Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016501.1 Corchorus capsularis cultivar CVL-1 contig16522, 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: 105995
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:735 original size:35 final size:35
Alignment explanation
Indices: 681--971 Score: 333
Period size: 35 Copynumber: 8.3 Consensus size: 35
671 AACTCCTCTG
* * * * *
681 GATCAAATCTGATCATTGGAAATTTCTTG-AAATGA
1 GATCAACTCTGATCGTTGGAAACTAC-TGAAAATGC
* * * *
716 GATCACCTCTGTTTGTTGGAAACTACTGAAAATGT
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
751 GATCAACTCTGATCGTTGGAAACTACTG-AAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
785 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
*
820 GATCAACTCTGATCGTTGGAGAA-TGCTGAAAATGC
1 GATCAACTCTGATCGTTGGA-AACTACTGAAAATGC
*
855 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
* * *
890 GATCAACTCTGATCGTTGGAAACTTCTTG-GAATGA
1 GATCAACTCTGATCGTTGGAAACTAC-TGAAAATGC
* * * *
925 GATCAACTCTGA-CCTCTGAAAACTTCTTG-AAATGA
1 GATCAACTCTGATCGT-TGGAAACTAC-TGAAAATGC
960 GATCAACTCTGA
1 GATCAACTCTGA
972 CCTCTGAAAA
Statistics
Matches: 229, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
34 39 0.17
35 186 0.81
36 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (35 bp):
GATCAACTCTGATCGTTGGAAACTACTGAAAATGC
Found at i:770 original size:70 final size:69
Alignment explanation
Indices: 681--1707 Score: 543
Period size: 70 Copynumber: 14.7 Consensus size: 69
671 AACTCCTCTG
* * * * * *
681 GATCAAATCTGATCATTGGAAATTTCTTGAAATGAGATCACCTCTGTTTGTTGGAAACTACTGAA
1 GATCAACTCTGATCGTTGGAAACTTC-TGAAATGAGATCAACTCTGATCGTTGGAAACTACTGAA
*
746 AATGT
65 AATGC
* *
751 GATCAACTCTGATCGTTGGAAACTACTGAAATGCGATCAACTCTGATCGTTGGAAACTACTGAAA
1 GATCAACTCTGATCGTTGGAAACTTCTGAAATGAGATCAACTCTGATCGTTGGAAACTACTGAAA
816 ATGC
66 ATGC
* * *
820 GATCAACTCTGATCGTTGGAGAA-TGCTGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGA
1 GATCAACTCTGATCGTTGGA-AACTTCTG-AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
884 AAATGC
64 AAATGC
* * * *
890 GATCAACTCTGATCGTTGGAAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG
1 GATCAACTCTGATCGTTGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAACTAC-TG
*
954 -AAATGA
63 AAAATGC
* * * * * *
960 GATCAACTCTGA-CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGAAAACTTCTT
1 GATCAACTCTGATCGT-TGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAACTAC-T
*
1023 G-AAATGA
62 GAAAATGC
* * * * * * *
1030 GATCAACTCTGA-CCTCTGAAAACTTCTTGGAATGAGATCAAATCTGA-CCTCTGAAAACTTCTT
1 GATCAACTCTGATCGT-TGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAACTAC-T
*
1093 G-AAATGA
62 GAAAATGC
* * * *
1100 GATCAACTCTGA-CCTCTGAAAACTTCTTTAAAATGAGATCAACTCTGACCTC-TT-GAAACTTC
1 GATCAACTCTGATCGT-TGGAAACTTC--TGAAATGAGATCAACTCTGA--TCGTTGGAAACTAC
* * *
1162 TTAATATGA
61 TGAAAATGC
* * * * **
1171 GATCAACTCTGA-CCTCTGGAAACTTCTTGATATGAGATCAACTCTGA-CCTCTGAAAACTTGTT
1 GATCAACTCTGATCGT-TGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAAC-TACT
*
1234 G-AAATGA
62 GAAAATGC
* ** * * * *
1241 GATCAACTCTGA-CCTCTAAAAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGAAAACTTCTT
1 GATCAACTCTGATCGT-TGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAACTAC-T
*
1304 G-AAATGA
62 GAAAATGC
* * * * * *
1311 GATCAACTCTGA-CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGAAAACTTATT
1 GATCAACTCTGATCGT-TGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAAC-TACT
*
1374 G-AAATGA
62 GAAAATGC
* * * * * * *
1381 GATCAACTCTGA-CCTCTGAAAACTTCTTGCAATGAGATCAACTCTGA-CCTCGGAAAACTTCTT
1 GATCAACTCTGATCGT-TGGAAACTTC-TGAAATGAGATCAACTCTGATCGTTGG-AAACTACTG
* *
1444 AGAATGA
63 AAAATGC
* * * * * * * *
1451 GATCAATTCTGACCTTTGAAAACTTCTTGCAATGAGATCAACTCTGA-CCTCTGAAAACTTCATG
1 GATCAACTCTGATCGTTGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAACTAC-TG
*
1515 -AAATGA
63 AAAATGC
* * * * *
1521 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGATCAACTCTGA-CCTCTGAAAACTTCTT
1 GATCAACTCTGATCGT-TGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAACTAC-T
* *
1584 G-ATATGA
62 GAAAATGC
* * * * * *
1591 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAAGGAGATCAACTCTGA-CCTCTGAAAACTTCTT
1 GATCAACTCTGATCGT-TGGAAACTTC-TGAAATGAGATCAACTCTGATCGT-TGGAAACTAC-T
* *
1654 G-ATATGA
62 GAAAATGC
* *
1661 GATCAACTCTGA-CCTCGGAAAACTTCTTGAAATGAGATCAACTCTGA
