Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1153
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: 54064
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:798 original size:20 final size:20
Alignment explanation
Indices: 773--810 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
763 GTCAAAACCC
*
773 ATAATGTATCGATACAATGA
1 ATAATGTATCAATACAATGA
*
793 ATAATGTTTCAATACAAT
1 ATAATGTATCAATACAAT
811 TGTGAGCATG
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:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (20 bp):
ATAATGTATCAATACAATGA
Found at i:7813 original size:13 final size:13
Alignment explanation
Indices: 7795--7820 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7785 CAGGGTAGCT
7795 TTGTATCGATACA
1 TTGTATCGATACA
7808 TTGTATCGATACA
1 TTGTATCGATACA
7821 ACACTTATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:8660 original size:49 final size:49
Alignment explanation
Indices: 8491--8843 Score: 347
Period size: 49 Copynumber: 7.1 Consensus size: 49
8481 AGTGATAAAT
* * * * * * *
8491 GTGCCAATATGTTGTTTCAAGACTAGTGATATTGGGCTTAAAGATGTAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATG--AAG
* * * * *
8542 AATGTCAATGTGCTGATTCACGG-T--CAGACATTAGACTTGAAGATGAGAAG
1 -GTGCCAATGTGCTGATTCAAGGCTAGC-GACATTGGACTTAAAGAT--GAAG
*
8592 AATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAG
1 -GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAG
* * *
8642 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAG
* * * *
8691 GTGCTAATATGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATT-GGACTTAAAGATGAAG
* *
8740 GTGCCAATGTGCTGATTCAAGGCCTA-CAACATTGGACTTAAAGGTGAAG
1 GTGCCAATGTGCTGATTCAAGG-CTAGCGACATTGGACTTAAAGATGAAG
* * * * *
8789 GTGCTAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAG
8838 GTGCCA
1 GTGCCA
8844 CCAACTTGTG
Statistics
Matches: 252, Mismatches: 39, Indels: 23
0.80 0.12 0.07
Matches are distributed among these distances:
48 4 0.02
49 167 0.66
50 46 0.18
51 2 0.01
52 32 0.13
53 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (49 bp):
GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAG
Found at i:8719 original size:98 final size:98
Alignment explanation
Indices: 8602--8843 Score: 425
Period size: 98 Copynumber: 2.5 Consensus size: 98
8592 AATGCCAATG
* *
8602 TGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC-
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCT
8666 AGCAACATTGGACTTAAAGGTGAAGGTGCTAATA
66 A-CAACATTGGACTTAAAGGTGAAGGTGCTAATA
8700 TGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 TGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
8764 TACAACATTGGACTTAAAGGTGAAGGTGCTAATA
65 TACAACATTGGACTTAAAGGTGAAGGTGCTAATA
*
8798 TGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGAAGGTGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCA
8844 CCAACTTGTG
Statistics
Matches: 138, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
97 1 0.01
98 134 0.97
99 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.25
Consensus pattern (98 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCT
ACAACATTGGACTTAAAGGTGAAGGTGCTAATA
Found at i:8911 original size:28 final size:29
Alignment explanation
Indices: 8852--9088 Score: 220
Period size: 28 Copynumber: 8.3 Consensus size: 29
8842 CACCAACTTG
**
8852 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
* *
8881 TGTGTGCTTTTG-AAGGTTGCCACTGCCT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * **
8909 TGTGGGC-TTTGAAAGGGGTGCCGCCAACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
*
8938 TGTGGGC-TTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACT
* * * *
8966 TGTGGGCTTTTGAAAAGATGCCATTGATT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
8995 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
9023 TGTGGGCTTTT-AAAGGTTCCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
