Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011849.1 Corchorus capsularis cultivar CVL-1 contig11870, 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: 134458
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:6068 original size:17 final size:17
Alignment explanation
Indices: 6046--6100 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
6036 TGTAAGTTGT
6046 TTAAAACTTGTTTAGGA
1 TTAAAACTTGTTTAGGA
*
6063 TTAAAACTTGTTTAGGC
1 TTAAAACTTGTTTAGGA
*
6080 TTTAAACTTGTTTAGGA
1 TTAAAACTTGTTTAGGA
6097 TTAA
1 TTAA
6101 GCAAATCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (17 bp):
TTAAAACTTGTTTAGGA
Found at i:6324 original size:9 final size:9
Alignment explanation
Indices: 6310--6335 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6300 TTAATCATAG
6310 ATAACATTT
1 ATAACATTT
6319 ATAACATTT
1 ATAACATTT
6328 ATAACATT
1 ATAACATT
6336 CGTATTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (9 bp):
ATAACATTT
Found at i:7370 original size:22 final size:21
Alignment explanation
Indices: 7344--7388 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
7334 GCAAAAGTGT
7344 AAAAAGTAGGGCGGTGTTTAGC
1 AAAAAG-AGGGCGGTGTTTAGC
*
7366 AAAAAGGGGGCGGTGTTTAGC
1 AAAAAGAGGGCGGTGTTTAGC
7387 AA
1 AA
7389 CATCCTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.33, C:0.09, G:0.38, T:0.20
Consensus pattern (21 bp):
AAAAAGAGGGCGGTGTTTAGC
Found at i:9698 original size:44 final size:44
Alignment explanation
Indices: 9635--9725 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
9625 TCCTTCAAGA
9635 ATTCTTCCATCCTTCCATCGTTCACCAAAGTGGGGATGGGTATT
1 ATTCTTCCATCCTTCCATCGTTCACCAAAGTGGGGATGGGTATT
9679 ATTCTTCCATCCTTCCATCGTTCACCAAAGTGGGGATGGGTATT
1 ATTCTTCCATCCTTCCATCGTTCACCAAAGTGGGGATGGGTATT
9723 ATT
1 ATT
9726 TAGTTAGGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (44 bp):
ATTCTTCCATCCTTCCATCGTTCACCAAAGTGGGGATGGGTATT
Found at i:10729 original size:89 final size:89
Alignment explanation
Indices: 10625--10802 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
10615 TTCTTTGTAA
*
10625 TTTGTTTATTTATTTGGTAGGTAGGTAGTTTATTTAAGATATAGTTTCTAGTTTGGATTGTATTC
1 TTTGTTTATTTATTTGGTAGGTAGGTAATTTATTTAAGATATAGTTTCTAGTTTGGATTGTATTC
10690 TCATTTAGATGTTTGTGCATAGAG
66 TCATTTAGATGTTTGTGCATAGAG
*
10714 TTTGTTTATTTATTTGGTAGGTAGGTAATTTATTTAAGATATAGTTTCTAGTTTGGGTTGTATTC
1 TTTGTTTATTTATTTGGTAGGTAGGTAATTTATTTAAGATATAGTTTCTAGTTTGGATTGTATTC
10779 TCATTTAGATGTTTGTGCATAGAG
66 TCATTTAGATGTTTGTGCATAGAG
10803 ATTTATATTG
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.51
Consensus pattern (89 bp):
TTTGTTTATTTATTTGGTAGGTAGGTAATTTATTTAAGATATAGTTTCTAGTTTGGATTGTATTC
TCATTTAGATGTTTGTGCATAGAG
Found at i:10883 original size:59 final size:59
Alignment explanation
Indices: 10819--10937 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
10809 ATTGCAATGA
10819 GATTTCAATGGGTTTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCGTTTCG
1 GATTTCAATGGGTTTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCGTTTCG
10878 GATTTCAATGGGTTTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCGTTTCG
1 GATTTCAATGGGTTTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCGTTTCG
10937 G
1 G
10938 TAATGTAACT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.15, C:0.08, G:0.36, T:0.40
Consensus pattern (59 bp):
GATTTCAATGGGTTTGTTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCGTTTCG
Found at i:11939 original size:16 final size:16
Alignment explanation
Indices: 11850--11956 Score: 94
Period size: 16 Copynumber: 6.8 Consensus size: 16
11840 ATTGGGCGGG
***
11850 TTCGGGTTCGGGCGCT
1 TTCGGGTTCGGGTATT
11866 TT-GGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
* *
11881 TTCGGTTTCGAGT-TCT
1 TTCGGGTTCGGGTAT-T
* *
11897 GTCGGGTTGGGGTATT
1 TTCGGGTTCGGGTATT
11913 TT-GGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
11928 TTCGGATTCGGGTATT
1 TTCGGGTTCGGGTATT
* *
11944 TCCAGGTTCGGGT
1 TTCGGGTTCGGGT
11957 CCGGGTCGAG
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
15 27 0.38
16 44 0.61
17 1 0.01
ACGTcount: A:0.07, C:0.14, G:0.38, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:13039 original size:7 final size:6
Alignment explanation
Indices: 13002--13038 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
12992 TTCAGGTAAT
13002 TTCGGG TTCGGG TTCGGG TTCGGG -T-GGG TTTCGGG TT
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG -TTCGGG TT
13039 TTGGGTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.11
5 1 0.04
6 21 0.75
7 3 0.11
ACGTcount: A:0.00, C:0.14, G:0.49, T:0.38
Consensus pattern (6 bp):
TTCGGG
Found at i:14012 original size:2 final size:2
Alignment explanation
Indices: 14005--14056 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
13995 ATTTTCTTTA
* * *
14005 AT AT AT AT AT AT AT AT AT AT AT AT TT AT CT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14047 AT AT AT AT AT
1 AT AT AT AT AT