1 GATCAACTCTGATCGTTGG-AAACTTC-TGAAATGAGATCAACTCTGA
1708 CCTCTGAAAA
Statistics
Matches: 865, Mismatches: 67, Indels: 50
0.88 0.07 0.05
Matches are distributed among these distances:
67 1 0.00
68 1 0.00
69 76 0.09
70 718 0.83
71 66 0.08
72 1 0.00
73 1 0.00
74 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (69 bp):
GATCAACTCTGATCGTTGGAAACTTCTGAAATGAGATCAACTCTGATCGTTGGAAACTACTGAAA
ATGC
Found at i:972 original size:35 final size:35
Alignment explanation
Indices: 884--1727 Score: 1390
Period size: 35 Copynumber: 24.1 Consensus size: 35
874 AAAATACTGA
* * *
884 AAATGCGATCAACTCTGATCGT-TGGAAACTTCTTG
1 AAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG
*
919 GAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
954 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
989 GAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1024 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1059 GAATGAGATCAAATCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1094 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTTA
1 AAATGAGATCAACTCTGACCTCTGAAAACTTC-TTG
1130 AAATGAGATCAACTCTGACCTCTTG-AAACTTCTT-
1 AAATGAGATCAACTCTGACCTC-TGAAAACTTCTTG
*
1164 AATATGAGATCAACTCTGACCTCTGGAAACTTCTTG
1 AA-ATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1200 ATATGAGATCAACTCTGACCTCTGAAAACTTGTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1235 AAATGAGATCAACTCTGACCTCTAAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1270 GAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1305 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1340 GAATGAGATCAACTCTGACCTCTGAAAACTTATTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1375 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1410 CAATGAGATCAACTCTGACCTCGGAAAACTTCTT-
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1444 AGAATGAGATCAATTCTGACCTTTGAAAACTTCTTG
1 A-AATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1480 CAATGAGATCAACTCTGACCTCTGAAAACTTCATG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1515 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1550 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1585 ATATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1620 AAAGGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1655 ATATGAGATCAACTCTGACCTCGGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1690 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1725 AAA
1 AAA
1728 GACCGCATAG
Statistics
Matches: 756, Mismatches: 45, Indels: 16
0.93 0.06 0.02
Matches are distributed among these distances:
34 6 0.01
35 716 0.95
36 32 0.04
37 2 0.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (35 bp):
AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
Found at i:2950 original size:37 final size:36
Alignment explanation
Indices: 2883--2959 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
2873 AAATTTTTGA
** *
2883 AAAACATTTTTCTTTTGAAAAAATTGCACTTCGAGG
1 AAAACATTTTTCTTTTGAAAAAATCACACTTCGAAG
* *
2919 AAAACATTTTTTCTTTTGAAAAGATCACACTTTGAAG
1 AAAACA-TTTTTCTTTTGAAAAAATCACACTTCGAAG
2956 AAAA
1 AAAA
2960 TCTTCTTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 6 0.17
37 29 0.83
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (36 bp):
AAAACATTTTTCTTTTGAAAAAATCACACTTCGAAG
Found at i:3680 original size:20 final size:19
Alignment explanation
Indices: 3655--3711 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
3645 ATCAGTCCAT
3655 TTCTTTCATTTTTTTTTTGC
1 TTCTTTC-TTTTTTTTTTGC
*
3675 TTCTTT-TTTTTTTCTTGC
1 TTCTTTCTTTTTTTTTTGC
3693 -T-TTTCTTTTTTCTTTTGC
1 TTCTTTCTTTTTT-TTTTGC
3711 T
1 T
3712 GATGGGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 3 0.09
17 7 0.22
18 16 0.50
20 6 0.19
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (19 bp):
TTCTTTCTTTTTTTTTTGC
Found at i:3683 original size:14 final size:15
Alignment explanation
Indices: 3664--3702 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
3654 TTTCTTTCAT
3664 TTTTTTTTTGCTT-C
1 TTTTTTTTTGCTTGC
*
3678 TTTTTTTTTTCTTGC
1 TTTTTTTTTGCTTGC
3693 TTTTCTTTTT
1 TTTT-TTTTT
3703 TCTTTTGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 5 0.23
16 5 0.23
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTGCTTGC
Found at i:3683 original size:15 final size:15
Alignment explanation
