Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2646
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: 32602
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1134 original size:30 final size:30
Alignment explanation
Indices: 1094--1152 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1084 CAGTTGGAGC
*
1094 TGGAGTTGGAGCTGGGAGCTGTAACAGAAT
1 TGGAGCTGGAGCTGGGAGCTGTAACAGAAT
1124 TGGAGCTGGAGCTGGGAGCTGTAACAGAA
1 TGGAGCTGGAGCTGGGAGCTGTAACAGAA
1153 AGAGCCAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.41, T:0.20
Consensus pattern (30 bp):
TGGAGCTGGAGCTGGGAGCTGTAACAGAAT
Found at i:1371 original size:11 final size:11
Alignment explanation
Indices: 1339--1388 Score: 57
Period size: 11 Copynumber: 4.4 Consensus size: 11
1329 AATATCAGTT
*
1339 TTCTCCTCTTAA
1 TTCTCTTCTT-A
1351 TTCTTCTTCTTA
1 TTC-TCTTCTTA
1363 TTCTCTTC-TA
1 TTCTCTTCTTA
1373 TTTCTCTTCTTA
1 -TTCTCTTCTTA
1385 TTCT
1 TTCT
1389 TCATAGTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 2 0.06
11 17 0.50
12 9 0.26
13 6 0.18
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (11 bp):
TTCTCTTCTTA
Found at i:6342 original size:30 final size:30
Alignment explanation
Indices: 6299--6358 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6289 ACAGTTGGAG
* *
6299 TTGGAGTTGGAGCTGGGAGCTGTAACAGAA
1 TTGGAGCTAGAGCTGGGAGCTGTAACAGAA
6329 TTGGAGCTAGAGCTGGGAGCTGTAACAGAA
1 TTGGAGCTAGAGCTGGGAGCTGTAACAGAA
6359 AGAGCCAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.12, G:0.38, T:0.22
Consensus pattern (30 bp):
TTGGAGCTAGAGCTGGGAGCTGTAACAGAA
Found at i:6594 original size:11 final size:11
Alignment explanation
Indices: 6561--6594 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
6551 TCTTAAATCT
6561 TCTTCTTATTC
1 TCTTCTTATTC
6572 TCTT-TTATTTC
1 TCTTCTTA-TTC
6583 TCTTCTTATTC
1 TCTTCTTATTC
6594 T
1 T
6595 TCATAGTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (11 bp):
TCTTCTTATTC
Found at i:8205 original size:16 final size:16
Alignment explanation
Indices: 8184--8215 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8174 TGGCGATCCG
8184 AGGTTTAAATCAATAT
1 AGGTTTAAATCAATAT
8200 AGGTTTAAATCAATAT
1 AGGTTTAAATCAATAT
8216 TGATCGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
AGGTTTAAATCAATAT
Found at i:9468 original size:2 final size:2
Alignment explanation
Indices: 9463--9493 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9453 TGTGTGTGTG
9463 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 T
9494 TATGATATTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9654 original size:31 final size:31
Alignment explanation
Indices: 9616--9677 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
9606 TTTTTCATTC
*
9616 TGTCCATGTAGATATATTAGAACTTATTGAT
