Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2622
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: 40664
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:857 original size:26 final size:26
Alignment explanation
Indices: 828--880 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
818 TTTTTGAAAA
828 TAAATTTGTAAAAAGGGGAGAGATAT
1 TAAATTTGTAAAAAGGGGAGAGATAT
* *
854 TAAATTTGTTAAAGGGGGAGAGATAT
1 TAAATTTGTAAAAAGGGGAGAGATAT
880 T
1 T
881 TTGAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (26 bp):
TAAATTTGTAAAAAGGGGAGAGATAT
Found at i:940 original size:14 final size:13
Alignment explanation
Indices: 913--937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
903 AAAAGGGGAG
913 ATTATTTTTGAAC
1 ATTATTTTTGAAC
926 ATTATTTTTGAA
1 ATTATTTTTGAA
938 ACAAAAAGGG
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:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTATTTTTGAAC
Found at i:5863 original size:27 final size:28
Alignment explanation
Indices: 5801--5863 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
5791 ACAAAAGTTC
*
5801 TATTTTAATATCTAATTAAAATATAAAT
1 TATTTTAATATCTAAATAAAATATAAAT
* *
5829 T-TTTTAATAT-TAAATAAAATTTTAAT
1 TATTTTAATATCTAAATAAAATATAAAT
*
5855 TATTATAAT
1 TATTTTAAT
5864 CTATATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 14 0.47
27 15 0.50
28 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTTTAATATCTAAATAAAATATAAAT
Found at i:9048 original size:20 final size:20
Alignment explanation
Indices: 9020--9057 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9010 GAAAACGGTT
*
9020 AATTGTCTTTAACAATAAAA
1 AATTATCTTTAACAATAAAA
*
9040 AATTATCTTTAATAATAA
1 AATTATCTTTAACAATAA
9058 TTTTTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (20 bp):
AATTATCTTTAACAATAAAA
Found at i:16672 original size:9 final size:9
Alignment explanation
Indices: 16614--16672 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
16604 TCTCTCTCAT
*
16614 TATCTCTCA
1 TATCTCTCC
16623 TATCTCTCC
1 TATCTCTCC
* *
16632 T-CCTAT-C
1 TATCTCTCC
*
16639 -ATCCCTCC
1 TATCTCTCC
*
16647 TATCTCTAC
1 TATCTCTCC
16656 TATCTCTCC
1 TATCTCTCC
16665 TATCTCTC
1 TATCTCTC
16673 ATCCTATCAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.11
9 31 0.82
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (9 bp):
TATCTCTCC
Found at i:16678 original size:42 final size:42
Alignment explanation
Indices: 16591--16704 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 42
16581 TCTTTCCTCC
* * *
16591 TCCTATCATCCCTTCTCTCTC-ATTATCTCTCATATCTCTCC
1 TCCTATCATCCCTTCTATCTCTACTATCTCTCATATCTCTCA
* *
16632 TCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCA
1 TCCTATCATCCCTTCTATCTCTACTATCTCTCATATCTCTCA
* * *
16674 TCCTATCATCCCTTTTATCTCTTCTTTCTCT
1 TCCTATCATCCCTTCTATCTCTACTATCTCT
16705 TTGAGGGCTA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
41 19 0.30
42 44 0.70
ACGTcount: A:0.14, C:0.40, G:0.00, T:0.46
Consensus pattern (42 bp):
TCCTATCATCCCTTCTATCTCTACTATCTCTCATATCTCTCA
Found at i:19998 original size:18 final size:17
Alignment explanation
Indices: 19975--20008 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19965 AAATGGCATG
*
19975 GAAAAAAGAAAATGAAAT
1 GAAAAAA-AAAAAGAAAT
19993 GAAAAAAAAAAAGAAA
1 GAAAAAAAAAAAGAAA
20009 AATAAAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAAAAAAAAAGAAAT
Found at i:20021 original size:24 final size:23
Alignment explanation
Indices: 19976--20023 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19966 AATGGCATGG
*
19976 AAAAAAGAAAATGAAATGAAAAA
1 AAAAAAGAAAATGAAAAGAAAAA
*
19999 AAAAAAGAAAAAT-AAAAGCAAAA
1 AAAAAAG-AAAATGAAAAGAAAAA