Indices: 3663--3706 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
3653 ATTTCTTTCA
3663 TTTTTTTTTTGCTT-C
1 TTTTTTTTTT-CTTGC
3678 TTTTTTTTTTCTTGC
1 TTTTTTTTTTCTTGC
3693 TTTTCTTTTTTCTT
1 TTTT-TTTTTTCTT
3707 TTGCTGATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.11
15 15 0.56
16 9 0.33
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTCTTGC
Found at i:7053 original size:25 final size:25
Alignment explanation
Indices: 7014--7069 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
7004 CAAATCTCAC
*
7014 TTTTAGGTTTCGAATTTTAATGATA
1 TTTTAGGTTTCGAATTTTAATCATA
* *
7039 TTTTAGTTTTTGAATTTTAATCATA
1 TTTTAGGTTTCGAATTTTAATCATA
7064 TCTTTA
1 T-TTTA
7070 TTATTTAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (25 bp):
TTTTAGGTTTCGAATTTTAATCATA
Found at i:7173 original size:66 final size:66
Alignment explanation
Indices: 7080--7204 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
7070 TTATTTAGTC
*
7080 TCCCACAAATTGGCAAGACCCCAAATTAT-TATTTAATTAATTATGTTT-TTATGATTTTTCTAG
1 TCCCACAAATTGGCAAGAACCCAAATTATCT-TTTAATTAATTAT-TTTATTATGATTTTTCTAG
7143 ACT
64 ACT
* * * *
7146 TCCCACAAATTGGCAA-AATCTAGAATTATCTTTTAATTATTTATTTTATTATTATTTTT
1 TCCCACAAATTGGCAAGAACCCA-AATTATCTTTTAATTAATTATTTTATTATGATTTTT
7205 ATAATTGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
65 6 0.12
66 44 0.86
67 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (66 bp):
TCCCACAAATTGGCAAGAACCCAAATTATCTTTTAATTAATTATTTTATTATGATTTTTCTAGAC
T
Found at i:22874 original size:58 final size:58
Alignment explanation
Indices: 22804--23148 Score: 654
Period size: 58 Copynumber: 5.9 Consensus size: 58
22794 TATTCTCTTC
22804 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
22862 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
22920 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
*
22978 AAAAGTCCTCAAACACAAGGGTATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
*
23036 AAAAGTCCTCAAACACAAGGGCATTCATAGGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
* *
23094 AAAAGTCCTCAAACACAAGGGTATTCATAAGTCCCTAAACACAGAGACATCTATA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
23149 TCAAAGTCCC
Statistics
Matches: 281, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 281 1.00
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.19
Consensus pattern (58 bp):
AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
Found at i:24524 original size:72 final size:73
Alignment explanation
Indices: 24422--24906 Score: 669
Period size: 72 Copynumber: 6.7 Consensus size: 73
24412 GTCCTCTTCT
24422 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
24487 ATCTTCCA
66 ATCTTCCA
*
24495 T-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
24559 ATCTTCCA
66 ATCTTCCA
* *
24567 T-ATTGCGGTTGTAGTCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
24631 ATCTTCCA
66 ATCTTCCA
* * * *** *
24639 T-ATTGCGGTTGTAGTCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTATGCGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
*
24703 ATGTT-CA
66 ATCTTCCA
* * * * *** *
24710 TCATTGCGATTGTAGCCGAGGTAGTTCCCACATCTAGCAGTCCTTCGCACAACCCTTATGCGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
*
24775 ATATT-CA
66 ATCTTCCA
* * * ** *
24782 TCATTACGATTGTAGCCGAGCCAGTTCCCACATTTGGCAGTCTTTCGCACAATCCTTATGTGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
24847 ATCTTCC-
66 ATCTTCCA
* *
24854 TCATTGCGATTGTAGCCGAGGTAGTTCCCACA-TTGGCAGTCTTTCGCACAATC
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATC
24907 TATGCTACTA
Statistics
Matches: 384, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
71 24 0.06
72 358 0.93
73 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (73 bp):
TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
ATCTTCCA
Found at i:28240 original size:39 final size:39
Alignment explanation
Indices: 28148--28257 Score: 116
Period size: 39 Copynumber: 2.8 Consensus size: 39
28138 CTCTCTCCCC
* * * *
28148 AAAGTCCCCAAACACATATAACATAGGGGCAATTCTTTCT
1 AAAGTCCCTAAACACATATAACACAAGGGC-ATTCTTACT
*
28188 AAAGT-CCTCAAACACATATAACACAAAGGCA-TCTATACT
1 AAAGTCCCT-AAACACATATAACACAAGGGCATTCT-TACT
**
28227 AAAGTCCCTAAACACATGCAACACAAGGGCA
1 AAAGTCCCTAAACACATATAACACAAGGGCA
28258 ATTTTCTCTA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 3 0.05
39 30 0.51
40 26 0.44