14057 TTATCTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:14039 original size:28 final size:28
Alignment explanation
Indices: 14008--14066 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
13998 TTCTTTAATA
14008 TATATATATATATATATATATTTATCTT
1 TATATATATATATATATATATTTATCTT
14036 TATATATATATATATATATATTTATCTT
1 TATATATATATATATATATATTTATCTT
14064 TAT
1 TAT
14067 CGGCTAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATATATATATATATATATTTATCTT
Found at i:29605 original size:1 final size:1
Alignment explanation
Indices: 29599--29625 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
29589 TTCAAATTAG
29599 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
29626 GTGTTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:37694 original size:8 final size:8
Alignment explanation
Indices: 37681--37705 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
37671 CCTTCTTTTC
37681 TTTTCTTT
1 TTTTCTTT
37689 TTTTCTTT
1 TTTTCTTT
37697 TTTTCTTT
1 TTTTCTTT
37705 T
1 T
37706 CACCCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTCTTT
Found at i:37694 original size:13 final size:14
Alignment explanation
Indices: 37673--37706 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
37663 AACCTTCTCC
37673 TTCTTTTCTTTTCT
1 TTCTTTTCTTTTCT
37687 TT-TTTTCTTTT-T
1 TTCTTTTCTTTTCT
37699 TTCTTTTC
1 TTCTTTTC
37707 ACCCTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 14 0.74
14 2 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTCTTTTCTTTTCT
Found at i:41143 original size:9 final size:9
Alignment explanation
Indices: 41081--41144 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
41071 AATCATCAAC
41081 AAGAAGAGG
1 AAGAAGAGG
* *
41090 AGGAGGAGG
1 AAGAAGAGG
* *
41099 AGGAGGAGG
1 AAGAAGAGG
*
41108 AAGAAGAAG
1 AAGAAGAGG
*
41117 AAGAAGAAG
1 AAGAAGAGG
*
41126 AGGAAGAGG
1 AAGAAGAGG
*
41135 AAGATGAGG
1 AAGAAGAGG
41144 A
1 A
41145 TGAAATAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (9 bp):
AAGAAGAGG
Found at i:48753 original size:60 final size:60
Alignment explanation
Indices: 48645--48803 Score: 212
Period size: 60 Copynumber: 2.6 Consensus size: 60
48635 GCTAATTGCT
** * **
48645 CAAATAAGGGGCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGACTCTGATCTTTTAATTTGGC
* * *
48705 CAAATAAGGACTTAACGTTTGCCAAAATGCTTACATAACGACTC-GATCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAA-GACTCTGATCTTTTAATTTGGC
* *
48765 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAG
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAG
48804 GGTCTGGCAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.01
60 81 0.95
61 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (60 bp):
CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGACTCTGATCTTTTAATTTGGC
Found at i:48926 original size:60 final size:60
Alignment explanation
Indices: 48852--48969 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
48842 ACTTAGGCCC
48852 TTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGG-CCAAATTAAAAGATCGGGGCT
1 TTATTTGAGCATTTTCGATAACGTTAGGCCCTTA-TTGGACCAAATTAAAAGATCGGGGCT
* * * *
48912 TTATTTGAGTATTTTCGATAACGTTAGGCCTTTATTGGATCGAATTTAAAAGATCGGG
1 TTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTGGA-CCAAATTAAAAGATCGGG
48970 TTCTTATTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 4 0.08
60 32 0.62
61 16 0.31
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (60 bp):
TTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTGGACCAAATTAAAAGATCGGGGCT
Found at i:70025 original size:11 final size:11
Alignment explanation
Indices: 70009--70038 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
69999 GACTCGGCTT
70009 TTTTTTTTTTC
1 TTTTTTTTTTC
70020 TTTTTTTTTTC
1 TTTTTTTTTTC
70031 TTTTTTTT
1 TTTTTTTT
70039 CTTTTCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:73089 original size:19 final size:19
Alignment explanation
Indices: 73065--73108 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
73055 CAGACCAGAC
73065 AATAACAAGAAACACGTGT
1 AATAACAAGAAACACGTGT
73084 AATAACAAGAAACACGTGT
1 AATAACAAGAAACACGTGT
73103 AATAAC
1 AATAAC
73109 TATCGTAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.16
Consensus pattern (19 bp):
AATAACAAGAAACACGTGT
Found at i:74713 original size:29 final size:30
Alignment explanation
Indices: 74680--74741 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
74670 AAATAAAAAC
* *
74680 TACCAATTTTAG-ATAAAAACTACTCATTA
1 TACCAATTTTAGAAAAAAAACTACCCATTA
74709 TACCAATTTTAGAAAAAAAAACTACCCATTA
1 TACCAATTTTAG-AAAAAAAACTACCCATTA
74740 TA
1 TA
74742 AGATAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (30 bp):
TACCAATTTTAGAAAAAAAACTACCCATTA
Found at i:75386 original size:25 final size:27
Alignment explanation
Indices: 75358--75412 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
75348 GCTACAAATG
*
75358 TTTTTGTGA-TTA-ACTATAATTAGTA
1 TTTTTGTGACTAACACTATAATTAGTA
*
75383 TTTTTTTGACTAACTACTATAATTAGTA
1 TTTTTGTGACTAAC-ACTATAATTAGTA
