Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014628.1 Kokia drynarioides strain JFW-HI SEQ_129667, whole genome shotgun sequence
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: 761112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 101 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:640660 original size:21 final size:21
Alignment explanation
Indices: 640636--640692 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
640626 AGTGCAGACT
*
640636 TCTACCGAAACAAGTGACAGG
1 TCTACCGAAACAAGTGACACG
* * *
640657 TCTACCGATACAAGTGACTCT
1 TCTACCGAAACAAGTGACACG
*
640678 TCTACCGAAATAAGT
1 TCTACCGAAACAAGT
640693 ATTACTTCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (21 bp):
TCTACCGAAACAAGTGACACG
Found at i:641511 original size:52 final size:52
Alignment explanation
Indices: 641440--641668 Score: 332
Period size: 52 Copynumber: 4.4 Consensus size: 52
641430 TTCATCTAAA
* * * * * *
641440 ACTCATGATGACACATAGTCATCTGACCTCTTAATTCGTACAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
* * * *
641492 ACTCACGATGACACATAGTCATCGGATCTCATGATCCATAAAAGATTCATAC
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
* *
641544 ACTCACGATGACACATAATCATCAGACCTCATAATCCATAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
*
641596 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
*
641648 ACTCATGATGACACATAGTCA
1 ACTCACGATGACACATAGTCA
641669 ACGAACCTTT
Statistics
Matches: 157, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 157 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
Found at i:644803 original size:26 final size:26
Alignment explanation
Indices: 644774--644922 Score: 95
Period size: 29 Copynumber: 5.4 Consensus size: 26
644764 GAAGTCCGTC
*
644774 AGGATTATCTTTTGTGAAAGTTCGCA
1 AGGACTATCTTTTGTGAAAGTTCGCA
* *
644800 AGGACTATCTGATATGTGGAAAGTCCGGC-
1 AGGACTATCT--TTTGT-GAAAGTTC-GCA
* *
644829 AGGGCTATCTTTTGTGGAAGTTCGCA
1 AGGACTATCTTTTGTGAAAGTTCGCA
* *
644855 AGGACTATCTCATTTGGGGAAAGTCCGCCA
1 AGGACTATCT--TTT-GTGAAAGTTCG-CA
* * *
644885 A-GACTATCATTATGAGGAAAGTTCGCC
1 AGGACTATC-TTTTG-TGAAAGTTCGCA
*
644912 AGAACTATCTT
1 AGGACTATCTT
644923 CTAAATATGA
Statistics
Matches: 96, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
25 2 0.02
26 24 0.25
27 9 0.09
28 24 0.25
29 31 0.32
30 6 0.06
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (26 bp):
AGGACTATCTTTTGTGAAAGTTCGCA
Found at i:644838 original size:55 final size:55
Alignment explanation
Indices: 644765--644921 Score: 179
Period size: 55 Copynumber: 2.8 Consensus size: 55
644755 GTAAATGTAG
* * * *
644765 AAGTCCGTCAGGATTATCTTTTGTGAAAGTTCGCAAGGACTATCTGATATGTGGA
1 AAGTCCGGCAGGACTATCTTTTGTGAAAGTTCGCAAGGACTATCTCATATGGGGA
* * *
644820 AAGTCCGGCAGGGCTATCTTTTGTGGAAGTTCGCAAGGACTATCTCATTTGGGGA
1 AAGTCCGGCAGGACTATCTTTTGTGAAAGTTCGCAAGGACTATCTCATATGGGGA
* * * * * *
644875 AAGTCCGCCAAGACTATCATTATGAGGAAAGTTCGCCAGAACTATCT
1 AAGTCCGGCAGGACTATC-TTTTG-TGAAAGTTCGCAAGGACTATCT
644922 TCTAAATATG
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
55 63 0.74
56 4 0.05
57 18 0.21
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (55 bp):
AAGTCCGGCAGGACTATCTTTTGTGAAAGTTCGCAAGGACTATCTCATATGGGGA
Found at i:644889 original size:29 final size:28
Alignment explanation
Indices: 644784--644921 Score: 99
Period size: 28 Copynumber: 4.9 Consensus size: 28
644774 AGGATTATCT
*
644784 TTTGT-GAAAGTTCGCAAGGACTATCTGA
1 TTTGTGGAAAGTTCGCAA-GACTATCTCA
* * * *
644812 TATGTGGAAAGTCCGGCAGGGCTATCT--
1 TTTGTGGAAAGTTC-GCAAGACTATCTCA
644839 TTTGTGG-AAGTTCGCAAGGACTATCTCA
1 TTTGTGGAAAGTTCGCAA-GACTATCTCA
* *
644867 TTTGGGGAAAGTCCGCCAAGACTA--TCA
1 TTTGTGGAAAGTTCG-CAAGACTATCTCA
* *
644894 TTATGAGGAAAGTTCGCCAGAACTATCT
1 TT-TGTGGAAAGTTCGCAAG-ACTATCT
644922 TCTAAATATG
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
25 3 0.03
26 12 0.14
27 14 0.16
28 25 0.29
29 25 0.29
30 7 0.08
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (28 bp):
TTTGTGGAAAGTTCGCAAGACTATCTCA
Found at i:645901 original size:25 final size:25
Alignment explanation
Indices: 645850--645902 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
645840 ATAAAGAAAG
* **
645850 ATGGATTTTTCTCCCGTTGGCGTGA
1 ATGGATTATTCTCCCGTTGGCAAGA
645875 ATGGATTATTCTCCCGTTGGCAAGA
1 ATGGATTATTCTCCCGTTGGCAAGA
645900 ATG
1 ATG
645903 AATAAACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (25 bp):
ATGGATTATTCTCCCGTTGGCAAGA
Found at i:650474 original size:6 final size:6
Alignment explanation
Indices: 650463--650500 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
650453 AGAACAAAGC
650463 ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT AT
1 ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT AT
650501 CACAATCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATTAGT
Found at i:650508 original size:6 final size:6
Alignment explanation
Indices: 650499--650536 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
650489 TAGTATTAGT
650499 ATCACA ATCACA ATCACA ATCACA ATCACA ATCACA AT
1 ATCACA ATCACA ATCACA ATCACA ATCACA ATCACA AT
650537 AATAACAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
ATCACA
Found at i:652521 original size:5 final size:5
Alignment explanation
Indices: 652511--652540 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
652501 AATCAAAGCT
*
652511 TTTTC TTTTC TTTTC TTTTC TTTCC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
652541 GTTGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:659859 original size:213 final size:213
Alignment explanation
Indices: 659487--659916 Score: 826
Period size: 213 Copynumber: 2.0 Consensus size: 213
659477 CAAATCAGAT
659487 TATTCTTCTTGAAAAAAAATTAAATCTAACTAAAAATACTAAAAATCAGGAGGAAAAATCTGATT
1 TATTCTTCTTGAAAAAAAATTAAATCTAACTAAAAATACTAAAAATCAGGAGGAAAAATCTGATT
*
659552 TGTCATTCTCCTATTAGAAAGGGATAGTGATGACATAAAATCACAGTTTCGTACAATCCTTTCTC
66 TGTCATTCTCCTATTAGAAAGGGATAGTGATGACATAAAATCACAGTTTCATACAATCCTTTCTC
659617 TTCTTGTAAGTTAACAACATTAAGAAAATATAAGAATAACAATTAAATCATGTAAAATAATTTAG
131 TTCTTGTAAGTTAACAACATTAAGAAAATATAAGAATAACAATTAAATCATGTAAAATAATTTAG
659682 TGTGAAGAATGAGAAATTC
196 TGTGAAGAA-GAGAAATTC
*
659701 TATT-TTCTTGAAAAAAATTTAAATCTAACTAAAAATACTAAAAATCAGGAGGAAAAATCTGATT
1 TATTCTTCTTGAAAAAAAATTAAATCTAACTAAAAATACTAAAAATCAGGAGGAAAAATCTGATT
659765 TGTCATTCTCCTATTAGAAAGGGATAGTGATGACATAAAATCACAGTTTCATACAATCCTTTCTC
66 TGTCATTCTCCTATTAGAAAGGGATAGTGATGACATAAAATCACAGTTTCATACAATCCTTTCTC
659830 TTCTTGTAAGTTAACAACATTAAGAAAATATAAGAATAACAATTAAATCATGTAAAATAATTTAG
131 TTCTTGTAAGTTAACAACATTAAGAAAATATAAGAATAACAATTAAATCATGTAAAATAATTTAG
659895 TGTGAAGAAGAGAAATTC
196 TGTGAAGAAGAGAAATTC
659913 TATT