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (39 bp):
AAAGTCCCTAAACACATATAACACAAGGGCATTCTTACT
Found at i:29774 original size:28 final size:28
Alignment explanation
Indices: 29725--29778 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
29715 ACATGTGTAC
* *
29725 ATAATTCTGTTTGACATGTACATAATTA
1 ATAATTCTGTATGACATATACATAATTA
* *
29753 ATAATTTTGTATGATATATACATAAT
1 ATAATTCTGTATGACATATACATAAT
29779 ATTATAGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (28 bp):
ATAATTCTGTATGACATATACATAATTA
Found at i:30676 original size:107 final size:107
Alignment explanation
Indices: 30490--30754 Score: 401
Period size: 107 Copynumber: 2.5 Consensus size: 107
30480 AATTTTTCTA
* ** *
30490 ACCCTTAAAATAAAATTTTAATTTTAATTTGG-GTTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTAATTATATATTTTA
* *
30553 TTTCTAAAACTCTATAACAATAAATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
* * * *
30595 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGCGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTAATTATATATTTTA
*
30660 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
30702 ACCCTTAAAATAAAAATAAAATTTTAATTT-GAGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGA-GCTAAACTTAGTGAAATTAA
30755 GGTTAAACTT
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
105 29 0.20
106 13 0.09
107 102 0.71
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (107 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
Found at i:31002 original size:18 final size:16
Alignment explanation
Indices: 30965--30995 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
30955 AATAAAAATT
30965 AAATATTATTATTTTA
1 AAATATTATTATTTTA
30981 AAATATT-TTATTTTA
1 AAATATTATTATTTTA
30996 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATATTATTATTTTA
Found at i:32161 original size:15 final size:16
Alignment explanation
Indices: 32143--32173 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
32133 TAAATTTCAA
32143 TAAAATAA-AATATTT
1 TAAAATAATAATATTT
32158 TAAAATAATAATATTT
1 TAAAATAATAATATTT
32174 AATTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATAATAATATTT
Found at i:33316 original size:15 final size:15
Alignment explanation
Indices: 33298--33330 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
33288 GTGATATTTC
*
33298 CAGAGTTGATTCCAA
1 CAGAGCTGATTCCAA
33313 CAGAGCTGATTCCAA
1 CAGAGCTGATTCCAA
33328 CAG
1 CAG
33331 TAAATATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (15 bp):
CAGAGCTGATTCCAA
Found at i:34233 original size:50 final size:50
Alignment explanation
Indices: 34158--34257 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
34148 AAAAAGGTCA
* * *
34158 AGCTAGAATGATTATGAAGACAAGATGATTAACAAAATGGCTCAAGCTTT
1 AGCTAGAATGATCATGAAGACAAGATGATCAACAAAATGCCTCAAGCTTT
* * *
34208 AGCTAGACTGATCCTGAAGACAAGATGATCAACAAAATGCCTCGAGCTTT
1 AGCTAGAATGATCATGAAGACAAGATGATCAACAAAATGCCTCAAGCTTT
34258 GAATGACTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (50 bp):
AGCTAGAATGATCATGAAGACAAGATGATCAACAAAATGCCTCAAGCTTT
Found at i:36416 original size:2 final size:2
Alignment explanation
Indices: 36409--36433 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36399 CTTGGAAATG
36409 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 A
36434 ACTGTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39683 original size:14 final size:14
Alignment explanation
Indices: 39664--39717 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
39654 GTCTTGATTT
39664 AAATAA-AAGTACAA
1 AAATAATAA-TACAA
39678 AAATAATAATACAA
1 AAATAATAATACAA
* *
39692 AAA-AAT-ATATAG
1 AAATAATAATACAA
*
39704 TAATAATAATACAA
1 AAATAATAATACAA
39718 GAATTGCATA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 18 0.56
15 2 0.06
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATAATAATACAA
Found at i:42085 original size:2 final size:2
Alignment explanation
Indices: 42078--42106 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42068 CTCTAGTATG
42078 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
42107 TAAGCAAATG
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:43058 original size:41 final size:42
Alignment explanation
Indices: 42979--43090 Score: 124
Period size: 41 Copynumber: 2.7 Consensus size: 42
42969 TTTGATAATC
* * * *
42979 AAGAGTCAAGGTAAGAG-ATTAATCAGTGAAATCAGTAATTA