9051 TTTGGGC-TTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
*
9079 TGTGAGCTTT
1 TGTGGGCTTT
9089 GGATGGTGAG
Statistics
Matches: 170, Mismatches: 29, Indels: 18
0.78 0.13 0.08
Matches are distributed among these distances:
27 12 0.07
28 96 0.56
29 59 0.35
30 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTGACT
Found at i:8936 original size:57 final size:58
Alignment explanation
Indices: 8852--9088 Score: 229
Period size: 57 Copynumber: 4.2 Consensus size: 58
8842 CACCAACTTG
* * *
8852 TGTGGGCTTTTGAAAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCACTGCCT
1 TGTGGGCTTTTGAAAGGGATGCCACCAACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
8909 TGTGGGC-TTTGAAAGGGGTGCCGCCAACTTGTGGGC-TTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTTGAAAGGGATGCCACCAACTTGTGGGCTTTTG--AAGGTTGCCACTGACT
* *** *
8966 TGTGGGCTTTTGAAA-AGATGCCATTGATTTGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGGATGCCACCAACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* * * * * *
9023 TGTGGGCTTTT-AAA-GGTTCCCACTAACTTTTGGGC-TTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGGATGCCACCAACTTGTGGGCTTTTG-AAGGTTGCCACTGACT
*
9079 TGTGAGCTTT
1 TGTGGGCTTT
9089 GGATGGTGAG
Statistics
Matches: 150, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
55 4 0.03
56 60 0.40
57 71 0.47
58 15 0.10
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (58 bp):
TGTGGGCTTTTGAAAGGGATGCCACCAACTTGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:9026 original size:85 final size:88
Alignment explanation
Indices: 8837--9088 Score: 277
Period size: 85 Copynumber: 2.9 Consensus size: 88
8827 TAAAGATGAA
* * * * *
8837 GGTGCCACCAACTTGTGTGGGCTTTTGAAAGGGTTG-CACCAACTTGTGTGCTTTTG-AAGGTTG
1 GGTGCCACCAAC-T-TGTGGGC-TTTGAAAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATG
*
8900 CCACTGCCTTGTGGGC-TTTGAAAGG
63 CCACTGACTTGTGGGCTTTTGAAAGG
*
8925 GGTGCCGCCAACTTGTGGGCTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTTGAAAAGATGCCA
1 GGTGCCACCAACTTGTGGGCTTTGAAAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCA
* *
8989 TTGATTTGTGGGCTTTTG-AA-G
66 CTGACTTGTGGGCTTTTGAAAGG
* ** * * *
9010 GTTGCCACTGACTTGTGGGCTTT-TAAAGGTTCCCACTAACTTTTGGGC-TTTGAAAAGATGCCA
1 GGTGCCACCAACTTGTGGGCTTTGAAAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCA
*
9073 CTGACTTGTGAGCTTT
66 CTGACTTGTGGGCTTT
9089 GGATGGTGAG
Statistics
Matches: 141, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
84 35 0.25
85 63 0.45
86 27 0.19
87 5 0.04
88 11 0.08
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (88 bp):
GGTGCCACCAACTTGTGGGCTTTGAAAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCA
CTGACTTGTGGGCTTTTGAAAGG
Found at i:9496 original size:37 final size:37
Alignment explanation
Indices: 9454--9538 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
9444 AAAGATGAAG
*
9454 CACAAATGCATCATGCAAAATGAAATCTTATGAATGT
1 CACAAATGCATCATGCAAAATAAAATCTTATGAATGT
*
9491 CACAAATGCATCATGCAAAATAAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATAAAATCTTATGAATGT
*
9528 CATAAATGCAT
1 CACAAATGCAT
9539 GATTGTGGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (37 bp):
CACAAATGCATCATGCAAAATAAAATCTTATGAATGT
Found at i:10580 original size:8 final size:8
Alignment explanation
Indices: 10558--10632 Score: 66
Period size: 8 Copynumber: 8.9 Consensus size: 8
10548 ATCCGGACCC
10558 TTTTTTTG
1 TTTTTTTG
10566 TTATTTTT-
1 TT-TTTTTG
10574 TTCTTTTTG
1 TT-TTTTTG
10583 -TTTTTTG
1 TTTTTTTG
10590 TTTTTTTG
1 TTTTTTTG
10598 TTTTTTT-
1 TTTTTTTG
10605 TTGGTTTTTGG
1 TT--TTTTT-G
10616 TTTTTTTAG
1 TTTTTTT-G
10625 TCTTTTTT
1 T-TTTTTT
10633 TTGCGGAAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
7 8 0.14
8 24 0.42
9 17 0.30
10 6 0.11
11 2 0.04
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:10598 original size:32 final size:33
Alignment explanation
Indices: 10558--10621 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