1 TATT
659917 ACTTATTTAG
Statistics
Matches: 214, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
212 13 0.06
213 197 0.92
214 4 0.02
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (213 bp):
TATTCTTCTTGAAAAAAAATTAAATCTAACTAAAAATACTAAAAATCAGGAGGAAAAATCTGATT
TGTCATTCTCCTATTAGAAAGGGATAGTGATGACATAAAATCACAGTTTCATACAATCCTTTCTC
TTCTTGTAAGTTAACAACATTAAGAAAATATAAGAATAACAATTAAATCATGTAAAATAATTTAG
TGTGAAGAAGAGAAATTC
Found at i:660635 original size:62 final size:61
Alignment explanation
Indices: 660551--660765 Score: 201
Period size: 62 Copynumber: 3.5 Consensus size: 61
660541 TGGACTCGAT
660551 AATTTTTC-CTACATTGGGGCCTAAACTTTTTTGTTTGTCCAAGTTA-AGCCTTGAACTTGAG
1 AATTTTTCTC-ACATTGGGGCCTAAACTTTTTTGTTTGTCCAAGTTAGA-CCTTGAACTTGAG
* ** *
660612 AATTGTTTCTTACA-TGGGAGCCTAAACTTGGCAATTG-TT-TCCACA-TTGGGACC-TGAACTT
1 AATT-TTTCTCACATTGGG-GCCTAAACTT---TTTTGTTTGTCCA-AGTT-AGACCTTGAACTT
*
660672 GAT
59 GAG
* * *
660675 AATTTTTCTCACATTGGGGCCTAAAGTTTTTTGTTTGCCCAAGTTAGATCTTGAACTTGAG
1 AATTTTTCTCACATTGGGGCCTAAACTTTTTTGTTTGTCCAAGTTAGACCTTGAACTTGAG
* *
660736 AATTGTTCCTCACATTGGAGCCTAAACTTT
1 AATT-TTTCTCACATTGGGGCCTAAACTTT
660766 GCAATTGTTC
Statistics
Matches: 123, Mismatches: 16, Indels: 29
0.73 0.10 0.17
Matches are distributed among these distances:
59 3 0.02
60 6 0.05
61 26 0.21
62 56 0.46
63 23 0.19
64 5 0.04
65 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (61 bp):
AATTTTTCTCACATTGGGGCCTAAACTTTTTTGTTTGTCCAAGTTAGACCTTGAACTTGAG
Found at i:660688 original size:31 final size:33
Alignment explanation
Indices: 660597--660696 Score: 111
Period size: 31 Copynumber: 3.2 Consensus size: 33
660587 GTCCAAGTTA
* *
660597 AGCCTTGAACTTGAGAATTGTTTCTTACA-TGGG
1 AGCC-TGAACTTGACAATTGTTTCTCACATTGGG
* *
660630 AGCCTAAACTTGGCAATTGTTTC-CACATTGGG
1 AGCCTGAACTTGACAATTGTTTCTCACATTGGG
*
660662 A-CCTGAACTTGATAATT-TTTCTCACATTGGG
1 AGCCTGAACTTGACAATTGTTTCTCACATTGGG
660693 -GCCT
1 AGCCT
660697 AAAGTTTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
30 4 0.07
31 28 0.49
32 21 0.37
33 4 0.07
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (33 bp):
AGCCTGAACTTGACAATTGTTTCTCACATTGGG
Found at i:660728 original size:124 final size:124
Alignment explanation
Indices: 660508--660782 Score: 410
Period size: 124 Copynumber: 2.2 Consensus size: 124
660498 CAAGATAGGT
*
660508 CCTAAACTTGGCAATTGTTCCCACATTGAAACCTGGACTCGATAATTTTTCCTACATTGGGGCCT
1 CCTAAACTTGGCAATTGTTCCCACATTGAAACCTGAACTCGATAATTTTTCCTACATTGGGGCCT
* * *
660573 AAACTTTTTTGTTTGTCCAAGTTAAGCCTTGAACTTGAGAATTGTTTCTTACATGGGAG
66 AAACTTTTTTGTTTGCCCAAGTTAAGCCTTGAACTTGAGAATTGTTCCTCACATGGGAG
* ** *
660632 CCTAAACTTGGCAATTGTTTCCACATTGGGACCTGAACTTGATAATTTTT-CTCACATTGGGGCC
1 CCTAAACTTGGCAATTGTTCCCACATTGAAACCTGAACTCGATAATTTTTCCT-ACATTGGGGCC
* * *
660696 TAAAGTTTTTTGTTTGCCCAAGTT-AGATCTTGAACTTGAGAATTGTTCCTCACATTGGAG
65 TAAACTTTTTTGTTTGCCCAAGTTAAG-CCTTGAACTTGAGAATTGTTCCTCACATGGGAG
*
660756 CCTAAACTTTGCAATTGTTCCCACATT
1 CCTAAACTTGGCAATTGTTCCCACATT
660783 AAGGCTTGAA
Statistics
Matches: 136, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
123 4 0.03
124 132 0.97
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (124 bp):
CCTAAACTTGGCAATTGTTCCCACATTGAAACCTGAACTCGATAATTTTTCCTACATTGGGGCCT
AAACTTTTTTGTTTGCCCAAGTTAAGCCTTGAACTTGAGAATTGTTCCTCACATGGGAG
Found at i:660764 original size:32 final size:30
Alignment explanation
Indices: 660604--660782 Score: 78
Period size: 31 Copynumber: 5.7 Consensus size: 30
660594 TTAAGCCTTG
** *
660604 AACTTGAGAATTGTTTCTTACATGGGAGCCTA
1 AACTTG-GAATTG-TTCCCACATTGGAGCCTA
* *
660636 AACTTGGCAATTGTTTCCACATTGG-GACCTG
1 AACTTGG-AATTGTTCCCACATTGGAG-CCTA
* * * *
660667 AACTTGATAATTTTTCTCACATTGGGGCCTA
1 AACTTG-GAATTGTTCCCACATTGGAGCCTA
* ** * * * *
660698 AAGTT--TTTTGTTTGCCCA-AGTTAGATCTTG
1 AACTTGGAATTG-TT-CCCACA-TTGGAGCCTA
660728 AACTTGAGAATTGTTCCTCACATTGGAGCCTA
1 AACTTG-GAATTGTTCC-CACATTGGAGCCTA
*
660760 AACTTTGCAATTGTTCCCACATT
1 AAC-TTGGAATTGTTCCCACATT
660783 AAGGCTTGAA
Statistics
Matches: 106, Mismatches: 28, Indels: 27
0.66 0.17 0.17
Matches are distributed among these distances:
28 2 0.02
29 3 0.03
30 13 0.12
31 47 0.44
32 34 0.32
33 7 0.07
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (30 bp):
AACTTGGAATTGTTCCCACATTGGAGCCTA
Found at i:661565 original size:4 final size:4
Alignment explanation
Indices: 661556--661598 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
661546 TTCTCATCTC
*
661556 CTTT CTTT CTTT CTTT CTTT CTTT CGTTT -GTT CTTT CTCTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CT-TT CT
661599 CTAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
3 2 0.06
4 25 0.74
5 7 0.21
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:662557 original size:6 final size:6
Alignment explanation
Indices: 662546--662598 Score: 61
Period size: 6 Copynumber: 8.0 Consensus size: 6
662536 GCTAGGGAAG
662546 GAAAAA GAAAAAA GAGAAAA GAAAAA GAGGAAAA TGAAAAA GAAAAA GAAAAA
1 GAAAAA G-AAAAA GA-AAAA GAAAAA GA--AAAA -GAAAAA GAAAAA GAAAAA
662599 AAAGTTGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
6 20 0.48
7 16 0.38
8 4 0.10
9 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:662559 original size:7 final size:7
Alignment explanation
Indices: 662547--662599 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
662537 CTAGGGAAGG
662547 AAAAAGA
1 AAAAAGA
662554 AAAAAGA
1 AAAAAGA
*
662561 GAAAAGA
1 AAAAAGA
*
662568 AAAAGAGG
1 AAAA-AGA
*
662576 AAAATG-
1 AAAAAGA
662582 AAAAAG-
1 AAAAAGA
662588 AAAAAGA
1 AAAAAGA
662595 AAAAA
1 AAAAA
662600 AAGTTGCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 11 0.28
7 22 0.56
8 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:662567 original size:14 final size:13
Alignment explanation
Indices: 662548--662598 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
662538 TAGGGAAGGA
662548 AAAAGAAAAAAGAG
1 AAAAG-AAAAAGAG
662562 AAAAGAAAAAGAGG
1 AAAAGAAAAAGA-G
662576 AAAATGAAAAAGA-
1 AAAA-GAAAAAGAG
662589 AAAAGAAAAA
1 AAAAGAAAAA
662599 AAAGTTGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.17
13 11 0.31
14 10 0.29
15 8 0.23
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:662579 original size:21 final size:20
Alignment explanation
Indices: 662546--662599 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
662536 GCTAGGGAAG
662546 GAAAAAGAAAAAA-GAGAAAA
1 GAAAAAGAAAAAATGA-AAAA
*
662566 GAAAAAGAGGAAAATGAAAAA
1 GAAAAAGA-AAAAATGAAAAA
662587 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
662600 AAGTTGCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
21 16 0.53
22 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
