Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2672
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: 86202
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1649 original size:21 final size:20
Alignment explanation
Indices: 1616--1663 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
1606 AGCTAGATGT
1616 TGGACAT-G-TTAAAATGCA
1 TGGACATGGCTTAAAATGCA
1634 TGGTACATGGCTTAAAATGCA
1 TGG-ACATGGCTTAAAATGCA
1655 TGGACATGG
1 TGGACATGG
1664 GTTGTTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.11
19 4 0.15
20 7 0.26
21 13 0.48
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (20 bp):
TGGACATGGCTTAAAATGCA
Found at i:2579 original size:20 final size:20
Alignment explanation
Indices: 2554--2624 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
2544 AAATAGAATG
*
2554 TATCGATACATTAAAAAATG
1 TATCGATACATTAAAAAATA
* * * *
2574 TGTCGATACATTCATACATA
1 TATCGATACATTAAAAAATA
*
2594 TATCGATACATTGAAAAATA
1 TATCGATACATTAAAAAATA
2614 TATCGATACAT
1 TATCGATACAT
2625 CTGGGTAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (20 bp):
TATCGATACATTAAAAAATA
Found at i:3123 original size:10 final size:10
Alignment explanation
Indices: 3108--3133 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3098 TGCACCTCTT
3108 TTTTTTTGTA
1 TTTTTTTGTA
3118 TTTTTTTGTA
1 TTTTTTTGTA
3128 TTTTTT
1 TTTTTT
3134 CAAATAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTA
Found at i:5987 original size:80 final size:79
Alignment explanation
Indices: 5861--6011 Score: 189
Period size: 80 Copynumber: 1.9 Consensus size: 79
5851 TGTCTTGGAA
* *
5861 GGATACTCTAACCCATTTTTACCTTTAAAACACTGAAATTTTCATCTCAGGGGATACTCCAACCC
1 GGATACTCTAACCCATTTTTACCTTTAAAACACTCAAATTTTCATCTCAGCGGATACTCCAACCC
5926 CACCATTTTTAAGG
66 CACCATTTTTAAGG
* * * ** *
5940 GGATACTCTAGCCTTATTTTT-GCTTTCAAAACAC-CAAATTTTACATCTCTTCGGATACTCTAA
1 GGATACTCTAACC-CATTTTTACCTTT-AAAACACTCAAATTTT-CATCTCAGCGGATACTCCAA
6003 CCCCACCAT
63 CCCCACCAT
6012 CTCCGAAGGG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
79 23 0.38
80 38 0.62
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (79 bp):
GGATACTCTAACCCATTTTTACCTTTAAAACACTCAAATTTTCATCTCAGCGGATACTCCAACCC
CACCATTTTTAAGG
Found at i:6023 original size:80 final size:79
Alignment explanation
Indices: 5861--6032 Score: 179
Period size: 80 Copynumber: 2.2 Consensus size: 79
5851 TGTCTTGGAA
* *
5861 GGATACTCTAACCCATTTTTACCTTTAAAACACTGAAATTTTCATCTCAGGGGATACTCCAACCC
1 GGATACTCTAACCCATTTTTACCTTTAAAACACTCAAATTTTCATCTCAGCGGATACTCCAACCC
***
5926 CACCATTTTTAAGG
66 CACCATTCCGAAGG
* * * ** *
5940 GGATACTCTAGCCTTATTTTT-GCTTTCAAAACAC-CAAATTTTACATCTCTTCGGATACTCTAA
1 GGATACTCTAACC-CATTTTTACCTTT-AAAACACTCAAATTTT-CATCTCAGCGGATACTCCAA
6003 CCCCACCATCTCCGAA-G
63 CCCCACCAT-TCCGAAGG
*
6020 GGATACTTTAACC
1 GGATACTCTAACC
6033 TCCATTTTCA
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
79 23 0.30
80 50 0.66
81 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (79 bp):
GGATACTCTAACCCATTTTTACCTTTAAAACACTCAAATTTTCATCTCAGCGGATACTCCAACCC
CACCATTCCGAAGG
Found at i:7456 original size:17 final size:17
Alignment explanation
