Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1556
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: 28704
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:1321 original size:28 final size:28
Alignment explanation
Indices: 1290--1472 Score: 197
Period size: 28 Copynumber: 6.5 Consensus size: 28
1280 CGTTCATCTC
* * *
1290 TTCAAAGCCCATAGGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTTAGTGGCACCCT
* * * *
1318 TTCAAAGCCTATAAATTAGTGGCACACT
1 TTCAAAGCCCACAAGTTAGTGGCACCCT
* *
1346 TTCAAATCCTACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTTAGTGGCACCCT
* * *
1374 TTCAAAGCCCACAAGTCAATGGTACCCCT
1 TTCAAAGCCCACAAGTTAGTGGCA-CCCT
* *
1403 TT-AAAGACTACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTTAGTGGCACCCT
*
1430 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTTAGTGGC--ACCCT
1460 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1473 CAAGTCGGTG
Statistics
Matches: 129, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 6 0.05
28 99 0.77
29 6 0.05
30 18 0.14
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTTAGTGGCACCCT
Found at i:1432 original size:84 final size:86
Alignment explanation
Indices: 1315--1472 Score: 230
Period size: 84 Copynumber: 1.8 Consensus size: 86
1305 TTAGTGGCAT
* * * * *
1315 CCTTTCAAAGCCTATAAATTAGTGGCACACTTTCAAATCCTACAAGTTAGTGGC-ACCCTTTCAA
1 CCTTTCAAAGACTACAAATTAGTGGCACACTTTCAAAGCCCACAAGTCAGTGGCAACCCTTTCAA
1379 AGCCCACAAGTCAATGGTACC
66 AGCCCACAAGTCAATGGTACC
* *
1400 CCTTT-AAAGACTACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCA
1 CCTTTCAAAGACTACAAATTAGTGGCACACTTTCAAAGCCCACAAGTCAGTGGCA-ACCCTTTCA
1464 AAGCCCACA
65 AAGCCCACA
1473 CAAGTCGGTG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
84 41 0.64
85 5 0.08
86 18 0.28
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.24
Consensus pattern (86 bp):
CCTTTCAAAGACTACAAATTAGTGGCACACTTTCAAAGCCCACAAGTCAGTGGCAACCCTTTCAA
AGCCCACAAGTCAATGGTACC
Found at i:1495 original size:32 final size:32
Alignment explanation
Indices: 1356--1509 Score: 113
Period size: 28 Copynumber: 5.2 Consensus size: 32
1346 TTCAAATCCT
*
1356 ACAAGTTAGTGGC--ACCCTTTCAAAG-CC-C
1 ACAAGTCAGTGGCATACCCTTTCAAAGCCCAC
*
1384 ACAAGTCAATGG--TACCCCTTT-AAAG---AC
1 ACAAGTCAGTGGCATA-CCCTTTCAAAGCCCAC
*
1411 TACAAGTTAGTGGC--ACCCTTTCAAAG-CC-C
1 -ACAAGTCAGTGGCATACCCTTTCAAAGCCCAC
1440 ACAAGTCAGTGGCATACCCTTTCAAAGCCCAC
1 ACAAGTCAGTGGCATACCCTTTCAAAGCCCAC
* * * *
1472 ACAAGTCGGTGGTA-ACTCTTTTCAAAGCCCAT
1 ACAAGTCAGTGGCATAC-CCTTTCAAAGCCCAC
1504 ACAAGT
1 ACAAGT
1510 TAATGGCACC
Statistics
Matches: 104, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
27 7 0.07
28 42 0.40
29 7 0.07
30 12 0.12
31 4 0.04
32 32 0.31
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (32 bp):
ACAAGTCAGTGGCATACCCTTTCAAAGCCCAC
Found at i:2409 original size:20 final size:20
Alignment explanation
Indices: 2384--2642 Score: 133
Period size: 20 Copynumber: 11.8 Consensus size: 20
2374 TTTTTACCTA
2384 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
2404 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* * *
2424 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
2444 AATGTATCGATACATTATATCTTTTTTACCC
1 AATGTATCGATAC-----A---TTTTT---C
*
2475 AGATGTATTGATACATTTTTC
1 A-ATGTATCGATACATTTTTC
* * *
2496 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
*
2516 AATGCATCGATACATTCTGTCTTTTTACC
1 AATGTATCGATACA-------TTTTT--C
*
2545 TAGATGTATCGATACATTTTTT
1 -A-ATGTATCGATACATTTTTC
* * *
2567 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* *
2587 AATGTATCGATACA-TGTAC
1 AATGTATCGATACATTTTTC
*
2606 GAATGTATCGATACATTCTTC
1 -AATGTATCGATACATTTTTC
2627 AATGTATCGATACATT
1 AATGTATCGATACATT
2643 CTGTCTTTTT
Statistics
Matches: 187, Mismatches: 27, Indels: 50
0.71 0.10 0.19
Matches are distributed among these distances:
20 138 0.74
21 6 0.03
24 10 0.05
25 1 0.01
27 4 0.02
28 3 0.02
30 1 0.01
31 13 0.07
32 11 0.06
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:2422 original size:12 final size:12
Alignment explanation
Indices: 2405--2458 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
2395 ACATTTTTCA
2405 ATGTATCGATAC
1 ATGTATCGATAC
2417 ATGTAT-G--A-
1 ATGTATCGATAC
2425 ATGTATCGATAC
1 ATGTATCGATAC
2437 ATGTAT-G--A-
1 ATGTATCGATAC