20022 AA
1 AA
20024 TCAAGATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.06
Consensus pattern (23 bp):
AAAAAAGAAAATGAAAAGAAAAA
Found at i:20864 original size:36 final size:36
Alignment explanation
Indices: 20817--20889 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
20807 GTGGGGACTA
20817 AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
1 AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
20853 AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
1 AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
20889 A
1 A
20890 ATTTTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.27
Consensus pattern (36 bp):
AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
Found at i:21385 original size:19 final size:19
Alignment explanation
Indices: 21361--21425 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
21351 TAGCCAAACT
21361 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
21380 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
21393 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
21414 TGTATCGATACA
1 TGTATCGATACA
21426 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:21397 original size:13 final size:13
Alignment explanation
Indices: 21379--21404 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21369 TACACAAAAT
21379 ATGTATCGATACA
1 ATGTATCGATACA
21392 ATGTATCGATACA
1 ATGTATCGATACA
21405 CAAAAAATAT
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:21402 original size:32 final size:33
Alignment explanation
Indices: 21361--21425 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
21351 TAGCCAAACT
21361 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
21393 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
21426 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:24913 original size:15 final size:15
Alignment explanation
Indices: 24893--24923 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24883 TAAAAATATC
*
24893 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
24908 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
24923 C
1 C
24924 CAAACGGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:26964 original size:20 final size:20
Alignment explanation
Indices: 26939--26990 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
26929 ATGTCCAAAA
26939 TGTATCGATACATGTTTT-TG
1 TGTATCGATACAT-TTTTCTG
*
26959 TGTATCGATACATTTTTCTT
1 TGTATCGATACATTTTTCTG
26979 TGTATCGATACA
1 TGTATCGATACA
26991 ATGTATCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.48
Consensus pattern (20 bp):
TGTATCGATACATTTTTCTG
Found at i:26997 original size:13 final size:13
Alignment explanation
Indices: 26979--27016 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
26969 CATTTTTCTT
26979 TGTATCGATACAA
1 TGTATCGATACAA
* *
26992 TGTATCAATACAC
1 TGTATCGATACAA
27005 TGTATCGATACA
1 TGTATCGATACA
27017 GGGGGATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:27171 original size:20 final size:20
Alignment explanation
Indices: 27128--27173 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
27118 AAATCTTTTG
27128 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
27149 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
27169 CAAAA
1 CAAAA
27174 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:29565 original size:19 final size:19
Alignment explanation
Indices: 29541--29605 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
29531 TAGCCAAACT
29541 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
29560 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