Indices: 7434--7479 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
7424 TTATTGAACT
7434 TAATAAATA-ATATTACC
1 TAATAAATATA-ATTACC
*
7451 TAATAAATATAATTATC
1 TAATAAATATAATTACC
*
7468 TAATAATTATAA
1 TAATAAATATAA
7480 AAAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 25 0.96
18 1 0.04
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATAATTACC
Found at i:17224 original size:97 final size:97
Alignment explanation
Indices: 17055--17242 Score: 288
Period size: 97 Copynumber: 1.9 Consensus size: 97
17045 TCAGGCACAA
17055 GTGTTGGACATGGTACTTCGAAAAAAAAAGAGTCATTGCTAAATAGACTATGATTGACAAAATAG
1 GTGTTGGACATGGTACTTCGAAAAAAAAAGAGTCATTGCTAAATAGACTATGATTGACAAAATAG
* *
17120 AAACGCAATGCTTTTGTAATGCCTTTTTTTAG
66 AAACGCAATGCTTTCGTAATGACTTTTTTTAG
* * * * * *
17152 GTGTTGGAGATGGTACTTCGAAAAATAAATAGTCATTGTTACATAGGCTATGATTGACAAAATA-
1 GTGTTGGACATGGTACTTCGAAAAAAAAAGAGTCATTGCTAAATAGACTATGATTGACAAAATAG
17216 AAAGCGCAATGCTTTCGTAATGACTTT
66 AAA-CGCAATGCTTTCGTAATGACTTT
17243 CTTGAAGATT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 3 0.04
97 79 0.96
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (97 bp):
GTGTTGGACATGGTACTTCGAAAAAAAAAGAGTCATTGCTAAATAGACTATGATTGACAAAATAG
AAACGCAATGCTTTCGTAATGACTTTTTTTAG
Found at i:19617 original size:2 final size:2
Alignment explanation
Indices: 19610--19639 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19600 AATAGAAGAC
19610 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
19640 TGAAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25313 original size:17 final size:16
Alignment explanation
Indices: 25277--25324 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
25267 TGGTTTCAGC
*
25277 ATTTTAGTTTTTAAATTT
1 ATTTTA-TTTTT-TATTT
25295 ATTTTATTTATTTATTT
1 ATTTTATTT-TTTATTT
25312 ATTTTATTTTTTA
1 ATTTTATTTTTTA
25325 GTCATCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
18 8 0.29
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
ATTTTATTTTTTATTT
Found at i:25578 original size:22 final size:22
Alignment explanation
Indices: 25520--25596 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
25510 AAAAAATAGT
*
25520 AGCAAAACAATAGCAACACAGCA
1 AGCAAAACAACAGC-ACACAGCA
* * *
25543 AGCAAAATAGCAGCACACAGTA
1 AGCAAAACAACAGCACACAGCA
* *
25565 AGCAAAACAACAGCAAATAGCA
1 AGCAAAACAACAGCACACAGCA
25587 AGCAAAACAA
1 AGCAAAACAA
25597 TAAGCATGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 34 0.76
23 11 0.24
ACGTcount: A:0.57, C:0.23, G:0.14, T:0.05
Consensus pattern (22 bp):
AGCAAAACAACAGCACACAGCA
Found at i:25683 original size:23 final size:23
Alignment explanation
Indices: 25651--25699 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
25641 ATAGCAAGTA
* *
25651 AAAAGTAGCAACAAACAGCAAGC
1 AAAAGCAGCAACAAACAGCAAAC
25674 AAAAGCAGCAACAAACAGCAAAC
1 AAAAGCAGCAACAAACAGCAAAC
25697 AAA
1 AAA
25700 GAAACACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.61, C:0.22, G:0.14, T:0.02
Consensus pattern (23 bp):
AAAAGCAGCAACAAACAGCAAAC
Found at i:27912 original size:156 final size:154
Alignment explanation
Indices: 27571--28034 Score: 408
Period size: 156 Copynumber: 3.0 Consensus size: 154
