAGCCAAAATC
1 AGAATATCGCTCTCACCGAGCCAAAATCAGAGTATCACTCTTTCCAAGCCAAAATC
* * * *
67735 AGAATATCGCTCTTACCGAGCTAAAATACAGAGTATCGCTCTTTCCGAGCCAAAAT
1 AGAATATCGCTCTCACCGAGCCAAAAT-CAGAGTATCACTCTTTCCAAGCCAAAAT
67791 ACAAAGTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 23 0.47
57 26 0.53
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (56 bp):
AGAATATCGCTCTCACCGAGCCAAAATCAGAGTATCACTCTTTCCAAGCCAAAATC
Found at i:67793 original size:29 final size:28
Alignment explanation
Indices: 67683--67790 Score: 135
Period size: 28 Copynumber: 3.8 Consensus size: 28
67673 AGCAAAAGAA
** *
67683 TATCGCTCTCCCCGAGCCAGAATCAGAG
1 TATCGCTCTTTCCGAGCCAAAATCAGAG
* * *
67711 TATCACTCTTTCCAAGCCAAAATCAGAA
1 TATCGCTCTTTCCGAGCCAAAATCAGAG
* *
67739 TATCGCTCTTACCGAGCTAAAATACAGAG
1 TATCGCTCTTTCCGAGCCAAAAT-CAGAG
67768 TATCGCTCTTTCCGAGCCAAAAT
1 TATCGCTCTTTCCGAGCCAAAAT
67791 ACAAAGTAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
28 41 0.62
29 25 0.38
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (28 bp):
TATCGCTCTTTCCGAGCCAAAATCAGAG
Found at i:70454 original size:11 final size:11
Alignment explanation
Indices: 70430--70473 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
70420 TGTTATACAT
70430 AATTCTTTTAA
1 AATTCTTTTAA
70441 AATT-TTTTAGA
1 AATTCTTTTA-A
*
70452 AATTCTTTTTA
1 AATTCTTTTAA
70463 AATT-TTTTAA
1 AATTCTTTTAA
70473 A
1 A
70474 TCTAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 11 0.38
11 14 0.48
12 4 0.14
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (11 bp):
AATTCTTTTAA
Found at i:70458 original size:22 final size:22
Alignment explanation
Indices: 70430--70471 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
70420 TGTTATACAT
70430 AATTCTTTTAAAATTTTTTAGA
1 AATTCTTTTAAAATTTTTTAGA
*
70452 AATTCTTTTTAAATTTTTTA
1 AATTCTTTTAAAATTTTTTA
70472 AATCTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTCTTTTAAAATTTTTTAGA
Found at i:70490 original size:17 final size:18
Alignment explanation
Indices: 70464--70505 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
70454 TTCTTTTTAA
*
70464 ATTT-TTTAAATCTA-AT
1 ATTTATTTAAAACTATAT
70480 ATTTATTTAAAACTATAT
1 ATTTATTTAAAACTATAT
*
70498 TTTTATTT
1 ATTTATTT
70506 GAAGGGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATTTAAAACTATAT
Found at i:70497 original size:16 final size:16
Alignment explanation
Indices: 70464--70501 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
70454 TTCTTTTTAA
*
70464 ATTTTTTAAATCTAAT
1 ATTTTTTAAAACTAAT
70480 ATTTATTTAAAACT-AT
1 ATTT-TTTAAAACTAAT
70496 ATTTTT
1 ATTTTT
70502 ATTTGAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 10 0.50
17 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTTAAAACTAAT
Found at i:71397 original size:17 final size:17
Alignment explanation
Indices: 71375--71410 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
71365 AGCGGCAATG
71375 TGTGATTGATGCATGTT
1 TGTGATTGATGCATGTT
71392 TGTGATTGATGCATGTT
1 TGTGATTGATGCATGTT
71409 TG
1 TG
71411 AGATGCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.47
Consensus pattern (17 bp):
TGTGATTGATGCATGTT
Found at i:84845 original size:23 final size:23
Alignment explanation
Indices: 84802--84846 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
84792 TTTGCTGTAA
*
84802 TTGTTGTTTTTGCTATGTTTTTG
1 TTGTTGTTTTTGCTATATTTTTG
84825 TTGTTG-TTTTGCTATTATTTTT
1 TTGTTGTTTTTGCTA-TATTTTT
84847 CTATTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.07, C:0.04, G:0.18, T:0.71