GAAAAAGAAAAAATGAAAAA
Found at i:662599 original size:13 final size:13
Alignment explanation
Indices: 662546--662599 Score: 65
Period size: 14 Copynumber: 4.0 Consensus size: 13
662536 GCTAGGGAAG
662546 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
662559 GAGAAAAGAAAAAGA
1 GA-AAAAGAAAAA-A
*
662574 GGAAAATG-AAAAA
1 -GAAAAAGAAAAAA
662587 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
662600 AAGTTGCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
12 6 0.17
13 8 0.23
14 14 0.40
15 5 0.14
16 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
GAAAAAGAAAAAA
Found at i:664214 original size:40 final size:40
Alignment explanation
Indices: 664053--664214 Score: 252
Period size: 40 Copynumber: 4.0 Consensus size: 40
664043 TTAAATTCAA
*
664053 TGTTAATATTCAAGCTTCGGCTTAGCAGGCTATGAGCCGA
1 TGTTAATATTCAAGCTTCGGCTTAGCAGGCTATGAGCCGG
* * *
664093 TGTTAATATTCAAGCTTCGGTTTAGCAGGCTACGAGTCGG
1 TGTTAATATTCAAGCTTCGGCTTAGCAGGCTATGAGCCGG
*
664133 TGTTAATATTTAAGCTTCGGCTTAGCAGGCTATGAGCCGG
1 TGTTAATATTCAAGCTTCGGCTTAGCAGGCTATGAGCCGG
* * *
664173 TGTTAATATTCAAGCTTCGACTTAGCAGGCCATGAGTCGG
1 TGTTAATATTCAAGCTTCGGCTTAGCAGGCTATGAGCCGG
664213 TG
1 TG
664215 AATGCGTAAG
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 110 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (40 bp):
TGTTAATATTCAAGCTTCGGCTTAGCAGGCTATGAGCCGG
Found at i:667389 original size:23 final size:22
Alignment explanation
Indices: 667345--667391 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
667335 CATAATTTTT
667345 AAAATAATTATAAAAAAAATAG
1 AAAATAATTATAAAAAAAATAG
*
667367 AAAATTATT-TAAAAAATATATAG
1 AAAATAATTATAAAAAA-A-ATAG
667390 AA
1 AA
667392 TTATAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 9 0.41
23 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (22 bp):
AAAATAATTATAAAAAAAATAG
Found at i:667430 original size:10 final size:9
Alignment explanation
Indices: 667350--667438 Score: 54
Period size: 10 Copynumber: 9.2 Consensus size: 9
667340 TTTTTAAAAT
667350 AATTATAAA
1 AATTATAAA
**
667359 AAAAATAGAA
1 AATTATA-AA
667369 AATTATTTAAA
1 AATTA--TAAA
* *
667380 AAATATATAG
1 AATTATA-AA
667390 AATTATAAGA
1 AATTATAA-A
*
667400 AGTTATAAA
1 AATTATAAA
*
667409 AA-TATTAA
1 AATTATAAA
667417 AATTATTAAA
1 AATTA-TAAA
667427 AATTCATAAA
1 AATT-ATAAA
667437 AA
1 AA
667439 AATAAAATAG
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
8 7 0.12
9 12 0.20
10 32 0.53
11 7 0.12
12 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (9 bp):
AATTATAAA
Found at i:667435 original size:28 final size:26
Alignment explanation
Indices: 667378--667455 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 26
667368 AAATTATTTA
* *
667378 AAAAATATATAGAATTATAAGAAGTTAT
1 AAAAATAT-TAAAATTATAA-AAATTAT
667406 AAAAATATTAAAATTATTAAAAATTCAT
1 AAAAATATTAAAATTA-TAAAAATT-AT
*
667434 AAAAA-AATAAAA-TAGTAAAAAT
1 AAAAATATTAAAATTA-TAAAAAT
667456 AAAGTCCATG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 9 0.20
27 17 0.39
28 18 0.41
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (26 bp):
AAAAATATTAAAATTATAAAAATTAT
Found at i:670105 original size:15 final size:14
Alignment explanation
Indices: 670079--670114 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
670069 TTGTTTGACT
* *
670079 GAAAATGGTTTTCG
1 GAAAATGATTTTTG
670093 GAAAATGATTTTTG
1 GAAAATGATTTTTG
670107 GAAAATGA
1 GAAAATGA
670115 ATTACTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTTTG
Found at i:674136 original size:50 final size:48
Alignment explanation
Indices: 674008--674277 Score: 164
Period size: 43 Copynumber: 6.0 Consensus size: 48
673998 AAAAACGCCA
*
674008 CTAAAGAACATGGTCTTTAGC-GGCGCTTAACCACAAACG-C-C----G
1 CTAAAGAACATGGTCTTTAGCAGG-GCTTTACCACAAACGTCGCTAAAG
*
674050 CTAAAGAACATGGTCTTTAGC-GGCGCTTTCCACACAAACGTCGCTAAACG
1 CTAAAGAACATGGTCTTTAGCAGG-GCTTTAC-CACAAACGTCGCTAAA-G
* *
674100 TTAAAGAATATGGTCTTTAGCAGGGCTTCTACCACAAA---CGCT---G
1 CTAAAGAACATGGTCTTTAGCAGGGCTT-TACCACAAACGTCGCTAAAG
* *
674143 CTAAAGAACATGGTCTTTAACAGCGCTTTTACCACAAACGT--C----G
1 CTAAAGAACATGGTCTTTAGCAGGGC-TTTACCACAAACGTCGCTAAAG
*
674186 CTAAAGAACATGGTTTTTAGC-GGTGCTTATACCACAAACG-C-C----G
1 CTAAAGAACATGGTCTTTAGCAGG-GCTT-TACCACAAACGTCGCTAAAG
* * *
674229 CTAAAGAACATGGTCTTTAGC-GGCGCTTTTGCCACAAACGCCACTAAAG
1 CTAAAGAACATGGTCTTTAGCAGG-GC-TTTACCACAAACGTCGCTAAAG
674278 AACATGTTCT
Statistics
Matches: 189, Mismatches: 15, Indels: 41
0.77 0.06 0.17
Matches are distributed among these distances:
42 32 0.17
43 109 0.58
44 7 0.04
45 2 0.01
47 4 0.02
49 1 0.01
50 30 0.16
51 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (48 bp):
CTAAAGAACATGGTCTTTAGCAGGGCTTTACCACAAACGTCGCTAAAG
Found at i:674156 original size:43 final size:43
Alignment explanation
Indices: 674101--674364 Score: 298
Period size: 43 Copynumber: 6.1 Consensus size: 43
674091 CGCTAAACGT
* * *
674101 TAAAGAATATGGTCTTTAGCAGG-GCTTCTACCACAAACGCTGC
1 TAAAGAACATGGTCTTTAGC-GGCGCTTTTACCACAAACGCCGC
* * *
674144 TAAAGAACATGGTCTTTAACAGCGCTTTTACCACAAACGTCGC
1 TAAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGC
* * *
674187 TAAAGAACATGGTTTTTAGCGGTGCTTATACCACAAACGCCGC
1 TAAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGC
* *
674230 TAAAGAACATGGTCTTTAGCGGCGCTTTTGCCACAAACGCCAC
1 TAAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGC
* * *
674273 TAAAGAACATGTTCTTTAGCGGCGTTTTTACCCACAAACACCGC
1 TAAAGAACATGGTCTTTAGCGGCGCTTTTA-CCACAAACGCCGC
* * * * ** *
674317 TATAGATA-ATGTTCTTTAGCGACGTTTTTTTCACAAACGCCGT
1 TAAAGA-ACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGC
674360 TAAAG
1 TAAAG
674365 TTAACAGATT
Statistics
Matches: 189, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.01
43 151 0.80
44 36 0.19
45 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
TAAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGC
Found at i:675777 original size:19 final size:20
Alignment explanation
Indices: 675738--675778 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
675728 TTAATGATAT
*
675738 TTTATTAAATGAAAATAATA
1 TTTAATAAATGAAAATAATA
*
675758 TTTAATAAAT-AAAATTATA
1 TTTAATAAATGAAAATAATA
675777 TT
1 TT
675779 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTAATAAATGAAAATAATA
Found at i:676690 original size:41 final size:41
Alignment explanation
Indices: 676584--676933 Score: 325
Period size: 41 Copynumber: 8.6 Consensus size: 41
676574 GTGCTTTCTC
* *
676584 ATGACCTGACCTTTAGCGGCGCTTATGAGAAAGCA-CCACTA
1 ATGACCTGACCTTTAGCGGCGCTTATGGGAAAG-AGCCGCTA
* ** * * *
676625 ATG-CCTTGACCTTTAACGATGCTTATTGCAAAGAGCCGTTA
1 ATGACC-TGACCTTTAGCGGCGCTTATGGGAAAGAGCCGCTA
* * *
676666 ATGACCTAACCTTTAGCGGCGCTTATGGGGAAGCA-CTGCTA