27561 TCCTTTAGGG
* * * ** *
27571 TATTTTTTTAGAACCAAGTCCTAGGTCATCACCGGGTCTACTTTTATGCTAAAGGTAGACATTTC
1 TATTTTTTTAGAATCGAGTCCTAGGTCATCACCGGATCTACTTTTATGCTAAAGGTAGGTATTTA
* * * * *
27636 GGATAAGTTCATCCCA-TCTAATCCTTTTAAA-TCTTTTAAGGGTATAGGGCATTTTGACATCGA
66 GGATAGGTTCATCTCATTATAATCCTTTTAAAGTCTTTT-AGGGTATAGGACATTCTGACATCGA
**
27699 AAGTATCCCCTAGGGGTATTTTCAA
130 AAGTATCCCCTAAAGGTATTTTCAA
* * * ** * * *
27724 AATTTTTTTAAAATTGAGTCCTAGGTTGTCACCGGATCCACTTTTATGCTGATGGTAGGTATTTA
1 TATTTTTTTAGAATCGAGTCCTAGGTCATCACCGGATCTACTTTTATGCTAAAGGTAGGTATTTA
* *
27789 GGATAGGTTCATCTCATTTTGTAATCCTTTTAAAGTCTTTTAGGGATATCAGGA-ACTTCT-ACG
66 GGATAGGTTCATCTCA--TTATAATCCTTTTAAAGTCTTTTAGGG-TAT-AGGACA-TTCTGACA
* *
27852 T-TAAAGATATCCCTTAAAGGTATTTT-AA
126 TCGAAAG-TATCCCCTAAAGGTATTTTCAA
* * * * *
27880 TATTTTTTTAGAATCGAGTCCTAGGTCATCACC-AAGTTTGCTTTTATGCCAAAGGTGGGTATTT
1 TATTTTTTTAGAATCGAGTCCTAGGTCATCACCGGA-TCTACTTTTATGCTAAAGGTAGGTATTT
* * * * *
27944 AAGATAGGTTCATCTCATCTATAATCCTTTTTAAGTAC-TTTAGGGGTCTCAAGTAC-TT-TTAC
65 AGGATAGGTTCATCTCAT-TATAATCCTTTTAAAGT-CTTTTA-GGGTAT--AGGACATTCTGAC
* *
28006 ATCGAAAGTATCTCCTAAGGGTATTTTCA
125 ATCGAAAGTATCCCCTAAAGGTATTTTCA
28035 TAATTTTCCT
Statistics
Matches: 246, Mismatches: 48, Indels: 31
0.76 0.15 0.10
Matches are distributed among these distances:
153 65 0.26
154 2 0.01
155 43 0.17
156 101 0.41
157 29 0.12
158 6 0.02
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (154 bp):
TATTTTTTTAGAATCGAGTCCTAGGTCATCACCGGATCTACTTTTATGCTAAAGGTAGGTATTTA
GGATAGGTTCATCTCATTATAATCCTTTTAAAGTCTTTTAGGGTATAGGACATTCTGACATCGAA
AGTATCCCCTAAAGGTATTTTCAA
Found at i:31662 original size:15 final size:16
Alignment explanation
Indices: 31621--31682 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
31611 TGGGAAAAGT
* *
31621 AAAGAAAAAAAAGAAA
1 AAAGAAAAAAATGAGA
31637 AAATGACAAAAAAATGAG-
1 AAA-G--AAAAAAATGAGA
*
31655 AAAGAAAAAATTGAGAA
1 AAAGAAAAAAATGAG-A
31672 AAAGAAAAAAA
1 AAAGAAAAAAA
31683 AGATATGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
15 10 0.27
16 3 0.08
17 12 0.32
18 3 0.08
19 9 0.24
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAAATGAGA
Found at i:33422 original size:35 final size:34
Alignment explanation
Indices: 33346--33537 Score: 115
Period size: 35 Copynumber: 5.5 Consensus size: 34
33336 TTACAAATTT
** * * *
33346 AGTTTTTCATTTTTATTGTTGAATCCTCGATGGAAG
1 AGTTTTTCA-TTTTAAAGTTAAAGCCTCAAT-GAAG
* * * *
33382 GGTTTTTTATTTTAAAGTTAAAGTCTTAATGAAAG
1 AGTTTTTCATTTTAAAGTTAAAGCCTCAATG-AAG
* * *
33417 AGTTTTTCA-TGTAAAGTTAAAGCCTCGATGGAGG
1 AGTTTTTCATTTTAAAGTTAAAGCCTCAAT-GAAG
*
33451 AGTTTTT--TTATTCAAAGTTAAAGCCTCAATGGAG
1 AGTTTTTCATT-TT-AAAGTTAAAGCCTCAATGAAG
* * * *
33485 AGTTTTTCAATTTAAA-TTAGAAACCTCGATAGAGG
1 AGTTTTTCATTTTAAAGTTA-AAGCCTCAAT-GAAG
33520 AGTTTTTTCA-TTTAAAGT
1 AG-TTTTTCATTTTAAAGT
33538 AGAAGTCTTG
Statistics
Matches: 120, Mismatches: 25, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
33 4 0.03
34 47 0.39
35 53 0.44
36 16 0.13
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (34 bp):
AGTTTTTCATTTTAAAGTTAAAGCCTCAATGAAG
Found at i:33443 original size:69 final size:69