1 TGTCCATGTACATATATTAGAACTTATTGAT
*
9647 TGTCCATGTACATTTATTAGAACTTATTGAT
1 TGTCCATGTACATATATTAGAACTTATTGAT
9678 AGTTCATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (31 bp):
TGTCCATGTACATATATTAGAACTTATTGAT
Found at i:9695 original size:31 final size:31
Alignment explanation
Indices: 9617--9685 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
9607 TTTTCATTCT
* * *
9617 GTCCATGTAGATATATTAGAACTTATTGATT
1 GTCCATGTACATTTATTAGAACTTATTGATA
9648 GTCCATGTACATTTATTAGAACTTATTGATA
1 GTCCATGTACATTTATTAGAACTTATTGATA
*
9679 GTTCATG
1 GTCCATG
9686 GTTGTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (31 bp):
GTCCATGTACATTTATTAGAACTTATTGATA
Found at i:10855 original size:3 final size:3
Alignment explanation
Indices: 10841--10883 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
10831 AAACTGGTAT
10841 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10884 ATAAATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10888 original size:4 final size:4
Alignment explanation
Indices: 10879--10904 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
10869 TAATAATAAT
10879 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
10905 ATGGCAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:15669 original size:196 final size:196
Alignment explanation
Indices: 15335--15730 Score: 767
Period size: 196 Copynumber: 2.0 Consensus size: 196
15325 TTTCCCAAGT
*
15335 CAGCCTCTTCACTTAAACTAATTCTCTTGGTGCAACAATAAAAACAAAATCAATATTACAAGGAA
1 CAGCCTCTTCACTTAAACTAATTCTCTCGGTGCAACAATAAAAACAAAATCAATATTACAAGGAA
*
15400 AGTAATGGAAGAGAACTAGCGTTCAGGCACATTTCCAATGAGAACCAGCATTTTCCCAAAGAGCC
66 AGTAATGGAAGAAAACTAGCGTTCAGGCACATTTCCAATGAGAACCAGCATTTTCCCAAAGAGCC
15465 TTTATGGCCACCAATATAGCATCTTAGACACCAGAAAAGCTGATGTTACATATCATACATGGTTC
131 TTTATGGCCACCAATATAGCATCTTAGACACCAGAAAAGCTGATGTTACATATCATACATGGTTC
15530 G
196 G
15531 CAGCCTCTTCACTTAAACTAATTCTCTCGGTGCAACAATAAAAACAAAATCAATATTACAAGGAA
1 CAGCCTCTTCACTTAAACTAATTCTCTCGGTGCAACAATAAAAACAAAATCAATATTACAAGGAA
15596 AGTAATGGAAGAAAACTAGCGTTCAGGCACATTTCCAATGAGAACCAGCATTTTCCCAAAGAGCC
66 AGTAATGGAAGAAAACTAGCGTTCAGGCACATTTCCAATGAGAACCAGCATTTTCCCAAAGAGCC
15661 TTTATGGCCACCAATATAGCATCTTAGACACCAGAAAAGCTGATGTTACATATCATACATGGTTC
131 TTTATGGCCACCAATATAGCATCTTAGACACCAGAAAAGCTGATGTTACATATCATACATGGTTC
15726 G
196 G
15727 -AGCC
1 CAGCC
15731 CCTTAACATG
Statistics
Matches: 198, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
195 4 0.02
196 194 0.98
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (196 bp):
CAGCCTCTTCACTTAAACTAATTCTCTCGGTGCAACAATAAAAACAAAATCAATATTACAAGGAA
AGTAATGGAAGAAAACTAGCGTTCAGGCACATTTCCAATGAGAACCAGCATTTTCCCAAAGAGCC
TTTATGGCCACCAATATAGCATCTTAGACACCAGAAAAGCTGATGTTACATATCATACATGGTTC
