Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold364
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: 2089110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1558862 original size:14 final size:13
Alignment explanation
Indices: 1558830--1558854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1558820 AACCAAAAAC
1558830 AAAAAAAAAACAA
1 AAAAAAAAAACAA
1558843 AAAAAAAAAACA
1 AAAAAAAAAACA
1558855 GAATAAAATG
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:1572052 original size:25 final size:27
Alignment explanation
Indices: 1571996--1572052 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
1571986 TTGAGTAATG
* *
1571996 AAAA-TATATTGATTTATACTTTATTT
1 AAAATTATATTGATTTATAATTTATTA
*
1572022 ATAATTATA-TGATTT-TAATTTATTA
1 AAAATTATATTGATTTATAATTTATTA
1572047 AAAATT
1 AAAATT
1572053 TAAAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 13 0.50
26 9 0.35
27 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (27 bp):
AAAATTATATTGATTTATAATTTATTA
Found at i:1574623 original size:33 final size:33
Alignment explanation
Indices: 1574581--1574649 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
1574571 TGATAAAGTT
*
1574581 TATAAATAAATCTAGTACATACTATTCAAAAAC
1 TATAAATAAATATAGTACATACTATTCAAAAAC
1574614 TATAAATAAATATAGTACATACTATTCAAAAAC
1 TATAAATAAATATAGTACATACTATTCAAAAAC
1574647 TAT
1 TAT
1574650 CTCTAAGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (33 bp):
TATAAATAAATATAGTACATACTATTCAAAAAC
Found at i:1576906 original size:3 final size:3
Alignment explanation
Indices: 1576898--1576937 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1576888 ATGTTCCCCC
*
1576898 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1576938 TTCTTTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1582516 original size:2 final size:2
Alignment explanation
Indices: 1582511--1582553 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1582501 TATATATATA
*
1582511 TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1582553 T
1 T
1582554 ATTATATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1585015 original size:17 final size:17
Alignment explanation
Indices: 1584956--1585017 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
1584946 TTTTGAATAT
*
1584956 ATAAT-TAT-ATATTTA
1 ATAATATATAATAATTA
*
1584971 ATAATTAAATAA-AATTA
1 ATAA-TATATAATAATTA
1584988 ATAATATATAATAATTA
1 ATAATATATAATAATTA
1585005 A-AATATGATAATA
1 ATAATAT-ATAATA
1585018 TGTATAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 4 0.10
16 12 0.31
17 22 0.56
18 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAATATATAATAATTA
Found at i:1585016 original size:27 final size:26
Alignment explanation
Indices: 1584951--1585023 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
1584941 TATCATTTTG
*
1584951 AATATATAATTATATATTTAATAATTA
1 AATATATAA-TATATATATAATAATTA
*
1584978 AATAAAATTAATA-ATATATAATAATTAA
1 AAT-ATA-TAATATATATATAATAATT-A
*
1585006 AATATGATAATATGTATA
1 AATAT-ATAATATATATA
1585024 AATTACTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
27 21 0.57
28 13 0.35
29 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
AATATATAATATATATATAATAATTA
Found at i:1585027 original size:24 final size:24
Alignment explanation
Indices: 1584971--1585028 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1584961 TATATATTTA
1584971 ATAATTAAA-TAAAATTAATAATAT
1 ATAA-TAAATTAAAATTAATAATAT
*
1584995 ATAAT-AATTAAAATATGATAATAT
1 ATAATAAATTAAAAT-TAATAATAT
*
1585019 GT-ATAAATTA
1 ATAATAAATTA
1585029 CTGTATATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 2 0.07
23 9 0.31
24 18 0.62
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAATAAATTAAAATTAATAATAT
Found at i:1592012 original size:75 final size:75
Alignment explanation
Indices: 1591858--1592035 Score: 196
Period size: 75 Copynumber: 2.4 Consensus size: 75
1591848 AACGATCAGG
** * * * * * *
1591858 ATTTATGTGATGAGTACAAGTCTGACAACCATAGTGAATGTTGGCTACCAGAATTCCATCTTTCT
1 ATTTATGTGGCGAGTACAAGTCTGGCAGCCAGAGTGAATGTTGACTACAAGAATTCCATCCTTCT
* * * *
1591923 GGCTACTAGG
66 GACAACCAGA
* *
1591933 ATTTATGTGGCGAGCACAGGTCTGGCAGCCAGAGTGAATGTTGACTAACAAG-ATTCCATCCTTC
1 ATTTATGTGGCGAGTACAAGTCTGGCAGCCAGAGTGAATGTTGACT-ACAAGAATTCCATCCTTC
1591997 TGACAACCAGA
65 TGACAACCAGA
* *
1592008 ATTTATGTCGCGAGTACAAGTGTGGCAG
1 ATTTATGTGGCGAGTACAAGTCTGGCAG
1592036 TCAAAATAAG
Statistics
Matches: 84, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
75 80 0.95
76 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (75 bp):
ATTTATGTGGCGAGTACAAGTCTGGCAGCCAGAGTGAATGTTGACTACAAGAATTCCATCCTTCT
GACAACCAGA
Found at i:1592658 original size:26 final size:26
Alignment explanation
Indices: 1592542--1592658 Score: 87
Period size: 26 Copynumber: 4.5 Consensus size: 26
1592532 GATGTCGTGA
*
1592542 TGGCGATCAGGATCGTAATGCCATGG
1 TGGCGAGCAGGATCGTAATGCCATGG
* * *
1592568 TGGCTAGCAGGATCGGAGTGCCATGG
1 TGGCGAGCAGGATCGTAATGCCATGG
* *
1592594 TGTAACTGA-CAGTAT--TAATGCCATGG
1 TG--GC-GAGCAGGATCGTAATGCCATGG
* * * **
1592620 TGACGATCGGGATCGTGGTGCCATGG
1 TGGCGAGCAGGATCGTAATGCCATGG
1592646 TGGCGAGCAGGAT
1 TGGCGAGCAGGAT
1592659 TGGATTGACT
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
23 2 0.03
24 6 0.09
26 54 0.78
28 6 0.09
29 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (26 bp):
TGGCGAGCAGGATCGTAATGCCATGG
Found at i:1592707 original size:78 final size:78
Alignment explanation
Indices: 1592423--1592705 Score: 287