2445 ATGTATCGATAC
1 ATGTATCGATAC
2457 AT
1 AT
2459 TATATCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
8 12 0.35
9 4 0.12
11 4 0.12
12 14 0.41
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:2448 original size:40 final size:39
Alignment explanation
Indices: 2384--2642 Score: 154
Period size: 40 Copynumber: 6.9 Consensus size: 39
2374 TTTTTACCTA
* * *
2384 AATGTATCGATACATTTTTCAATGTATCGATACATGTATG
1 AATGTATCGATACATGTATGAATGTATCGATACAT-TATG
2424 AATGTATCGATACATGTATGAATGTATCGATACATTAT-
1 AATGTATCGATACATGTATGAATGTATCGATACATTATG
* *** ** * * *
2462 -ATCT-TTTTTAC--CCA-G-ATGTATTGATACATTTTTC
1 AATGTATCGATACATGTATGAATGTATCGATACA-TTATG
* *
2496 AATGTATCGATACATGTATGAATGCATCGATACATTCTG
1 AATGTATCGATACATGTATGAATGTATCGATACATTATG
* ** * * *
2535 --TCT-T-TTTAC--CTA-G-ATGTATCGATACATTTTTT
1 AATGTATCGATACATGTATGAATGTATCGATACA-TTATG
*
2567 AATGTATCGATACATGTATGAATGTATCGATACATGTACG
1 AATGTATCGATACATGTATGAATGTATCGATACAT-TATG
* *
2607 AATGTATCGATACAT-TCTTCAATGTATCGATACATT
1 AATGTATCGATACATGT-ATGAATGTATCGATACATT
2643 CTGTCTTTTT
Statistics
Matches: 163, Mismatches: 37, Indels: 39
0.68 0.15 0.16
Matches are distributed among these distances:
31 12 0.07
32 16 0.10
33 6 0.04
34 3 0.02
35 7 0.04
36 12 0.07
37 5 0.03
38 3 0.02
39 11 0.07
40 88 0.54
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (39 bp):
AATGTATCGATACATGTATGAATGTATCGATACATTATG
Found at i:2582 original size:71 final size:72
Alignment explanation
Indices: 2405--2601 Score: 306
Period size: 71 Copynumber: 2.8 Consensus size: 72
2395 ACATTTTTCA
* * *
2405 ATGTATCGATACATGTATGAATGTATCGATACATGTATGAATGTATCGATACATTATATCTTTTT
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATTATATCTTTTT
2470 TACCCAG
66 TACCCAG
* * * *
2477 ATGTATTGATACATTTTTCAATGTATCGATACATGTATGAATGCATCGATACATTCTGTC-TTTT
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATTATATCTTTTT
*
2541 TACCTAG
66 TACCCAG
*
2548 ATGTATCGATACATTTTTTAATGTATCGATACATGTATGAATGTATCGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
2602 GTACGAATGT
Statistics
Matches: 114, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 61 0.54
72 53 0.46
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (72 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATTATATCTTTTT
TACCCAG
Found at i:6581 original size:21 final size:22
Alignment explanation
Indices: 6557--6606 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
6547 ATCAAATCTT
* *
6557 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
6578 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
6600 --TCAAAAT
1 CTTCAAAAT
6607 CATCCACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:8941 original size:20 final size:19
Alignment explanation
Indices: 8898--8951 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
8888 ACATTATGCT
**
8898 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGGACA
*
8917 TTGTATTGATACATGGACAA
1 TTGTATCGATACATGGAC-A
8937 TTGTATCGATACATG
1 TTGTATCGATACATG
8952 AAACTGGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:18004 original size:78 final size:78
Alignment explanation
Indices: 17900--18105 Score: 243
Period size: 78 Copynumber: 2.6 Consensus size: 78
17890 GTGATAATAA
* * * * * *
17900 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGATTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
17965 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* *
17978 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * * *
18043 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* * *
18057 CGGGGTTGGAGTATCCTCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
18106 GAAATAACAA
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
77 1 0.01
78 55 0.51
79 52 0.48
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:18097 original size:28 final size:28
Alignment explanation
Indices: 18057--18130 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
18047 GGAATAAAGC
*
18057 CGGGGTTGGAGTATCCTCTCG-GAAGTAA
1 CGGGGTTGGAGTATCCTC-CGAGAAATAA
18085 CGGGGTTGGAGTATCC-CCGATGAAATAA
1 CGGGGTTGGAGTATCCTCCGA-GAAATAA
**
18113 CAAGGTTGGAGTATCCTC
1 CGGGGTTGGAGTATCCTC
18131 GACTGTGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 36 0.90
29 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCTCCGAGAAATAA
Found at i:18265 original size:104 final size:102
Alignment explanation
Indices: 18116--18448 Score: 375
Period size: 104 Copynumber: 3.2 Consensus size: 102
18106 GAAATAACAA
* * *
18116 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAATCGGAGTTGGAGTATCC
* *
18181 CCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
65 CCGATTAAAGGAAAATTAGTGTTT-GAAAATAAAATCGG
* * * * *
18220 GGTTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTTAGCAATAAAACCGG-GATTGGAATATC
1 GGTTGGAGTATCCCCGATTGTG-AAAAATTGGTGTTTTGGAAATAAAATCGGAG-TTGGAGTATC
* * * * * * *
18284 CCCGATT-ATGAAAAATCAATATTTTGGAAATAAAGTCGG
64 CCCGATTAAAGGAAAATTAGT-GTTTGAAAATAAAATCGG
*
18323 GGTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTG--TTTTGGAAATAAAATCGGAGTTGGAGTATC
*
18388 CCCGATTATA-GAAAATTAGTGTCTTGAAAATAAAATCGG
64 CCCGATTAAAGGAAAATTAGTGT-TTGAAAATAAAATCGG
* * *
18427 AGTTGGAATTTCCCCGATTGTG
1 GGTTGGAGTATCCCCGATTGTG
18449 GAGAATTGAG
Statistics
Matches: 187, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
102 9 0.05
103 43 0.23
104 125 0.67
105 10 0.05
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (102 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
CGATTAAAGGAAAATTAGTGTTTGAAAATAAAATCGG
Found at i:18329 original size:51 final size:51
Alignment explanation
Indices: 18117--18445 Score: 320
Period size: 52 Copynumber: 6.4 Consensus size: 51
18107 AAATAACAAG
* * * * *
18117 GTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAATCGGA
* * * * * * *
18169 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAATCGGA
* * * *
18221 GTTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTTAGCAATAAAACCGG-
1 GTTGGAGTATCCCCGATTATG-AAAAATTAGTGTTTTGGAAATAAAATCGGA
* * * * * *
18272 GATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGG
1 G-TTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGGA
* * *
18324 GTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG--TTTTGGAAATAAAATCGGA
* *
18377 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAATCGGA
* *
18428 GTTGGAATTTCCCCGATT
1 GTTGGAGTATCCCCGATT
18446 GTGGAGAATT
Statistics
Matches: 227, Mismatches: 43, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
51 81 0.36
52 92 0.41
53 54 0.24
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGGA
Found at i:20827 original size:33 final size:33
Alignment explanation
Indices: 20785--20847 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
20775 TTTCCAAATG
***
20785 TATCGATACAAAGATCCATGTATCGATACAATA
1 TATCGATACAAAGAAAAATGTATCGATACAATA
*
20818 TATCGATACACAGAAAAATGTATCGATACA
1 TATCGATACAAAGAAAAATGTATCGATACA
20848 TTTCCTTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (33 bp):
TATCGATACAAAGAAAAATGTATCGATACAATA
Found at i:20891 original size:19 final size:19
Alignment explanation
Indices: 20867--20934 Score: 94
Period size: 19 Copynumber: 3.9 Consensus size: 19
20857 CAGTAGCTAA
20867 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
20886 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
20901 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
20918 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
20935 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 1 0.02
19 28 0.65
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:20907 original size:13 final size:13
Alignment explanation
Indices: 20889--20913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20879 ACAAAACTTA
20889 TGTATCGATACAT
1 TGTATCGATACAT
20902 TGTATCGATACA
1 TGTATCGATACA
20914 AAACTTATGT
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:20911 original size:32 final size:32
Alignment explanation
Indices: 20870--20932 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
20860 TAGCTAATTA
20870 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
20902 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
20933 AATTGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:21014 original size:21 final size:21
Alignment explanation
Indices: 20990--21046 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
20980 CATTTGTAGG
20990 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
21011 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
21032 ATGTATCGATACATT
1 ATGTATCGATACATT