G
Found at i:18689 original size:150 final size:153
Alignment explanation
Indices: 18509--18869 Score: 373
Period size: 150 Copynumber: 2.4 Consensus size: 153
18499 TTGGATATAT
*
18509 TTTTGATATGAAAGTATCTCAGTAATCTTAAAAGACTCGAAAATGATCAAAAAATGA-TAAATC-
1 TTTTGACATGAAAGTATCTCAGTAATCTTAAAAGACTCGAAAATGAT-AAAAAATGAGTAAA-CA
* * *
18572 TATTATAAATGTACACTTTTGGCATAAAAGCAT-TCTGGTGACTACATCGAACTCAG-TTCTA-A
64 TATCATAAATGCACACTTTTGGCATAAAAGCATCTC-AGTGACTACATCGAACT-AGATTCTAGA
18634 -AAAATTACTAAAATGC-CCT-TAATA
127 GAAAATTACTAAAATGCTCCTCTAATA
* ** * * * *
18658 CTTTTGACATGAAAGTATCTCAATTGTCTT-AAAGAACTCAAAAATAATTATAAAA-GAGTGAAC
1 -TTTTGACATGAAAGTATCTCAGTAATCTTAAAAG-ACTCGAAAATGA-TAAAAAATGAGTAAAC
* * * *
18721 ATATCCTAAATGCACACTTTTGGTATAAAAGCATCTCAGTGACTAGATCGGACTAGATTCTAGGA
63 ATATCATAAATGCACACTTTTGGCATAAAAGCATCTCAGTGACTACATCGAACTAGATTCTA-GA
* *
18786 GAAAATTATTAAAATGCTCTTCTAATA
127 GAAAATTACTAAAATGCTCCTCTAATA
* * *
18813 TATCTTCGACATTAAAGTATCTCAGTAACCTTAAAGGACTCGAAAATGATAAAAAAT
1 T-T-TT-GACATGAAAGTATCTCAGTAATCTTAAAAGACTCGAAAATGATAAAAAAT
18870 AATCATTTGA
Statistics
Matches: 169, Mismatches: 26, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
149 9 0.05
150 91 0.54
151 3 0.02
152 1 0.01
153 15 0.09
154 3 0.02
155 6 0.04
156 8 0.05
157 30 0.18
158 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (153 bp):
TTTTGACATGAAAGTATCTCAGTAATCTTAAAAGACTCGAAAATGATAAAAAATGAGTAAACATA
TCATAAATGCACACTTTTGGCATAAAAGCATCTCAGTGACTACATCGAACTAGATTCTAGAGAAA
ATTACTAAAATGCTCCTCTAATA
Found at i:19503 original size:13 final size:13
Alignment explanation
Indices: 19485--19510 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19475 TACAGCAAGT
19485 ATGTATCGATACA
1 ATGTATCGATACA
19498 ATGTATCGATACA
1 ATGTATCGATACA
19511 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21759 original size:21 final size:21
Alignment explanation
Indices: 21726--21770 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21716 TTGCAAGTTG
*
21726 AAATAAAGAAGTTGGCTAACGA
1 AAATAAAGAAGTTAGCTAA-GA
*
21748 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
21768 AAA
1 AAA
21771 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:23354 original size:65 final size:65
Alignment explanation
Indices: 23285--24045 Score: 397
Period size: 66 Copynumber: 11.7 Consensus size: 65
23275 TTGTTTTTTT
* * * * *
23285 TTTTTTACTTAGGTTTTGTCTTGGTCACATTTTGTTGGTTCGTATGGTTTCGTCCCAGCCAACTC
1 TTTTTTACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAACTC
* * * * * * *
23350 TTTTTCACTTAGGTTTTTACCTT-GATCACCTTTTGTTGGTTTG-CTGGTTTTATCCCAACCAA-
1 TTTTTTACTTAGG-TTTTGCCTTAG-TCACCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAAC
*
23412 TT
64 TC