75411 TT
1 TT
75413 AGATTGTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.32
26 2 0.08
28 15 0.60
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (27 bp):
TTTTTGTGACTAACACTATAATTAGTA
Found at i:75942 original size:3 final size:3
Alignment explanation
Indices: 75934--75996 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
75924 AAGAGGAAAA
75934 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
75982 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
75997 ATATGGTGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:81059 original size:21 final size:21
Alignment explanation
Indices: 81033--81074 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
81023 GATACGGGTT
*
81033 CGAGTCTTGCAAATGAAAAAA
1 CGAGTCTTACAAATGAAAAAA
81054 CGAGTCTTACAAATGAAAAAA
1 CGAGTCTTACAAATGAAAAAA
81075 ATAAACATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (21 bp):
CGAGTCTTACAAATGAAAAAA
Found at i:81191 original size:43 final size:43
Alignment explanation
Indices: 81130--81215 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
81120 TATTTACTTT
81130 AGGATCAATGTGATTACCAAAAAACTACCATCTCCATAAGTAA
1 AGGATCAATGTGATTACCAAAAAACTACCATCTCCATAAGTAA
*
81173 AGGATCAATGTGATTACCAAAAAACTACCATGTCCATAAGTAA
1 AGGATCAATGTGATTACCAAAAAACTACCATCTCCATAAGTAA
81216 GGTTTCAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (43 bp):
AGGATCAATGTGATTACCAAAAAACTACCATCTCCATAAGTAA
Found at i:81436 original size:16 final size:16
Alignment explanation
Indices: 81415--81515 Score: 89
Period size: 16 Copynumber: 6.3 Consensus size: 16
81405 CCGCCCGATT
*
81415 CGAGACCTGAATGACC
1 CGAGACCCGAATGACC
81431 CGAGACCCGAATGACC
1 CGAGACCCGAATGACC
81447 CGTA-ACCCGAATGACC
1 CG-AGACCCGAATGACC
* * *
81463 TGTA-ACCGGAGTGACC
1 CG-AGACCCGAATGACC
* *
81479 CAAGACCCGTATGACC
1 CGAGACCCGAATGACC
* * *
81495 TGAAACCCGAATAACC
1 CGAGACCCGAATGACC
81511 CGAGA
1 CGAGA
81516 AGTTAACCCG
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
15 1 0.01
16 65 0.97
17 1 0.01
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.12
Consensus pattern (16 bp):
CGAGACCCGAATGACC
Found at i:87718 original size:6 final size:6
Alignment explanation
Indices: 87707--87731 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
87697 GTGTTTTGAG
87707 AAATGA AAATGA AAATGA AAATGA A
1 AAATGA AAATGA AAATGA AAATGA A
87732 GAATAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAATGA
Found at i:92739 original size:25 final size:25
Alignment explanation
Indices: 92694--92741 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
92684 TTGGGCATGG
*
92694 CAAGAAGAAAGAAGGGTAAGAAGGC
1 CAAGAAGAAAGAAGAGTAAGAAGGC
*
92719 CAAGAAGAATGATAGAG-AAGAAG
1 CAAGAAGAAAGA-AGAGTAAGAAG
92742 AAGAGGATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.54, C:0.06, G:0.33, T:0.06
Consensus pattern (25 bp):
CAAGAAGAAAGAAGAGTAAGAAGGC
Found at i:93777 original size:30 final size:30
Alignment explanation
Indices: 93741--93816 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 30
93731 TCAGAAAAGC
93741 GCTTATTTGGCCTTTTTAA-AGAGTTCAGGG
1 GCTTATTTGGCC-TTTTAATAGAGTTCAGGG
**
93771 GCTTATTTGG-C-TGCAATTAGAGTTCAGGG
1 GCTTATTTGGCCTTTTAA-TAGAGTTCAGGG
93800 GCTTATTTGGCCGTTTT
1 GCTTATTTGGCC-TTTT
93817 GTATAAGTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
29 22 0.59
30 11 0.30
32 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (30 bp):
GCTTATTTGGCCTTTTAATAGAGTTCAGGG
Found at i:97683 original size:15 final size:15
Alignment explanation
Indices: 97663--97699 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
97653 TTCGTACTTT
97663 TATATATAGTATAAA
1 TATATATAGTATAAA
*
97678 TATATATAGTATAGA
1 TATATATAGTATAAA
97693 TATATAT
1 TATATAT
97700 TAGCTCCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (15 bp):
TATATATAGTATAAA
Found at i:104515 original size:12 final size:12
Alignment explanation
Indices: 104498--104524 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
104488 TCCCTGTCAA
104498 CAAATTCACTTG
1 CAAATTCACTTG
104510 CAAATTCACTTG
1 CAAATTCACTTG
104522 CAA
1 CAA
104525 GTACTATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (12 bp):
CAAATTCACTTG
Found at i:108667 original size:75 final size:75
Alignment explanation
Indices: 108544--108693 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
108534 ATCATGTTTG
* * *
108544 TAATGCATTTAGGTATTTATTAACCAACCCCTACACATCACTTTAACCATCTCATGCTCATTTCA
1 TAATGCATTTAGGTATTTACTAACCAACCCCTACACATCACTTTAACCATCTCATGCCCATTGCA
108609 CTGCCAAATA
66 CTGCCAAATA
*
108619 TAATGCATTTAGGTATTTACTAACCAACCCTTACACATCACTTTAACCATCTCATGCCCATTGCA
1 TAATGCATTTAGGTATTTACTAACCAACCCCTACACATCACTTTAACCATCTCATGCCCATTGCA
108684 CTGCCAAATA
66 CTGCCAAATA
108694 GCAATGGTTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (75 bp):
TAATGCATTTAGGTATTTACTAACCAACCCCTACACATCACTTTAACCATCTCATGCCCATTGCA
CTGCCAAATA
Found at i:108949 original size:13 final size:13
Alignment explanation