Period size: 78 Copynumber: 3.6 Consensus size: 78
1592413 GGCGGGCAAA
** * * * * ** * *
1592423 ATTGGAGTGACTTAATGTCACTGATAATATTAATACCGTGGTGGCGATTAGGATCGTGGTGCTAT
1 ATTGGAGTGACTTGGTGTCACTAACAGTATTGATGTCGTGGTGGCGATCAGGATCGTGGTGCCAT
* *
1592488 GGTGACGAGTAGG
66 GGTGGCGAGCAGG
* * * * **
1592501 GTTGAAGTGACTTGGTGTCGCTAACAGTATTGATGTCGTGATGGCGATCAGGATCGTAATGCCAT
1 ATTGGAGTGACTTGGTGTCACTAACAGTATTGATGTCGTGGTGGCGATCAGGATCGTGGTGCCAT
*
1592566 GGTGGCTAGCAGG
66 GGTGGCGAGCAGG
* * * * * * * * * *
1592579 ATCGGAGTGCCATGGTGTAACTGACAGTATTAATGCCATGGTGACGATCGGGATCGTGGTGCCAT
1 ATTGGAGTGACTTGGTGTCACTAACAGTATTGATGTCGTGGTGGCGATCAGGATCGTGGTGCCAT
1592644 GGTGGCGAGCAGG
66 GGTGGCGAGCAGG
* *
1592657 ATTGGATTGACTTGGTGTCACTAACAGTACTGATGTCGTGGTGGCGATC
1 ATTGGAGTGACTTGGTGTCACTAACAGTATTGATGTCGTGGTGGCGATC
1592706 GGAGTGACTT
Statistics
Matches: 158, Mismatches: 47, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
78 158 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (78 bp):
ATTGGAGTGACTTGGTGTCACTAACAGTATTGATGTCGTGGTGGCGATCAGGATCGTGGTGCCAT
GGTGGCGAGCAGG
Found at i:1592733 original size:124 final size:124
Alignment explanation
Indices: 1592578--1592828 Score: 304
Period size: 124 Copynumber: 2.0 Consensus size: 124
1592568 TGGCTAGCAG
* * * *
1592578 GATCGGAGTGCCATGGTGTAACTGACAGTATTAATGCCATGGTGACGATCGGGATCGTGGTGCCA
1 GATCGGAGTGACATGGTGTAACTAACAGTATTAATGCCATGGTGACGATCAGGATCGTAGTGCCA
* ** ** * * *
1592643 TGGTGGCGAGCAGGATTGGATTGACTTGGTGTCACTAACAGTACTGATGTCGTGGTGGC
66 TGGTGACGAGCAGGATCAGAGCGACTTGCTGCCACTAACAGTACTGATGTCGTAGTGGC
* * * * ** *
1592702 GATCGGAGTGACTTGGTGTCACTAACAGTATTGATGCTATGGTGGTGATCATGATCGTAGTGCCA
1 GATCGGAGTGACATGGTGTAACTAACAGTATTAATGCCATGGTGACGATCAGGATCGTAGTGCCA
* * *
1592767 TGGTGACTAGCAGGATCAGAGCGACTTGCTGCCACTGACAGTATTGATGTCGTAGTGGC
66 TGGTGACGAGCAGGATCAGAGCGACTTGCTGCCACTAACAGTACTGATGTCGTAGTGGC
1592826 GAT
1 GAT
1592829 TAGAATCGTA
Statistics
Matches: 105, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
124 105 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.27
Consensus pattern (124 bp):
GATCGGAGTGACATGGTGTAACTAACAGTATTAATGCCATGGTGACGATCAGGATCGTAGTGCCA
TGGTGACGAGCAGGATCAGAGCGACTTGCTGCCACTAACAGTACTGATGTCGTAGTGGC
Found at i:1592745 original size:46 final size:46
Alignment explanation
Indices: 1592664--1592751 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
1592654 AGGATTGGAT
*
1592664 TGACTTGGTGTCACTAACAGTACTGATGTCGTGGTGGCGATCGGAG
1 TGACTTGGTGTCACTAACAGTACTGATGTCATGGTGGCGATCGGAG
* *
1592710 TGACTTGGTGTCACTAACAGTATTGATG-CTATGGTGGTGATC
1 TGACTTGGTGTCACTAACAGTACTGATGTC-ATGGTGGCGATC
1592752 ATGATCGTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (46 bp):
TGACTTGGTGTCACTAACAGTACTGATGTCATGGTGGCGATCGGAG
Found at i:1592810 original size:78 final size:77
Alignment explanation
Indices: 1592702--1593004 Score: 319
Period size: 78 Copynumber: 3.9 Consensus size: 77
1592692 TCGTGGTGGC
* * *
1592702 GATCGGAGTGACTTGGTGTCACTAACAGTATTGATGCTATGGTGGTGATCATGATCGTAGTGCCA
1 GATCAGAGTGACTTGGTGTCACTGACAGTATTGATGCTATGGTGGCGATCA-GATCGTAGTGCCA
1592767 TGGTGACTAGCAG
65 TGGTGACTAGCAG
* * * * *
1592780 GATCAGAGCGACTTGCTGCCACTGACAGTATTGATGTCGTA--GTGGCGATTAGAATCGTAATGC
1 GATCAGAGTGACTTGGTGTCACTGACAGTATTGATG-C-TATGGTGGCGATCAG-ATCGTAGTGC
1592843 CATGGT-AGCTAGCAG
63 CATGGTGA-CTAGCAG
* * ** *
1592858 GATCGGAGTGACTTGGTGTCACTGACAATATTGATGCCGTGGTGACGATCAGGATCGTAGTGCCA
1 GATCAGAGTGACTTGGTGTCACTGACAGTATTGATGCTATGGTGGCGATCA-GATCGTAGTGCCA
* *
1592923 TGATGGCTAG-AG
65 TGGTGACTAGCAG
* * * * *
1592935 GATCAGAGTGCCATGGTGTCACTGACAGTAGTGATGCTATGGTGGCAATTAGGATCGT-GATGCC
1 GATCAGAGTGACTTGGTGTCACTGACAGTATTGATGCTATGGTGGCGATCA-GATCGTAG-TGCC
1592999 ATGGTG
64 ATGGTG
1593005 GCGAACAGAA
Statistics
Matches: 185, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
76 1 0.01
77 62 0.34
78 118 0.64
79 2 0.01
80 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (77 bp):
GATCAGAGTGACTTGGTGTCACTGACAGTATTGATGCTATGGTGGCGATCAGATCGTAGTGCCAT
GGTGACTAGCAG
Found at i:1592859 original size:202 final size:202
Alignment explanation
Indices: 1592506--1592907 Score: 491
Period size: 202 Copynumber: 2.0 Consensus size: 202
1592496 GTAGGGTTGA
* * *
1592506 AGTGACTTGGTGTCGCTAACAGTATTGATGTCGTGATGGCGATCAGGATCGTAATGCCATGGTGG
1 AGTGACTTGGTGTCACTAACAGTATTGATGTCATGATGGCGATCAGGATCGTAATGCCATGGTGA
* * * * * * * *
1592571 CTAGCAGGATCGGAGTGCCATGGTGTAACTGACAGTATTAATGCCATGGTGACGATCGGGATCGT
66 CTAGCAGGATCAGAGCGACATGCTGCAACTGACAGTATTAATGCCATAGTGACGATCAGAATCGT
** * * * * * *
1592636 GGTGCCATGGTGGCGAGCAGGATTGGATTGACTTGGTGTCACTAACAGTACTGATGTCGTGGTGG
131 AATGCCATGGTAGCGAGCAGGATCGGAGTGACTTGGTGTCACTAACAATACTGATGCCGTGGTGA
1592701 CGATCGG
196 CGATCGG
* * * *
1592708 AGTGACTTGGTGTCACTAACAGTATTGATG-CTATGGTGGTGATCATGATCGTAGTGCCATGGTG
1 AGTGACTTGGTGTCACTAACAGTATTGATGTC-ATGATGGCGATCAGGATCGTAATGCCATGGTG
* * * * * * *
1592772 ACTAGCAGGATCAGAGCGACTTGCTGCCACTGACAGTATTGATGTCGTAGTGGCGATTAGAATCG
65 ACTAGCAGGATCAGAGCGACATGCTGCAACTGACAGTATTAATGCCATAGTGACGATCAGAATCG
* * *
1592837 TAATGCCATGGTAGCTAGCAGGATCGGAGTGACTTGGTGTCACTGACAATATTGATGCCGTGGTG
130 TAATGCCATGGTAGCGAGCAGGATCGGAGTGACTTGGTGTCACTAACAATACTGATGCCGTGGTG
1592902 ACGATC
195 ACGATC
1592908 AGGATCGTAG
Statistics
Matches: 166, Mismatches: 33, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
201 1 0.01
202 165 0.99
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (202 bp):
AGTGACTTGGTGTCACTAACAGTATTGATGTCATGATGGCGATCAGGATCGTAATGCCATGGTGA