21047 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:21883 original size:55 final size:55
Alignment explanation
Indices: 21788--22542 Score: 947
Period size: 55 Copynumber: 13.4 Consensus size: 55
21778 ATAAAGTGTA
* * * * *
21788 TCCTTCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGTG
** *
21843 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* ** **
21898 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTG
* * *
21959 TCCTGCTCTTTTAGGACTGAAAAATGCCACCAACCTATGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
22014 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* ** * * **
22069 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACCTATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTG
*
22130 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
22185 TCCTGCTCTTTGAGGACTG-GAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
** **
22239 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTG
* * *
22300 TCCTGCTTTTTGAGGACTGAAAAATGCCACCAACCTGTGTAGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* * *
22355 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAAATTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
*
22410 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
22465 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
*
22520 TCCTGCTCTTTGGGGACTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
22543 GCGGAAGGAG
Statistics
Matches: 613, Mismatches: 67, Indels: 40
0.85 0.09 0.06
Matches are distributed among these distances:
54 51 0.08
55 403 0.66
56 15 0.02
60 15 0.02
61 129 0.21
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
Found at i:21922 original size:26 final size:26
Alignment explanation
Indices: 21836--21923 Score: 63
Period size: 26 Copynumber: 3.3 Consensus size: 26
21826 GTGGGCTTTA
* *
21836 AAAGGCGTCCTGCTCTTTGAGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** * *
21862 AAAGGTG-CCACCAACTTGTGTGGG-CTTT
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
21890 AAGAGGTGTCCTGCTCTTTGGGGACTG
1 AA-AGGTGTCCTGCTCTTTGGGGACTG
21917 AAAGGTG
1 AAAGGTG
21924 CCACCAACTT
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
25 3 0.07
26 14 0.31
27 9 0.20
28 8 0.18
29 8 0.18
30 3 0.07
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:21947 original size:29 final size:29
Alignment explanation
Indices: 21860--21948 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
21850 CTTTGAGGAC
21860 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
21889 T-AAGAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGG-CTT
21915 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
21944 TGAAA
1 TGAAA
21949 AGAAAAAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 8 0.18
28 8 0.18
29 14 0.31
30 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:22019 original size:171 final size:171
Alignment explanation
Indices: 21787--22542 Score: 1194
Period size: 171 Copynumber: 4.5 Consensus size: 171
21777 AATAAAGTGT
* * * *
21787 ATCCTTCTCATTGAGGAGT-AAAAAGTGCCACCAA-CTCGTGTGGGCTTTAAAAGGCGTCCTGCT
1 ATCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACCT-GTGTGGGCTTTAAAAGGTGTCCTGCT
* *
21850 CTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGG
64 CTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGG
21913 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
127 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
* *
21958 ATCCTGCTCTTTTAGGACTGAAAAATGCCACCAACCTATGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
22023 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTG
66 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
* *
22088 AAAGGTGCCACCAACCTATGTGGGCTTTGAAAAGAAAAAGC
131 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
22129 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
22194 TTGAGGACTGG-AAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
66 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
22258 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
131 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
* *
22299 ATCCTGCTTTTTGAGGACTGAAAAATGCCACCAACCTGTGTAGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
22364 TTGAGGACTGGAAAATGCCACCAAATTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