Indices: 108931--108956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
108921 GGTACGGTTA
108931 AACACTATTTTTG
1 AACACTATTTTTG
108944 AACACTATTTTTG
1 AACACTATTTTTG
108957 CCCAACCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
AACACTATTTTTG
Found at i:110773 original size:2 final size:2
Alignment explanation
Indices: 110766--110796 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
110756 GTAAGGTTAG
110766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
110797 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:110927 original size:22 final size:22
Alignment explanation
Indices: 110897--110968 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
110887 ATTATACTAT
*
110897 TTTTTATAATCCTATTATGAAA
1 TTTTGATAATCCTATTATGAAA
110919 TTTTGATAA-CCT-TCCTATGAAA
1 TTTTGATAATCCTAT--TATGAAA
* ** * *
110941 TTTTAATAATGATACTATGGAA
1 TTTTGATAATCCTATTATGAAA
110963 TTTTGA
1 TTTTGA
110969 AAACCTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 3 0.08
22 34 0.87
23 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTGATAATCCTATTATGAAA
Found at i:111008 original size:22 final size:20
Alignment explanation
Indices: 110970--111016 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
110960 GAATTTTGAA
* *
110970 AACCTTTTATAATTTTTTTT
1 AACCTTTTATAAATTTTGTT
110990 AACCTTCTTATGAAATTTTGTT
1 AACCTT-TTAT-AAATTTTGTT
111012 AACCT
1 AACCT
111017 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 4 0.17
22 13 0.57
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (20 bp):
AACCTTTTATAAATTTTGTT
Found at i:111278 original size:45 final size:46
Alignment explanation
Indices: 111157--111280 Score: 132
Period size: 45 Copynumber: 2.8 Consensus size: 46
111147 TCATACTCTG
* *
111157 AAATTTTGAT-AATC-ACACTATGAAATTTTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATTTTGATAAACCTCGCTATA
* *
111201 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAATCTTC-CTATA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAAA-CCTCGCTATA
* * *
111247 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAA
111281 CTACAAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 10 0.15
45 35 0.51
46 20 0.29
47 3 0.04
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (46 bp):
AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCGCTATA
Found at i:111281 original size:22 final size:23
Alignment explanation
Indices: 111155--111282 Score: 140
Period size: 22 Copynumber: 5.7 Consensus size: 23
111145 AATCATACTC
*
111155 TGAAATTTTGATAA-TC-ACACTA
1 TGAAATTTTGATAACTCTTC-CTA
111177 TGAAATTTTGATAAC-C-TCGCTA
1 TGAAATTTTGATAACTCTTC-CTA
*
111199 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAACTCTTCCTA
* *
111222 TAAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAACTCTTCCTA
* *
111245 TAAAATTTTGATAACT-TTCTTA
1 TGAAATTTTGATAACTCTTCCTA
*
111267 TGAAATCTTGATAACT
1 TGAAATTTTGATAACT
111283 ACAAATTTTG
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
22 52 0.55
23 41 0.43
24 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (23 bp):
TGAAATTTTGATAACTCTTCCTA
Found at i:111395 original size:22 final size:23
Alignment explanation
Indices: 111311--111404 Score: 72
Period size: 22 Copynumber: 4.3 Consensus size: 23
111301 CCCATGTTTT
111311 TTTTGATAA-CCT-CATTATGAAA
1 TTTTGATAACCCTAC-TTATGAAA
* * * *
111333 TTTTG-TTACTCTCCCTATGAAA
1 TTTTGATAACCCTACTTATGAAA
*** *
111355 TTTTGATCTGCATAC-TATGAAA
1 TTTTGATAACCCTACTTATGAAA
111377 TTTTGATAACCCT-CTTATGAAA
1 TTTTGATAACCCTACTTATGAAA
111399 TTTTGA
1 TTTTGA
111405 AAACTAAACT
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
21 3 0.05
22 48 0.87
23 4 0.07
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (23 bp):
TTTTGATAACCCTACTTATGAAA
Found at i:111607 original size:22 final size:22
Alignment explanation
Indices: 111556--111721 Score: 110
Period size: 22 Copynumber: 7.6 Consensus size: 22
111546 TCACATTCTA
* *
111556 GAAAATTTGATAACCTCTTTCT
1 GAAATTTTGATAACCTCTTTAT
111578 GAAATTTTGATAACCTCTTTAT
1 GAAATTTTGATAACCTCTTTAT
* * * *
111600 AAAATTTTGTTGATCC-CTCTAT
1 GAAATTTTGAT-AACCTCTTTAT
* * * *
111622 GAAATTCTGATAATCGCATTAT
1 GAAATTTTGATAACCTCTTTAT
*
111644 -ATAATTTTGATAACCTCACTT-T
1 GA-AATTTTGATAACCTC-TTTAT
* ** *
111666 GGAATTTTGATAACAACATTAT
1 GAAATTTTGATAACCTCTTTAT
111688 GAAATTTTGATAA--TCTTCCTAT
1 GAAATTTTGATAACCTCTT--TAT
111710 -AAATTTTGATAA
1 GAAATTTTGATAA
111722 TCTGATCTCT
Statistics
Matches: 112, Mismatches: 24, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.02
21 17 0.15
22 88 0.79
23 5 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTTTAT
Found at i:111850 original size:22 final size:22
Alignment explanation
Indices: 111821--111946 Score: 123
Period size: 22 Copynumber: 5.7 Consensus size: 22
111811 ATAATCTTCA
*
111821 TATGAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACCTCGC
* *
111843 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCGC
* *