1 AAGAGTCAAAGTAAAAGAAGTAATCAGTAAAATCAGTAATTA
*
43020 AAGAGTCAAAGTAAAAGAAGTAATCAGTAAAAT-GGTAATTA
1 AAGAGTCAAAGTAAAAGAAGTAATCAGTAAAATCAGTAATTA
* *
43061 AA-AGT-AAGAGTAAAAAAAGCAATCAGTAAA
1 AAGAGTCAA-AGTAAAAGAAGTAATCAGTAAA
43091 TCGGTAAAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.03
40 23 0.37
41 24 0.39
42 13 0.21
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.21
Consensus pattern (42 bp):
AAGAGTCAAAGTAAAAGAAGTAATCAGTAAAATCAGTAATTA
Found at i:43097 original size:40 final size:42
Alignment explanation
Indices: 42999--43097 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 42
42989 GTAAGAGATT
* * * *
42999 AATCAGTGAAATCAGTAATTAAAGAGTCAAAGTAAAAGAAGT
1 AATCAGTAAAATCGGTAATTAAAGAGTCAAAGTAAAAAAAGC
43041 AATCAGTAAAAT-GGTAATTAAA-AGT-AAGAGTAAAAAAAGC
1 AATCAGTAAAATCGGTAATTAAAGAGTCAA-AGTAAAAAAAGC
43081 AATCAGT-AAATCGGTAA
1 AATCAGTAAAATCGGTAA
43098 AGAGTAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
39 6 0.12
40 25 0.49
41 9 0.18
42 11 0.22
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (42 bp):
AATCAGTAAAATCGGTAATTAAAGAGTCAAAGTAAAAAAAGC
Found at i:43141 original size:22 final size:22
Alignment explanation
Indices: 43106--43483 Score: 220
Period size: 22 Copynumber: 17.1 Consensus size: 22
43096 AAAGAGTAAA
43106 AATCAGTAAA-AGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
*
43127 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
* *
43149 AATCAGTGAAG-GCAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
43170 AATCAGTAAAGAGTAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
*
43192 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
*
43214 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
* *
43236 AATTAGTAAA-AGGT--AATCAGT
1 AATCAGTAAAGA-GTAAAAT-GGT
* * *
43257 AA-GAGCAAA-ATGGTAAAATAGT
1 AATCAGTAAAGA--GTAAAATGGT
* *
43279 AATTAGTAAAAAGTAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
43301 AATCAGTAAAAAGTAAAATCGT
1 AATCAGTAAAGAGTAAAATGGT
** *
43323 AAAAAGTGATAATAATCAGTAAAA-GGT
1 AATCA--G-T-A-AA-GAGTAAAATGGT
*
43350 AAAATGGTAATCAGT-AAGAGCAAAATGGT
1 --AA---T---CAGTAAAGAGTAAAATGGT
*
43379 AATCAGTAAAGGGTAAAA-GGT
1 AATCAGTAAAGAGTAAAATGGT
*
43400 AATCAGT-AAGAGCAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
43421 AATCAGTAAAGAGT-AAA----
1 AATCAGTAAAGAGTAAAATGGT
43438 AATCAGTAAA-AGGTAAGAA-GGT
1 AATCAGTAAAGA-GTAA-AATGGT
* *
43460 TATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
43482 AA
1 AA
43484 AAAGTAATCA
Statistics
Matches: 286, Mismatches: 33, Indels: 75
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.00
17 12 0.04
18 1 0.00
19 2 0.01
20 17 0.06
21 70 0.24
22 138 0.48
23 11 0.04
24 3 0.01
25 1 0.00
26 1 0.00
27 6 0.02
28 13 0.05
29 7 0.02
32 1 0.00
33 1 0.00
35 1 0.00
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGGT
Found at i:43222 original size:87 final size:86
Alignment explanation
Indices: 43106--43483 Score: 357
Period size: 87 Copynumber: 4.5 Consensus size: 86
43096 AAAGAGTAAA
43106 AATCAGT-AAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTGAAG-GCAAAATGG
1 AATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGT-AAGAG-AAAATGG
43169 TAATCAGT-AAAGAGTAAAATGGT
64 TAATCAGTAAAAG-GTAAAATGGT
* * ** *
43192 AATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATTAGTAAAAGGTAATCAGT
1 AATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAGAGAAAAT-GGT
* * *
43257 AA-GAGCAAAATGGTAAAATAGT
65 AATCAGTAAAA-GGTAAAATGGT
* * * * *
43279 AATTAGTAAAAAGTAA-AATGGTAATCAGTAAAAAGTAAAATCGTAA--A--AAGTGATAA---T
1 AATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAGAGAAAATGGT
43336 AATCAGTAAAAGGTAAAATGGT
65 AATCAGTAAAAGGTAAAATGGT
* * * *
43358 AATCAGT-AAGAGCAA-AATGGTAATCAGTAAAGGGTAAAA-GGTAATCAGTAAGAGCAAAATGG
1 AATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAGAG-AAAATGG
43420 TAATCAGT-AAAGAGT-AAA----
64 TAATCAGTAAAAG-GTAAAATGGT
* *
43438 AATCAGTAAAAGGTAAGAAGGTTATCAGTAAAGAGTAAAATAGTAA
1 AATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAA
43484 AAAGTAATCA
Statistics
Matches: 242, Mismatches: 31, Indels: 42
0.77 0.10 0.13
Matches are distributed among these distances:
77 4 0.02
78 28 0.12
79 20 0.08
80 13 0.05
81 28 0.12
82 9 0.04
83 6 0.02
84 7 0.03
85 11 0.05
86 16 0.07
87 99 0.41
88 1 0.00
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (86 bp):
AATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAGAGAAAATGGTA
ATCAGTAAAAGGTAAAATGGT
Found at i:43279 original size:36 final size:38
Alignment explanation
Indices: 43196--43280 Score: 115
Period size: 36 Copynumber: 2.3 Consensus size: 38
43186 AATGGTAATC
*
43196 AGTAAAA-AGTAAGAAGGTAATCAGTAAAGAGTAAAAT
1 AGTAAAATAGTAAGAAGGTAATCAGTAAAGAGCAAAAT
*
43233 AGT-AATTAGTAA-AAGGTAATCAGT-AAGAGCAAAAT
1 AGTAAAATAGTAAGAAGGTAATCAGTAAAGAGCAAAAT
*
43268 GGTAAAATAGTAA
1 AGTAAAATAGTAA
43281 TTAGTAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 12 0.29
36 22 0.52
37 8 0.19
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (38 bp):
AGTAAAATAGTAAGAAGGTAATCAGTAAAGAGCAAAAT
Found at i:43376 original size:21 final size:21
Alignment explanation
Indices: 43361--43438 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
43351 AAATGGTAAT
*
43361 CAGTAAGAGCAAAATGGTAAT
1 CAGTAAGAGTAAAATGGTAAT
*
43382 CAGTAAAGGGTAAAA-GGTAAT
1 CAGT-AAGAGTAAAATGGTAAT
*
43403 CAGTAAGAGCAAAATGGTAAT
1 CAGTAAGAGTAAAATGGTAAT
43424 CAGTAAAGAGTAAAA
1 CAGT-AAGAGTAAAA
43439 ATCAGTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.16
21 24 0.49
22 17 0.35
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.18
Consensus pattern (21 bp):
CAGTAAGAGTAAAATGGTAAT
Found at i:43390 original size:42 final size:41
Alignment explanation
Indices: 43335--43438 Score: 172
Period size: 42 Copynumber: 2.4 Consensus size: 41
43325 AAAGTGATAA
43335 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
1 TAATCAGT-AAAGGTAAAA-GGTAATCAGTAAGAGCAAAATGG
43378 TAATCAGTAAAGGGTAAAAGGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAA-GGTAAAAGGTAATCAGTAAGAGCAAAATGG
43420 TAATCAGTAAAGAGTAAAA
1 TAATCAGTAAAG-GTAAAA
43439 ATCAGTAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
41 1 0.02
42 43 0.73
43 15 0.25
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (41 bp):
TAATCAGTAAAGGTAAAAGGTAATCAGTAAGAGCAAAATGG
Found at i:43489 original size:22 final size:22
Alignment explanation
Indices: 43464--43519 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 22
43454 GAAGGTTATC
* *
43464 AGTAAAGAGTAAAATAGT-AAAA
1 AGTAAACAGTAAAA-AGTAAAAT
* *
43486 AGTAATCAGTAAAAGGTAAAAT
1 AGTAAACAGTAAAAAGTAAAAT
*
43508 AGTAATCAGTAA
1 AGTAAACAGTAA
43520 GAGCAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.21
Consensus pattern (22 bp):
AGTAAACAGTAAAAAGTAAAAT
Found at i:43528 original size:22 final size:21
Alignment explanation
Indices: 43482--43529 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
43472 GTAAAATAGT
*
43482 AAAAAGTAATCAGTAAAAGGTA
1 AAAAAGTAATCAGTAAAA-GCA
* *
43504 AAATAGTAATCAGTAAGAGCA
1 AAAAAGTAATCAGTAAAAGCA
43525 AAAAA
1 AAAAA
43530 ATGGTTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (21 bp):
AAAAAGTAATCAGTAAAAGCA
Found at i:50865 original size:62 final size:62
Alignment explanation
Indices: 50768--50894 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
50758 GAAGGGTATC
50768 AGGTCTGTTTCATATTCAATTCTGATAAATGGACAGCAAACTGCTAGGTTTAGCCCTACAAG
1 AGGTCTGTTTCATATTCAATTCTGATAAATGGACAGCAAACTGCTAGGTTTAGCCCTACAAG
50830 AGGTCTGTTTCATATTCAATTCTGATAAATGGACAGCAAACTGCTAGGTTTAGCCCTACAAG
1 AGGTCTGTTTCATATTCAATTCTGATAAATGGACAGCAAACTGCTAGGTTTAGCCCTACAAG
50892 AGG
1 AGG
50895 AATTAGACAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (62 bp):
AGGTCTGTTTCATATTCAATTCTGATAAATGGACAGCAAACTGCTAGGTTTAGCCCTACAAG
Found at i:54323 original size:17 final size:19
Alignment explanation
Indices: 54287--54323 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
54277 CACACATTAT
*
54287 ATTAGAAGAGAGGTTAAAA
1 ATTAGAAGAGAGGCTAAAA
54306 ATTAG-AGA-AGGCTAAAA
1 ATTAGAAGAGAGGCTAAAA
54323 A
1 A
54324 GTTTCTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (19 bp):
ATTAGAAGAGAGGCTAAAA
Found at i:54878 original size:8 final size:8
Alignment explanation
Indices: 54865--54902 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
54855 ATTAGAGAGA
54865 TAATTATC
1 TAATTATC
54873 TAATTATC
1 TAATTATC
54881 TAATTATC
1 TAATTATC
54889 TAATTATC
1 TAATTATC
54897 TAATTA
1 TAATTA
54903 GGGTCGTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (8 bp):
TAATTATC
Found at i:55545 original size:2 final size:2
Alignment explanation
Indices: 55538--55590 Score: 70
Period size: 2 Copynumber: 24.5 Consensus size: 2
55528 TAGTATAAGC