CTAGCAGGATCAGAGCGACATGCTGCAACTGACAGTATTAATGCCATAGTGACGATCAGAATCGT
AATGCCATGGTAGCGAGCAGGATCGGAGTGACTTGGTGTCACTAACAATACTGATGCCGTGGTGA
CGATCGG
Found at i:1592908 original size:156 final size:154
Alignment explanation
Indices: 1592702--1593003 Score: 399
Period size: 156 Copynumber: 1.9 Consensus size: 154
1592692 TCGTGGTGGC
* * ** *
1592702 GATCGGAGTGACTTGGTGTCACTAACAGTATTGATGCTATGGTGGTGATCATGATCGTAGTGCCA
1 GATCGGAGTGACTTGGTGTCACTAACAATATTGATGCCATGGTGACGATCAGGATCGTAGTGCCA
* * * *
1592767 TGGTGACTAGCAGGATCAGAGCGACTTGCTGCCACTGACAGTATTGATGTCGTA-GTGGCGATTA
66 TGATGACTAG-AGGATCAGAGCGACATGCTGCCACTGACAGTAGTGATG-C-TAGGTGGCAATTA
1592831 GAATCGTAATGCCATGGTAGCTAGCAG
128 GAATCGTAATGCCATGGTAGCTAGCAG
* *
1592858 GATCGGAGTGACTTGGTGTCACTGACAATATTGATGCCGTGGTGACGATCAGGATCGTAGTGCCA
1 GATCGGAGTGACTTGGTGTCACTAACAATATTGATGCCATGGTGACGATCAGGATCGTAGTGCCA
* * * * * *
1592923 TGATGGCTAGAGGATCAGAGTGCCATGGTGTCACTGACAGTAGTGATGCTATGGTGGCAATTAGG
66 TGATGACTAGAGGATCAGAGCGACATGCTGCCACTGACAGTAGTGATGCTA-GGTGGCAATTAGA
*
1592988 ATCGTGATGCCATGGT
130 ATCGTAATGCCATGGT
1593004 GGCGAACAGA
Statistics
Matches: 126, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
153 2 0.02
154 1 0.01
155 57 0.45
156 66 0.52
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (154 bp):
GATCGGAGTGACTTGGTGTCACTAACAATATTGATGCCATGGTGACGATCAGGATCGTAGTGCCA
TGATGACTAGAGGATCAGAGCGACATGCTGCCACTGACAGTAGTGATGCTAGGTGGCAATTAGAA
TCGTAATGCCATGGTAGCTAGCAG
Found at i:1594531 original size:75 final size:74
Alignment explanation
Indices: 1594335--1594562 Score: 217
Period size: 75 Copynumber: 3.1 Consensus size: 74
1594325 TTTGTCAGAT
* * * * *
1594335 ATTCATCTTTCTGACGACCAGGATTTAAGTGACGAACACAAGTTTGACAACCAGAGTGAGTGTTG
1 ATTCATCTTTCTGACGATCAGGATTTATGTGACGAACACAAGTCTGACAGCCAGAGTGAATGTTG
*
1594400 TCTACTAAG
66 GCTACTAAG
* * * * * * * *
1594409 ATTCTGTCTTTTTGGCGATC-GAGATTTATATGGC-AAGTACAAATCTGACAGCCAGAGTAAATG
1 ATTC-ATCTTTCTGACGATCAG-GATTTATGTGACGAA-CACAAGTCTGACAGCCAGAGTGAATG
* *
1594472 GTGGCTACTAGG
63 TTGGCTACTAAG
* * * *
1594484 ATTTCATCATTCTGACGATCAGGATTTATGTGACGAACACAGGTCTGATAGCCATAGTGAATGTT
1 A-TTCATCTTTCTGACGATCAGGATTTATGTGACGAACACAAGTCTGACAGCCAGAGTGAATGTT
*
1594549 GGCTACCAAG
65 GGCTACTAAG
1594559 ATTC
1 ATTC
1594563 TATCCATTTG
Statistics
Matches: 117, Mismatches: 31, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
74 10 0.09
75 101 0.86
76 6 0.05
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (74 bp):
ATTCATCTTTCTGACGATCAGGATTTATGTGACGAACACAAGTCTGACAGCCAGAGTGAATGTTG
GCTACTAAG
Found at i:1594607 original size:150 final size:150
Alignment explanation
Indices: 1594336--1594621 Score: 349
Period size: 150 Copynumber: 1.9 Consensus size: 150
1594326 TTGTCAGATA
* * * *
1594336 TTCATCTTTCTGACGACCAGGATTTAAGTGACGAACACAAGTTTGACAACCAGAGTGAGTGTTGT
1 TTCATCATTCTGACGACCAGGATTTAAGTGACGAACACAAGTCTGACAACCAGAGTGAATGTTGG
* * ** * * * * * *
1594401 CTACTAAGATTCTGTCTTTTTGGCGATCGAGATTTATATGGCAAGTACAAATCTGACAGCCAGAG
66 CTACCAAGATTCTATCCATTTGACAATCAAAATTTATATAGCAAGTACAAATCTGACAGCCAGAA
1594466 TAAATGGTGGCTACTAGGAT
131 TAAATGGTGGCTACTAGGAT
* * * * * *
1594486 TTCATCATTCTGACGATCAGGATTTATGTGACGAACACAGGTCTGATAGCCATAGTGAATGTTGG
1 TTCATCATTCTGACGACCAGGATTTAAGTGACGAACACAAGTCTGACAACCAGAGTGAATGTTGG
* * *
1594551 CTACCAAGATTCTATCCATTTGACAA-CTAAAATTTATATAGCGAGTACAGATCTGACAGTCAGA
66 CTACCAAGATTCTATCCATTTGACAATC-AAAATTTATATAGCAAGTACAAATCTGACAGCCAGA
1594615 ATAAATG
130 ATAAATG
1594622 TTAATTACCA
Statistics
Matches: 112, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
149 1 0.01
150 111 0.99
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (150 bp):
TTCATCATTCTGACGACCAGGATTTAAGTGACGAACACAAGTCTGACAACCAGAGTGAATGTTGG
CTACCAAGATTCTATCCATTTGACAATCAAAATTTATATAGCAAGTACAAATCTGACAGCCAGAA
TAAATGGTGGCTACTAGGAT
Found at i:1596344 original size:22 final size:22
Alignment explanation
Indices: 1596318--1596363 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1596308 TGTATTTTTA
1596318 TTATATTTAAATAAATTTTAAT
1 TTATATTTAAATAAATTTTAAT
*
1596340 TTATATTTAAATAAATTTTTAT
1 TTATATTTAAATAAATTTTAAT
1596362 TT
1 TT
1596364 TAAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATTTAAATAAATTTTAAT
Found at i:1596367 original size:17 final size:19
Alignment explanation
Indices: 1596339--1596373 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1596329 TAAATTTTAA
1596339 TTTATATTTAAA-TAAATT
1 TTTATATTTAAATTAAATT
1596357 TTTAT-TTTAAATTAAAT
1 TTTATATTTAAATTAAAT
1596374 ATTAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATATTTAAATTAAATT
Found at i:1596371 original size:22 final size:22
Alignment explanation
Indices: 1596311--1596374 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
1596301 ATGCGTATGT
*
1596311 ATTTTTATTAT-ATTTAAATAA
1 ATTTTTATTTTAATTTAAATAA
*
1596332 A-TTTTAATTTATATTTAAATAA
1 ATTTTTATTTTA-ATTTAAATAA
*
1596354 ATTTTTATTTTAAATTAAATA
1 ATTTTTATTTTAATTTAAATA
1596375 TTAATATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.19
21 1 0.03
22 19 0.53
23 9 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTATTTTAATTTAAATAA
Found at i:1596383 original size:38 final size:37
Alignment explanation
Indices: 1596314--1596418 Score: 99
Period size: 38 Copynumber: 2.8 Consensus size: 37
1596304 CGTATGTATT
* *
1596314 TTTATTATATTTAAA-TAAATTTTAATTTATATTTAAATAAA
1 TTTATTAT-TTTAAATTAAATATTAA--TATATGT-AA-AAA
*
1596355 TTT-TTATTTTAAATTAAATATTAATATATGTAAAAG