*** * * * * *
23414 TTTTTTCAACTT---TTCCACCCTAATCATCTTTT-TT-TTTCATATGGTTTCATCCCAGCTAAC
1 TTTTTT--ACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAAC
23474 TC
64 TC
* ** * * * * *
23476 CTTTCAACTTAGCTTTTACCTTGGTCAACC-TTTGTTGGTTCGTATGGTTTCATACTAGCTAACT
1 TTTTTTACTTAGGTTTTGCCTTAGTC-ACCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAACT
23540 AC
65 -C
* * * * * * * *
23542 TTTTTGACTT---TTTCGCCTTAATCATCCTTTTTTTCGTTCATGTGGTTTCATCCAAGCTAACT
1 TTTTTTACTTAGGTTTTGCCTTAGTCA-CCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAACT
23604 C
65 C
* * * * * ** *
23605 TTTTTTGACTTAGGTTATGCCCTGGTTACCCTTTG-TGGTTTATATGGTTTCATCCTAGCTAACT
1 TTTTTT-ACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAACT
23669 CC
65 -C
* * * * * *
23671 TTTTTTCCCTAGGTTCTGACTTAGTTAGCC-TTTGTTGGTTCATATGGTTTCATCCCAGCTAACC
1 TTTTTTACTTAGGTTTTGCCTTAGTCA-CCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAA-C
23735 TC
64 TC
* ** * * * * * * * ** * *
23737 CTTTCGACTTAAGTTTCGCCCTGGTCACCCTTTGTTGGTTTGTATGTTTTCATCCTGGCCAATCC
1 TTTTTTACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAA-CT
23802 C
65 C
** * * * * *
23803 TTTTCAACTTAAGTTTTGCCCTAGTCACCTTTTGTTGGTTTGTATGGTTTCATCCCCGCCAACTC
1 TTTTTTACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAACT-
23868 C
65 C
** * * * * * ***
23869 TTTTCGACTTAAGTTCT-ACTCTAGTTA-CTCTTTGTTGATT-GTATGGTTTCATCTTGGCTAAC
1 TTTTTTACTTAGGTTTTGCCT-TAGTCACCT-TTTGTTGGTTCGTATGGTTTCATCCCAGCTAAC
23931 TC
64 TC
** * * * ** * *
23933 TTTTTTTACTTAGGTTTTGCCCAAGTTA-CTCTTTGTTGGTTTGCATGGTTTTGTCCCGGCCAAC
1 -TTTTTTACTTAGGTTTTGCCTTAGTCACCT-TTTGTTGGTTCGTATGGTTTCATCCCAGCTAAC
23997 TC
64 TC
* *
23999 TTTTTTGACCTAGGTTTCGCCTTAGTCACCTTTTGTTGGTTCGTATG
1 TTTTTT-ACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCGTATG
24046 TTCACTCTTT
Statistics
Matches: 532, Mismatches: 131, Indels: 65
0.73 0.18 0.09
Matches are distributed among these distances:
60 6 0.01
61 17 0.03
62 19 0.04
63 28 0.05
64 43 0.08
65 156 0.29
66 251 0.47
67 12 0.02
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (65 bp):
TTTTTTACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCGTATGGTTTCATCCCAGCTAACTC
Found at i:23644 original size:129 final size:126
Alignment explanation
Indices: 23434--23675 Score: 306
Period size: 129 Copynumber: 1.9 Consensus size: 126
23424 TTTTCCACCC
* * *
23434 TAATCATCTTTTTTTTTCATATGGTTTCATCCCAGCTAACTCCTTTCAACTTAGCTTTTACCTTG
1 TAATCATCTTTTTTTTTCATATGGTTTCATCCAAGCTAACTCCTTTCAACTTAGCTTATACCCTG
*
23499 GTCAACCTTTGTTGGTTCGTATGGTTTCATACTAGCTAACTACTTTTTGACTTTTTCGCCT
66 GTCAACCTTTGTTGGTTCATATGGTTTCATACTAGCTAACTACTTTTTGACTTTTTCGCCT
* * ** * *
23560 TAATCATCCTTTTTTTCGTTCATGTGGTTTCATCCAAGCTAACTCTTTTTTGACTTAGGTTATGC
1 TAATCAT-CTTTTTTT--TTCATATGGTTTCATCCAAGCTAACTC-CTTTCAACTTAGCTTATAC