10548 ATCCGGACCC
10558 TTTTTTTGTTATTTTTTT-CTTTTT-GTTTTTTG
1 TTTTTTTGTT-TTTTTTTGCTTTTTGGTTTTTTG
*
10590 TTTTTTTGTTTTTTTTTGGTTTTTGGTTTTTT
1 TTTTTTTGTTTTTTTTTGCTTTTTGGTTTTTT
10622 TAGTCTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 7 0.24
32 15 0.52
33 7 0.24
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (33 bp):
TTTTTTTGTTTTTTTTTGCTTTTTGGTTTTTTG
Found at i:10611 original size:11 final size:10
Alignment explanation
Indices: 10558--10613 Score: 60
Period size: 11 Copynumber: 5.3 Consensus size: 10
10548 ATCCGGACCC
10558 TTTTTTTGTT
1 TTTTTTTGTT
*
10568 ATTTTTTTCTT
1 -TTTTTTTGTT
10579 TTTGTTTT-TT
1 TTT-TTTTGTT
10589 GTTTTTTTGTT
1 -TTTTTTTGTT
10600 TTTTTTTGGTT
1 TTTTTTT-GTT
10611 TTT
1 TTT
10614 GGTTTTTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 16 0.40
11 24 0.60
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:10612 original size:17 final size:15
Alignment explanation
Indices: 10558--10622 Score: 76
Period size: 15 Copynumber: 4.0 Consensus size: 15
10548 ATCCGGACCC
10558 TTTTTTTGTTATTTTT
1 TTTTTTTGTT-TTTTT
*
10574 TTCTTTTTGTTTTTTG
1 TT-TTTTTGTTTTTTT
10590 TTTTTTTGTTTTTTT
1 TTTTTTTGTTTTTTT
10605 TTGGTTTTTGGTTTTTTT
1 TT--TTTTT-GTTTTTTT
10623 AGTCTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
15 14 0.33
16 8 0.19
17 13 0.30
18 8 0.19
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.85
Consensus pattern (15 bp):
TTTTTTTGTTTTTTT
Found at i:10630 original size:18 final size:17
Alignment explanation
Indices: 10559--10631 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 17
10549 TCCGGACCCT
* *
10559 TTTTTTGTTATTTTTTTC
1 TTTTTGGTT-TTTTTGTC
10577 TTTTT-G-TTTTTTGT-
1 TTTTTGGTTTTTTTGTC
* * *
10591 TTTTTTGTTTTTTTTTGG
1 TTTTTGGTTTTTTTGT-C
10609 TTTTTGGTTTTTTTAGTC
1 TTTTTGGTTTTTTT-GTC
10627 TTTTT
1 TTTTT
10632 TTTGCGGAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.11
15 7 0.16
16 8 0.18
17 1 0.02
18 23 0.51
19 1 0.02
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (17 bp):
TTTTTGGTTTTTTTGTC
Found at i:15123 original size:12 final size:12
Alignment explanation
Indices: 15090--15123 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
15080 TTCTCTAAAT
*
15090 AAGAAAAACAAA
1 AAGAAAAAAAAA
15102 AAGACAAAAAAAA
1 AAGA-AAAAAAAA
15115 AAGAAAAAA
1 AAGAAAAAA
15124 GCATGAAATG
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:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:16702 original size:93 final size:94
Alignment explanation
Indices: 16524--16788 Score: 278
Period size: 93 Copynumber: 2.9 Consensus size: 94
16514 CATATACTAT
* * * ** * * *
16524 TAGATGATATTGGTGCATCACAAAGCCT-ATTTTCCTTAGGGAAAG--GGT-GCAACCCATACAT
1 TAGATGGTATTGATGCATCACAAAGCCTAATTTTCATTAGGGAAAGAATATCCCGA-CCACACAT
*
16585 TCCC-AATCATATCTCCTTTATCCAACCAA
65 TCCCTAATCATATCTCCTTCATCCAACCAA
* ** * **
16614 TAGATGGTATTGATGTATCACAAAGGTTAATTTTC-TTGGGGCAAA-AATATGTCGACCACACAT
1 TAGATGGTATTGATGCATCACAAAGCCTAATTTTCATTAGGG-AAAGAATATCCCGACCACACAT
*
16677 TCCCTAATCATATCTCCTTCATCCAACCAC
65 TCCCTAATCATATCTCCTTCATCCAACCAA
* * *
16707 TAGATGGTATTGATGCATCACAAAGCCTGATTTTCATTAGGGAAAGGATATCCCGACCACTCATT
1 TAGATGGTATTGATGCATCACAAAGCCTAATTTTCATTAGGGAAAGAATATCCCGACCACACATT
16772 -CCTAATCATAT-TCCTTC
66 CCCTAATCATATCTCCTTC
16789 TTTTAGCCAC
Statistics
Matches: 145, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
90 28 0.19
91 9 0.06
92 18 0.12
93 70 0.48
94 20 0.14
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (94 bp):
TAGATGGTATTGATGCATCACAAAGCCTAATTTTCATTAGGGAAAGAATATCCCGACCACACATT
CCCTAATCATATCTCCTTCATCCAACCAA
Found at i:17071 original size:47 final size:46
Alignment explanation
Indices: 16994--17268 Score: 236
Period size: 47 Copynumber: 5.9 Consensus size: 46
16984 TTTACATTCG
***
16994 TTTGACTATATTGGCATTAAAACCTAGTCAAACT-TTTTCTACCTTCA
1 TTTGACTATATTGGCATTAGGGCCTAGTCAAACTCTTTTC-ACCTT-A
* * *
17041 TTTGACTATATTGGCATTAGGGCCTGGTCAAACTCTTATCACCCTTG