1 ATGACCTGACCTTTAGCGGCGCTTATGGGAAAG-AGCCGCTA
* * *
676707 ATGACCTAACCTTTAGCGGCGCTTATGGTAAAGCGCCGCTA
1 ATGACCTGACCTTTAGCGGCGCTTATGGGAAAGAGCCGCTA
* ** * *
676748 ATGGCCTGACCTTTAGCGGTACTTATGTGAAAGTGCCGCTA
1 ATGACCTGACCTTTAGCGGCGCTTATGGGAAAGAGCCGCTA
* * * *
676789 AT-ACTTGACCTTTAGCGGCGCTTATGGTAAAGCGCCACTA
1 ATGACCTGACCTTTAGCGGCGCTTATGGGAAAGAGCCGCTA
* * *
676829 ATGACCTAACCTTTAGCGGCGCTTATGGTAAAGCA-CTGCTA
1 ATGACCTGACCTTTAGCGGCGCTTATGGGAAAG-AGCCGCTA
* *** * * *
676870 ATGACCAGACCTTTAATAGCGCTTATGGGAAAGCGTCGCAA
1 ATGACCTGACCTTTAGCGGCGCTTATGGGAAAGAGCCGCTA
676911 ATG-CCTGACCTTTAGCGGCGCTT
1 ATGACCTGACCTTTAGCGGCGCTT
676934 TGAAATAAAC
Statistics
Matches: 246, Mismatches: 55, Indels: 17
0.77 0.17 0.05
Matches are distributed among these distances:
40 51 0.21
41 192 0.78
42 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (41 bp):
ATGACCTGACCTTTAGCGGCGCTTATGGGAAAGAGCCGCTA
Found at i:676721 original size:82 final size:82
Alignment explanation
Indices: 676584--676933 Score: 366
Period size: 82 Copynumber: 4.3 Consensus size: 82
676574 GTGCTTTCTC
* * * * **
676584 ATGACCTGACCTTTAGCGGCGCTTATGAGAAAGCACCACTAATG-CCTTGACCTTTAACGATGCT
1 ATGACCTAACCTTTAGCGGCGCTTATGGGAAAGCACCGCTAATGACC-TAACCTTTAACGGCGCT
* * * *
676648 TATTGCAAAGAGCCGTTA
65 TATGGTAAAGCGCCGCTA
* * *
676666 ATGACCTAACCTTTAGCGGCGCTTATGGGGAAGCACTGCTAATGACCTAACCTTTAGCGGCGCTT
1 ATGACCTAACCTTTAGCGGCGCTTATGGGAAAGCACCGCTAATGACCTAACCTTTAACGGCGCTT
676731 ATGGTAAAGCGCCGCTA
66 ATGGTAAAGCGCCGCTA
* * ** * ** * * *
676748 ATGGCCTGACCTTTAGCGGTACTTATGTGAAAGTGCCGCTAAT-ACTTGACCTTTAGCGGCGCTT
1 ATGACCTAACCTTTAGCGGCGCTTATGGGAAAGCACCGCTAATGACCTAACCTTTAACGGCGCTT
*
676812 ATGGTAAAGCGCCACTA
66 ATGGTAAAGCGCCGCTA
* * **
676829 ATGACCTAACCTTTAGCGGCGCTTATGGTAAAGCACTGCTAATGACC-AGACCTTTAATAGCGCT
1 ATGACCTAACCTTTAGCGGCGCTTATGGGAAAGCACCGCTAATGACCTA-ACCTTTAACGGCGCT
* * *
676893 TATGGGAAAGCGTCGCAA
65 TATGGTAAAGCGCCGCTA
*
676911 ATG-CCTGACCTTTAGCGGCGCTT
1 ATGACCTAACCTTTAGCGGCGCTT
676934 TGAAATAAAC
Statistics
Matches: 221, Mismatches: 44, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
81 88 0.40
82 131 0.59
83 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (82 bp):
ATGACCTAACCTTTAGCGGCGCTTATGGGAAAGCACCGCTAATGACCTAACCTTTAACGGCGCTT
ATGGTAAAGCGCCGCTA
Found at i:676895 original size:122 final size:120
Alignment explanation
Indices: 676584--676933 Score: 389
Period size: 122 Copynumber: 2.9 Consensus size: 120
676574 GTGCTTTCTC
* * *
676584 ATGACCTGACCTTTAGCGGCGCTTATGAG-AAAGCACCACTAATGCCTTGACCTTTAACGATGCT
1 ATGACCTAACCTTTAGCGGCGCTTATG-GTAAAGCACCGCTAATGCC-TGACCTTTAAAG-TGCT
* * * **
676648 TAT-TGCAAAGAGCCGTTAATGACCTAACCTTTAGCGGCGCTTATGGGGAAGCACTGCTA
63 TATGTG-AAAGAGCCGCTAAT-ACCTGACCTTTAGCGGCGCTTATGGGAAAGCACCACTA
* ** *
676707 ATGACCTAACCTTTAGCGGCGCTTATGGTAAAGCGCCGCTAATGGCCTGACCTTTAGCGGTACTT
1 ATGACCTAACCTTTAGCGGCGCTTATGGTAAAGCACCGCTAAT-GCCTGACCTTTA-AAGTGCTT
* * * *
676772 ATGTGAAAGTGCCGCTAATACTTGACCTTTAGCGGCGCTTATGGTAAAGCGCCACTA
64 ATGTGAAAGAGCCGCTAATACCTGACCTTTAGCGGCGCTTATGGGAAAGCACCACTA
* * *
676829 ATGACCTAACCTTTAGCGGCGCTTATGGTAAAGCACTGCTAATGACCAGACCTTTAATAGCGCTT
1 ATGACCTAACCTTTAGCGGCGCTTATGGTAAAGCACCGCTAATG-CCTGACCTTTAA-AGTGCTT
* * * * *
676894 ATGGGAAAGCGTCGCAAATGCCTGACCTTTAGCGGCGCTT
64 ATGTGAAAGAGCCGCTAATACCTGACCTTTAGCGGCGCTT
676934 TGAAATAAAC
Statistics
Matches: 193, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
121 1 0.01
122 121 0.63
123 65 0.34
124 6 0.03
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (120 bp):
ATGACCTAACCTTTAGCGGCGCTTATGGTAAAGCACCGCTAATGCCTGACCTTTAAAGTGCTTAT
GTGAAAGAGCCGCTAATACCTGACCTTTAGCGGCGCTTATGGGAAAGCACCACTA
Found at i:677095 original size:40 final size:40
Alignment explanation
Indices: 676987--677095 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
676977 CCTATAAATG
* * * *
676987 CCGCTATTGCTTTACCTGTTGCGGCGCTTATGGACAAACG
1 CCGCTATTGCTTTACCTTTTGCGGCGTTTATGGAAAAACA
* *
677027 TCGCTATTGCTTTACCTTTTGCGACGTTTATGGAAAAACA
1 CCGCTATTGCTTTACCTTTTGCGGCGTTTATGGAAAAACA
*
677067 CCGCTATTACTTTACCTTTTGCGGCGTTT
1 CCGCTATTGCTTTACCTTTTGCGGCGTTT
677096 TCTTTCCAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (40 bp):
CCGCTATTGCTTTACCTTTTGCGGCGTTTATGGAAAAACA
Found at i:687900 original size:17 final size:18
Alignment explanation
Indices: 687880--687919 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
687870 TTTGGGAGGG
*
687880 TTTGA-AAAAAAATTAGA
1 TTTGAGAAAAAAATTAAA
687897 TTTGAGTAAAAAAATTAAA
1 TTTGAG-AAAAAAATTAAA
687916 TTTG
1 TTTG
687920 TTTAAGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
19 15 0.75
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (18 bp):
TTTGAGAAAAAAATTAAA
Found at i:688466 original size:29 final size:30
Alignment explanation
Indices: 688414--688491 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 30
688404 AATTGAAATT
* *
688414 AAAATTATTT-AATAATTTTATATTTT-AA
1 AAAATAATTTAAAAAATTTTATATTTTAAA
688442 AAAATAATTTAAAAAATTTTATATTTTAAA
1 AAAATAATTTAAAAAATTTTATATTTTAAA
*
688472 AAAATAATTTTAATAAATTT
1 AAAATAA-TTTAAAAAATTT
688492 AAAATCATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.20
29 15 0.34
30 9 0.20
31 11 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AAAATAATTTAAAAAATTTTATATTTTAAA
Found at i:693836 original size:50 final size:50
Alignment explanation
Indices: 693782--693892 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
693772 TTCATCGTAA
*
693782 CTTCATCTTGCCCCACTGCATCTTCAAGGAG-ATAAGATTTGCTTCTGTAG
1 CTTCATCTTGCCCCACTGCAACTTCAAGG-GTATAAGATTTGCTTCTGTAG
* * * *
693832 CTTCA-CTCTGACCCATTGCAACTTCAAGGGTATAGGATTTGGTTCTGTAG
1 CTTCATCT-TGCCCCACTGCAACTTCAAGGGTATAAGATTTGCTTCTGTAG
693882 CTTCATCTTGC
1 CTTCATCTTGC
693893 TCTACAACAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
49 3 0.06
50 47 0.90
51 2 0.04
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (50 bp):
CTTCATCTTGCCCCACTGCAACTTCAAGGGTATAAGATTTGCTTCTGTAG
Found at i:694706 original size:36 final size:36
Alignment explanation
Indices: 694651--694787 Score: 193
Period size: 36 Copynumber: 3.8 Consensus size: 36
694641 TGGTAACAGA
* * *
694651 CATGTCCTTTGGGTTAACAGGGAGTAAAATAAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
*
694687 CATGACCTTTGGGTCAACAGAGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* *
694723 AACGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* * *
694759 CATGACTTTTCGATCAACAGGGAGTAAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAAA
694788 CGAATAACGA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 89 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:695496 original size:21 final size:21