111865 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCTCGC
* * *
111886 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCTCGC
111909 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCGC
*
111931 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
111947 TCTTTTTGAT
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
21 4 0.05
22 76 0.90
23 4 0.05
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCGC
Found at i:111871 original size:44 final size:43
Alignment explanation
Indices: 111821--112164 Score: 174
Period size: 44 Copynumber: 7.9 Consensus size: 43
111811 ATAATCTTCA
*
111821 TATGAAATTTTGATAACCACGCTATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCAC-CTATGAAATTTTGATAACCTCCC
* * * * * *
111865 CATGAAATATT-AGTAACCTCCTAATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGA-TAACCACCT-ATGAAATTTTGATAACCTCCC
* *
111909 TATGAAATTCTT-ATAACCTCGCTATGACATTTTGATAA--T--C
1 TATGAAATT-TTGATAACCAC-CTATGAAATTTTGATAACCTCCC
** * * *
111949 --T----TTTTGATAACCTTTCTATAAAATTGTGAAAATTAACCACCC
1 TATGAAATTTTGATAACC-ACCTATGAAATTTTG---A-TAACCTCCC
** * * * *
111991 TATGAAATTTCAATAACCAACCTAAGATATTTTAATAACCTGATCC
1 TATGAAATTTTGATAACC-ACCTATGAAATTTTGATAACCT--CCC
* * *
112037 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTCCA
1 TATGAAATTTTGATAACCAC-CTATGAAATTTTGATAACCTCCC
* * *
112081 TATGAAATTTTGGTAACCACGCTATGGAATTTTGATAAACT-CC
1 TATGAAATTTTGATAACCAC-CTATGAAATTTTGATAACCTCCC
* * * *
112124 TCAAGAAATTATAATAACCATCTTATGAAATTTTGATAACC
1 T-ATGAAATTTTGATAACCA-CCTATGAAATTTTGATAACC
112165 ACATAGAGAC
Statistics
Matches: 225, Mismatches: 50, Indels: 50
0.69 0.15 0.15
Matches are distributed among these distances:
33 2 0.01
34 18 0.08
35 1 0.00
37 1 0.00
38 4 0.02
40 1 0.00
42 1 0.00
43 5 0.02
44 133 0.59
45 9 0.04
46 33 0.15
48 17 0.08
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (43 bp):
TATGAAATTTTGATAACCACCTATGAAATTTTGATAACCTCCC
Found at i:112014 original size:22 final size:22
Alignment explanation
Indices: 111982--112165 Score: 97
Period size: 22 Copynumber: 8.3 Consensus size: 22
111972 TTGTGAAAAT
* *
111982 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
112004 TAACCAACCTAAGATATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
112026 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
*
112050 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
** **
112072 TAA-CTTCCATATGAAATTTTGG
1 TAACCAACC-TATGAAATTTTAA
* *
112094 TAACC-ACGCTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * * *
112116 TAAAC-TCCTCAAGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
112138 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
112160 TAACCA
1 TAACCA
112166 CATAGAGACA
Statistics
Matches: 126, Mismatches: 27, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
21 5 0.04
22 99 0.79
23 5 0.04
24 17 0.13
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:112054 original size:46 final size:44
Alignment explanation
Indices: 111989--112099 Score: 118
Period size: 46 Copynumber: 2.5 Consensus size: 44
111979 AATTAACCAC
*** *
111989 CCTATGAAATTTCAATAACCAAC-CTAAGATATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCAACACTAAGAAATTTTAATAA-CT--T
* *
112035 CCTATGAAATTTTGGTAACC-ACACTATGAAATTTTGATAACTT
1 CCTATGAAATTTTGGTAACCAACACTAAGAAATTTTAATAACTT
112078 CCATATGAAATTTTGGTAACCA
1 CC-TATGAAATTTTGGTAACCA
112100 CGCTATGGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
43 3 0.05
44 18 0.32
45 4 0.07
46 31 0.55
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCAACACTAAGAAATTTTAATAACTT
Found at i:112362 original size:19 final size:20
Alignment explanation
Indices: 112331--112368 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
112321 TATTGACATT
112331 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
112350 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
112369 ACTGATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:112689 original size:2 final size:2
Alignment explanation
Indices: 112647--112675 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
112637 ATACATAGTG
112647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
112676 CTTACTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:114529 original size:22 final size:22
Alignment explanation
Indices: 114504--114562 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
114494 ATTCAAAGGT
* * *
114504 TATCGAAATTTTATAATGTGGC
1 TATCAAAATTTCATAATGTGAC
114526 TATCAAAATTTCATAATGTGAC
1 TATCAAAATTTCATAATGTGAC
114548 TATCAAAATTTCATA
1 TATCAAAATTTCATA
114563 GGGTGGGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (22 bp):
TATCAAAATTTCATAATGTGAC
Found at i:114631 original size:22 final size:22
Alignment explanation
Indices: 114606--114647 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
114596 AATTTCCTAA
114606 GGAGGTTAACAAAATTTTATAG
1 GGAGGTTAACAAAATTTTATAG
**
114628 GGAGGTTATGAAAATTTTAT
1 GGAGGTTAACAAAATTTTAT