55538 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA CTA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA -TA
55581 TA CTA TA TA T
1 TA -TA TA TA T
55591 TATTTTCAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 39 0.83
3 8 0.17
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:62843 original size:11 final size:11
Alignment explanation
Indices: 62827--62853 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
62817 ACCCCAAATA
62827 ATAATAATAAT
1 ATAATAATAAT
62838 ATAATAATAAT
1 ATAATAATAAT
62849 ATAAT
1 ATAAT
62854 TAACAGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:64170 original size:3 final size:3
Alignment explanation
Indices: 64162--64210 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
64152 TACCCTTTAT
* *
64162 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATC ATA ATC ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
64209 AT
1 AT
64211 TATTTTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:64185 original size:20 final size:20
Alignment explanation
Indices: 64160--64198 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
64150 ATTACCCTTT
64160 ATATAATAATAATAATAATA
1 ATATAATAATAATAATAATA
64180 ATATAATAATAATAATAAT
1 ATATAATAATAATAATAAT
64199 CATAATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAATAATAATAATAATA
Found at i:66565 original size:2 final size:2
Alignment explanation
Indices: 66558--66624 Score: 64
Period size: 2 Copynumber: 33.0 Consensus size: 2
66548 CTTTGAATAC
* * * * *
66558 AT AT AT AT AT AT AT AT AC AT AT AT AT GCT -T CT AT CT CT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT -AT AT
66601 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
66625 GTATTAAAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.02
2 53 0.95
3 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70811 original size:25 final size:25
Alignment explanation
Indices: 70783--70834 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
70773 ATCAACTTTC
70783 CTTCGAAAAAAAAAAATCCAAAT-AA
1 CTTC-AAAAAAAAAAATCCAAATCAA
***
70808 CTTCACTCAAAAAAATCCAAATCAA
1 CTTCAAAAAAAAAAATCCAAATCAA
70833 CT
1 CT
70835 AACGAATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.56, C:0.23, G:0.02, T:0.19
Consensus pattern (25 bp):
CTTCAAAAAAAAAAATCCAAATCAA
Found at i:82245 original size:74 final size:74
Alignment explanation
Indices: 82124--82271 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
82114 CAACATCTAT
*
82124 ACCTTTTACTTTAAAGAGAGGCCAGCGGGTTCCTTATTCATGTAACAGTGCGAACTCTCAAAATT
1 ACCTTTTACTTTAAAGAGAGGCCAGCGGGTTCCCTATTCATGTAACAGTGCGAACTCTCAAAATT
82189 CAATTAACA
66 CAATTAACA
*
82198 ACCTTTTACTTTAAAGAGAGGCCAGCGGGTTCCCTGTTCATGTAACAGTGCGAACTCTCAAAATT
1 ACCTTTTACTTTAAAGAGAGGCCAGCGGGTTCCCTATTCATGTAACAGTGCGAACTCTCAAAATT
82263 CAATTAACA
66 CAATTAACA
82272 CATCTCATCC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (74 bp):
ACCTTTTACTTTAAAGAGAGGCCAGCGGGTTCCCTATTCATGTAACAGTGCGAACTCTCAAAATT
CAATTAACA
Found at i:84691 original size:8 final size:8
Alignment explanation
Indices: 84678--84711 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
84668 ACCAGTAGCT
84678 TTTTTTTA
1 TTTTTTTA
84686 TTTTTTTA
1 TTTTTTTA
84694 TTTTTTTTA
1 -TTTTTTTA
84703 TTTTTTTA
1 TTTTTTTA
84711 T
1 T
84712 ATATTCCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:84691 original size:9 final size:9
Alignment explanation
Indices: 84677--84709 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
84667 AACCAGTAGC
84677 TTTTTTTTA
1 TTTTTTTTA
84686 -TTTTTTTA
1 TTTTTTTTA
84694 TTTTTTTTA
1 TTTTTTTTA
84703 TTTTTTT
1 TTTTTTT
84710 ATATATTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:84699 original size:17 final size:17
Alignment explanation
Indices: 84677--84711 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
84667 AACCAGTAGC
84677 TTTTTTTTATTTTTTTA
1 TTTTTTTTATTTTTTTA
84694 TTTTTTTTATTTTTTTA
1 TTTTTTTTATTTTTTTA
84711 T
1 T
84712 ATATTCCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTTTTATTTTTTTA
Found at i:99297 original size:17 final size:17
Alignment explanation
Indices: 99228--99300 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
99218 ACTGGGCCTA
*
99228 AAAAAGAAAGAGGTCGC
1 AAAAAGAAAGAGGTCAC
**
99245 AAAAAGAAAGA-GAAAC
1 AAAAAGAAAGAGGTCAC
* *
99261 AAAAA-AATTG-GGCCTA-
1 AAAAAGAA-AGAGGTC-AC