Alignment explanation
Indices: 695456--695529 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
695446 GAGTTTTTAG
* **
695456 TATCGGTAGAAATAAGACTTA
1 TATCGGTAGAACTATCACTTA
* *
695477 TTTCGGTAGAA-TAGTCACTTG
1 TATCGGTAGAACTA-TCACTTA
*
695498 TATCGGTAGAACTATCACTTG
1 TATCGGTAGAACTATCACTTA
*
695519 TATCGATAGAA
1 TATCGGTAGAA
695530 GTCTGTACCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (21 bp):
TATCGGTAGAACTATCACTTA
Found at i:700327 original size:18 final size:18
Alignment explanation
Indices: 700306--700347 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
700296 CCTTCTCTTG
700306 ACCTTCTTCCTGTTCTAC
1 ACCTTCTTCCTGTTCTAC
*
700324 ACCTTCTTCTTGTTCTAC
1 ACCTTCTTCCTGTTCTAC
700342 ACCTTC
1 ACCTTC
700348 ATCCCCATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.38, G:0.05, T:0.45
Consensus pattern (18 bp):
ACCTTCTTCCTGTTCTAC
Found at i:702508 original size:81 final size:81
Alignment explanation
Indices: 702373--702524 Score: 295
Period size: 81 Copynumber: 1.9 Consensus size: 81
702363 ATCTTGAACG
702373 TAATTTACCTGGGTACAGTGTTAGACATGAGTTAAACAAAAGTACTAACTGACCAGGGTTAAATT
1 TAATTTACCTGGGTACAGTGTTAGACATGAGTTAAACAAAAGTACTAACTGACCAGGGTTAAATT
702438 GTTAACTGACCAGGGT
66 GTTAACTGACCAGGGT
*
702454 TAATTTACCTGGGTACAGTTTTAGACATGAGTTAAACAAAAGTACTAACTGACCAGGGTTAAATT
1 TAATTTACCTGGGTACAGTGTTAGACATGAGTTAAACAAAAGTACTAACTGACCAGGGTTAAATT
702519 GTTAAC
66 GTTAAC
702525 GCAAGATGAT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (81 bp):
TAATTTACCTGGGTACAGTGTTAGACATGAGTTAAACAAAAGTACTAACTGACCAGGGTTAAATT
GTTAACTGACCAGGGT
Found at i:704268 original size:38 final size:38
Alignment explanation
Indices: 704219--704293 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
704209 GATGATTTCA
* *
704219 ACTATTACTTTATTTACCTCAATG-CCTTGACATGATAG
1 ACTATTACTTTATCTACCTCAATGACC-TAACATGATAG
* *
704257 ACTATTGCTTTATCTACCTCCATGACCTAACATGATA
1 ACTATTACTTTATCTACCTCAATGACCTAACATGATA
704294 TGCGATGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 30 0.94
39 2 0.06
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.37
Consensus pattern (38 bp):
ACTATTACTTTATCTACCTCAATGACCTAACATGATAG
Found at i:713962 original size:36 final size:35
Alignment explanation
Indices: 713915--714050 Score: 177
Period size: 36 Copynumber: 3.8 Consensus size: 35
713905 GGTAATAGGC
* *
713915 ATGACCTTTGGGTCAATAGAGAGTAAAATAAGCAT
1 ATGACCTTTGGGTCAACAGAGAGTAAAATGAGCAT
*
713950 AATGACCTTTGGGTCAACA-AGGGGTAAAATGAGCATT
1 -ATGACCTTTGGGTCAACAGA-GAGTAAAATGAGCA-T
*
713987 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCACT
1 ATGACCTTTGGGTCAACAGAGAGTAAAATGAGCA-T
714023 ATGACCTTTGGGTCAACAG-GCAGTAAAA
1 ATGACCTTTGGGTCAACAGAG-AGTAAAA
714051 CAAACAATGA
Statistics
Matches: 90, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
35 2 0.02
36 87 0.97
37 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.24
Consensus pattern (35 bp):
ATGACCTTTGGGTCAACAGAGAGTAAAATGAGCAT
Found at i:714049 original size:72 final size:72
Alignment explanation
Indices: 713915--714050 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
713905 GGTAATAGGC
* *
713915 ATGACCTTTGGGTCAATAGAGAGTAAAATAAGCATAATGACCTTTGGGTCAACAAGGGGTAAAAT
1 ATGACCTTTGGGTCAACAGAGAGTAAAATAAGCATAATGACCTTTGGGTCAACAAGGAGTAAAAT
713980 GAGCATT
66 GAGCATT
* *
713987 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCACT-ATGACCTTTGGGTCAAC-AGGCAGTAAA
1 ATGACCTTTGGGTCAACAGAGAGTAAAATAAGCA-TAATGACCTTTGGGTCAACAAGG-AGTAAA
714050 A
64 A
714051 CAAACAATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
71 3 0.05
72 54 0.93
73 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.24
Consensus pattern (72 bp):
ATGACCTTTGGGTCAACAGAGAGTAAAATAAGCATAATGACCTTTGGGTCAACAAGGAGTAAAAT
GAGCATT
Found at i:714772 original size:21 final size:21
Alignment explanation
Indices: 714746--714786 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
714736 ACTCGTTTCG
714746 GTAAAA-TAGTCACTTGTATCA
1 GTAAAACT-GTCACTTGTATCA
714767 GTAAAACTGTCACTTGTATC
1 GTAAAACTGTCACTTGTATC
714787 GGTAGAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (21 bp):
GTAAAACTGTCACTTGTATCA
Found at i:715204 original size:101 final size:101
Alignment explanation
Indices: 715063--715374 Score: 349
Period size: 101 Copynumber: 3.1 Consensus size: 101
715053 GGGTGTTACA
* * * *
715063 GATTTGATGTCATAGCTTCATCTTGCTTCACTGCATCTTCACAAAGATAAATATTTGCTTTTGTA
1 GATTTGATGTCATAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAATATTTGCTTTTGTA
*
715128 GCTTCAATTTGATCCATTGAAACTTCAGGGATATAG
66 GCTTCAATCTGATCCATTGAAACTTCAGGGATATAG
* * * * *
715164 GATTTTATGTCATAGCTTCATCTTTCTCCACTGCAACTTCAGGGAGATAAATATTTGCTTCTATA
1 GATTTGATGTCATAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAATATTTGCTTTTGTA
* * * * * *
715229 GCTTCAATCCGACCCACT-ACAACATCAGGGGTGTAG
66 GCTTCAATCTGATCCATTGA-AACTTCAGGGATATAG
* * ** * * * **
715265 GATTTGGTTTTGTAGCTTCATCCTGCTCTACTACAACTTCAGAGAGATAAGGATTTGCTTTTGTA
1 GATTTGATGTCATAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAATATTTGCTTTTGTA
* * *
715330 GTTTCAATCTGATCC-TTGCAACTTCAAGGATATAG
66 GCTTCAATCTGATCCATTGAAACTTCAGGGATATAG
715365 GATTTGATGT
1 GATTTGATGT
715375 TGTAACTTTA
Statistics
Matches: 168, Mismatches: 41, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
100 22 0.13
101 146 0.87
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (101 bp):
GATTTGATGTCATAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAATATTTGCTTTTGTA
GCTTCAATCTGATCCATTGAAACTTCAGGGATATAG
Found at i:715330 original size:51 final size:50
Alignment explanation
Indices: 715115--715335 Score: 139
Period size: 50 Copynumber: 4.4 Consensus size: 50
715105 AAAGATAAAT
* * *
715115 ATTTGCTTTTGTAGCTTCAAT-TTGATCCATTGA-AACTTCAGG-GATATAGG
1 ATTTGCTTTTGTAGCTTC-ATCCTGCTCCACT-ACAACTTCAGGAGATA-AGG
** * ** * * * **
715165 ATTTTATGTCATAGCTTCATCTTTCTCCACTGCAACTTCAGGGAGATAAAT
1 ATTTGCTTTTGTAGCTTCATCCTGCTCCACTACAACTTCA-GGAGATAAGG
* * * * *
715216 ATTTGCTTCTATAGCTTCAATCC-GAC-CCACTACAACATCAGG-GGTGTAGG
1 ATTTGCTTTTGTAGCTTC-ATCCTG-CTCCACTACAACTTCAGGAGAT-AAGG
* *
715266 ATTTGGTTTTGTAGCTTCATCCTGCTCTACTACAACTTCAGAGAGATAAGG
1 ATTTGCTTTTGTAGCTTCATCCTGCTCCACTACAACTTCAG-GAGATAAGG
*
715317 ATTTGCTTTTGTAGTTTCA
1 ATTTGCTTTTGTAGCTTCA
715336 ATCTGATCCT
Statistics
Matches: 127, Mismatches: 33, Indels: 21
0.70 0.18 0.12
Matches are distributed among these distances:
49 9 0.07
50 59 0.46
51 49 0.39
52 10 0.08
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (50 bp):
ATTTGCTTTTGTAGCTTCATCCTGCTCCACTACAACTTCAGGAGATAAGG
Found at i:718721 original size:156 final size:151
Alignment explanation
Indices: 718489--718770 Score: 438