Alignment explanation
Indices: 33370--33546 Score: 195
Period size: 69 Copynumber: 2.6 Consensus size: 69
33360 ATTGTTGAAT
33370 CCTCGATGGAAGG-GTTTTTTATTTTAAAGTTAAAGTCTTAATGAAAGAGTTTTTC-ATGTAAAG
1 CCTCGATGG-AGGAGTTTTTTATTTTAAAGTTAAAGTCTTAATG-AAGAGTTTTTCAATGTAAA-
*
33433 TTA-AAG
63 TTAGAAA
* * * * *
33439 CCTCGATGGAGGAGTTTTTT-TATTCAAAGTTAAAGCCTCAATGGAGAGTTTTTCAATTTAAATT
1 CCTCGATGGAGGAGTTTTTTAT-TTTAAAGTTAAAGTCTTAATGAAGAGTTTTTCAATGTAAATT
33503 AGAAA
65 AGAAA
*
33508 CCTCGATAGAGGAGTTTTTTCA-TTTAAAG-TAGAAGTCTT
1 CCTCGATGGAGGAGTTTTTT-ATTTTAAAGTTA-AAGTCTT
33547 GGTAGAGGAG
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
68 19 0.21
69 72 0.79
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (69 bp):
CCTCGATGGAGGAGTTTTTTATTTTAAAGTTAAAGTCTTAATGAAGAGTTTTTCAATGTAAATTA
GAAA
Found at i:33454 original size:34 final size:34
Alignment explanation
Indices: 33370--33604 Score: 156
Period size: 35 Copynumber: 6.8 Consensus size: 34
33360 ATTGTTGAAT
*
33370 CCTCGATGGAAGG-GTTTTTTATTTTAAAGTTAAAG
1 CCTCGATGG-AGGAGTTTTTCA-TTTAAAGTTAAAG
* ** * * *
33405 TCTTAATGAAAGAGTTTTTCATGTAAAGTTAAAG
1 CCTCGATGGAGGAGTTTTTCATTTAAAGTTAAAG
* *
33439 CCTCGATGGAGGAGTTTTTTTATTCAAAGTTAAAG
1 CCTCGATGGAGGAG-TTTTTCATTTAAAGTTAAAG
* *
33474 CCTCAATGGA-GAGTTTTTCAATTTAAA-TTAGAAA
1 CCTCGATGGAGGAGTTTTTC-ATTTAAAGTTA-AAG
*
33508 CCTCGATAGAGGAGTTTTTTCATTTAAAG-TAGAAG
1 CCTCGATGGAGGAG-TTTTTCATTTAAAGTTA-AAG
* * * * * *
33543 TCTTGGTAGAGGAGTTTTTTACTTTAAAAGTTGAAG
1 CCTCGATGGAGGAGTTTTTCA-TTT-AAAGTTAAAG
* * * *
33579 CCTTGGTGAAAGAG-TTTTCATTTAAA
1 CCTCGATGGAGGAGTTTTTCATTTAAA
33605 ATTGAAACCT
Statistics
Matches: 158, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
33 11 0.07
34 51 0.32
35 72 0.46
36 23 0.15
37 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (34 bp):
CCTCGATGGAGGAGTTTTTCATTTAAAGTTAAAG
Found at i:33594 original size:36 final size:35
Alignment explanation
Indices: 33483--33637 Score: 104
Period size: 35 Copynumber: 4.4 Consensus size: 35
33473 GCCTCAATGG
* * * *
33483 AGAG-TTTTTCAATTTAAATTAGAAACCTCGATAGA
1 AGAGTTTTTTC-ATTTAAAGTAGAAGCCTTGGTAGA
* *
33518 GGAGTTTTTTCATTTAAAGTAGAAGTCTTGGTAGA
1 AGAGTTTTTTCATTTAAAGTAGAAGCCTTGGTAGA
* *
33553 GGAGTTTTTT-ACTTTAAAAGTTGAAGCCTTGGT-GAA
1 AGAGTTTTTTCA-TTT-AAAGTAGAAGCCTTGGTAG-A
* * * ** *
33589 AGAG--TTTTCATTTAAAATTGAAACCTTAATACA
1 AGAGTTTTTTCATTTAAAGTAGAAGCCTTGGTAGA
33622 AGAGTTTTTTTCATTT
1 AGAG-TTTTTTCATTT
33638 TAAATTTATG
Statistics
Matches: 97, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
33 18 0.19
34 8 0.08
35 37 0.38
36 34 0.35
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (35 bp):
AGAGTTTTTTCATTTAAAGTAGAAGCCTTGGTAGA
Found at i:33820 original size:6 final size:6
Alignment explanation
Indices: 33811--33857 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
33801 AAATTTTGAC
* *
33811 TTTAAT TTTAAT TTTAA- TTTAA- -TTAGT TTCAAT TTTAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
33856 TT
1 TT
33858 CAAGAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 3 0.09
5 5 0.14
6 27 0.77
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (6 bp):
TTTAAT