Consensus pattern (23 bp):
TTGTTGTTTTTGCTATATTTTTG
Found at i:84877 original size:34 final size:34
Alignment explanation
Indices: 84803--84880 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
84793 TTGCTGTAAT
* * * *
84803 TGTTGTTTTTGCTATGTTTTTGTTGTTGTTTTGC
1 TGTTATTTTTGCTATGTTTTGGTTATTGTTTGGC
* *
84837 TATTATTTTT-CTATTGTTTTGGTTATTGTTTGGG
1 TGTTATTTTTGCTA-TGTTTTGGTTATTGTTTGGC
84871 TGTTATTTTT
1 TGTTATTTTT
84881 TATGCGCTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 3 0.08
34 33 0.92
ACGTcount: A:0.08, C:0.04, G:0.21, T:0.68
Consensus pattern (34 bp):
TGTTATTTTTGCTATGTTTTGGTTATTGTTTGGC
Found at i:86049 original size:13 final size:12
Alignment explanation
Indices: 86021--86045 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
86011 AATGTAGTGT
86021 ATTTATTTTTAA
1 ATTTATTTTTAA
86033 ATTTATTTTTAA
1 ATTTATTTTTAA
86045 A
1 A
86046 ATTTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:86347 original size:21 final size:21
Alignment explanation
Indices: 86321--86360 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
86311 TAATTTATTT
86321 TAATTTAATTTTGTTAGTAAG
1 TAATTTAATTTTGTTAGTAAG
*
86342 TAATTTTATTTTGTTAGTA
1 TAATTTAATTTTGTTAGTA
86361 GTAGTAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTAAG
Found at i:86787 original size:16 final size:16
Alignment explanation
Indices: 86742--86789 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
86732 TAAACCTAGC
86742 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
86758 T-A-TAA-TA-TAAAA
1 TAATTAATTACCAAAA
86770 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
86786 TAAT
1 TAAT
86790 ATTCTCATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 5 0.19
13 3 0.12
14 6 0.23
15 3 0.12
16 9 0.35
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:86856 original size:30 final size:30
Alignment explanation
Indices: 86822--86916 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
86812 AAATGATACA
*
86822 AAATAAATATTTATTTTGTACCATTTTGGT
1 AAATAAATATTTATTTTGTACCATTTTGAT
** * * *
86852 AAAT-AAT-GGTGTGTGGATACCATTTTGAT
1 AAATAAATATTTATTTTG-TACCATTTTGAT
* *
86881 ATATAAATATTTATTTTGTACCATTTTAAT
1 AAATAAATATTTATTTTGTACCATTTTGAT
86911 AAATAA
1 AAATAA
86917 CTCATTTTGA
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
28 4 0.08
29 17 0.35
30 23 0.48
31 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTGAT
Found at i:88188 original size:43 final size:43
Alignment explanation
Indices: 88106--88190 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
88096 CATTAACAGT
*
88106 TAAATTATATTACTTGACTCGTATTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* * *
88149 TAAATTATATTATTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
88191 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:88670 original size:6 final size:6
Alignment explanation
Indices: 88661--88700 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
88651 AGCCAGAGCT
88661 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAG
88701 AAATTGGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:88676 original size:18 final size:18
Alignment explanation
Indices: 88655--88700 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
88645 CTCTAGAGCC
*
88655 AGAGCTAGAGGAAGAGGA
1 AGAGCAAGAGGAAGAGGA
*
88673 AGAGGAAGAGGAAGAGGA
1 AGAGCAAGAGGAAGAGGA
*
88691 AGAGGAAGAG
1 AGAGCAAGAG