* * * * *
23625 CCTGGTTACCCTTTG-TGGTTTATATGGTTTCATCCTAGCTAACTCCTTTTT
62 CCTGGTCAACCTTTGTTGGTTCATATGGTTTCATACTAGCTAACTACTTTTT
23676 TCCCTAGGTT
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
126 7 0.07
127 8 0.08
129 57 0.59
130 25 0.26
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.47
Consensus pattern (126 bp):
TAATCATCTTTTTTTTTCATATGGTTTCATCCAAGCTAACTCCTTTCAACTTAGCTTATACCCTG
GTCAACCTTTGTTGGTTCATATGGTTTCATACTAGCTAACTACTTTTTGACTTTTTCGCCT
Found at i:23974 original size:131 final size:129
Alignment explanation
Indices: 23453--24003 Score: 414
Period size: 131 Copynumber: 4.2 Consensus size: 129
23443 TTTTTTTTCA
* * * * * *
23453 TATGGTTTCATCCCAGCTAACTCC-TTTCAACTT-AGCTTTTACCTTGGTCAACCTTTGTTGGTT
1 TATGGTTTCATCCCAGCCAACTCCTTTTCGACTTAAG--TTTGCCCTGGTTACCCTTTGTT-GTT
* * * * * * * * * * *
23516 CGTATGGTTTCATACTAGCTAACTACTTTTTGACTT---TTTCGCCTTAATCATCCTTTTTTTCG
63 TGTATGGTTTCATCCTGGCTAACTCCTTTTTTACTTAGGTTTTGCCCTAGTTA-CC-TTTGTTGG
**
23578 TTCA
126 TTTG
* * * * * * * *
23582 TGTGGTTTCATCCAAGCTAACTCTTTTTTGACTTAGGTTATGCCCTGGTTACCCTTTGTGGTTTA
1 TATGGTTTCATCCCAGCCAACTCCTTTTCGACTTAAGTT-TGCCCTGGTTACCCTTTGTTGTTTG
* * * * * * *
23647 TATGGTTTCATCCTAGCTAACTCCTTTTTTCCCTAGGTTCTGACTTAGTTAGCCTTTGTTGGTTC
65 TATGGTTTCATCCTGGCTAACTCCTTTTTTACTTAGGTTTTGCCCTAGTTA-CCTTTGTTGGTTT
*
23712 A
129 G
* *
23713 TATGGTTTCATCCCAGCTAACCTCC-TTTCGACTTAAGTTTCGCCCTGGTCACCCTTTGTTGGTT
1 TATGGTTTCATCCCAGCCAA-CTCCTTTTCGACTTAAGTTT-GCCCTGGTTACCCTTTGTT-GTT
* * ** * *
23777 TGTATGTTTTCATCCTGGCCAA-TCCCTTTTCAACTTAAGTTTTGCCCTAGTCACCTTTTGTTGG
63 TGTATGGTTTCATCCTGGCTAACT-CCTTTTTTACTTAGGTTTTGCCCTAGTTACC-TTTGTTGG
23841 TTTG
126 TTTG
* * * * * *
23845 TATGGTTTCATCCCCGCCAACTCCTTTTCGACTTAAGTTCTACTCTAGTTACTCTTTGTTGATTG
1 TATGGTTTCATCCCAGCCAACTCCTTTTCGACTTAAGTT-TGCCCTGGTTACCCTTTGTTGTTTG
* * *
23910 TATGGTTTCATCTTGGCTAACTCTTTTTTTACTTAGGTTTTGCCCAAGTTACTCTTTGTTGGTTT
65 TATGGTTTCATCCTGGCTAACTCCTTTTTTACTTAGGTTTTGCCCTAGTTAC-CTTTGTTGGTTT
23975 G
129 G
* ** * *
23976 CATGGTTTTGTCCCGGCCAACTCTTTTT
1 TATGGTTTCATCCCAGCCAACTCCTTTT
24004 TGACCTAGGT
Statistics
Matches: 337, Mismatches: 70, Indels: 28
0.77 0.16 0.06
Matches are distributed among these distances:
129 55 0.16
130 23 0.07
131 145 0.43
132 113 0.34
133 1 0.00
ACGTcount: A:0.15, C:0.24, G:0.16, T:0.45
Consensus pattern (129 bp):
TATGGTTTCATCCCAGCCAACTCCTTTTCGACTTAAGTTTGCCCTGGTTACCCTTTGTTGTTTGT
ATGGTTTCATCCTGGCTAACTCCTTTTTTACTTAGGTTTTGCCCTAGTTACCTTTGTTGGTTTG
Found at i:23983 original size:263 final size:260
Alignment explanation
Indices: 23449--24047 Score: 576
Period size: 263 Copynumber: 2.3 Consensus size: 260
23439 ATCTTTTTTT
* * ** *
23449 TTCATATGGTTTCATCCCAGCTAACTCCTTTCAACTT-AGCTTTTACCTTGGTCAACCTTTGTTG