1 TTTATTATTTTAAATTAAATATTAATATATGTAAAAA
*
1596391 TTTAGTAATTTTAAATTAAA-ATTAATAT
1 TTTA-TTATTTTAAATTAAATATTAATAT
1596419 TTCTTTAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
36 5 0.09
37 10 0.18
38 20 0.35
39 6 0.11
40 13 0.23
41 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (37 bp):
TTTATTATTTTAAATTAAATATTAATATATGTAAAAA
Found at i:1596425 original size:22 final size:23
Alignment explanation
Indices: 1596400--1596442 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1596390 GTTTAGTAAT
1596400 TTTAAAT-TAAAATT-AATATTTC
1 TTTAAATAT-AAATTAAATATTTC
1596422 TTTAAATATAAATTAAATATT
1 TTTAAATATAAATTAAATATT
1596443 AATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAATATAAATTAAATATTTC
Found at i:1596448 original size:29 final size:28
Alignment explanation
Indices: 1596402--1596462 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
1596392 TTAGTAATTT
*
1596402 TAAATTAAAATTAATATTTCTTTAAATA
1 TAAATTAAAATTAATATTTATTTAAATA
*
1596430 TAAATTAAATATTAATATTTATTTATATA
1 TAAATTAAA-ATTAATATTTATTTAAATA
1596459 TAAA
1 TAAA
1596463 ATTATCTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAATTAAAATTAATATTTATTTAAATA
Found at i:1596517 original size:20 final size:19
Alignment explanation
Indices: 1596489--1596529 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1596479 AAGCATATAT
1596489 TTAAATAAAAATTTAATAAA
1 TTAAAT-AAAATTTAATAAA
*
1596509 TTAATTAAAATTTAATAAA
1 TTAAATAAAATTTAATAAA
1596528 TT
1 TT
1596530 TTTAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAAATAAAATTTAATAAA
Found at i:1596541 original size:18 final size:19
Alignment explanation
Indices: 1596497--1596541 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1596487 ATTTAAATAA
1596497 AAAT-TTAATAAATTAATT
1 AAATATTAATAAATTAATT
*
1596515 AAA-ATTTAATAAATT-TTT
1 AAATA-TTAATAAATTAATT
1596533 AAATATTAA
1 AAATATTAA
1596542 AATTTTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATATTAATAAATTAATT
Found at i:1597135 original size:29 final size:28
Alignment explanation
Indices: 1597098--1597220 Score: 83
Period size: 29 Copynumber: 4.2 Consensus size: 28
1597088 AATTAAAATA
*
1597098 TTAACTATATTAAAAAATTTAAAAATTAT
1 TTAAATATA-TAAAAAATTTAAAAATTAT
* *
1597127 TTAAGTATA-AATTAAAA-TTAATAATTTAT
1 TTAAATATATAA--AAAATTTAA-AAATTAT
* *
1597156 TTAAATATA-AATTAATATTAAAAAATTAT
1 TTAAATATATAA--AAAATTTAAAAATTAT
* *
1597185 TTAAATATA-ATAAAAATATAAAAATTTAA
1 TTAAATATATA-AAAAATTTAAAAA-TTAT
1597214 TTAAATA
1 TTAAATA
1597221 AAATTATAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.03
28 13 0.17
29 59 0.76
30 4 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
TTAAATATATAAAAAATTTAAAAATTAT
Found at i:1597181 original size:58 final size:57
Alignment explanation
Indices: 1597118--1597226 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 57
1597108 TAAAAAATTT
* * * *
1597118 AAAAATTATTTAAGTATAAATTAAAAT-TAATAATTTATTTAAATATAAATTAATATTA
1 AAAAATTATTTAAATAT-AATAAAAATATAAAAATTTAATTAAATA-AAATTAATATTA
1597176 AAAAATTATTTAAATATAATAAAAATATAAAAATTTAATTAAATAAAATTA
1 AAAAATTATTTAAATATAATAAAAATATAAAAATTTAATTAAATAAAATTA
1597227 TAAAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
57 14 0.30
58 32 0.70
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (57 bp):
AAAAATTATTTAAATATAATAAAAATATAAAAATTTAATTAAATAAAATTAATATTA
Found at i:1597231 original size:23 final size:25
Alignment explanation
Indices: 1597183--1597238 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
1597173 TTAAAAAATT
1597183 ATTTAAATATAATAAAAATATAAAA
1 ATTTAAATATAATAAAAATATAAAA
* *
1597208 ATTTAATTA-AATAAAATTAT-AAA
1 ATTTAAATATAATAAAAATATAAAA
1597231 ATTTAAAT
1 ATTTAAAT
1597239 TTTTTTTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 10 0.36
24 10 0.36
25 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTTAAATATAATAAAAATATAAAA
Found at i:1597239 original size:24 final size:26
Alignment explanation
Indices: 1597183--1597239 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
1597173 TTAAAAAATT
1597183 ATTTAAA-TATAATAAAAATATAAAA
1 ATTTAAATTATAATAAAAATATAAAA
*
1597208 ATTT-AATTA-AATAAAATTAT-AAA
1 ATTTAAATTATAATAAAAATATAAAA
1597231 ATTTAAATT
1 ATTTAAATT
1597240 TTTTTTACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.24
24 16 0.55
25 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTTAAATTATAATAAAAATATAAAA
Found at i:1598554 original size:2 final size:2
Alignment explanation
Indices: 1598547--1598576 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1598537 AATATGGAGG
*
1598547 GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1598577 CTTAGTAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1598560 original size:12 final size:12
Alignment explanation
Indices: 1598543--1598576 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1598533 GAGGAATATG
1598543 GAGGGAGAGAGA
1 GAGGGAGAGAGA
1598555 GAGGGAGAGAGA
1 GAGGGAGAGAGA
*
1598567 GAGAGAGAGA
1 GAGGGAGAGA
1598577 CTTAGTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (12 bp):
GAGGGAGAGAGA
Found at i:1599368 original size:106 final size:106
Alignment explanation
Indices: 1599183--1599387 Score: 410
Period size: 106 Copynumber: 1.9 Consensus size: 106
1599173 CTCCATAGCA
1599183 TTTTATAGAACTCTTAACATTAAATCAAAATGATTGGGTCTAATTGCAATTCAGTGCCAATTTGC
1 TTTTATAGAACTCTTAACATTAAATCAAAATGATTGGGTCTAATTGCAATTCAGTGCCAATTTGC
1599248 TGTATGATTTTTGTCCTGAACCATTCCTTTTGCTGTATGAT
66 TGTATGATTTTTGTCCTGAACCATTCCTTTTGCTGTATGAT