88701 AAATTGGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.02, G:0.48, T:0.02
Consensus pattern (18 bp):
AGAGCAAGAGGAAGAGGA
Found at i:89094 original size:14 final size:14
Alignment explanation
Indices: 89074--89126 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
89064 TTTCATACTT
89074 ATAAATCTTAAACC
1 ATAAATCTTAAACC
* *
89088 CTAAATCATAAACC
1 ATAAATCTTAAACC
*
89102 ATAAACCTTAAACC
1 ATAAATCTTAAACC
*
89116 TTAAAT-TTAAA
1 ATAAATCTTAAA
89127 ACCTTAAACC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 5 0.16
14 27 0.84
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAATCTTAAACC
Found at i:89135 original size:7 final size:7
Alignment explanation
Indices: 89075--89141 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
89065 TTCATACTTA
*
89075 TAAATCT
1 TAAACCT
*
89082 TAAACCC
1 TAAACCT
* *
89089 TAAATCA
1 TAAACCT
*
89096 TAAACCA
1 TAAACCT
89103 TAAACCT
1 TAAACCT
89110 TAAACCT
1 TAAACCT
*
89117 TAAA-TT
1 TAAACCT
89123 TAAAACCT
1 T-AAACCT
*
89131 TAAACCA
1 TAAACCT
89138 TAAA
1 TAAA
89142 TTTAAAACCC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 2 0.04
7 45 0.92
8 2 0.04
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:89142 original size:21 final size:21
Alignment explanation
Indices: 89104--89150 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
89094 CATAAACCAT
*
89104 AAACCTTAAACCTTAAATTTA
1 AAACCTTAAACCATAAATTTA
89125 AAACCTTAAACCATAAATTTA
1 AAACCTTAAACCATAAATTTA
89146 AAACC
1 AAACC
89151 CTAAGCCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (21 bp):
AAACCTTAAACCATAAATTTA
Found at i:91674 original size:24 final size:24
Alignment explanation
Indices: 91646--91691 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
91636 CACCATACAC
91646 GGAGTTGGATCCTCATTTTCTACT
1 GGAGTTGGATCCTCATTTTCTACT
*
91670 GGAGTTGGATCTTCATTTTCTA
1 GGAGTTGGATCCTCATTTTCTA
91692 TAAGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.43
Consensus pattern (24 bp):
GGAGTTGGATCCTCATTTTCTACT
Found at i:93422 original size:20 final size:20
Alignment explanation
Indices: 93397--93434 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
93387 GAAAAAAATA
93397 AAAATATTTGTAATATTTCG
1 AAAATATTTGTAATATTTCG
*
93417 AAAATATTTGTATTATTT
1 AAAATATTTGTAATATTT
93435 AATTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
AAAATATTTGTAATATTTCG
Found at i:103256 original size:24 final size:23
Alignment explanation
Indices: 103196--103265 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
103186 ATATAAAAAT
103196 AATTATATTAAAA-ATGTTATTA
1 AATTATATTAAAATATGTTATTA
103218 AATTATACATT--AATATGTTTATTA
1 AATTAT--ATTAAAATATG-TTATTA
103242 AATTATATTAAAATATG--ATTA
1 AATTATATTAAAATATGTTATTA
103263 AAT
1 AAT
103266 CATTTATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
21 7 0.17
22 11 0.26
23 3 0.07
24 21 0.50
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (23 bp):
AATTATATTAAAATATGTTATTA
Found at i:103326 original size:25 final size:25
Alignment explanation
Indices: 103278--103327 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
103268 TTTATTATCT
* ** *
103278 TTTTATTAAATTTTTTTAATAATAA
1 TTTTATTAAAATTTAATAACAATAA
103303 TTTTATTAAAATTTAATAACAATAA
1 TTTTATTAAAATTTAATAACAATAA
103328 CAAAATCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTATTAAAATTTAATAACAATAA
Found at i:103899 original size:13 final size:13
Alignment explanation
Indices: 103883--103931 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