Period size: 156 Copynumber: 1.8 Consensus size: 151
718479 GGCACGACCA
* *
718489 TAAATGTATATGCCTTATGTAAAGAAATTCATTTTCTAGTAAAGTTGTTCTAACAGAATTGAACT
1 TAAATGTATATGCCTTATGTAAAGAAATTCATTTTCTAATAAAGTTGTTCTAAAAGAATTGAACT
* * *
718554 AAGAATCAATGTCTTTCTTGCATATGCATACATGCATTCATTAGCATTGCATTTCATTACATGCA
66 AAGAATAAATGTATTTC-T---TATGCATACATACATTCATTAGCATTGCATTTCATTACATGCA
718619 CTAAATTAGGGCAAGGCCGTAAATG
127 CTAAATTAGGGCAAGGCCGTAAATG
* **
718644 TAAACTGTATCTGCCTTATGTAAAGAAATTTGTTTTCTAATAAAGTTGTTCTAAAAGAATTGAAC
1 TAAA-TGTATATGCCTTATGTAAAGAAATTCATTTTCTAATAAAGTTGTTCTAAAAGAATTGAAC
*
718709 TAAGAATAAATGTATTTCTTATGCATACATACATTCATTAGCATTTCATTTCATTACATGCA
65 TAAGAATAAATGTATTTCTTATGCATACATACATTCATTAGCATTGCATTTCATTACATGCA
718771 TTAATTTTTT
Statistics
Matches: 117, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
152 41 0.35
155 5 0.04
156 71 0.61
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (151 bp):
TAAATGTATATGCCTTATGTAAAGAAATTCATTTTCTAATAAAGTTGTTCTAAAAGAATTGAACT
AAGAATAAATGTATTTCTTATGCATACATACATTCATTAGCATTGCATTTCATTACATGCACTAA
ATTAGGGCAAGGCCGTAAATG
Found at i:719118 original size:32 final size:32
Alignment explanation
Indices: 719072--719138 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
719062 ATAAGGATCC
* *
719072 TTTTGTAAATGGCACATGACCACTGTCTTTTA
1 TTTTGTAAAGGGCACATGACCACTATCTTTTA
719104 TTTTGTAAAGGGCACATGACCACTATCTTTTA
1 TTTTGTAAAGGGCACATGACCACTATCTTTTA
719136 TTT
1 TTT
719139 CAATAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (32 bp):
TTTTGTAAAGGGCACATGACCACTATCTTTTA
Found at i:719801 original size:67 final size:67
Alignment explanation
Indices: 719691--719844 Score: 192
Period size: 67 Copynumber: 2.3 Consensus size: 67
719681 GAGGAGACTA
* * *
719691 AAAAAAAGAAAA-AAAGGAAAAATG-G-TCGAGATGAAAACCCGTAAAGGGCATCTTGAAACAAA
1 AAAAAAAGAAAAGAAAAGAAAAA-GAGATCAAGATGAAAACCCGTAAAGGGCATCTTAAAACAAA
719753 AAC
65 AAC
* **
719756 AAAAACAA-AAATA-AAAAGAAAAAGAGATCAAGATGAAAACTCGTAAAGGGCATCTTAAAACCC
1 AAAAA-AAGAAA-AGAAAAGAAAAAGAGATCAAGATGAAAACCCGTAAAGGGCATCTTAAAACAA
719819 AAAC
64 AAAC
719823 AAAAAAAGAAAAGAAAAGAAAA
1 AAAAAAAGAAAAGAAAAGAAAA
719845 GAAAAGGTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
65 9 0.12
66 16 0.21
67 52 0.68
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.10
Consensus pattern (67 bp):
AAAAAAAGAAAAGAAAAGAAAAAGAGATCAAGATGAAAACCCGTAAAGGGCATCTTAAAACAAAA
AC
Found at i:719836 original size:5 final size:5
Alignment explanation
Indices: 719826--719850 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
719816 CCCAAACAAA
719826 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
719851 GTAAAAGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:721132 original size:6 final size:6
Alignment explanation
Indices: 721104--721166 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
721094 ATTCGATAAA
* * * *
721104 AAAAAG -AAAAT AAAAAT AAAAAG AAAAAG AGAAAAG AACAAG -AGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG
*
721151 GAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAA
721167 TGAGAGGTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 8 0.17
6 34 0.71
7 6 0.12
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:722103 original size:102 final size:100
Alignment explanation
Indices: 721975--722174 Score: 242
Period size: 100 Copynumber: 2.0 Consensus size: 100
721965 ATCAGTACAA
* * * * * *
721975 CATCAAATCCTATATCCCTGAAGTTAC-AGT-GGATTGGATTAAAAATTACAGTAGCAAATCTTT
1 CATCAAATCCTATAACCCTAAAGTTACAAATGGGA--GGATT-AAAACTACAGAAGAAAATC-TT
** *
722038 ATCTCTTTGGAGTTGCAGTAGAGCTAGATAAAGCTACCT
62 ATCTCTTTAAAGTTGCAGTAGAGCAAGATAAAGCTACCT
722077 CATCAAATCCTATAACCCTAAAGTTACAAATGGGAGGATTAAAACTACAGAAGAAAATCTTATCT
1 CATCAAATCCTATAACCCTAAAGTTACAAATGGGAGGATTAAAACTACAGAAGAAAATCTTATCT
* * *
722142 CTTTAAAGTTGCAGTGGATCAAGATGAAGCTAC
66 CTTTAAAGTTGCAGTAGAGCAAGATAAAGCTAC
722175 GACAATCCTA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
100 33 0.39
101 16 0.19
102 30 0.36
103 2 0.02
104 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (100 bp):
CATCAAATCCTATAACCCTAAAGTTACAAATGGGAGGATTAAAACTACAGAAGAAAATCTTATCT
CTTTAAAGTTGCAGTAGAGCAAGATAAAGCTACCT
Found at i:722324 original size:50 final size:51
Alignment explanation
Indices: 722220--722378 Score: 153
Period size: 50 Copynumber: 3.1 Consensus size: 51
722210 TTAAAATAAT
* * * ** *
722220 AAAAACAAATCTTTATCTCTCTAAAGATCCAGTAGAGCAAGATTAAAGCTAC
1 AAAATCAAATC-TTATCTCCCTAAAGTTATAGTAGAGCAAGATTGAAGCTAC
* * * * *
722272 AAAATCTAATTTTATAC-CCCTAAAGTTATA-TAGGGCCAGATTGAAGATAC
1 AAAATCAAATCTTAT-CTCCCTAAAGTTATAGTAGAGCAAGATTGAAGCTAC
**
722322 AAAAGAAAATCTTATCTCCCTAAAGTTATAGTAGAGCAAGA-TGAAGCTAC
1 AAAATCAAATCTTATCTCCCTAAAGTTATAGTAGAGCAAGATTGAAGCTAC
722372 AACAATC
1 AA-AATC
722379 CTACGTCCTT
Statistics
Matches: 83, Mismatches: 20, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
49 1 0.01
50 50 0.60
51 23 0.28
52 9 0.11
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (51 bp):
AAAATCAAATCTTATCTCCCTAAAGTTATAGTAGAGCAAGATTGAAGCTAC
Found at i:722608 original size:102 final size:102
Alignment explanation
Indices: 722434--723200 Score: 617
Period size: 102 Copynumber: 7.5 Consensus size: 102
722424 AATCCTACTC
* * * *
722434 CCCTGAAGTTGCAGTGG-GTCGGATTAAAACTAACACTAGCAGATCTCAATCTCCATGAAGTTGA
1 CCCTGAAGTTGCAGTGGAG-CAGATTAAAACTAACAGTAGCAGATCTCAATCTCCTTGAAGTTGC
*
722498 AGTGGAATGGAGTGAAGCC-CTGACCCTAAATCTTATAT
65 AGTGGAATGGAGTGAAGCCAC-GACCCCAAATCTTATAT
* * * *
722536 CCCTGAAGTTGTAGTGGAGCAGATTAAAATTAACAGTAGCAGATCTTAATCT-CTCTGAAGTTGT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCT-TGAAGTTGC
* **
722600 AGTAGAATGGAGTGAA-CCACGACCCCAAATCCAATAT
65 AGTGGAATGGAGTGAAGCCACGACCCCAAATCTTATAT
* * * * ** * *
722637 CCTTGAAGTTGCAGTGGATCAAATTAAAATTAACAGTAAAAAATCTCAATCT-CTCTGAAGTTAC
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCT-TGAAGTTGC
* * * *
722701 AGTGGAATAGAGTGAAGCCACGACCCTAATTCCTATAT
65 AGTGGAATGGAGTGAAGCCACGACCCCAAATCTTATAT
* * * * * *
722739 CCCT-AAGGTTACAATGGATCGGATTAAAACCAACAGTAGCAGATCTCAATCT-CTCTGGAGTTG
1 CCCTGAA-GTTGCAGTGGAGCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCT-TGAAGTTG
* * * * *
722802 TAATGGAATGGAGTGAAGCCATGACCCCAGATCTTGTAT
64 CAGTGGAATGGAGTGAAGCCACGACCCCAAATCTTATAT
* * * * * *
722841 CCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAATAGCATATCTCAATCTCCTTAAAGTTGCA
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCTTGAAGTTGCA
* * *
722906 ATGGAATAGAGTGAAGCCACAACCCCAAATCTTATAT
66 GTGGAATGGAGTGAAGCCACGACCCCAAATCTTATAT
* * * *
722943 CCCTAAAGTTGTAGAGG-G-ACGAATTAAAACTAACCA-TAGCAAATCTCAATCTCCTTGAAGTT