66 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
** *
22429 AAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GT
131 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
* * * *
22464 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
22529 TTGGGGACT-GAAAA
66 TTGAGGACTGGAAAA
22543 GCGGAAGGAG
Statistics
Matches: 553, Mismatches: 27, Indels: 17
0.93 0.05 0.03
Matches are distributed among these distances:
164 5 0.01
165 68 0.12
170 169 0.31
171 298 0.54
172 13 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (171 bp):
ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
Found at i:22421 original size:341 final size:336
Alignment explanation
Indices: 21787--22543 Score: 1193
Period size: 341 Copynumber: 2.2 Consensus size: 336
21777 AATAAAGTGT
* * * *
21787 ATCCTTCTCATTGAGGAGT-AAAAAGTGCCACCAA-CTCGTGTGGGCTTTAAAAGGCGTCCTGCT
1 ATCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACCT-GTGTGGGCTTTAAAAGGTGTCCTGCT
*
21850 CTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGA
64 CTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGA
21914 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTTAGGACTGA
128 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTTAGGACTGA
*
21979 AAAATGCCACCAACCTATGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCAC
193 AAAATGCCACCAACCTATGTAGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCAC
* * **
22044 CAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACCTATGT
258 CAAATTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTATGT
22109 GGGCTTTGAAAAGAAAAAGC
323 GGGCTTTG-AAAG-----GC
22129 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
22194 TTGAGGACTGGAAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACT
66 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACT
22257 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCT-TTTTGAGGACTGAA
130 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTT-AGGACTGAA
*
22321 AAATGCCACCAACCTGTGTAGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACC
194 AAATGCCACCAACCTATGTAGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACC
* *
22386 AAATTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTG
259 AAATTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTATGTG
*
22451 GGCTTTGAAAGGT
324 GGCTTTGAAAGGC
* * * *
22464 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
* *
22529 TTGGGGACTGAAAAG
66 TTGAGGACTGGAAAG
22544 CGGAAGGAGA
Statistics
Matches: 389, Mismatches: 20, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
335 74 0.19
340 8 0.02
341 233 0.60
342 63 0.16
343 11 0.03
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (336 bp):
ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTG
AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTTAGGACTGAAAA
ATGCCACCAACCTATGTAGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
ATTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTATGTGGG
CTTTGAAAGGC
Found at i:23543 original size:8 final size:8
Alignment explanation
Indices: 23520--23571 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
23510 CTTTTCTCTC
*
23520 TTTTTCTT
1 TTTTTGTT
23528 TGTTTTGTT
1 T-TTTTGTT
23537 TTTTTG-T
1 TTTTTGTT
23544 TTTTT-TT
1 TTTTTGTT
*
23551 TTTTTGCT
1 TTTTTGTT
*
23559 TTTTTCTT
1 TTTTTGTT
23567 TTTTT
1 TTTTT
23572 TGAAGAGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 12 0.32
8 18 0.49
9 7 0.19
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.87
Consensus pattern (8 bp):
TTTTTGTT
Found at i:23544 original size:13 final size:12
Alignment explanation
Indices: 23520--23553 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
23510 CTTTTCTCTC
*
23520 TTTTTCTTTGTT
1 TTTTTTTTTGTT
23532 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
23545 TTTTTTTTT
1 TTTTTTTTT
23554 TTGCTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:23555 original size:22 final size:22
Alignment explanation
Indices: 23518--23573 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
23508 TTCTTTTCTC
*
23518 TCTTTTTCTTTGTTTTGTTTTTT
1 TCTTTTT-TTTGTTTTGCTTTTT
* *
23541 TGTTTTTTTTTTTTTGCTTTTT
1 TCTTTTTTTTGTTTTGCTTTTT
23563 TCTTTTTTTTG
1 TCTTTTTTTTG
23574 AAGAGAAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (22 bp):
TCTTTTTTTTGTTTTGCTTTTT
Done.