Found at i:33879 original size:15 final size:15
Alignment explanation
Indices: 33859--33888 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33849 TTTTAATTTC
33859 AAGAAAATAAAAAAA
1 AAGAAAATAAAAAAA
33874 AAGAAAATAAAAAAA
1 AAGAAAATAAAAAAA
33889 TTCAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (15 bp):
AAGAAAATAAAAAAA
Found at i:42452 original size:13 final size:13
Alignment explanation
Indices: 42434--42458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42424 TTTGAGACCA
42434 TGTATCGATACAT
1 TGTATCGATACAT
42447 TGTATCGATACA
1 TGTATCGATACA
42459 AACAGTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:42535 original size:19 final size:20
Alignment explanation
Indices: 42511--42560 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
42501 AATTGTGTAA
* *
42511 GTATCGATACAATG-ATCAT
1 GTATCGATACAAAGCATAAT
42530 GTATCGATACAAAGCATAAT
1 GTATCGATACAAAGCATAAT
*
42550 ATATCGATACA
1 GTATCGATACA
42561 TCTGGATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (20 bp):
GTATCGATACAAAGCATAAT
Found at i:44160 original size:2 final size:2
Alignment explanation
Indices: 44153--44191 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
44143 TTAAAAAGAG
44153 AT AT AT AT 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 AT AT AT AT A
44192 AATAACTAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47518 original size:28 final size:29
Alignment explanation
Indices: 47481--47538 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
47471 GTTATAATCA
* *
47481 TATTTAAAATATTTTATA-TTTATATAAAT
1 TATTTAAAAT-TTTAAAATTTTATATAAAT
47510 TATTT-AAATTTTAAAATTTTATATAAAT
1 TATTTAAAATTTTAAAATTTTATATAAAT
47538 T
1 T
47539 CTTAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
28 16 0.62
29 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TATTTAAAATTTTAAAATTTTATATAAAT
Found at i:47531 original size:19 final size:19
Alignment explanation
Indices: 47509--47548 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
47499 TTTATATAAA
*
47509 TTATTTAAATT-TTAAAATT
1 TTATATAAATTCTT-AAATT
47528 TTATATAAATTCTTAAATT
1 TTATATAAATTCTTAAATT
47547 TT
1 TT
47549 GAATTGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATATAAATTCTTAAATT
Found at i:52762 original size:22 final size:23
Alignment explanation
Indices: 52723--52768 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
52713 ATGTTAAAAA
52723 AAACATAATAAAAAAAAATGCATG
1 AAACATAAT-AAAAAAAATGCATG
52747 AAACATAAT-AAAAAAATGCATG
1 AAACATAATAAAAAAAATGCATG
52769 GTCAAAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.59
24 9 0.41
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (23 bp):
AAACATAATAAAAAAAATGCATG
Found at i:53724 original size:20 final size:20
Alignment explanation
Indices: 53677--53751 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
53667 AAAAAGACAT
*
53677 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
53696 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
53717 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
53737 AATGTATCGATACAT
1 AATGTATCGATACAT
53752 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:53745 original size:40 final size:39