99277 AAAAAGAAAGAGGTCAC
1 AAAAAGAAAGAGGTCAC
99294 AAAAAGA
1 AAAAAGA
99301 GAAATGAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
15 2 0.05
16 16 0.38
17 24 0.57
ACGTcount: A:0.62, C:0.10, G:0.22, T:0.07
Consensus pattern (17 bp):
AAAAAGAAAGAGGTCAC
Found at i:99573 original size:22 final size:22
Alignment explanation
Indices: 99548--99592 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
99538 ACGTCACAAA
99548 ACCGTCGTCGGAGTATTCATCG
1 ACCGTCGTCGGAGTATTCATCG
99570 ACCGTCGTCGGAGTATTCATCG
1 ACCGTCGTCGGAGTATTCATCG
99592 A
1 A
99593 TATGAGGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
ACCGTCGTCGGAGTATTCATCG
Found at i:99655 original size:4 final size:4
Alignment explanation
Indices: 99648--99702 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
99638 TATATATATA
99648 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
99696 TATG TAT
1 TATG TAT
99703 TAAATTCCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:100510 original size:36 final size:36
Alignment explanation
Indices: 100463--100574 Score: 100
Period size: 36 Copynumber: 3.4 Consensus size: 36
100453 GTAGATAGGT
100463 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAA
1 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAA
* * *
100499 TCTGAAGACAGTT-C---ACG-TA---GATAG-G-T
1 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAA
* *
100525 TCTGAAGACAGTTCCTAAATGATATTTAAGAGTGAA
1 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAA
*
100561 TCTGAAGACGGTTC
1 TCTGAAGACAGTTC
100575 ACGTAGATAG
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
26 13 0.22
27 2 0.03
28 4 0.07
30 2 0.03
31 4 0.07
32 2 0.03
34 3 0.05
35 2 0.03
36 26 0.45
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (36 bp):
TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAA
Found at i:100510 original size:62 final size:62
Alignment explanation
Indices: 100402--100669 Score: 389
Period size: 62 Copynumber: 4.3 Consensus size: 62
100392 AGTCCATGGA
* * *
100402 TCTGAAGACAGTTCCTGACAGAT-TTTAAGAATGAATCTGAAGACAGTTCACGTAGATAGGT
1 TCTGAAGACAGTTCCTAAAAGATATTTAAGAGTGAATCTGAAGACAGTTCACGTAGATAGGT
*
100463 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAATCTGAAGACAGTTCACGTAGATAGGT
1 TCTGAAGACAGTTCCTAAAAGATATTTAAGAGTGAATCTGAAGACAGTTCACGTAGATAGGT
* *
100525 TCTGAAGACAGTTCCTAAATGATATTTAAGAGTGAATCTGAAGACGGTTCACGTAGATAGGT
1 TCTGAAGACAGTTCCTAAAAGATATTTAAGAGTGAATCTGAAGACAGTTCACGTAGATAGGT
* * * * * *
100587 TTTGAAGACAGTTCCTAAATGATATTTAAGGGTGAATCCGAAGACAGTTCATGAAGA-AGGAT
1 TCTGAAGACAGTTCCTAAAAGATATTTAAGAGTGAATCTGAAGACAGTTCACGTAGATAGG-T
100649 T-TGAAGACAGTTCCTATAAAG
1 TCTGAAGACAGTTCCTA-AAAG
100670 CCTCGAGAGA
Statistics
Matches: 190, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
61 39 0.21
62 151 0.79
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (62 bp):
TCTGAAGACAGTTCCTAAAAGATATTTAAGAGTGAATCTGAAGACAGTTCACGTAGATAGGT
Found at i:102879 original size:88 final size:88
Alignment explanation
Indices: 102751--102929 Score: 358
Period size: 88 Copynumber: 2.0 Consensus size: 88
102741 CGTTATGTCC
102751 ATAGCTTTAATATATATATGGCTGTCAAGTATACCGTTTTGGCTTCTGTTTAGAATTATAGCCTT
1 ATAGCTTTAATATATATATGGCTGTCAAGTATACCGTTTTGGCTTCTGTTTAGAATTATAGCCTT
102816 GTATTTATGCTTAAAATTAGGGG
66 GTATTTATGCTTAAAATTAGGGG
102839 ATAGCTTTAATATATATATGGCTGTCAAGTATACCGTTTTGGCTTCTGTTTAGAATTATAGCCTT
1 ATAGCTTTAATATATATATGGCTGTCAAGTATACCGTTTTGGCTTCTGTTTAGAATTATAGCCTT
102904 GTATTTATGCTTAAAATTAGGGG
66 GTATTTATGCTTAAAATTAGGGG
102927 ATA
1 ATA
102930 TTGTTTGTTG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (88 bp):
ATAGCTTTAATATATATATGGCTGTCAAGTATACCGTTTTGGCTTCTGTTTAGAATTATAGCCTT
GTATTTATGCTTAAAATTAGGGG
Found at i:104407 original size:41 final size:38
Alignment explanation
Indices: 104361--104464 Score: 154
Period size: 41 Copynumber: 2.7 Consensus size: 38
104351 CTATTTAAGC
*
104361 AATTCCAAGAGAAGACTTTTGGAAAATAAAAATTTTTTAGT
1 AATTCCAAGAGAAGACTTTTGGAAAATAAAAA--TTTTA-A
*
104402 AATTCCAAGAGAAGACTTTTGGGAAATAAAAATTTTAA
1 AATTCCAAGAGAAGACTTTTGGAAAATAAAAATTTTAA
*
104440 AAATCCAAGAGAAGACTTTTGGAAA
1 AATTCCAAGAGAAGACTTTTGGAAA
104465 TTAATAAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
38 23 0.39
39 5 0.08
41 31 0.53
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (38 bp):
AATTCCAAGAGAAGACTTTTGGAAAATAAAAATTTTAA
Done.