1 TTTGACTATATTGGCATTAGGGCCTAGTCAAACTCTTTTCA-CCTTA
** *
17088 TTTGACTATATTGGTGTTAGGTCCTAGTCAAACTCTTTTCACTCTTA
1 TTTGACTATATTGGCATTAGGGCCTAGTCAAACTCTTTTCAC-CTTA
*
17135 TTTGAC-AGTATTGGCATTAGGAG-CTAGTCAAACT-TTTTCCACCTTCG
1 TTTGACTA-TATTGGCATTAGG-GCCTAGTCAAACTCTTTT-CACCTT-A
** * * * *
17182 TTTGACTGCATTAGCATTAAGGCCTAGTCAAACTCTTCTCACCATTG
1 TTTGACTATATTGGCATTAGGGCCTAGTCAAACTCTTTTCACC-TTA
* * * * * *
17229 TTTGATTGTATTAGCATTA-GTCCTGGTCGAACTCTTTTCA
1 TTTGACTATATTGGCATTAGGGCCTAGTCAAACTCTTTTCA
17269 TCCTCATTCG
Statistics
Matches: 190, Mismatches: 27, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
46 27 0.14
47 150 0.79
48 13 0.07
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (46 bp):
TTTGACTATATTGGCATTAGGGCCTAGTCAAACTCTTTTCACCTTA
Found at i:17154 original size:94 final size:93
Alignment explanation
Indices: 16990--17264 Score: 267
Period size: 94 Copynumber: 2.9 Consensus size: 93
16980 TAAATTTACA
**
16990 TTCGTTTGACTATATTGGCATTAAAACCTAGTCAAACT-TTTTCTACCTTCATTTGACTA-TATT
1 TTCGTTTGACTATATTGGCATT-AGGCCTAGTCAAACTCTTTTC-ACCTT-ATTTGAC-AGTATT
17053 GGCATTAGGGCCTGGTCAAACTCTTAT-CACCC
62 GGCATTAGGGCCTGGTCAAACTCTTATCCA-CC
**
17085 TT-GTTTGACTATATTGGTGTTAGGTCCTAGTCAAACTCTTTTCACTCTTATTTGACAGTATTGG
1 TTCGTTTGACTATATTGGCATTAGG-CCTAGTCAAACTCTTTTCAC-CTTATTTGACAGTATTGG
* *
17149 CATTAGGAG-CTAGTCAAACT-TTTTCCACC
64 CATTAGG-GCCTGGTCAAACTCTTATCCACC
** * * * ** *
17178 TTCGTTTGACTGCATTAGCATTAAGGCCTAGTCAAACTCTTCTCACCATTGTTTGATTGTATTAG
1 TTCGTTTGACTATATTGGCATT-AGGCCTAGTCAAACTCTTTTCACC-TTATTTGACAGTATTGG
* *
17243 CATTA-GTCCTGGTCGAACTCTT
64 CATTAGGGCCTGGTCAAACTCTT
17265 TTCATCCTCA
Statistics
Matches: 150, Mismatches: 19, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
93 20 0.13
94 116 0.77
95 14 0.09
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (93 bp):
TTCGTTTGACTATATTGGCATTAGGCCTAGTCAAACTCTTTTCACCTTATTTGACAGTATTGGCA
TTAGGGCCTGGTCAAACTCTTATCCACC
Found at i:17546 original size:85 final size:83
Alignment explanation
Indices: 17337--17892 Score: 331
Period size: 85 Copynumber: 6.6 Consensus size: 83
17327 AGTATCGCTT
* * * * *
17337 TTCATCCCTTGTTTACCTATTGGCTCAGT-CCTCAGAAAACCCCTTATCCCCTCA--GTGACCTA
1 TTCATCCCTTGTTTACCTATCGGCTCAATCCCT-AGTAAACCCCTTA-CACCT-ATGGTGACCTG
* * * * *
17399 TCAGTTTATTCTCGGTCAACC
63 TCAGCTTAGTCCCAGTAAACC
* * * * * * *
17420 TTTCATCCTTTGTTTACTTATTGACTTAGTCCC-CGATAAACCCCTTACACCTATGGTGACCTGT
1 -TTCATCCCTTGTTTACCTATCGGCTCAATCCCTAG-TAAACCCCTTACACCTATGGTGACCTGT
*
17484 TAGCTTAGTCACCAGTAAACC
64 CAGCTTAGTC-CCAGTAAACC
* * * * * * *
17505 TGCATCCCATTGTTCACCTGTCGGCTCAGTCCCTAGTAAACCCCTTATC-CTCTCT-GTGACTTA
1 TTCATCCC-TTGTTTACCTATCGGCTCAATCCCTAGTAAACCCCTTA-CAC-CTATGGTGACCTG
* *
17568 TCGGCTTAGTCCCTAAGTCAACCC
63 TCAGCTTAGTCCC--AGT-AAACC
* * *
17592 TTCATCCCTTGTTTACCTATCGGCTTAATCCC-AGTAAACCACTTACACATATGGTGACCTGTCA
1 TTCATCCCTTGTTTACCTATCGGCTCAATCCCTAGTAAACCCCTTACACCTATGGTGACCTGTCA
* *
17656 GCTTAGTCTCTAGTCAACC
66 GCTTAGTC-CCAGTAAACC
* * * * **
17675 TTCATTCCTTGTTTACCTATTGGCTCAATCCCTGGTAAACCCCTTACACCTATGTTGACCTACCA
1 TTCATCCCTTGTTTACCTATCGGCTCAATCCCTAGTAAACCCCTTACACCTATGGTGACCTGTCA
*** *
17740 GCTTAGTCTTTGATCAACC
66 GCTTAGTCCCAG-TAAACC
* * * * * ** * * *
17759 TTTATCTCATTGTTTACCTGTCAGCTCAGTCCCCGGTAAACCCCTTTTCCCCT-TGGTGACCTAT
1 TTCATC-CCTTGTTTACCTATCGGCTCAATCCCTAGTAAACCCC-TTACACCTATGGTGACCTGT
* * *
17823 C-GATTTAGTCCCCGATCAACCC
64 CAG-CTTAGTCCCAG-T-AAACC
* * * * *
17845 TTCATCCCTTGTTTACTTATCAGATCAGTCCC-CGTAAACCCCTTACAC
1 TTCATCCCTTGTTTACCTATCGGCTCAATCCCTAGTAAACCCCTTACAC
17893 GTAAGCTCAG
Statistics
Matches: 371, Mismatches: 80, Indels: 43
0.75 0.16 0.09
Matches are distributed among these distances:
82 1 0.00
83 43 0.12
84 118 0.32
85 155 0.42
86 43 0.12
87 11 0.03
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.34
Consensus pattern (83 bp):
TTCATCCCTTGTTTACCTATCGGCTCAATCCCTAGTAAACCCCTTACACCTATGGTGACCTGTCA