29573 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
29594 TGTATCGATACA
1 TGTATCGATACA
29606 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:29577 original size:13 final size:13
Alignment explanation
Indices: 29559--29584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29549 TACACAAAAT
29559 ATGTATCGATACA
1 ATGTATCGATACA
29572 ATGTATCGATACA
1 ATGTATCGATACA
29585 CAAAAAATAT
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:29582 original size:32 final size:33
Alignment explanation
Indices: 29541--29605 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
29531 TAGCCAAACT
29541 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
29573 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
29606 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:31499 original size:22 final size:21
Alignment explanation
Indices: 31463--31524 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
31453 TTTTCTTAGT
31463 TAATTC-TTTATTTTCTTTTGGC
1 TAATTCATTTATTTTCTTTT--C
*
31485 -AATTCATTAATTTTCTTTTC
1 TAATTCATTTATTTTCTTTTC
31505 TAATTCATTTATTTTCTTTT
1 TAATTCATTTATTTTCTTTT
31525 TAAGAAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 23 0.64
22 12 0.33
ACGTcount: A:0.19, C:0.13, G:0.03, T:0.65
Consensus pattern (21 bp):
TAATTCATTTATTTTCTTTTC
Found at i:31997 original size:3 final size:3
Alignment explanation
Indices: 31989--32013 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31979 AACCTCTTGC
31989 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
32014 TATTACCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:34102 original size:92 final size:92
Alignment explanation
Indices: 33936--34171 Score: 366
Period size: 92 Copynumber: 2.6 Consensus size: 92
33926 CCACCCATAT
* * * *
33936 ATTCCTAAT-ATATCCCTTTCTTTTAGCCATTACATGGTATTGATGCATCATAAAGCCTGATTTC
1 ATTCCTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACAAAGCCTAATTTC
*
34000 CTTAGGGCAAGGATATCCTGACCACTC
66 CTTAGGGCAAGGATATCCCGACCACTC
*
34027 ATTCCTAATCATATCCCTTTCTTTTGGCCACTAGATGGTATTGATGCATCACAAAGCCTAATTTC
1 ATTCCTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACAAAGCCTAATTTC
* * *
34092 CTTTGGGCAAGGATATCCCGACCATTT
66 CTTAGGGCAAGGATATCCCGACCACTC
* *
34119 ATTCCCAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGTATCACA
1 ATTCCTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACA
34172 TGACCATAAA
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 9 0.07
92 123 0.93
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (92 bp):
ATTCCTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACAAAGCCTAATTTC
CTTAGGGCAAGGATATCCCGACCACTC
Found at i:34647 original size:47 final size:46
Alignment explanation
Indices: 34576--34686 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 46
34566 ATTTTACTTG
* * *
34576 GTCAAAC-CTTTTTCATTATCGTTTGACGTGATGGTTCTTGCCTTA
1 GTCAAACATTTTTTCATTCTCGTTTGACGTGATGGTTCTTGCCCTA
* * *
34621 TTCAAACATTTTTTTCATTCTTGTTTGACGTTATGGTTCTTGCCCTA
1 GTCAAACA-TTTTTTCATTCTCGTTTGACGTGATGGTTCTTGCCCTA
34668 GTCAAACATTTTTTCATTC
1 GTCAAACATTTTTTCATTC
34687 CTATTTAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
45 6 0.11
46 11 0.19
47 40 0.70
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.48
Consensus pattern (46 bp):
GTCAAACATTTTTTCATTCTCGTTTGACGTGATGGTTCTTGCCCTA
Found at i:34767 original size:81 final size:81
Alignment explanation
Indices: 34644--34961 Score: 317
Period size: 80 Copynumber: 4.0 Consensus size: 81
34634 TTCATTCTTG
* * *
34644 TTTGACGTTATGGTTCTTGCCCTAGTCAAACATTTTTTCATTCCTATTTAACTATACCTAGTCAA
1 TTTGACGTGATGGTTCTTGACCTAGTCAAACATCTTTTCATTCCTATTTAACTATACCTAGTCAA
34709 ACTCTTTTCATTACCA