114648 GGAGAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (22 bp):
GGAGGTTAACAAAATTTTATAG
Found at i:114658 original size:22 final size:22
Alignment explanation
Indices: 114615--114665 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
114605 AGGAGGTTAA
**
114615 CAAAATTTTATAGGGAGGTTAT
1 CAAAATTTTATAGGGAAATTAT
*
114637 GAAAATTTTAT-GGAGAAATTAT
1 CAAAATTTTATAGG-GAAATTAT
114659 CAAAATT
1 CAAAATT
114666 ACATAGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (22 bp):
CAAAATTTTATAGGGAAATTAT
Found at i:114817 original size:22 final size:22
Alignment explanation
Indices: 114701--114915 Score: 106
Period size: 22 Copynumber: 9.8 Consensus size: 22
114691 TTCTCAAAGC
* * **
114701 GAGGTTATCGAAATTGCATGGT
1 GAGGTTATCAAAATTTCATACT
* *
114723 GTGGTTATCAAAATTTTCATAGT
1 GAGGTTATCAAAA-TTTCATACT
* * *
114746 GCGGTTA-C-CAATTTTATAGCGT
1 GAGGTTATCAAAATTTCATA-C-T
**
114768 GA--TTATCAAAATTTCATAGG
1 GAGGTTATCAAAATTTCATACT
** *
114788 GAAATTATCAAAATTTCACACT
1 GAGGTTATCAAAATTTCATACT
*
114810 GAGGTTATCAAAATTT-ATTAGT
1 GAGGTTATCAAAATTTCA-TACT
*
114832 -ATGGTTATCAAAATTTCATGGTCT
1 GA-GGTTATCAAAATTTCAT--ACT
**
114856 GA--TTAT-AAAATTTGCATAGG
1 GAGGTTATCAAAATTT-CATACT
* *
114876 GAGGTTATCGAAATTTCATAAT
1 GAGGTTATCAAAATTTCATACT
*
114898 GAGGTTATCAAATTTTCA
1 GAGGTTATCAAAATTTCA
114916 CGGTGTGATT
Statistics
Matches: 146, Mismatches: 30, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
20 13 0.09
21 12 0.08
22 99 0.68
23 20 0.14
24 1 0.01
25 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATACT
Found at i:114820 original size:44 final size:44
Alignment explanation
Indices: 114770--114915 Score: 131
Period size: 44 Copynumber: 3.3 Consensus size: 44
114760 TATAGCGTGA
**
114770 TTATCAAAATTTCATAGGGAAATTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACACTGAGG
* **
114814 TTATCAAAATTT-ATTA-GTATGGTTATCAAAATTTCATGGTCTGA--
1 TTATCAAAATTTCA-TAGGGA-GGTTATCAAAATTTCA--CACTGAGG
* * *
114858 TTAT-AAAATTTGCATAGGGAGGTTATCGAAATTTCATAATGAGG
1 TTATCAAAATTT-CATAGGGAGGTTATCAAAATTTCACACTGAGG
*
114902 TTATCAAATTTTCA
1 TTATCAAAATTTCA
114916 CGGTGTGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
42 3 0.04
43 10 0.12
44 55 0.68
45 9 0.11
46 4 0.05
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACACTGAGG
Found at i:114861 original size:66 final size:65
Alignment explanation
Indices: 114703--114935 Score: 195
Period size: 66 Copynumber: 3.6 Consensus size: 65
114693 CTCAAAGCGA
* * * * * * **
114703 GGTTATCGAAATTGCATGGTGTGGTTATCAAAATTTTCATAGTGCGGTTA-CCAATTTTATAGCG
1 GGTTATCAAAATTTCATGGTGTGATTATCAAAA-TTTCATAGTGAGGTTATCAAAATTTATAGTA
114767 T
65 T
* ** * *
114768 GATTATCAAAATTTCATAGG-GAAATTATCAAAATTTCACACTGAGGTTATCAAAATTTATTAGT
1 GGTTATCAAAATTTCAT-GGTGTGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTA-TAGT
114832 AT
64 AT
* * * *
114834 GGTTATCAAAATTTCATGGTCTGATTAT-AAAATTTGCATAGGGAGGTTATCGAAATTTCATAAT
1 GGTTATCAAAATTTCATGGTGTGATTATCAAAATTT-CATAGTGAGGTTATCAAAATTT-ATAGT
114898 GA-
64 -AT
* * * *
114900 GGTTATCAAATTTTCACGGTGTGATTGTCAATATTT
1 GGTTATCAAAATTTCATGGTGTGATTATCAAAATTT
114936 TTACGTTGTA
Statistics
Matches: 133, Mismatches: 27, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
64 13 0.10
65 40 0.30
66 72 0.54
67 8 0.06
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (65 bp):
GGTTATCAAAATTTCATGGTGTGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTATAGTAT
Found at i:116577 original size:39 final size:39
Alignment explanation
Indices: 116518--116595 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
116508 AATCGTGAAC
*
116518 CGCCCCAATCGTTTATTTTTATTTTTTGCAATTTGACAA
1 CGCCCCAATCGTTTAGTTTTATTTTTTGCAATTTGACAA
116557 CGCCCCAATCGTTTAGTTTTATTTTTTGCAATTTGACAA
1 CGCCCCAATCGTTTAGTTTTATTTTTTGCAATTTGACAA
116596 TAAGTAGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.45
Consensus pattern (39 bp):
CGCCCCAATCGTTTAGTTTTATTTTTTGCAATTTGACAA
Found at i:119907 original size:22 final size:22
Alignment explanation
Indices: 119448--119989 Score: 227
Period size: 22 Copynumber: 24.6 Consensus size: 22
119438 AATAGAAAGT
*
119448 TTATCAAAATTTCATAGTGTAG
1 TTATCAAAATTTCATAGTGTGG
*
119470 TTA-CAAAAATTTCATACG-GAGG
1 TTATC-AAAATTTCATA-GTGTGG
* * * *
119492 TTATCAAAACTTCAAAGTATAG
1 TTATCAAAATTTCATAGTGTGG
* * *
119514 TTATCAAAATTTCTTAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
* **
119536 TTAACAAAATTTCATACG-AAGG
1 TTATCAAAATTTCATA-GTGTGG
*
119558 TTATCGAAAGTTT-ATAGTGTGG
1 TTATC-AAAATTTCATAGTGTGG
****
119580 TTATCAAAATTTCATAAAAAGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
119602 TTAACAAAATATCATAAGGAGGGAG
1 TTATCAAAATTTCAT-A-GTGTG-G
*
119627 ATTATCAAAA--T--T--TGTGC
1 -TTATCAAAATTTCATAGTGTGG
* *
119644 TTATCAAAATTTCCTA--GAGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
119664 TTAACAATATTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
* * * * *
119686 TTATGAAAATTTTATGGAGAGG
1 TTATCAAAATTTCATAGTGTGG
* *