1599289 TTTTATAGAACTCTTAACATTAAATCAAAATGATTGGGTCTAATTGCAATTCAGTGCCAATTTGC
1 TTTTATAGAACTCTTAACATTAAATCAAAATGATTGGGTCTAATTGCAATTCAGTGCCAATTTGC
1599354 TGTATGATTTTTGTCCTGAACCATTCCTTTTGCT
66 TGTATGATTTTTGTCCTGAACCATTCCTTTTGCT
1599388 ATCAAGAAAT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (106 bp):
TTTTATAGAACTCTTAACATTAAATCAAAATGATTGGGTCTAATTGCAATTCAGTGCCAATTTGC
TGTATGATTTTTGTCCTGAACCATTCCTTTTGCTGTATGAT
Found at i:1603524 original size:94 final size:94
Alignment explanation
Indices: 1603363--1603551 Score: 369
Period size: 94 Copynumber: 2.0 Consensus size: 94
1603353 TTGATAGCTA
*
1603363 GAGGTACAGACTGTGTGATGTGTGGCCTTGAATAGAAGCTTCGTTTGATTTAATAATAATTTCTT
1 GAGGTACAGACTGTGTGATGTGTGGCCTTGAATAGAAGCTTCGTTTGATTTAATAATAACTTCTT
1603428 TTTTGCTTTTTTAAGTCATTAGATTTAAG
66 TTTTGCTTTTTTAAGTCATTAGATTTAAG
1603457 GAGGTACAGACTGTGTGATGTGTGGCCTTGAATAGAAGCTTCGTTTGATTTAATAATAACTTCTT
1 GAGGTACAGACTGTGTGATGTGTGGCCTTGAATAGAAGCTTCGTTTGATTTAATAATAACTTCTT
1603522 TTTTGCTTTTTTAAGTCATTAGATTTAAG
66 TTTTGCTTTTTTAAGTCATTAGATTTAAG
1603551 G
1 G
1603552 GACGCCAGTT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (94 bp):
GAGGTACAGACTGTGTGATGTGTGGCCTTGAATAGAAGCTTCGTTTGATTTAATAATAACTTCTT
TTTTGCTTTTTTAAGTCATTAGATTTAAG
Found at i:1603778 original size:15 final size:14
Alignment explanation
Indices: 1603740--1603767 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1603730 TTAATTCTAA
1603740 AATATAAAAATATT
1 AATATAAAAATATT
1603754 AATATAAAAATATT
1 AATATAAAAATATT
1603768 TTTAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:1604910 original size:22 final size:22
Alignment explanation
Indices: 1604867--1604915 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
1604857 AAAATTCAAG
* * *
1604867 ATTTATTTTAATTAATTTATAT
1 ATTTATTTTAATAAAATAATAT
*
1604889 ATTTATTTTTATAAAATAATAT
1 ATTTATTTTAATAAAATAATAT
1604911 -TTTAT
1 ATTTAT
1604916 AAGTTTGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTATTTTAATAAAATAATAT
Found at i:1612234 original size:2 final size:2
Alignment explanation
Indices: 1612227--1612261 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1612217 GGCAAGAAAA
1612227 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1612262 CTTCTTAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1613105 original size:28 final size:28
Alignment explanation
Indices: 1613031--1613105 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
1613021 TTTTAATATT
*
1613031 AATA-TATATTTATATTATTATTTTTTTA
1 AATATTAT-TTTATATTATTAATTTTTTA
**
1613059 CTTATTATTTTA-ATTTATTAATTTTTTA
1 AATATTATTTTATA-TTATTAATTTTTTA
1613087 AATATT-TTTTATATATATT
1 AATATTATTTTATAT-TATT
1613106 TATAATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
27 7 0.18
28 28 0.74
29 3 0.08
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (28 bp):
AATATTATTTTATATTATTAATTTTTTA
Found at i:1613201 original size:16 final size:15
Alignment explanation
Indices: 1613172--1613216 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
1613162 ATACTTATAT
1613172 ATATAAATTTTAAAA
1 ATATAAATTTTAAAA
*
1613187 TTATAAATATTTAAAA
1 ATATAAAT-TTTAAAA
*
1613203 ATAAAAATTTTAAA
1 ATATAAATTTTAAA
1613217 TATCAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATAAATTTTAAAA
Found at i:1614050 original size:12 final size:12
Alignment explanation
Indices: 1614033--1614073 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1614023 TATAAATCAA
1614033 TTAAATTAAATT
1 TTAAATTAAATT
*
1614045 TTAAATT-TA-T
1 TTAAATTAAATT
1614055 TTAAATTAAATT
1 TTAAATTAAATT
1614067 TTAAATT
1 TTAAATT
1614074 TATTATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 8 0.32
11 2 0.08
12 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAAATTAAATT
Found at i:1614059 original size:22 final size:22
Alignment explanation
Indices: 1614033--1614077 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1614023 TATAAATCAA
1614033 TTAAATTAAATTTTAAATTTAT
1 TTAAATTAAATTTTAAATTTAT
1614055 TTAAATTAAATTTTAAATTTAT
1 TTAAATTAAATTTTAAATTTAT
1614077 T
1 T
1614078 ATTGATTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAATTAAATTTTAAATTTAT
Found at i:1616620 original size:15 final size:16
Alignment explanation
Indices: 1616577--1616621 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
1616567 GTTCAGATCT
*
1616577 TTTTGGGTTTGGGCCA
1 TTTTGGGTTTGGACCA
* *
1616593 TTCTGGATTTGGACC-
1 TTTTGGGTTTGGACCA
1616608 TTTTGGGTTTGGAC
1 TTTTGGGTTTGGAC
1616622 AGCATTGAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.09, C:0.13, G:0.33, T:0.44
Consensus pattern (16 bp):
TTTTGGGTTTGGACCA
Found at i:1618754 original size:23 final size:24
Alignment explanation
Indices: 1618727--1618777 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1618717 TCACTAAAAT
* *
1618727 TTTAAATAATAATA-ATTAATTAA
1 TTTAAATAAAAATATATTAATAAA
*
1618750 TTTAAATAAAAATATTTTAATAAA
1 TTTAAATAAAAATATATTAATAAA
1618774 TTTA
1 TTTA
1618778 TTTTAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAATAAAAATATATTAATAAA
Found at i:1621666 original size:24 final size:25
Alignment explanation
Indices: 1621638--1621701 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
1621628 AATTTGATTT
1621638 ATTTTATAATTATATAATA-TAT-TA
1 ATTTTAT-ATTATATAATATTATGTA
*
1621662 ATTTTATATGTTTAT-ATATTATGTA
1 ATTTTATAT-TATATAATATTATGTA
1621687 ATTTT-TATTATATAA
1 ATTTTATATTATATAA
1621702 AAAATACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 9 0.26
24 18 0.53
25 7 0.21