66 ACTCTTTTCATTACCA
* ** * * * * * *
34725 TTTGGCGTGATGGTTCTTGTTCTGGTCAAATAACTTTTCATT-CTCGTTTGACTATA-CTTGATC
1 TTTGACGTGATGGTTCTTGACCTAGTCAAACATCTTTTCATTCCT-ATTTAACTATACCTAG-TC
*
34788 AAACTC-TTTCATTACCG
64 AAACTCTTTTCATTACCA
* * * * * * *
34805 TTTGACGGGATAGTT-TTCACCTTAGTCAAACATCTTTTCATTCACGA-TTGACT-GACCAAGTC
1 TTTGACGTGATGGTTCTTGACC-TAGTCAAACATCTTTTCATTC-CTATTTAACTATACCTAGTC
*
34867 AAACTCTTTTCAGT-CCTA
64 AAACTCTTTTCATTACC-A
* * *
34885 TTTGATGTGATGGTTCTTGCCCTAGTCAAACATTTTTTCATTCCTATTTAACTATACCTAGTCAA
1 TTTGACGTGATGGTTCTTGACCTAGTCAAACATCTTTTCATTCCTATTTAACTATACCTAGTCAA
*
34950 ACTTTTTTCATT
66 ACTCTTTTCATT
34962 CTTGTTTGAC
Statistics
Matches: 186, Mismatches: 40, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
79 16 0.09
80 95 0.51
81 74 0.40
82 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (81 bp):
TTTGACGTGATGGTTCTTGACCTAGTCAAACATCTTTTCATTCCTATTTAACTATACCTAGTCAA
ACTCTTTTCATTACCA
Found at i:34952 original size:160 final size:162
Alignment explanation
Indices: 34666--34961 Score: 352
Period size: 160 Copynumber: 1.8 Consensus size: 162
34656 GTTCTTGCCC
* * * * * *
34666 TAGTCAAACATTTTTTCATTCCTATTTAACTATACCTAGTCAAACTCTTTTCATTACCATTTGGC
1 TAGTCAAACATCTTTTCATTCCGATTTAACTAGACCAAGTCAAACTCTTTTCAGTACCATTTGAC
** * * * * *
34731 GTGATGGTTCTTGTTCTGGTCAAATAACTTTTCATTCTCGTTTGACTATACTTGATCAAAC-TCT
66 GTGATGGTTCTTGCCCTAGTCAAACAACTTTTCATTCTCATTTAACTATACTAGATCAAACTTCT
34795 TTCATTACCGTTTGACGGGATAGTTTTCACCT
131 TTCATTACCGTTTGACGGGATAGTTTTCACCT
*
34827 TAGTCAAACATCTTTTCATTCACGA-TTGACT-GACCAAGTCAAACTCTTTTCAGT-CCTATTTG
1 TAGTCAAACATCTTTTCATTC-CGATTTAACTAGACCAAGTCAAACTCTTTTCAGTACC-ATTTG
* **
34889 ATGTGATGGTTCTTGCCCTAGTCAAACATTTTTTCATTC-CTATTTAACTATACCTAG-TCAAAC
64 ACGTGATGGTTCTTGCCCTAGTCAAACAACTTTTCATTCTC-ATTTAACTATA-CTAGATCAAAC
*
34952 TTTTTTCATT
127 TTCTTTCATT
34962 CTTGTTTGAC
Statistics
Matches: 112, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
159 3 0.03
160 71 0.63
161 36 0.32
162 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (162 bp):
TAGTCAAACATCTTTTCATTCCGATTTAACTAGACCAAGTCAAACTCTTTTCAGTACCATTTGAC
GTGATGGTTCTTGCCCTAGTCAAACAACTTTTCATTCTCATTTAACTATACTAGATCAAACTTCT
TTCATTACCGTTTGACGGGATAGTTTTCACCT
Found at i:34978 original size:35 final size:35
Alignment explanation
Indices: 34905--34996 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 35
34895 TGGTTCTTGC
34905 CCTAGTCAAACATTTTTTCATTCCTATTTAACTATA
1 CCTAGTCAAAC-TTTTTTCATTCCTATTTAACTATA
* * * *
34941 CCTAGTCAAACTTTTTTCATTCTTGTTTGACTGTA
1 CCTAGTCAAACTTTTTTCATTCCTATTTAACTATA
*
34976 CCTGGTCAAA-TTCTTTTCATT
1 CCTAGTCAAACTT-TTTTCATT
34997 ACCGTTTAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 2 0.04
35 37 0.74
36 11 0.22
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.47
Consensus pattern (35 bp):
CCTAGTCAAACTTTTTTCATTCCTATTTAACTATA
Found at i:34991 original size:116 final size:115
Alignment explanation
Indices: 34827--35077 Score: 272
Period size: 116 Copynumber: 2.2 Consensus size: 115
34817 GTTTTCACCT
* * *
34827 TAGTCAAACATCTTTTCATTCACGATTGACTGACCAAGTCAAACTCTTTTCAGT-CCTATTTGAT
1 TAGTCAAAC-TTTTTTCATTCACGATTGACTGACCAAGTCAAACTCTTTTCAGTACC-ATTTAAC
* * *
34891 GTGATGGTTCTTGCCCTAGTCAAACATTTTTTCATTC-CTATTTAACTATACC
64 GTGATGGTTATTGCCCTAGTCAAACATCTGTTCATTCTC-ATTTAACTATACC
** * ** * * *
34943 TAGTCAAACTTTTTTCATTCTTGTTTGACTGTACCTGGTCAAATTCTTTTCATTACCGTTTAACG
1 TAGTCAAACTTTTTTCATTCACGATTGACTG-ACCAAGTCAAACTCTTTTCAGTACCATTTAACG
* * * *
35008 TGATGGTTATTGCCTTGGTCAAACATCTGTTCATTCTCGTTTAACTATAGC
65 TGATGGTTATTGCCCTAGTCAAACATCTGTTCATTCTCATTTAACTATACC
* *
35059 TAATCAAACTTTTGTCATT