Alignment explanation
Indices: 53674--53751 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
53664 GGTAAAAAGA
* *
53674 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
53713 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
53752 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:58122 original size:6 final size:6
Alignment explanation
Indices: 58111--58153 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
58101 TTTATTTAGA
58111 TTATAT TTATAT TTATAT TTATAT TTATCAT TTAT-T TTATAT T
1 TTATAT TTATAT TTATAT TTATAT TTAT-AT TTATAT TTATAT T
58154 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
7 6 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:59504 original size:16 final size:16
Alignment explanation
Indices: 59475--59507 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59465 ATTTATAAAC
59475 ATATATAATAAAAATA
1 ATATATAATAAAAATA
59491 ATATA-AATATAAAATA
1 ATATATAATA-AAAATA
59507 A
1 A
59508 ATACGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATATAATAAAAATA
Found at i:59509 original size:20 final size:19
Alignment explanation
Indices: 59477--59525 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
59467 TTATAAACAT
*
59477 ATATAATAAAAATAATATAA
1 ATATAA-AAAAATAAGATAA
*
59497 ATATAAAATAAATACGATAA
1 ATATAAAA-AAATAAGATAA
59517 ATA-AAAAAA
1 ATATAAAAAA
59526 CACAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 6 0.23
20 18 0.69
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
ATATAAAAAAATAAGATAA
Found at i:60732 original size:2 final size:2
Alignment explanation
Indices: 60720--60780 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
60710 TTTGTTCTAC
60720 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
60761 T- TA AA TA TA -A TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
60781 AAAATAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:60797 original size:17 final size:17
Alignment explanation
Indices: 60756--60793 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
60746 ATATATATAT
*
60756 ATATATTAAATATAATAA
1 ATATA-TAAAAATAATAA
60774 ATATATAAAAATAA-AA
1 ATATATAAAAATAATAA
60790 ATAT
1 ATAT
60794 TATACACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATATAAAAATAATAA
Found at i:64673 original size:21 final size:20
Alignment explanation
Indices: 64640--64687 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
64630 AGCTAGATGT
64640 TGGACAT-G-TTAAAATGCA
1 TGGACATGGCTTAAAATGCA
64658 TGGTACATGGCTTAAAATGCA
1 TGG-ACATGGCTTAAAATGCA
64679 TGGACATGG
1 TGGACATGG
64688 GTTGTTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.11
19 4 0.15
20 7 0.26
21 13 0.48
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (20 bp):
TGGACATGGCTTAAAATGCA
Found at i:65604 original size:20 final size:20
Alignment explanation
Indices: 65575--65649 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
65565 AAAAAAATAG
65575 AATGTATCGATACATTAAAA
1 AATGTATCGATACATTAAAA
* * *
65595 AATGTGTCGATACATTCATA
1 AATGTATCGATACATTAAAA
* * *
65615 CATATATCGATACATTGAAA
1 AATGTATCGATACATTAAAA
65635 AATGTATCGATACAT