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
ATTTTATATTATATAATATTATGTA
Found at i:1621767 original size:18 final size:18
Alignment explanation
Indices: 1621746--1621780 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1621736 AAAAATATTT
* *
1621746 ATTTTTTAAAATTTAAAA
1 ATTTATTAAAAATTAAAA
1621764 ATTTATTAAAAATTAAA
1 ATTTATTAAAAATTAAA
1621781 TTTAAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTATTAAAAATTAAAA
Found at i:1621798 original size:36 final size:38
Alignment explanation
Indices: 1621758--1621834 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 38
1621748 TTTTTAAAAT
* * *
1621758 TTAAAAATTTATTA-AAAATTAAATTTAAA-AAA-TAAA
1 TTAAAAATATAATATAAAA-TAAATCTAAATAAATTAAA
1621794 TTAAAAATATAATATAAAATAAATCTAAATAAATTAAA
1 TTAAAAATATAATATAAAATAAATCTAAATAAATTAAA
1621832 TTA
1 TTA
1621835 CTTATTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 21 0.60
37 7 0.20
38 7 0.20
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (38 bp):
TTAAAAATATAATATAAAATAAATCTAAATAAATTAAA
Found at i:1621799 original size:24 final size:24
Alignment explanation
Indices: 1621754--1621833 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
1621744 TTATTTTTTA
**
1621754 AAATTTAAAAATTTATTAAAAATT
1 AAATTTAAAAATAAATTAAAAATT
1621778 AAATTTAAAAAATAAATTAAAAA-T
1 AAATTT-AAAAATAAATTAAAAATT
*
1621802 ATAATAT-AAAATAAATCTAAATAAATT
1 A-AATTTAAAAATAAAT-T-AA-AAATT
1621829 AAATT
1 AAATT
1621834 ACTTATTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
23 9 0.20
24 9 0.20
25 20 0.43
26 6 0.13
27 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATTTAAAAATAAATTAAAAATT
Found at i:1621805 original size:13 final size:13
Alignment explanation
Indices: 1621768--1621805 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1621758 TTAAAAATTT
1621768 ATTAAAAAT-TAA
1 ATTAAAAATATAA
1621780 ATTTAAAAA-ATAA
1 A-TTAAAAATATAA
1621793 ATTAAAAATATAA
1 ATTAAAAATATAA
1621806 TATAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAAATATAA
Found at i:1621811 original size:13 final size:11
Alignment explanation
Indices: 1621758--1621831 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 11
1621748 TTTTTAAAAT
**
1621758 TTAAAAATTTA
1 TTAAAAATAAA
1621769 TTAAAAATTAAA
1 TTAAAAA-TAAA
1621781 TTTAAAAAATAAA
1 -TT-AAAAATAAA
1621794 TTAAAAATATAA
1 TTAAAAATA-AA
1621806 -TATAAAATAAA
1 TTA-AAAATAAA
1621817 TCT--AAATAAA
1 T-TAAAAATAAA
1621827 TTAAA
1 TTAAA
1621832 TTACTTATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
9 1 0.02
10 8 0.15
11 19 0.37
12 12 0.23
13 7 0.13
14 5 0.10
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAAATAAA
Found at i:1631987 original size:5 final size:5
Alignment explanation
Indices: 1631971--1632047 Score: 70
Period size: 5 Copynumber: 15.2 Consensus size: 5
1631961 TTTATTCAAT
*
1631971 TTATA TTTATA TTATA TTA-A TTATTA TTATA -AATA TTTATA TTATA
1 TTATA -TTATA TTATA TTATA TTA-TA TTATA TTATA -TTATA TTATA
* *
1632017 TTATA TTTTAA TTATT TTAT- TTATA TTATA T
1 TTATA TTAT-A TTATA TTATA TTATA TTATA T
1632048 CAAGTATGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
4 11 0.18
5 33 0.55
6 16 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1631990 original size:30 final size:28
Alignment explanation
Indices: 1631956--1632047 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 28
1631946 ATTTGGATCA
1631956 ATTAATTTATTCAATTTATATTTATATTAT
1 ATTAATTTATT--ATTTATATTTATATTAT
1631986 ATTAA-TTATTATTATAAATATTTATATTAT
1 ATTAATTTATTATT-T--ATATTTATATTAT
1632016 ATTATATTTTAATTATTT-TATTTATATTAT
1 ATTA-A-TTT-ATTATTTATATTTATATTAT
1632046 AT
1 AT
1632048 CAAGTATGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
27 3 0.05
28 1 0.02
29 5 0.09
30 36 0.65
31 1 0.02
33 3 0.05
34 6 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTAATTTATTATTTATATTTATATTAT
Found at i:1641332 original size:24 final size:23
Alignment explanation
Indices: 1641315--1641363 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1641305 TTTATAATTT
1641315 TTTTAAA-TATAATATTTAATAAA
1 TTTTAAATTATAATATTT-ATAAA
*
1641338 TTTTAAATTTTAATATTTATGAAA
1 TTTTAAATTATAATATTTAT-AAA
1641362 TT
1 TT
1641364 ATAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTAAATTATAATATTTATAAA
Found at i:1642174 original size:2 final size:2
Alignment explanation
Indices: 1642167--1642198 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1642157 AATAAAAATA
1642167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1642199 CACCTTCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1642974 original size:23 final size:22
Alignment explanation
Indices: 1642932--1642974 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1642922 TTATATTACG
*
1642932 ATTAATTAAATTAATATTATAA
1 ATTAAATAAATTAATATTATAA
*
1642954 ATTAAATAATATTAATTTTAT
1 ATTAAATAA-ATTAATATTAT
1642975 TAAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAAATAAATTAATATTATAA
Found at i:1642995 original size:18 final size:21
Alignment explanation
Indices: 1642957--1642995 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1642947 ATTATAAATT
1642957 AAATAATATTAATTTTATTAA
1 AAATAATATTAATTTTATTAA
1642978 AAAT-ATATT-ATTTT-TTAA
1 AAATAATATTAATTTTATTAA
1642996 TTTTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 5 0.28
21 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAATATTAATTTTATTAA
Found at i:1643004 original size:28 final size:24
Alignment explanation
Indices: 1642965--1643019 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 24