GCTTAGTCCCAGTAAACC
Found at i:17579 original size:43 final size:42
Alignment explanation
Indices: 17508--17747 Score: 143
Period size: 43 Copynumber: 5.6 Consensus size: 42
17498 GTAAACCTGC
* * *
17508 ATCCCATTGTTCACCTGTCGGCTCAGTCCCTAGTAAACCCCTT
1 ATCCC-TTGTTGACCTATCGGCTTAGTCCCTAGTAAACCCCTT
* *
17551 ATCCTCTCTG-TGACTTATCGGCTTAGTCCCTAAGTCAA-CCCTT
1 ATCC-CT-TGTTGACCTATCGGCTTAGTCCCT-AGTAAACCCCTT
* * *
17594 CATCCCTTGTTTACCTATCGGCTTAATCCC-AGTAAACCACTT
1 -ATCCCTTGTTGACCTATCGGCTTAGTCCCTAGTAAACCCCTT
* * * * * *
17636 A-CACATATGGTGACCTGTCAGCTTAGTCTCTAGTCAA--CCTT
1 ATC-CCT-TGTTGACCTATCGGCTTAGTCCCTAGTAAACCCCTT
* * * * * *
17677 CATTCCTTGTTTACCTATTGGCTCAATCCCTGGTAAACCCCTT
1 -ATCCCTTGTTGACCTATCGGCTTAGTCCCTAGTAAACCCCTT
* *
17720 A-CACCTATGTTGACCTACCAGCTTAGTC
1 ATC-CCT-TGTTGACCTATCGGCTTAGTC
17748 TTTGATCAAC
Statistics
Matches: 144, Mismatches: 38, Indels: 30
0.68 0.18 0.14
Matches are distributed among these distances:
40 1 0.01
41 31 0.22
42 30 0.21
43 70 0.49
44 12 0.08
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (42 bp):
ATCCCTTGTTGACCTATCGGCTTAGTCCCTAGTAAACCCCTT
Found at i:17788 original size:254 final size:252
Alignment explanation
Indices: 17337--18130 Score: 627
Period size: 254 Copynumber: 3.2 Consensus size: 252
17327 AGTATCGCTT
* * * *
17337 TTCATCCCTTGTTTACCTATTGGCTCAGTCCTCAGAAAACCCCTTATCCCCTCAGTGACCTATCA
1 TTCATCCCTTGTTTACCTATCGGCTCAGTCC-CAGTAAACCCCTTA-CACATCAGTGACCTATCA
* * * * * *
17402 GTTTATTCTCGGTCAACCTTTCATCCTTTGTTTACTTATTGACTTAGTCCCCGATAAACCCCTTA
64 GCTTAGTCTCAGTCAACCTTTCATCCTTTGTTTACCTATTGACTCAATCCCCGATAAACCCCTTA
*** *
17467 CACCTATGGTGACCTGTTAGCTTAGTCACCAGTAAACCTGCATCCCATTGTTCACCTGTCGGCTC
129 CACCTATGGTGACCTACCAGCTTAGTCACCAGTAAACCTGCATCCCATTGTTCACCTGTCAGCTC
* * * * *
17532 AGTCCCTAGTAAACCCCTTATCCTCTCT-GTGACTTATCGGCTTAGTCCCTAAGTCAACCC
194 AGTCCCCAGTAAACCCCTTATCCCCT-TGGTGACCTATCGACTTAGTCCCCAA-TCAACCC
* * * *
17592 TTCATCCCTTGTTTACCTATCGGCTTAATCCCAGTAAACCACTTACACAT-ATGGTGACCTGTCA
1 TTCATCCCTTGTTTACCTATCGGCTCAGTCCCAGTAAACCCCTTACACATCA--GTGACCTATCA
* * *
17656 GCTTAGTCTCTAGTCAACC-TTCATTCC-TTGTTTACCTATTGGCTCAATCCCTGGTAAACCCCT
64 GCTTAGTCTC-AGTCAACCTTTCA-TCCTTTGTTTACCTATTGACTCAATCCCCGATAAACCCCT
* *** * ** * *
17719 TACACCTATGTTGACCTACCAGCTTAGTC-TTTGATCAACCTTTATCTCATTGTTTACCTGTCAG
127 TACACCTATGGTGACCTACCAGCTTAGTCACCAG-TAAACCTGCATCCCATTGTTCACCTGTCAG
* * * *
17783 CTCAGTCCCCGGTAAACCCCTTTTCCCCTTGGTGACCTATCGATTTAGTCCCCGATCAACCC
191 CTCAGTCCCCAGTAAACCCCTTATCCCCTTGGTGACCTATCGACTTAGTCCCCAATCAACCC
* * * *
17845 TTCATCCCTTGTTTACTTATCAGATCAGTCCCCGTAAACCCCTT--ACA-C---G---TA--AGC
1 TTCATCCCTTGTTTACCTATCGGCTCAGTCCCAGTAAACCCCTTACACATCAGTGACCTATCAGC
* * * * ** * * * * *
17899 TCAGTCTCCAATCAACCTTT-ATCTCATTATTTACCTATCAACTTAGTCTCCAATAAACCCTTTA
66 TTAGTCT-CAGTCAACCTTTCATC-CTTTGTTTACCTATTGACTCAATCCCCGATAAACCCCTTA
* * * * ** * * * * * * *
17963 CACCTATGGTGACCTGCCAGTTTAGCCTCTGGTCAACCTTCATCTCATTTTTTA-CTATTAGCTC
129 CACCTATGGTGACCTACCAGCTTAGTCACCAGTAAACCTGCATCCCATTGTTCACCTGTCAGCTC
* * * * * * * * ****
18027 AGTCCTCGGTAAACCCCTTAT-CCCTCGGTGTCTTGTCAACTTAATCTTTGATCAACCC
194 AGTCCCCAGTAAACCCCTTATCCCCTTGGTGACCTATCGACTTAGTCCCCAATCAACCC
*
18085 TTCATCCCTTATTTACCTATCGGCTCAGTCCCTAGTAAACCCCTTA
1 TTCATCCCTTGTTTACCTATCGGCTCAGTCCC-AGTAAACCCCTTA
18131 TCCTTTTGGT
Statistics
Matches: 438, Mismatches: 87, Indels: 41
0.77 0.15 0.07
Matches are distributed among these distances:
240 57 0.13
241 56 0.13
242 73 0.17
243 3 0.01
246 1 0.00
251 3 0.01
252 1 0.00
253 49 0.11
254 157 0.36
255 38 0.09
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (252 bp):
TTCATCCCTTGTTTACCTATCGGCTCAGTCCCAGTAAACCCCTTACACATCAGTGACCTATCAGC
TTAGTCTCAGTCAACCTTTCATCCTTTGTTTACCTATTGACTCAATCCCCGATAAACCCCTTACA
CCTATGGTGACCTACCAGCTTAGTCACCAGTAAACCTGCATCCCATTGTTCACCTGTCAGCTCAG
TCCCCAGTAAACCCCTTATCCCCTTGGTGACCTATCGACTTAGTCCCCAATCAACCC
Found at i:17888 original size:42 final size:42
Alignment explanation