1 AATGTATCGATACAT
65650 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:68897 original size:76 final size:76
Alignment explanation
Indices: 68721--68943 Score: 174
Period size: 77 Copynumber: 2.9 Consensus size: 76
68711 ATTGTTGAGG
* * * * ** *
68721 GGATACTCTATCCCCGTTTGTACTTCTAAAAAACTAAAATTTTCATCTCAGGGGATTGTCTAATC
1 GGATACTCCAACCCCGTTT-TACTT-TAAAACACTGAAATTTTCATCTCAGGGGATACTCCAA-C
*
68786 TTACCATT-T-TC-AA
63 --CCCATTGTCTCGAA
**
68799 GGGGATACTCCAACCCCGTTTTA-TTTCCCAACA-TCG-AATGTTTCATCTCTA-GGGATACTCC
1 --GGATACTCCAACCCCGTTTTACTTT-AAAACACT-GAAAT-TTTCATCTC-AGGGGATACTCC
68860 AACCCCATTGTCTCGAA
60 AACCCCATTGTCTCGAA
*
68877 GGATACTCTAA-CCCGTTTTTACCTTTAAAACACTGAAATTTTCATCTCAGGGGATACTCCAACC
1 GGATACTCCAACCCCG-TTTTA-CTTTAAAACACTGAAATTTTCATCTCAGGGGATACTCCAACC
68941 CCA
64 CCA
68944 CCATTTTTAA
Statistics
Matches: 117, Mismatches: 13, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
75 9 0.08
76 17 0.15
77 39 0.33
78 32 0.27
79 3 0.03
80 17 0.15
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (76 bp):
GGATACTCCAACCCCGTTTTACTTTAAAACACTGAAATTTTCATCTCAGGGGATACTCCAACCCC
ATTGTCTCGAA
Found at i:70474 original size:17 final size:17
Alignment explanation
Indices: 70452--70497 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
70442 TTATTGAACT
70452 TAATAAATA-ATATTACC
1 TAATAAATATA-ATTACC
*
70469 TAATAAATATAATTATC
1 TAATAAATATAATTACC
*
70486 TAATAATTATAA
1 TAATAAATATAA
70498 AAAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 25 0.96
18 1 0.04
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATAATTACC
Found at i:80426 original size:97 final size:98
Alignment explanation
Indices: 80255--80447 Score: 280
Period size: 97 Copynumber: 2.0 Consensus size: 98
80245 TGTCAAGCAC
80255 AGGTGTTGGACATGGTACTTCGAAAAAAAAAAAAGAGTCATTGCTAAATAGACTATGATTGACAA
1 AGGTGTTGGACATGGTACTTCG--AAAAAAAAAAGAGTCATTGCTAAATAGACTATGATTGACAA
* * *
80320 AATAGAAGCGCAATGCTTTTGTAATGCCTTTTTTT
64 AATAAAAGCGCAATGCTTTCGTAATGACTTTTTTT
* * * * * *
80355 AGGTGTTGGAGATGGTACTTCG-AAAAATAAATAGTCATTGTTACATAGGCTATGATTGACAAAA
1 AGGTGTTGGACATGGTACTTCGAAAAAAAAAAGAGTCATTGCTAAATAGACTATGATTGACAAAA
80419 TAAAAGCGCAATGCTTTCGTAATGACTTT
66 TAAAAGCGCAATGCTTTCGTAATGACTTT
80448 CTTGAAGATT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
97 63 0.75
100 21 0.25
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (98 bp):
AGGTGTTGGACATGGTACTTCGAAAAAAAAAAGAGTCATTGCTAAATAGACTATGATTGACAAAA
TAAAAGCGCAATGCTTTCGTAATGACTTTTTTT
Found at i:82517 original size:22 final size:21
Alignment explanation
Indices: 82475--82517 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
82465 GGTCTGACAA
82475 ATAAATTTATTTAAATGCAATG
1 ATAAATTTATTTAAA-GCAATG
82497 ATAAATTATAATTTAAA-CAAT
1 ATAAATT-T-ATTTAAAGCAAT
82518 CCAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
ATAAATTTATTTAAAGCAATG
Found at i:82814 original size:2 final size:2
Alignment explanation
Indices: 82807--82836 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
82797 AAATAGAGAC
82807 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
82837 TGAAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.