1642955 TTAAATAATA
1642965 TTAATTTTATTAAAAATATATTATTTT
1 TTAATTTTATT---AATATATTATTTT
1642992 TTAATTTTTATTAATATATTATTTT
1 TTAA-TTTTATTAATATATTATTTT
1643017 TTA
1 TTA
1643020 TTGAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 16 0.59
27 4 0.15
28 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTAATTTTATTAATATATTATTTT
Found at i:1643027 original size:23 final size:25
Alignment explanation
Indices: 1642979--1643028 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1642969 TTTTATTAAA
**
1642979 AATATATTATTTTTTAATTTTTATT
1 AATATATTATTTTTTAATTTGAATT
1643004 AATATATTATTTTTT-A-TTGAATT
1 AATATATTATTTTTTAATTTGAATT
1643027 AA
1 AA
1643029 AAAGTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
24 1 0.04
25 15 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
AATATATTATTTTTTAATTTGAATT
Found at i:1643168 original size:22 final size:20
Alignment explanation
Indices: 1643132--1643190 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 20
1643122 TAAAATTATT
1643132 AAATATAAAAAATTTAA-AAA
1 AAATAT-AAAAATTTAACAAA
1643152 ATAATAATAAAATATTTAACAAA
1 A-AAT-ATAAAA-ATTTAACAAA
*
1643175 AACTATAAAAATTTAA
1 AAATATAAAAATTTAA
1643191 TTAACATCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 7 0.21
21 13 0.38
22 10 0.29
23 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATATAAAAATTTAACAAA
Found at i:1644208 original size:47 final size:47
Alignment explanation
Indices: 1644152--1644245 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1644142 AATATTGAAT
1644152 TTCAATATTATAAATAAATAATTTAAATAATAACTAAATTTAGAGAC
1 TTCAATATTATAAATAAATAATTTAAATAATAACTAAATTTAGAGAC
1644199 TTCAATATTATAAATAAATAATTTAAATAATAACTAAATTTAGAGAC
1 TTCAATATTATAAATAAATAATTTAAATAATAACTAAATTTAGAGAC
1644246 AATTTAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (47 bp):
TTCAATATTATAAATAAATAATTTAAATAATAACTAAATTTAGAGAC
Found at i:1644471 original size:17 final size:17
Alignment explanation
Indices: 1644449--1644481 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1644439 GTATTTATAA
1644449 TAATTTGTT-AAATTTTT
1 TAATTT-TTAAAATTTTT
1644466 TAATTTTTAAAATTTT
1 TAATTTTTAAAATTTT
1644482 ATATATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TAATTTTTAAAATTTTT
Found at i:1652054 original size:2 final size:2
Alignment explanation
Indices: 1652047--1652092 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1652037 TGATACTACA
* *
1652047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1652089 AT AT
1 AT AT
1652093 GTTATATTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1658498 original size:18 final size:20
Alignment explanation
Indices: 1658463--1658499 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1658453 TATACATTAC
1658463 TAATATATAAATTTATATAT
1 TAATATATAAATTTATATAT
1658483 TAATA-ATAAA-TTATATA
1 TAATATATAAATTTATATA
1658500 ATATCACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATATAAATTTATATAT
Found at i:1662357 original size:10 final size:9
Alignment explanation
Indices: 1662333--1662392 Score: 60
Period size: 8 Copynumber: 7.3 Consensus size: 9
1662323 TAATTTCATA
1662333 TAAAT-TAT
1 TAAATATAT
1662341 TAAATATAT
1 TAAATATAT
1662350 TAAA-ATA-
1 TAAATATAT
1662357 TAAA-ATA-
1 TAAATATAT
*
1662364 TAAATATAA
1 TAAATATAT
1662373 TAAATATAT
1 TAAATATAT
*
1662382 T-ATTATAT
1 TAAATATAT
1662390 TAA
1 TAA
1662393 CGTAGTAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
7 11 0.24
8 18 0.39
9 17 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAATATAT
Found at i:1663069 original size:13 final size:13
Alignment explanation
Indices: 1663053--1663078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1663043 AAAATAAATT
1663053 TAAATAAATATAA
1 TAAATAAATATAA
1663066 TAAATAAATATAA
1 TAAATAAATATAA
1663079 GAATTTTTCA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:1663071 original size:23 final size:26
Alignment explanation
Indices: 1663021--1663074 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 26
1663011 AATAAATTAA
1663021 AAATTTAAATATAATGATTTAAAAAAT
1 AAATTTAAATATAATGA-TTAAAAAAT
*
1663048 AAATTTAAATA-AAT-A-TAATAAAT
1 AAATTTAAATATAATGATTAAAAAAT
1663071 AAAT
1 AAAT
1663075 ATAAGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 11 0.42
25 1 0.04
26 3 0.12
27 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AAATTTAAATATAATGATTAAAAAAT
Found at i:1663074 original size:27 final size:29
Alignment explanation
Indices: 1663011--1663075 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 29
1663001 ATAAAATTAA
*
1663011 AATAAATTAA-AAATTTAAATATAATGAT
1 AATAAATAAATAAATTTAAATATAATGAT
*
1663039 -TTAAA-AAATAAATTTAAATA-AAT-AT
1 AATAAATAAATAAATTTAAATATAATGAT
1663064 AATAAATAAATA
1 AATAAATAAATA
1663076 TAAGAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (29 bp):
AATAAATAAATAAATTTAAATATAATGAT
Found at i:1665153 original size:22 final size:23
Alignment explanation
Indices: 1665116--1665158 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1665106 TGTATAGTTG
*
1665116 TTTTTTATTTATAAATGGTAGAT
1 TTTTTTATTCATAAATGGTAGAT
1665139 TTTTTTATTCA-AAATGGTAG
1 TTTTTTATTCATAAATGGTAG
1665159 GACTTAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.53
Consensus pattern (23 bp):
TTTTTTATTCATAAATGGTAGAT
Found at i:1665287 original size:17 final size:18
Alignment explanation
Indices: 1665252--1665290 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
1665242 AACCTACCTT