103873 TTTAGTATTA
*
103883 TTTTTTAAAAGTG
1 TTTTTGAAAAGTG
103896 TTTTT-AAAATGTG
1 TTTTTGAAAA-GTG
* *
103909 ATTTTGAAGAGTG
1 TTTTTGAAAAGTG
103922 TTTTTGAAAA
1 TTTTTGAAAA
103932 ATTTGATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 4 0.13
13 23 0.77
14 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (13 bp):
TTTTTGAAAAGTG
Found at i:103944 original size:26 final size:25
Alignment explanation
Indices: 103885--103944 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
103875 TAGTATTATT
*
103885 TTTTAAAAGTGTTTTTAAAATGTGA
1 TTTTAAGAGTGTTTTTAAAATGTGA
*
103910 TTTTGAAGAGTGTTTTTGAAAAATTTGA
1 TTTT-AAGAGTGTTTTT--AAAATGTGA
103938 -TTTAAGA
1 TTTTAAGA
103945 TTTAAGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 4 0.13
26 15 0.50
27 3 0.10
28 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (25 bp):
TTTTAAGAGTGTTTTTAAAATGTGA
Found at i:104484 original size:31 final size:31
Alignment explanation
Indices: 104396--104484 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
104386 AATTAAAATT
* *
104396 TTGAATCCC-TTAAAAATTGAAAAGAAATTTT
1 TTGAA-CCCTTTAAAAATTGAAAAAAAATTTA
* * **
104427 TTAAACCCTTTAAAAGTTGGTAAAAAATTTA
1 TTGAACCCTTTAAAAATTGAAAAAAAATTTA
104458 TTGAACCCTTTAAAAATTGAAAAAAAA
1 TTGAACCCTTTAAAAATTGAAAAAAAA
104485 ATTAAACTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 3 0.06
31 44 0.94
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (31 bp):
TTGAACCCTTTAAAAATTGAAAAAAAATTTA
Found at i:104975 original size:92 final size:92
Alignment explanation
Indices: 104818--105001 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
104808 ATCTCCTGCA
104818 AAAAGATAATAAATAAAACAATTACGAATTCGATTTCATCATTATCGTGTTTAGTTTGAATCTAA
1 AAAAGATAATAAATAAAACAATTACGAATTCGATTTCATCATTATCGTGTTTAGTTTGAATCTAA
104883 ATCATCAAATGAGTTTAACAGTTGATT
66 ATCATCAAATGAGTTTAACAGTTGATT
104910 AAAAGATAATAAATAAAACAATTACGAATTCGATTTCATCATTATCGTGTTTAGTTTGAATCTAA
1 AAAAGATAATAAATAAAACAATTACGAATTCGATTTCATCATTATCGTGTTTAGTTTGAATCTAA
104975 ATCATCAAATGAGTTTAACAGTTGATT
66 ATCATCAAATGAGTTTAACAGTTGATT
105002 TGAAAAACCC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (92 bp):
AAAAGATAATAAATAAAACAATTACGAATTCGATTTCATCATTATCGTGTTTAGTTTGAATCTAA
ATCATCAAATGAGTTTAACAGTTGATT
Found at i:107563 original size:79 final size:79
Alignment explanation
Indices: 107440--107732 Score: 424
Period size: 79 Copynumber: 3.7 Consensus size: 79
107430 TAGCACCTAG
* * * **
107440 TGCCTTGCTGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAATATCTGTCAA
1 TGCCTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCTGTCAA
107505 ATCTTGGCACCCAA
66 ATCTTGGCACCCAA
* *
107519 TGCTTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCCGTCAA
1 TGCCTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCTGTCAA
* * *
107584 ATCGTAGCACCCAG
66 ATCTTGGCACCCAA
* *
107598 TGCCTAGCGGATAAACTGCAATTGTGAGCCTAGCTCTAGTTGGATTAACCAACAATATCTGTCAA
1 TGCCTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCTGTCAA
*
107663 ATCTTGACACCCAA
66 ATCTTGGCACCCAA
* * ** *
107677 TGCCTAGCGGATAAATCACAATTGTGAGTGCAGCTCTAGTTGGATTAACGAACAAT
1 TGCCTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTTGGATTAACCAACAAT
107733 GTCCATTAAA
Statistics
Matches: 189, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 189 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (79 bp):
TGCCTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCTGTCAA
ATCTTGGCACCCAA