Indices: 17768--17889 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
17758 CTTTATCTCA
* * *
17768 TTGTTTACCTGTCAGCTCAGTCCCCGGTAAACCCCTTTTCCCC
1 TTGTTTACCTATCAGATCAGTCCCC-GTAAACCCCTTATCCCC
* * * *
17811 TTGGTGACCTATC-GATTTAGTCCCCGATCAA-CCCTTCAT-CCC
1 TTGTTTACCTATCAGA-TCAGTCCCCG-TAAACCCCTT-ATCCCC
*
17853 TTGTTTACTTATCAGATCAGTCCCCGTAAACCCCTTA
1 TTGTTTACCTATCAGATCAGTCCCCGTAAACCCCTTA
17890 CACGTAAGCT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
41 4 0.06
42 34 0.55
43 24 0.39
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.33
Consensus pattern (42 bp):
TTGTTTACCTATCAGATCAGTCCCCGTAAACCCCTTATCCCC
Found at i:18039 original size:157 final size:157
Alignment explanation
Indices: 17752--18046 Score: 348
Period size: 157 Copynumber: 1.9 Consensus size: 157
17742 TTAGTCTTTG
* * * ** * *
17752 ATCAACCTTTATCTCATTGTTTACCTGTCAGCTCAGTCCCCGGTAAACCCCTTTTCCCCTTGGTG
1 ATCAACCTTTATCTCATTATTTACCTATCAACTCAGTCCCCAATAAACCCCTTTACACCTTGGTG
* *
17817 ACCTATCGATTTAGTCCCCGATCAACCCTTCATCCCTTGTTTACTTATCAGATCAGTCCCCGTAA
66 ACCTACCGATTTAGTCCCCGATCAACCCTTCATCCATTGTTTACTTATCAGATCAGTCCCCGTAA
17882 ACCCCTTACACGTAAGCTCAGTCTCCA
131 ACCCCTTACACGTAAGCTCAGTCTCCA
* *
17909 ATCAACCTTTATCTCATTATTTACCTATCAACTTAGTCTCCAATAAA-CCCTTTACACCTATGGT
1 ATCAACCTTTATCTCATTATTTACCTATCAACTCAGTCCCCAATAAACCCCTTTACACCT-TGGT
* * * * * *
17973 GACCTGCC-AGTTTAG-CCTCTGGTCAA-CCTTCATCTCATTTTTTAC-TATTAGCTCAGTCCTC
65 GACCTACCGA-TTTAGTCC-CCGATCAACCCTTCATC-CATTGTTTACTTATCAGATCAGTCC-C
*
18034 GGTAAACCCCTTA
126 CGTAAACCCCTTA
18047 TCCCTCGGTG
Statistics
Matches: 115, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
156 33 0.29
157 82 0.71
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.34
Consensus pattern (157 bp):
ATCAACCTTTATCTCATTATTTACCTATCAACTCAGTCCCCAATAAACCCCTTTACACCTTGGTG
ACCTACCGATTTAGTCCCCGATCAACCCTTCATCCATTGTTTACTTATCAGATCAGTCCCCGTAA
ACCCCTTACACGTAAGCTCAGTCTCCA
Found at i:18181 original size:84 final size:83
Alignment explanation
Indices: 17919--18221 Score: 240
Period size: 84 Copynumber: 3.6 Consensus size: 83
17909 ATCAACCTTT
* * * * * * * *
17919 ATCTCATTATTTACCTATCAACTTAGTCTCC-AATAAACCCTTTACACCTATGGTGACCTGCCAG
1 ATCTCATTATTTACCTATCAGCTCAGTC-CCTAGTAAACCCCTTA-TCCTTTGGTGACCTGTCAA
* * * *
17983 TTTAGCCTCTGGTCAACCTTC
64 CTTAGTCTTTGGTCAACC-CC
* * * * * * *
18004 ATCTCATTTTTTA-CTATTAGCTCAGT-CCTCGGTAAACCCCTTATCCCTCGGTGTCTTGTCAAC
1 ATCTCATTATTTACCTATCAGCTCAGTCCCT-AGTAAACCCCTTATCCTTTGGTGACCTGTCAAC
* *
18067 TTAATCTTTGATCAACCCTTC
65 TTAGTCTTTGGTCAACCC--C
* *
18088 ATC-CCTTATTTACCTATCGGCTCAGTCCCTAGTAAACCCCTTATCCTTTTGGTGACCTGTCAAC
1 ATCTCATTATTTACCTATCAGCTCAGTCCCTAGTAAACCCCTTATCC-TTTGGTGACCTGTCAAC
18152 TTAGTCTTTGGTCAACCCC
65 TTAGTCTTTGGTCAACCCC
* * **
18171 ATCTCATTATTTA-CTCATCAGC-CTAGTCCTTAGTAAATCTTTTATCCTTTG
1 ATCTCATTATTTACCT-ATCAGCTC-AGTCCCTAGTAAACCCCTTATCCTTTG
18222 TCGAGTTGTC
Statistics
Matches: 170, Mismatches: 38, Indels: 22
0.74 0.17 0.10
Matches are distributed among these distances:
82 2 0.01
83 42 0.25
84 82 0.48
85 44 0.26
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.38
Consensus pattern (83 bp):
ATCTCATTATTTACCTATCAGCTCAGTCCCTAGTAAACCCCTTATCCTTTGGTGACCTGTCAACT
TAGTCTTTGGTCAACCCC
Found at i:20057 original size:309 final size:311
Alignment explanation
Indices: 19422--20193 Score: 706
Period size: 309 Copynumber: 2.5 Consensus size: 311
19412 TTAGGATAGC
* * * * * * * *
19422 TTCATCCCATCTTTAATCTTTTTGAGTCCTTT-AGGGTTACC-AGATACTTTTACGTCGATGGTA
1 TTCATCTCATCTATAAACATTTTAAGTCCTTTAAGGG-TACCAAGATACTTTCACGTCGAAGGCA
* * * ** * * * ** * *
19485 TACCCAT-AGGGTATTTTTGTAATTTTTTAGAATTGAGTCTTAGGTTTTCACCGGGTTTGCTTTT
65 T-CCCATAAGGGTATTTCTATAA-TTTTTAAAACCGAGTCCTAGATTATCACTAGATTCGCTTTT
** * * * * *
19549 ATATC-GAAGATGGGTATTTAGGATAGGTTCATCTTTTTATGATCATTTTTAAGTCCTTTTTGGG
128 ATGCCAAAAG-TGGGTATTTAGGATAGATTCATATTTTTAGGATCATTTTTAAGTCCTTTTAGGG
* * * * *