119708 TTATCAAAATTAT-ATAGAGAGG
1 TTATCAAAATT-TCATAGTGTGG
* *
119730 ATATCATAATTTCATTCTCATAG-GCAGG
1 TTATCA-AA----ATT-TCATAGTG-TGG
* *
119758 TTATCGAAATTTCATGGTGTGG
1 TTATCAAAATTTCATAGTGTGG
*
119780 TTATCAAAATTTTCATAGTGCGG
1 TTATCAAAA-TTTCATAGTGTGG
* * *
119803 TTA-C-TAATTTTATAGTGTGA
1 TTATCAAAATTTCATAGTGTGG
* * * *
119823 TCATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGTGTGG
* * *
119845 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGTGTGG
119867 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* **
119889 TTATCAAAATTTCACAGTGTCA
1 TTATCAAAATTTCATAGTGTGG
* *
119911 TTATCAAACTTTCATAG-GAAGG
1 TTATCAAAATTTCATAGTG-TGG
* ** * *
119933 TAATTGAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
119955 TTATCAAATTTTCACAGTGTTG
1 TTATCAAAATTTCATAGTGTGG
*
119977 TTATCAATATTTC
1 TTATCAAAATTTC
119990 TACGTTTGAG
Statistics
Matches: 390, Mismatches: 97, Indels: 66
0.71 0.18 0.12
Matches are distributed among these distances:
16 9 0.02
18 3 0.01
20 28 0.07
21 13 0.03
22 275 0.71
23 32 0.08
24 3 0.01
25 1 0.00
26 8 0.02
27 7 0.02
28 11 0.03
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:121937 original size:2 final size:2
Alignment explanation
Indices: 121930--121968 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
121920 GATACTAGTG
121930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
121969 GTCTTCTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:127456 original size:332 final size:331
Alignment explanation
Indices: 126843--128250 Score: 2200
Period size: 332 Copynumber: 4.2 Consensus size: 331
126833 TGTACGTTGT
* *
126843 CTAAAAACGTGTTTCGGGGCTCCGTCTCAATTTTGCATGATTTTTGGTGTCGAGACTCCTTGAAA
1 CTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAA
* *
126908 TATCTATATTCATCTTATCAAATCTCAGCCACAATACATTTAAGGATTTGTTTTTACGAGCTTCT
66 TATCTATATTCATCTAATCAAATCTCAGCCACAATGCATTTAAGGATTTGTTTTTACGAGCTTCT
* *
126973 GAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAGTATGAAAAAGGATATGAAAAGCTC
131 GAATCTTGTTTCGATTTAATTAAAAATAAATTCAGAAAAAATATGAAAAAGGATATGAAAAGCTC
*
127038 GAAAAGTCCTTCAAATTTTGTGGTGTTAAATTATATATATTTAATGAGTATTTTAGCCAAAAATT
196 GAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATTTTAGCCAAAAATT
*
127103 GAAG-AAAAATTTTTCGGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCACG
261 GAAGAAAAAATTTTT-AGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-
127167 GTTTTTTA
324 GTTTTTTA
* * *
127175 CTAAAAACGCATTTCGGGGCTCCGTCTCAATTTTGCATGATTTTTGGCATCGAGACTTCTTGAAA
1 CTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAA
127240 TATCTATATTCATCTAATCAAATCTCAGCCACAATGCATTTAAGGATTTGTTTTTACGAGCTTCT
66 TATCTATATTCATCTAATCAAATCTCAGCCACAATGCATTTAAGGATTTGTTTTTACGAGCTTCT
*
127305 GAATCTTGTTTCGATTTAATTAAAAATAAATTCAGAAAAAATATGAAAAAGGATATGAAAAGGTC
131 GAATCTTGTTTCGATTTAATTAAAAATAAATTCAGAAAAAATATGAAAAAGGATATGAAAAGCTC
**
127370 GAAAAGTCCTTCAAATTTTTTGGTGTTAAATTAGGTATATTTAATGAGTATTTTAGCCAAAAATT
196 GAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATTTTAGCCAAAAATT
* *
127435 GAAG-AAAATTTTTTAGGGACATTTTTTGAAAAATATTAGCCGAAATCGTGTACTAACCATCACA
261 GAAGAAAAAATTTTTA-GGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-
*
127499 GTTTTTTG
324 GTTTTTTA
*
127507 CTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGATTTTTGGTGTCGAGACTCCTTGAAA
1 CTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAA
*
127572 TATCTATATTCATCTTATCAAATCTCAGCCACAATGCATTTAAGGATTTGTTTTTACGAGCTTCT
66 TATCTATATTCATCTAATCAAATCTCAGCCACAATGCATTTAAGGATTTGTTTTTACGAGCTTCT
* *
127637 GAATCTTGTTTTGATTTAATTAAAAATAAATTCAGAAAAAATGTGAAAAAGGATATGAAAAGCTC
131 GAATCTTGTTTCGATTTAATTAAAAATAAATTCAGAAAAAATATGAAAAAGGATATGAAAAGCTC
* *
127702 GAAAAGTCCTTTAAATTTTTTGGTGTTCAATTATATATATTTAATGAGTATTTTAGCCAAAAATT
196 GAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATTTTAGCCAAAAATT
* * *
127767 GAAG-CAAAATTTTTCAGGACA-TTTTTG-AAAATTTTAGCCGAAATCGTATACTAACTATCACG
261 GAAGAAAAAATTTTT-AGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCACG
*
127829 ATTTTTA
325 TTTTTTA
* * * ** * *
127836 CTACAAACGCGTTTCGGGGCTCCGTCTCAGTTTTGCTTGATACTTAGCATCGAGACTCCTTGAAA
1 CTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAA
* * * *
127901 TATCTATAATCATCTAACCAAATCTCAGCCACAATGCAATTAAGAATTTGTTTTTACGAGCTTCT
66 TATCTATATTCATCTAATCAAATCTCAGCCACAATGCATTTAAGGATTTGTTTTTACGAGCTTCT
* * *
127966 GAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAGTATGAAAAAGGTTATGAAAAGCTC
131 GAATCTTGTTTCGATTTAATTAAAAATAAATTCAGAAAAAATATGAAAAAGGATATGAAAAGCTC
* *
128031 GAAAAGTCCTTCAAATTTTTTGGTGTTAAATATATACATATATATAATGAGTATTTGAGGCC-AA
196 GAAAAGTCCTTCAAATTTTTTGGTGTTAAAT-TAT--ATATATTTAATGAGTATTTTA-GCCAAA
**
128095 AATTGAAGAAAAAATTTTTATCACATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATC
257 AATTGAAGAAAAAATTTTTAGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATC
*
128160 ACTGTTTTTTG
322 AC-GTTTTTTA
* * * * **
128171 CTAAAAACGCATTTCGGGGCTCCGCCTCAATTTTGCATCATTTTCT-GCGTCGAAACTTTTTGAA