Found at i:107718 original size:158 final size:158
Alignment explanation
Indices: 107430--107732 Score: 471
Period size: 158 Copynumber: 1.9 Consensus size: 158
107420 CCGACGATTA
* * *
107430 TAGCACCTAGTGCCTTGCTGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAA
1 TAGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAA
* * *
107495 TATCTGTCAAATCTTGGCACCCAATGCTTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTT
66 TATCTGTCAAATCTTGACACCCAATGCCTAGCGGATAAACCACAATTGTGAGCCCAGCTCTAGTT
107560 GGATTAACCAACAATATCCGTCAAATCG
131 GGATTAACCAACAATATCCGTCAAATCG
* * * **
107588 TAGCACCCAGTGCCTAGCGGATAAACTGCAATTGTGAGCCTAGCTCTAGTTGGATTAACCAACAA
1 TAGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAA
* **
107653 TATCTGTCAAATCTTGACACCCAATGCCTAGCGGATAAATCACAATTGTGAGTGCAGCTCTAGTT
66 TATCTGTCAAATCTTGACACCCAATGCCTAGCGGATAAACCACAATTGTGAGCCCAGCTCTAGTT
*
107718 GGATTAACGAACAAT
131 GGATTAACCAACAAT
107733 GTCCATTAAA
Statistics
Matches: 130, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
158 130 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (158 bp):
TAGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAA
TATCTGTCAAATCTTGACACCCAATGCCTAGCGGATAAACCACAATTGTGAGCCCAGCTCTAGTT
GGATTAACCAACAATATCCGTCAAATCG
Found at i:112280 original size:18 final size:19
Alignment explanation
Indices: 112246--112282 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
112236 AAAACCAAGA
112246 TATTTACAATATGCATTTT
1 TATTTACAATATGCATTTT
*
112265 TATTTA-AATATTCATTTT
1 TATTTACAATATGCATTTT
112283 AAAGTATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (19 bp):
TATTTACAATATGCATTTT
Found at i:123834 original size:28 final size:30
Alignment explanation
Indices: 123754--123844 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 30
123744 TGGTAACAGG
123754 CATGACCTTTGGGTCAACAGGGAGTAAAATAAGCA
1 CATGACCTTTGGGTCAACAGGGAG-----TAAGCA
*
123789 TCATGACCTTTGGATCAACAGGGAGTAAG-A
1 -CATGACCTTTGGGTCAACAGGGAGTAAGCA
*
123819 -ATGACCTTTGGGTCAATAGGGAGTAA
1 CATGACCTTTGGGTCAACAGGGAGTAA
123845 ATCAAATATC
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
28 24 0.46
30 1 0.02
31 4 0.08
36 23 0.44
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.23
Consensus pattern (30 bp):
CATGACCTTTGGGTCAACAGGGAGTAAGCA
Found at i:127625 original size:20 final size:20
Alignment explanation
Indices: 127580--127628 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
127570 AATTTATTAA
*
127580 AACATAGGCAAATGCTAAAT
1 AACATGGGCAAATGCTAAAT
127600 AACATGGGCAAATGCTAAAT
1 AACATGGGCAAATGCTAAAT
127620 AACATGGGC
1 AACATGGGC
127629 GAAGCCGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.18
Consensus pattern (20 bp):
AACATGGGCAAATGCTAAAT
Found at i:132650 original size:6 final size:6
Alignment explanation
Indices: 132634--132667 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
132624 ATTATAATAA
*
132634 AAGGA- AAGGAG AAGGAG AAGGAG AAGGAA AAGGA
1 AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGA
132668 AAAGATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
AAGGAG
Found at i:132666 original size:18 final size:17
Alignment explanation
Indices: 132632--132671 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
132622 AAATTATAAT
*
132632 AAAAGGAAAGGAGAAGG
1 AAAAGGAAAGGAAAAGG
*
132649 AGAAGGAGAAGGAAAAGG
1 AAAAGGA-AAGGAAAAGG
132667 AAAAG
1 AAAAG
132672 ATGAAGTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (17 bp):
AAAAGGAAAGGAAAAGG
Done.