19613 TTACTGGGATACTTTCACGTCGAAGGTATACCCATAAGGACATTTTCATAATTTTTCTAGAAATG
192 TTACCGAGATACTTTCACATCAAAGCTATACCCATAAGGACATTTTCATAATTTTTCTAGAAATG
* * * * * *
19678 AGTCTGGGTTGTCATTGAGTCCATTTTTATGCCGAAGGTGGATATTTAGGTTAGG
257 AGTCTAGGTTCTCATAGAGTCCACTTTTATGCCGAAAGTGGATATTTAGGTTAAG
* * *
19733 TTCATCTCATCTATAAACATTTTAAGTCTTTTAAGGGTACTAGGATACTTTCACGTCGAAGGCAT
1 TTCATCTCATCTATAAACATTTTAAGTCCTTTAAGGGTACCAAGATACTTTCACGTCGAAGGCAT
* *
19798 -CCAT-AGGGATATTTCTATAATTTTTAAAAATCGAGTCCTCGATTATCACTAGATTCGCTTTTA
66 CCCATAAGGG-TATTTCTATAATTTTT-AAAACCGAGTCCTAGATTATCACTAGATTCGCTTTTA
*
19861 TGCCAAAGGTGGGTATTTAGGATAGATTCATATTTTTAGGAT-ATTTTTAAGT-CTTTTAGGGTT
129 TGCCAAAAGTGGGTATTTAGGATAGATTCATATTTTTAGGATCATTTTTAAGTCCTTTTAGGGTT
* ** ** ** *
19924 ACCGAGATATTTTTGCATCAAAGCTATACCCATAATTACATTTTTGTAATTTTTCTAGAACCCT-
194 ACCGAGATACTTTCACATCAAAGCTATACCCATAAGGACATTTTCATAATTTTTCTAGAA--ATG
** *
19988 A-TCCTAGGTTCTCACTAG-GTCTGCTTTTATGTCGAAAGTGGATATTTAGGTTAAG
257 AGT-CTAGGTTCTCA-TAGAGTCCACTTTTATGCCGAAAGTGGATATTTAGGTTAAG
* * * * *
20043 TT-ATC-CTGTCTATAATCCTTTTAAGTCCTTTAAGGGTACCAAGATACTTTCACGTTGAAGGTA
1 TTCATCTC-ATCTATAAACATTTTAAGTCCTTTAAGGGTACCAAGATACTTTCACGTCGAAGGCA
* * * * * * * * * *
20106 TCCCCTAAGGGTATTTTTGTAATTTTTAAGACCTAGTCCTAGGTTGTCATTAGGTTTGCTTTTAT
65 TCCCATAAGGGTATTTCTATAATTTTTAAAACCGAGTCCTAGATTATCACTAGATTCGCTTTTAT
* *
20171 GCCAAAAGTGGATATTTAAGATA
130 GCCAAAAGTGGGTATTTAGGATA
20194 AGTTCATCCC
Statistics
Matches: 373, Mismatches: 76, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
308 1 0.00
309 160 0.43
310 83 0.22
311 104 0.28
312 25 0.07
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (311 bp):
TTCATCTCATCTATAAACATTTTAAGTCCTTTAAGGGTACCAAGATACTTTCACGTCGAAGGCAT
CCCATAAGGGTATTTCTATAATTTTTAAAACCGAGTCCTAGATTATCACTAGATTCGCTTTTATG
CCAAAAGTGGGTATTTAGGATAGATTCATATTTTTAGGATCATTTTTAAGTCCTTTTAGGGTTAC
CGAGATACTTTCACATCAAAGCTATACCCATAAGGACATTTTCATAATTTTTCTAGAAATGAGTC
TAGGTTCTCATAGAGTCCACTTTTATGCCGAAAGTGGATATTTAGGTTAAG
Found at i:20065 original size:156 final size:155
Alignment explanation
Indices: 19904--20230 Score: 338
Period size: 153 Copynumber: 2.1 Consensus size: 155
19894 TTTTAGGATA
* * ** **
19904 TTTTTAAGTCTTTTAGGGTTACCGAGATATTTTTGCATCAAAGCTATACCCATAATTACATTTTT
1 TTTTTAAGTCTTTTAGGG-TACCAAGATACTTTCACATCAAAGCTAT-CCCATAAGGACATTTTT
* * *
19969 GTAATTTTTCTAGAACCCTA-TCCTAGGTTCTCACTAGGTCTGCTTTTATGTCGAAAGTGGATAT
64 GTAATTTTT-AAG-A-CCTAGTCCTAGGTTCTCACTAGGTCTGCTTTTATGCCAAAAGTGGATAT
* * *
20033 TTAGGTTAAGTT-AT-CCTGTCTATAATCC
126 TTAAGATAAGTTCATCCCTGTCTAAAATCC
* * ** * * **
20061 -TTTTAAGTCCTTTAAGGGTACCAAGATACTTTCACGTTGAAGGTATCCCCTAAGGGTATTTTTG
1 TTTTTAAGT-CTTTTAGGGTACCAAGATACTTTCACATCAAAGCTATCCCATAAGGACATTTTTG
* * *
20125 TAATTTTTAAGACCTAGTCCTAGGTTGTCATTAGGTTTGCTTTTATGCCAAAAGTGGATATTTAA
65 TAATTTTTAAGACCTAGTCCTAGGTTCTCACTAGGTCTGCTTTTATGCCAAAAGTGGATATTTAA
* *
20190 GATAAGTTCATCCCTTTTTAAAATCC
130 GATAAGTTCATCCCTGTCTAAAATCC
20216 TTTTTAAGTTCTTTT
1 TTTTTAAG-TCTTTT
20231 TAAAACCATA
Statistics
Matches: 138, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
152 4 0.03
153 50 0.36
154 4 0.03
155 32 0.23
156 39 0.28
157 9 0.07
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (155 bp):
TTTTTAAGTCTTTTAGGGTACCAAGATACTTTCACATCAAAGCTATCCCATAAGGACATTTTTGT
AATTTTTAAGACCTAGTCCTAGGTTCTCACTAGGTCTGCTTTTATGCCAAAAGTGGATATTTAAG
ATAAGTTCATCCCTGTCTAAAATCC
Found at i:21215 original size:20 final size:20
Alignment explanation
Indices: 21192--21264 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
21182 ACAATTCAAA
21192 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
21212 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
21233 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
21253 GTATCGATACAT
1 GTATCGATACAT
21265 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:21235 original size:21 final size:21
Alignment explanation
Indices: 21209--21285 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