1 TTCACATGGTTTCATCCCAGCTAACTCCTTTCGACTTAAG-TTTCGCCTTGGTCACCCTTTGTTG
* * ** * *
23513 GTTCGTATGGTTTCATACTAGCTAACTACTTTTTGACTTTTTCGCCTTAATCATCCTTTTTTTCG
65 GTTCGTATGTTTTCATACTAGCCAACTACTTTTCAACTTTTTCGCCCTAATCATCCTTTTGTTCG
* * * * * * *
23578 TTCATGTGGTTTCATCCAAGCTAACTCTTTTTTGACTTAGGTTATGCCCTGGTTACCCTTTGTGG
130 TTCATATGGTTTCATCCAAGCCAACTCCTTTTCGACTTAAGTTATACCCTAGTTACCCTTTGTGG
* * **
23643 TTTATATGGTTTCATCCTAGCTAACTCCTTTTTTCCCTAGGTTCTGACTTAGTTAGCCTTTGTTG
195 ATTATATGGTTTCATCCTAGCTAACTCCTTTTTTACCTAGGTTCTGACCAAGTTAGCCTTTGTTG
23708 G
260 G
* *
23709 TTCATATGGTTTCATCCCAGCTAACCTCCTTTCGACTTAAGTTTCGCCCTGGTCACCCTTTGTTG
1 TTCACATGGTTTCATCCCAGCTAA-CTCCTTTCGACTTAAGTTTCGCCTTGGTCACCCTTTGTTG
* * * * * *
23774 GTTTGTATGTTTTCATCCTGGCCAA-TCCCTTTTCAACTTAAGTTTTGCCCTAGTCA-CCTTTTG
65 GTTCGTATGTTTTCATACTAGCCAACT-ACTTTTCAACTT---TTTCGCCCTAATCATCCTTTTG
* ** ** * * *
23837 TTGGTTTGTATGGTTTCATCCCCGCCAACTCCTTTTCGACTTAAGTTCTACTCTAGTTACTCTTT
126 TTCGTTCATATGGTTTCATCCAAGCCAACTCCTTTTCGACTTAAGTTATACCCTAGTTACCCTTT
* * * * * * * *
23902 GTTGATTGTATGGTTTCATCTTGGCTAACTCTTTTTTTACTTAGGTTTTGCCCAAGTTA-CTCTT
191 GTGGATTATATGGTTTCATCCTAGCTAACTCCTTTTTTACCTAGGTTCTGACCAAGTTAGC-CTT
23966 TGTTGG
255 TGTTGG
** ** * * * * * * * *
23972 TTTGCATGGTTTTGTCCCGGCCAACTCTTTTTTGACCTAGGTTTCGCCTTAGTCACCTTTTGTTG
1 TTCACATGGTTTCATCCCAGCTAACTC-CTTTCGACTTAAGTTTCGCCTTGGTCACCCTTTGTTG
24037 GTTCGTATGTT
65 GTTCGTATGTT
24048 CACTCTTTGT
Statistics
Matches: 272, Mismatches: 59, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
260 25 0.09
261 61 0.22
262 6 0.02
263 169 0.62
264 11 0.04
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (260 bp):
TTCACATGGTTTCATCCCAGCTAACTCCTTTCGACTTAAGTTTCGCCTTGGTCACCCTTTGTTGG
TTCGTATGTTTTCATACTAGCCAACTACTTTTCAACTTTTTCGCCCTAATCATCCTTTTGTTCGT
TCATATGGTTTCATCCAAGCCAACTCCTTTTCGACTTAAGTTATACCCTAGTTACCCTTTGTGGA
TTATATGGTTTCATCCTAGCTAACTCCTTTTTTACCTAGGTTCTGACCAAGTTAGCCTTTGTTGG
Found at i:24034 original size:131 final size:131
Alignment explanation
Indices: 23714--24045 Score: 314
Period size: 131 Copynumber: 2.5 Consensus size: 131
23704 GTTGGTTCAT
* * * * * * *
23714 ATGGTTTCATCCCAGCTAACCTCC-TTTCGACTTAAGTTTCGCCCTGGTCACCCTTTGTTGGTTT
1 ATGGTTTCATCCCCGCCAA-CTCCTTTTCGACCTAAGTTTCGCCTTAGTCACCTTTTGTT-GATT
* *
23778 GTATGTTTTCATCCTGGCCAATCCCTTTTCAACTTAAGTTTTGCCCTAGTCACCTTTTGTTGGTT
64 GTATGGTTTCATCCTGGCCAATCCCTTTTCAACTTAAGTTTTGCCCAAGTCACCTTTTGTTGGTT
*
23843 TGT
129 TGC
* ** *
23846 ATGGTTTCATCCCCGCCAACTCCTTTTCGACTTAAG-TTCTACTCTAGTTA-CTCTTTGTTGATT
1 ATGGTTTCATCCCCGCCAACTCCTTTTCGACCTAAGTTTCGCCT-TAGTCACCT-TTTGTTGATT
* * * ** * *
23909 GTATGGTTTCATCTTGGCTAA-CTCTTTTTTTACTTAGGTTTTGCCCAAGTTA-CTCTTTGTTGG
64 GTATGGTTTCATCCTGGCCAATC-CCTTTTCAACTTAAGTTTTGCCCAAGTCACCT-TTTGTTGG