1 CCCTGAAGTTGCAGTGGAGCA-G-ATTAAAACTAA-CAGTAGCAGATCTCAATCTCCTTGAAGTT
* *** * * *
723005 ACAGTGGAATGGAGTGAAATTA-TAGCACCAAATCCTATA-
63 GCAGTGGAATGGAGTGAAGCCACGA-CCCCAAATCTTATAT
* * * * * * *
723044 CCCTTAAAGTTGTAAATAG-GCAGATTAAGACTAAAAGTAGCAGATCTCAATCTCCTTAAAGTTG
1 CCC-TGAAGTTG-CAGTGGAGCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCTTGAAGTTG
* * * ** * * *
723108 AAGTGGAATGCAGTTAAGTTACAACACCAAATCTTATAC
64 CAGTGGAATGGAGTGAAGCCACGACCCCAAATCTTATAT
* * * * * * * *
723147 CCCTAAAGTTACAGAGGGGTAGGTTAAAACTAACCA-TAACAAATCTCAATCTCC
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAACTAA-CAGTAGCAGATCTCAATCTCC
723201 CTAAATTTAT
Statistics
Matches: 544, Mismatches: 102, Indels: 38
0.80 0.15 0.06
Matches are distributed among these distances:
101 95 0.17
102 432 0.79
103 16 0.03
104 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (102 bp):
CCCTGAAGTTGCAGTGGAGCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCTTGAAGTTGCA
GTGGAATGGAGTGAAGCCACGACCCCAAATCTTATAT
Found at i:722944 original size:204 final size:202
Alignment explanation
Indices: 722434--723159 Score: 684
Period size: 204 Copynumber: 3.6 Consensus size: 202
722424 AATCCTACTC
* * * * *
722434 CCCTGAAGTTGCAGTGGGTCGGATTAAAACTAACACTAGCAGATCTCAATCTCCATGAAGTTGAA
1 CCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAATAGCAGATCTCAATCTCCTTAAAGTTGAA
* * * * ** * *
722499 GTGGAATGGAGTGAAGCC-CTGACCCTAAATCTTATATCCCTGAAGTTGTAGTGGAGCAGATTAA
66 GTGGAATAGAGTGAAGCCAC-AACCCCAAATCTTATATCCCTAAAGTTACAATGGA-CGGATTAA
* * * *
722563 AATTAACAGTAGCAGATCTTAATCTCTCTGAAGTTGTAGTAGAATGGAGTGAACCACGACCCCAA
129 AACTAACAGTAGCAGATCTCAATCTCTCTGAAGTTGTAGTGGAATGGAGTGAACCATGACCCCAA
*
722628 ATCCAATAT
194 ATCCTATAT
* * * * ** * *
722637 CCTTGAAGTTGCAGTGGATCAAATTAAAATTAACAGTAAAAAATCTCAATCT-CTCTGAAGTT-A
1 CCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAATAGCAGATCTCAATCTCCT-TAAAGTTGA
* * * * *
722700 CAGTGGAATAGAGTGAAGCCACGACCCTAATTCCTATATCCCTAAGGTTACAATGGATCGGATTA
65 -AGTGGAATAGAGTGAAGCCACAACCCCAAATCTTATATCCCTAAAGTTACAATGGA-CGGATTA
* * *
722765 AAACCAACAGTAGCAGATCTCAATCTCTCTGGAGTTGTAATGGAATGGAGTGAAGCCATGACCCC
128 AAACTAACAGTAGCAGATCTCAATCTCTCTGAAGTTGTAGTGGAATGGAGTGAA-CCATGACCCC
* * *
722830 AGATCTTGTAT
192 AAATCCTATAT
* * *
722841 CCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAATAGCATATCTCAATCTCCTTAAAGTTGCA
1 CCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAATAGCAGATCTCAATCTCCTTAAAGTTG-A
** * *
722906 A-TGGAATAGAGTGAAGCCACAACCCCAAATCTTATATCCCTAAAGTTGTAGAGGGACGAATTAA
65 AGTGGAATAGAGTGAAGCCACAACCCCAAATCTTATATCCCTAAAGTTACA-ATGGACGGATTAA
* ** ** *
722970 AACTAACCA-TAGCAAATCTCAATCTC-CTTGAAGTTACAGTGGAATGGAGTGAAATTAT-AGCA
129 AACTAA-CAGTAGCAGATCTCAATCTCTC-TGAAGTTGTAGTGGAATGGAGTG-AACCATGA-CC
723032 CCAAATCCTATA-
190 CCAAATCCTATAT
* * * *
723044 CCCTTAAAGTTGTAAATAGG--CAGATTAAGACTAA-AAGTAGCAGATCTCAATCTCCTTAAAGT
1 CCC-TGAAGTTG-CAGT-GGATCAGATTAAAACTAACAA-TAGCAGATCTCAATCTCCTTAAAGT
* ** * *
723106 TGAAGTGGAAT-GCAGTTAAGTTACAACACCAAATCTTATACCCCTAAAGTTACA
62 TGAAGTGGAATAG-AGTGAAGCCACAACCCCAAATCTTATATCCCTAAAGTTACA
723160 GAGGGGTAGG
Statistics
Matches: 430, Mismatches: 75, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
202 2 0.00
203 160 0.37
204 252 0.59
205 13 0.03
206 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (202 bp):
CCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAATAGCAGATCTCAATCTCCTTAAAGTTGAA
GTGGAATAGAGTGAAGCCACAACCCCAAATCTTATATCCCTAAAGTTACAATGGACGGATTAAAA
CTAACAGTAGCAGATCTCAATCTCTCTGAAGTTGTAGTGGAATGGAGTGAACCATGACCCCAAAT
CCTATAT
Found at i:723243 original size:204 final size:204
Alignment explanation
Indices: 722862--723250 Score: 466
Period size: 204 Copynumber: 1.9 Consensus size: 204
722852 TAGTGGATCG
*
722862 GATTAAAACTAACAATAGCATATCTCAATCTCCTTAAAGTTGCAATGGAATAGAGTGAAGCCACA
1 GATTAAAACTAACAATAGCAGATCTCAATCTCCTTAAAGTTGCAATGGAATAGAGTGAAGCCACA
* * ** *
722927 ACCCCAAATCTTATATCCCTAAAGTTGTAGAGGGACGAATTAAAACTAACCATAGCAAATCTCAA
66 ACACCAAATCTTATACCCCTAAAGTTACAGAGGGACGAATTAAAACTAACCATAACAAATCTCAA
* * * * * ** * *
722992 TCTCCTTGAAGTTACAGTGGAATGGAGTGAAATTATAGCACCAAATCCTATACCCTTAAAGTTGT
131 TCTCCCTAAAGTTACAGTGAAATAGAGTAAAACCACAACACCAAATCCTATACCCTTAAAGTTGT
723057 AAATAGGCA
196 AAATAGGCA
* * **
723066 GATTAAGACTAA-AAGTAGCAGATCTCAATCTCCTTAAAGTTG-AAGTGGAAT-GCAGTTAAGTT
1 GATTAAAACTAACAA-TAGCAGATCTCAATCTCCTTAAAGTTGCAA-TGGAATAG-AGTGAAGCC
*
723128 ACAACACCAAATCTTATACCCCTAAAGTTACAGAGGG--GTAGGTTAAAACTAACCATAACAAAT
63 ACAACACCAAATCTTATACCCCTAAAGTTACAGAGGGACG-A-ATTAAAACTAACCATAACAAAT
* * * *
723191 CTCAATCTCCCTAAATTTATAGTGAAATAGAG-AAAAGCCACAATATCAAATCCTATACCC
126 CTCAATCTCCCTAAAGTTACAGTGAAATAGAGTAAAA-CCACAACACCAAATCCTATACCC
723251 CTACTACTGA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
202 1 0.01
203 9 0.06
204 145 0.94
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (204 bp):
GATTAAAACTAACAATAGCAGATCTCAATCTCCTTAAAGTTGCAATGGAATAGAGTGAAGCCACA
ACACCAAATCTTATACCCCTAAAGTTACAGAGGGACGAATTAAAACTAACCATAACAAATCTCAA
TCTCCCTAAAGTTACAGTGAAATAGAGTAAAACCACAACACCAAATCCTATACCCTTAAAGTTGT
AAATAGGCA
Found at i:727153 original size:21 final size:20
Alignment explanation
Indices: 727124--727174 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
727114 AAAAATAAAC
*
727124 CCAAACCCAAACAACACAAAT
1 CCAAGCCCAAAC-ACACAAAT
*
727145 CCAAGCCCAAACACCCAAAT
1 CCAAGCCCAAACACACAAAT
**
727165 ATAAGCCCAA
1 CCAAGCCCAA
727175 CTTAAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.51, C:0.39, G:0.04, T:0.06
Consensus pattern (20 bp):
CCAAGCCCAAACACACAAAT
Found at i:728445 original size:14 final size:13
Alignment explanation
Indices: 728426--728455 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
728416 ATTTATTGTT
728426 TTTTTCTTTTTTTC
1 TTTTTC-TTTTTTC
728440 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
728453 TTT
1 TTT
728456 ATTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:728534 original size:28 final size:30
Alignment explanation
Indices: 728494--728554 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
728484 TATTCTTGCC
* *
728494 TTTATTTACTTTTATTTATTTATTG-CTTT
1 TTTATGTACTTTTATTTACTTATTGTCTTT
*
728523 TTTATGTA-TTTTATTTACTTGTTGTCTTT
1 TTTATGTACTTTTATTTACTTATTGTCTTT
728552 TTT
1 TTT
728555 TTTCATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.72
Consensus pattern (30 bp):
TTTATGTACTTTTATTTACTTATTGTCTTT
Found at i:728721 original size:21 final size:21
Alignment explanation
Indices: 728684--728725 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
728674 ATTATATTGG
728684 TTATATTATTTGTTATCATTTT
1 TTATATTATTTGTTATC-TTTT
728706 TTAT-TTATTT-TATATCTTTT
1 TTATATTATTTGT-TATCTTTT