21199 TACATGTTGC
21209 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
21230 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
21250 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
21270 GGATGTATCGATACAT
1 -AATGTATCGATACAT
21286 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:21243 original size:41 final size:41
Alignment explanation
Indices: 21192--21285 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
21182 ACAATTCAAA
21192 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
21233 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
21274 GTATCGATACAT
1 GTATCGATACAT
21286 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:21342 original size:13 final size:13
Alignment explanation
Indices: 21324--21349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21314 TACAGCAAGT
21324 ATGTATCGATACA
1 ATGTATCGATACA
21337 ATGTATCGATACA
1 ATGTATCGATACA
21350 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:22798 original size:33 final size:33
Alignment explanation
Indices: 22756--22820 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
22746 TTTGGGACAA
22756 TGTATCGATACAAT-T-CTTCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
*
22789 TGTATCGATAGAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
22821 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:22898 original size:19 final size:18
Alignment explanation
Indices: 22849--22906 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
22839 ACTGCCAGTT
22849 TCATGTGTCGATACAATTG
1 TCATGTGTCGATACAA-TG
22868 TACATGTGTCGATACAATG
1 T-CATGTGTCGATACAATG
*
22887 ATCATGTATCGATACAATG
1 -TCATGTGTCGATACAATG
22906 T
1 T
22907 ATCGATACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.53
20 16 0.44
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (18 bp):
TCATGTGTCGATACAATG
Found at i:22908 original size:13 final size:13
Alignment explanation
Indices: 22890--22916 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22880 TACAATGATC
22890 ATGTATCGATACA
1 ATGTATCGATACA
22903 ATGTATCGATACA
1 ATGTATCGATACA
22916 A
1 A
22917 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:22931 original size:33 final size:32
Alignment explanation
Indices: 22871--22935 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
22861 ACAATTGTAC
* * *
22871 ATGTGTCGATACAATGATCATGTATCGATACA
1 ATGTATCGATACAAAGATAATGTATCGATACA
22903 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAG-ATAATGTATCGATACA
22936 TCTCGATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAAGATAATGTATCGATACA
Found at i:31689 original size:20 final size:19
Alignment explanation
Indices: 31647--31696 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
31637 GTTTAGGATA
31647 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTC-TC
31667 ATGTATCGATACAATGTGC-C
1 ATGTATCGATACAAT-T-CTC
31687 ATGTATCGAT
1 ATGTATCGAT
31697 GCAAACAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 26 0.93
21 1 0.04
22 1 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGTATCGATACAATTCTC
Found at i:35632 original size:21 final size:21
Alignment explanation
Indices: 35607--35657 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
35597 CCTAGAGTCA
35607 TTGGAAAATGTTAGAGCATGG
1 TTGGAAAATGTTAGAGCATGG
*
35628 TTGGAAAATGTTAGAGCATTG
1 TTGGAAAATGTTAGAGCATGG
*
35649 TTAGAAAAT
1 TTGGAAAAT
35658 CACCAACACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGGAAAATGTTAGAGCATGG
Found at i:46192 original size:20 final size:20
Alignment explanation
Indices: 46167--46204 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46157 TCAAAAACCC
*
46167 ATAATGTATCGATACAATGA
1 ATAATGTATCAATACAATGA
*
46187 ATAATGTTTCAATACAAT
1 ATAATGTATCAATACAAT
46205 TGTGAGCATG
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:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (20 bp):
ATAATGTATCAATACAATGA
Done.