1 CTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGATTTT-TGGCGTCGAGACTCCTTGAA
128235 ATATCTATATTCATCT
65 ATATCTATATTCATCT
128251 GATCGTGTCG
Statistics
Matches: 986, Mismatches: 79, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
329 212 0.22
330 34 0.03
331 6 0.01
332 611 0.62
333 19 0.02
334 32 0.03
335 71 0.07
336 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (331 bp):
CTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAA
TATCTATATTCATCTAATCAAATCTCAGCCACAATGCATTTAAGGATTTGTTTTTACGAGCTTCT
GAATCTTGTTTCGATTTAATTAAAAATAAATTCAGAAAAAATATGAAAAAGGATATGAAAAGCTC
GAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATTTTAGCCAAAAATT
GAAGAAAAAATTTTTAGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGT
TTTTTA
Found at i:128508 original size:13 final size:12
Alignment explanation
Indices: 128474--128512 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
128464 ATCTAAATCT
128474 AAATT-TAAAGC
1 AAATTATAAAGC
*
128485 AGATTATAAAGC
1 AAATTATAAAGC
128497 AAATTAATAAAGC
1 AAATT-ATAAAGC
128510 AAA
1 AAA
128513 CAATAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 4 0.17
12 10 0.42
13 10 0.42
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (12 bp):
AAATTATAAAGC
Found at i:131042 original size:11 final size:12
Alignment explanation
Indices: 131013--131040 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
131003 ATATAAAATC
131013 AAAAATTTCGAA
1 AAAAATTTCGAA
131025 AAAAATTTCGAA
1 AAAAATTTCGAA
131037 AAAA
1 AAAA
131041 TTATTCCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (12 bp):
AAAAATTTCGAA
Found at i:134052 original size:332 final size:331
Alignment explanation
Indices: 133433--134458 Score: 1732
Period size: 332 Copynumber: 3.1 Consensus size: 331
133423 GATGTTGACC
133433 TCACGATTTTTTACTAAAAACGCGTTTCGGGGCTCCGTCTCAGTTTTGCTTGATATTTGGCATCG
1 TCACG-TTTTTTACTAAAAACGCGTTTCGGGGCTCCGTCTCAGTTTTGCTTGATATTTGGCATCG
* *
133498 AGACACCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAATGCAATTAAGGATTTGTT
65 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGCAATTAAGGATTTGTT
* *
133563 TTTACGAGCTTCTGAATCTTGTTTTGATTTAATTAAAAATAAATTCAGAAAAAATATGAAAAAGG
130 TTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAAGG
133628 ATATGAAAAGCTCGAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATT
195 ATATGAAAAGCTCGAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATT
133693 TTAGCCAAAAATTGAAGAAAAATTTTTCGGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTA
260 TTAGCCAAAAATTGAAGAAAAATTTTTCGGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTA
133758 CTAACCA
325 CTAACCA
* * * **
133765 TCACAGTTTTTTGCTAAAAACGCGTTTCGGGGCTCCGTCTCAATTTTGCATGATATTTGGTGTCG
1 TCAC-GTTTTTTACTAAAAACGCGTTTCGGGGCTCCGTCTCAGTTTTGCTTGATATTTGGCATCG
* * *
133830 AGACTCCTTGAAATATCTATATTCATCTTATCAAATCTCAGCCACAATGCATTTAAGGATTTGTT
65 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGCAATTAAGGATTTGTT
133895 TTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAAGG
130 TTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAAGG
133960 ATATGAAAAGCTCGAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATT
195 ATATGAAAAGCTCGAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATT
134025 TTAGCCAAAAATTGAAGAAAAATTTTTCGGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTA
260 TTAGCCAAAAATTGAAGAAAAATTTTTCGGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTA
**
134090 CTAAGTA
325 CTAACCA
134097 TCACGATTTTTTACTAAAAACGCGTTTCGGGGCTCCGTCTCAGTTTTGCTTGATATTTGGCATCG
1 TCACG-TTTTTTACTAAAAACGCGTTTCGGGGCTCCGTCTCAGTTTTGCTTGATATTTGGCATCG
134162 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGCAATTAAGGATTTGTT
65 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGCAATTAAGGATTTGTT
*
134227 TTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAGTATGAAAAAGG
130 TTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAAGG
* * * *
134292 TTATAAAAAGCTCGAAAAGTTCTTC-AATTTTTTGGTGTTAAATTATATATATATATATATAATT
195 ATATGAAAAGCTCGAAAAGTCCTTCAAATTTTTTGGTGTT-AA--AT-TATATATAT-T-TAATG
* * * *
134356 AGTATTTGAGCCCATAATTGAAGAAAAAATTTTCGGGACATTTTTTGAAAAATTTTAGCCGAAAT
254 AGTATTTTAGCCAAAAATTGAAGAAAAATTTTTCGGGACATTTTTTGAAAAATTTTAGCCGAAAT
*
134421 CGTGTACTCACCA
319 CGTGTACTAACCA
134434 TCAC-TATTTTTACTAAAAACGCGTT
1 TCACGT-TTTTTACTAAAAACGCGTT
Statistics
Matches: 651, Mismatches: 34, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
331 15 0.02
332 524 0.80
333 1 0.00
334 2 0.00
335 10 0.02
336 20 0.03
337 79 0.12
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (331 bp):
TCACGTTTTTTACTAAAAACGCGTTTCGGGGCTCCGTCTCAGTTTTGCTTGATATTTGGCATCGA
GACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGCAATTAAGGATTTGTTT
TTACGAGCTTCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAAGGA
TATGAAAAGCTCGAAAAGTCCTTCAAATTTTTTGGTGTTAAATTATATATATTTAATGAGTATTT
TAGCCAAAAATTGAAGAAAAATTTTTCGGGACATTTTTTGAAAAATTTTAGCCGAAATCGTGTAC
TAACCA
Done.