1 TAGTCAAACTTTTTTCATT
35078 ACCATTTGAT
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
115 18 0.16
116 91 0.81
117 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (115 bp):
TAGTCAAACTTTTTTCATTCACGATTGACTGACCAAGTCAAACTCTTTTCAGTACCATTTAACGT
GATGGTTATTGCCCTAGTCAAACATCTGTTCATTCTCATTTAACTATACC
Found at i:38066 original size:16 final size:17
Alignment explanation
Indices: 38047--38079 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
38037 GATTTTTGAA
38047 AATTTTATTTA-GTTTT
1 AATTTTATTTATGTTTT
38063 AATTTTATTTATGTTTT
1 AATTTTATTTATGTTTT
38080 TAACTAGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
AATTTTATTTATGTTTT
Found at i:38395 original size:10 final size:10
Alignment explanation
Indices: 38380--38426 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
38370 CAGCAAGTGA
38380 AAGAAAAAAG
1 AAGAAAAAAG
38390 AAG-AAAAAG
1 AAGAAAAAAG
38399 AA-AGAAAAAG
1 AAGA-AAAAAG
38409 AGAGAAAAAAG
1 A-AGAAAAAAG
38420 AA-AAAAA
1 AAGAAAAA
38427 CTAAGCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 13 0.39
10 11 0.33
11 8 0.24
12 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:38398 original size:9 final size:9
Alignment explanation
Indices: 38384--38426 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
38374 AAGTGAAAGA
38384 AAAAAGAAG
1 AAAAAGAAG
38393 AAAAAGAAAG
1 AAAAAG-AAG
38403 AAAAAGAGAG
1 AAAAAGA-AG
38413 AAAAAAGAA-
1 -AAAAAGAAG
38422 AAAAA
1 AAAAA
38427 CTAAGCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.16
9 7 0.23
10 12 0.39
11 7 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:38403 original size:20 final size:19
Alignment explanation
Indices: 38378--38425 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
38368 TTCAGCAAGT
38378 GAAAGAAAAAAGAAGAAAAA
1 GAAAGAAAAAAG-AGAAAAA
*
38398 GAAAG-AAAAAGAGAGAAA
1 GAAAGAAAAAAGAGAAAAA
38416 -AAAGAAAAAA
1 GAAAGAAAAAA
38426 ACTAAGCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.15
18 11 0.42
19 6 0.23
20 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAAAGAGAAAAA
Found at i:39657 original size:145 final size:144
Alignment explanation
Indices: 39432--39861 Score: 643
Period size: 145 Copynumber: 3.0 Consensus size: 144
39422 TTTAGCCCTA
* * * * * * *
39432 TAGGGGTATTGGGTCCTTTTCCGTCGAAGGTA-CC-TCATAAGGCA-TTTTCGTAATTTTTTAGG
1 TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCA-AGGGCATTTTTTGTAA-TTTTTAGA
39494 ATCGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAA
64 ATCGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAA
39559 CCCTTTTCAAGTCTTT
129 CCCTTTTCAAGTCTTT
39575 TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTTGTAATTTTTAGAA
1 TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCA-TTTTTTGTAATTTTTAGAA
39640 TCGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAAC
65 TCGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAAC
39705 CCTTTTCAAGTCTTT
130 CCTTTTCAAGTCTTT
39720 TAGGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTGTAATTTTTAGAA
1 TA-GGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTGTAATTTTTAGAA
* * ** ** * * * *
39785 TCGAGTCCTAGGTTATGACTCTTACACCAAAGGTGCAGATATAGGATAGATTCACTC-TTTCAAC
65 TCGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAAC
39849 CCTTTTCAAGTCT
130 CCTTTTCAAGTCT
39862 CTTAAGATCA
Statistics
Matches: 265, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
143 28 0.11
144 27 0.10
145 159 0.60
146 51 0.19
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (144 bp):
TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTGTAATTTTTAGAAT
CGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAACC
CTTTTCAAGTCTTT
Done.