728726 ATTGTGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATATTATTTGTTATCTTTT
Found at i:728751 original size:22 final size:22
Alignment explanation
Indices: 728726--728772 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
728716 TATATCTTTT
728726 ATTGT-GTTATTAATTGCATTTA
1 ATTGTAGTTATTAATT-CATTTA
* *
728748 ATTGTATTTATTTATTCATTTA
1 ATTGTAGTTATTAATTCATTTA
728770 ATT
1 ATT
728773 CAAGTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.60
Consensus pattern (22 bp):
ATTGTAGTTATTAATTCATTTA
Found at i:729630 original size:32 final size:32
Alignment explanation
Indices: 729589--729650 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
729579 ATAAAGAAAG
729589 GTCGCAAATTAAATTAAACCGATTTCTCAAAT
1 GTCGCAAATTAAATTAAACCGATTTCTCAAAT
729621 GTCGCAAATTAAATTAAACCGATTTCTCAA
1 GTCGCAAATTAAATTAAACCGATTTCTCAA
729651 TTTCCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (32 bp):
GTCGCAAATTAAATTAAACCGATTTCTCAAAT
Found at i:730811 original size:20 final size:21
Alignment explanation
Indices: 730786--730860 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 21
730776 ATATACTAAG
730786 CAAT-AAAATAAAATAAGTAA
1 CAATAAAAATAAAATAAGTAA
730806 CAATAAATAAATAAAATAAAGCATGAA
1 CAAT-AA-AAATAAAAT-AAG--T-AA
**
730833 TGATAAAAATAAAATAAGTAA
1 CAATAAAAATAAAATAAGTAA
730854 CAATAAA
1 CAATAAA
730861 TACAATATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
20 4 0.09
21 7 0.16
22 2 0.05
23 9 0.20
24 6 0.14
25 9 0.20
26 3 0.07
27 4 0.09
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (21 bp):
CAATAAAAATAAAATAAGTAA
Found at i:730814 original size:24 final size:24
Alignment explanation
Indices: 730787--730867 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
730777 TATACTAAGC
730787 AATAAAATAAAATAAGTAACAATA
1 AATAAAATAAAATAAGTAACAATA
* **
730811 AAT-AAATAAAATAAAGCATGAAT-
1 AATAAAATAAAAT-AAGTAACAATA
*
730834 GATAAAAATAAAATAAGTAACAATA
1 AAT-AAAATAAAATAAGTAACAATA
*
730859 AATACAATA
1 AATAAAATA
730868 TTTTAATGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
23 11 0.25
24 22 0.50
25 11 0.25
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (24 bp):
AATAAAATAAAATAAGTAACAATA
Found at i:730815 original size:14 final size:15
Alignment explanation
Indices: 730792--730860 Score: 61
Period size: 15 Copynumber: 4.4 Consensus size: 15
730782 TAAGCAATAA
730792 AATAAAATAAGTAAC
1 AATAAAATAAGTAAC
*
730807 AAT-AAATAAATAA-
1 AATAAAATAAGTAAC
*
730820 AATAAAGCATGAATGATAAA
1 AATAAA--AT-AA-G-TAAC
730840 AATAAAATAAGTAAC
1 AATAAAATAAGTAAC
730855 AATAAA
1 AATAAA
730861 TACAATATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
13 3 0.07
14 11 0.25
15 12 0.27
16 3 0.07
17 4 0.09
18 2 0.05
19 3 0.07
20 6 0.14
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.20
Consensus pattern (15 bp):
AATAAAATAAGTAAC
Found at i:731277 original size:11 final size:11
Alignment explanation
Indices: 731258--731292 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
731248 AAATAATACT
*
731258 AAAGCAAAATA
1 AAAGTAAAATA
731269 AAAGTAAAATA
1 AAAGTAAAATA
*
731280 ACAGTAAAATA
1 AAAGTAAAATA
731291 AA
1 AA
731293 TAAATGACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (11 bp):
AAAGTAAAATA
Found at i:735808 original size:29 final size:30
Alignment explanation
Indices: 735762--735823 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
735752 ATTATTTTCG
*
735762 TAATTAATTTATCCTTTAA-ATCATTTTTA
1 TAATTAATTAATCCTTTAATATCATTTTTA
** *
735791 TAATTAATTAATTTTTTAATATTATTTTTA
1 TAATTAATTAATCCTTTAATATCATTTTTA
735821 TAA
1 TAA
735824 AAAAAGCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (30 bp):
TAATTAATTAATCCTTTAATATCATTTTTA
Found at i:742481 original size:2 final size:2
Alignment explanation
Indices: 742474--742511 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
742464 AGAACACAAA
742474 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
742512 TTTTGAGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:744740 original size:52 final size:52
Alignment explanation
Indices: 744662--744767 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
744652 CATCGGATGC
744662 CCATCTTGCATCAGTACTCCCCCAATTGCATAGTCTGATGCATTCGTGCGTA
1 CCATCTTGCATCAGTACTCCCCCAATTGCATAGTCTGATGCATTCGTGCGTA
744714 CCATCTTGCATCAGTACTCCCCCAATTGCATAGTCTGATGCATTCGTGCGTA
1 CCATCTTGCATCAGTACTCCCCCAATTGCATAGTCTGATGCATTCGTGCGTA
744766 CC
1 CC
744768 TCATACGCCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (52 bp):
CCATCTTGCATCAGTACTCCCCCAATTGCATAGTCTGATGCATTCGTGCGTA
Found at i:747625 original size:2 final size:2
Alignment explanation
Indices: 747618--747643 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
747608 AGAATAGAAA
747618 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
747644 TTTTTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:758459 original size:26 final size:26
Alignment explanation
Indices: 758406--758460 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
758396 TAGCTATCAA
* *
758406 ATGCTACGACAATTCTGGACACGTTC
1 ATGCAACGACAATTCTGGACACGCTC
* * *
758432 ATGCAACGACAATTTTGTACATGCTC
1 ATGCAACGACAATTCTGGACACGCTC
758458 ATG
1 ATG
758461 TAGCAACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (26 bp):
ATGCAACGACAATTCTGGACACGCTC
Found at i:758556 original size:38 final size:38
Alignment explanation
Indices: 758476--758557 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
758466 ACATTTCTAA
* *
758476 GTGCAA-TTGAAGAATACTTATGCAGTGATAGTTATGG
1 GTGCAATTTGAAGAATACTTATGCAGCGACAGTTATGG
* *
758513 ATGCAATTTGAAGAATATTTATGCAGCGACAGTCT-TGG
1 GTGCAATTTGAAGAATACTTATGCAGCGACAGT-TATGG
758551 GTGCAAT
1 GTGCAAT
758558 CTGGAAGTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 5 0.13
38 32 0.84
39 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (38 bp):
GTGCAATTTGAAGAATACTTATGCAGCGACAGTTATGG
Found at i:760778 original size:14 final size:15
Alignment explanation
Indices: 760755--760792 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
760745 TATAGCAATA
*
760755 TTTCT-TTTTTTTCT
1 TTTCTCTTTTTCTCT
760769 TTTCTCTTTTTCTCT
1 TTTCTCTTTTTCTCT
760784 TTT-TCTTTT
1 TTTCTCTTTT
760793 ATTCAACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTCTTTTTCTCT
Found at i:760778 original size:16 final size:15
Alignment explanation
Indices: 760755--760792 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
760745 TATAGCAATA
*
760755 TTTCTTTTTTTTC-T
1 TTTCTTTTTTCTCTT
760769 TTTCTCTTTTTCTCTT
1 TTTCT-TTTTTCTCTT
760785 TTTCTTTT
1 TTTCTTTT
760793 ATTCAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 5 0.24
15 10 0.48
16 6 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTTCTCTT
Done.