23972 TTTGC
127 TTTGC
** * * * * *
23977 ATGGTTTTGTCCCGGCCAACTCTTTTTTGACCTAGGTTTCGCCTTAGTCACCTTTTGTTGGTTCG
1 ATGGTTTCATCCCCGCCAACTCCTTTTCGACCTAAGTTTCGCCTTAGTCACCTTTTGTTGATT-G
24042 TATG
65 TATG
24046 TTCACTCTTT
Statistics
Matches: 162, Mismatches: 30, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
130 3 0.02
131 108 0.67
132 51 0.31
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (131 bp):
ATGGTTTCATCCCCGCCAACTCCTTTTCGACCTAAGTTTCGCCTTAGTCACCTTTTGTTGATTGT
ATGGTTTCATCCTGGCCAATCCCTTTTCAACTTAAGTTTTGCCCAAGTCACCTTTTGTTGGTTTG
C
Found at i:24185 original size:66 final size:64
Alignment explanation
Indices: 24047--24192 Score: 148
Period size: 66 Copynumber: 2.2 Consensus size: 64
24037 GTTCGTATGT
* ** * *
24047 TCACTCTTTGTTAATTCGTATGGTTTCATCCTGCCAACTTTTTTCGACTTAGGTTCCACCCTAG
1 TCACCCTTTGTTGGTTCATATGGTTTCATCCCGCCAACTTTTTTCGACTTAGGTTCCACCCTAG
* * * * * * * * *
24111 TTATCCTTTTTTGGTTCATATGGTTTCATCCCGATCAACTTCTTTTTGATTTAGGTTCTATCTTA
1 TCACCCTTTGTTGGTTCATATGGTTTCATCCCG-CCAACTT-TTTTCGACTTAGGTTCCACCCTA
24176 G
64 G
24177 TCACCCTTTGTTGGTT
1 TCACCCTTTGTTGGTT
24193 TGTATGATTT
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
64 25 0.40
65 6 0.10
66 32 0.51
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.47
Consensus pattern (64 bp):
TCACCCTTTGTTGGTTCATATGGTTTCATCCCGCCAACTTTTTTCGACTTAGGTTCCACCCTAG
Found at i:27513 original size:13 final size:13
Alignment explanation
Indices: 27495--27519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27485 CAATTTTTTG
27495 TGTATCGATACAT
1 TGTATCGATACAT
27508 TGTATCGATACA
1 TGTATCGATACA
27520 AGTTTGGCTA
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:28228 original size:21 final size:21
Alignment explanation
Indices: 28187--28230 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28177 CTCCCCTTTA
* *
28187 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
28208 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
28229 TC
1 TC
28231 ATATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:30020 original size:13 final size:13
Alignment explanation
Indices: 30002--30027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29992 ATAATCACCC
30002 TGTATCGATACAA
1 TGTATCGATACAA
30015 TGTATCGATACAA
1 TGTATCGATACAA
30028 AAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:32130 original size:16 final size:16
Alignment explanation
Indices: 32109--32139 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32099 ATTTCGTTTG
*
32109 GAGCTTCTTCATTTTT
1 GAGCTTCCTCATTTTT
32125 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
32140 GGACATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.52
Consensus pattern (16 bp):
GAGCTTCCTCATTTTT
Done.