1665252 ATATAAAACAAATTTAAA
1 ATATAAAACAAATTTAAA
1665270 ATATAAAA-ATAA-TTAAA
1 ATATAAAACA-AATTTAAA
1665287 ATAT
1 ATAT
1665291 TATAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATATAAAACAAATTTAAA
Found at i:1665641 original size:21 final size:23
Alignment explanation
Indices: 1665617--1665665 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
1665607 TGACATTTTC
*
1665617 TTATATTTA-ATAATTTA-TGTA
1 TTATATTTATATAATTTATTATA
*
1665638 TTATATTTATATATTTTATTATA
1 TTATATTTATATAATTTATTATA
1665661 TTATA
1 TTATA
1665666 ATCATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 7 0.29
23 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATATTTATATAATTTATTATA
Found at i:1665672 original size:21 final size:19
Alignment explanation
Indices: 1665611--1665674 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 19
1665601 TCATCTTGAC
*
1665611 ATTTTCTTATATTTAATA-
1 ATTTTATTATATTTAATAT
1665629 ATTTATGTATTATATTT-ATAT
1 A-TT-T-TATTATATTTAATAT
1665650 ATTTTATTATATTATAATCAT
1 ATTTTATTATATT-TAAT-AT
1665671 ATTT
1 ATTT
1665675 AAAATATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
18 10 0.26
19 4 0.11
20 8 0.21
21 16 0.42
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTTATTATATTTAATAT
Found at i:1666576 original size:21 final size:22
Alignment explanation
Indices: 1666541--1666585 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1666531 AATTATATAA
1666541 AATTAAAATATTTTA-TTTGTC
1 AATTAAAATATTTTACTTTGTC
*
1666562 AATTAAAATCA-TTTACTTTTTC
1 AATTAAAAT-ATTTTACTTTGTC
1666584 AA
1 AA
1666586 AATTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTAAAATATTTTACTTTGTC
Found at i:1668118 original size:31 final size:30
Alignment explanation
Indices: 1668083--1668162 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
1668073 AGTGGAATTG
1668083 AAAATTATTAATAATTATTTTAAAAAAATAA
1 AAAATTATTAATAATTATTTT-AAAAAATAA
* ** * *
1668114 AAAATTATTTATAAAAATTTTAATAACTAA
1 AAAATTATTAATAATTATTTTAAAAAATAA
1668144 AAAATTATCTTAATAATTA
1 AAAATTA--TTAATAATTA
1668163 CCTTTCAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 14 0.36
31 18 0.46
32 7 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATTATTAATAATTATTTTAAAAAATAA
Found at i:1668228 original size:33 final size:32
Alignment explanation
Indices: 1668191--1668289 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 32
1668181 CTAAAATTTT
*
1668191 TTAAAAATGATATTTGTCTTTCAAATTATTAAA
1 TTAAAAATGATATTTAT-TTTCAAATTATTAAA
* *
1668224 TTAAAAATGATATTTATATCCAAAATTATTAAA
1 TTAAAAATGATATTTATTTTC-AAATTATTAAA
1668257 TTAAAAATGATATTTATTTTCAAATTTATTAAA
1 TTAAAAATGATATTTATTTTCAAA-TTATTAAA
1668290 AATTTTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
32 5 0.08
33 54 0.92
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (32 bp):
TTAAAAATGATATTTATTTTCAAATTATTAAA
Found at i:1671507 original size:28 final size:27
Alignment explanation
Indices: 1671475--1671542 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
1671465 TAACTCATTG
1671475 AAAAAAAAATTAAATATAATTACTTTA-AC
1 AAAAAAAAATTAAA-A-AATTAC-TTACAC
*
1671504 AAAAATAAAATTAAAAATTTACTTACAC
1 AAAAA-AAAATTAAAAAATTACTTACAC
*
1671532 AAATAAAAATT
1 AAAAAAAAATT
1671543 TATCCTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.26
28 11 0.31
29 6 0.17
30 9 0.26
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAAAAAAATTAAAAAATTACTTACAC
Found at i:1672006 original size:3 final size:3
Alignment explanation
Indices: 1671998--1672024 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1671988 GAAGATGTTG
1671998 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1672025 GTTGTTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1672542 original size:21 final size:21
Alignment explanation
Indices: 1672514--1672561 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1672504 TTTATTAACA
*
1672514 AAATATTAAAATTTTAAT-TT
1 AAATATTAAAATTTAAATATT
1672534 AAATAATTAAAATTTAAATATT
1 AAAT-ATTAAAATTTAAATATT
1672556 -AATATT
1 AAATATT
1672562 TTTAATTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
21 16 0.64
22 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAAAATTTAAATATT
Found at i:1672562 original size:14 final size:15
Alignment explanation
Indices: 1672529--1672562 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1672519 TTAAAATTTT
1672529 AATTTAAATAATTAA
1 AATTTAAATAATTAA
1672544 AATTTAAAT-ATTAA
1 AATTTAAATAATTAA
*
1672558 TATTT
1 AATTT
1672563 TTAATTATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAAATAATTAA
Found at i:1673333 original size:21 final size:21
Alignment explanation
Indices: 1673304--1673348 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1673294 TTTATTAAAA
1673304 ATAAATTTTAT-ATTAAAATTT
1 ATAAATTTTATAATT-AAATTT
*
1673325 ATAATTTTTATAATTAAATTT
1 ATAAATTTTATAATTAAATTT
1673346 ATA
1 ATA
1673349 TAAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAATTTTATAATTAAATTT
Found at i:1673831 original size:16 final size:16
Alignment explanation
Indices: 1673810--1673844 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1673800 ATCCTTTTAT
1673810 ATACATACATACACAC
1 ATACATACATACACAC
* *
1673826 ATACATATATATACAC
1 ATACATACATACACAC
1673842 ATA
1 ATA
1673845 TATTGCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
ATACATACATACACAC
Found at i:1673949 original size:2 final size:2
Alignment explanation
Indices: 1673942--1673976 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1673932 AAAGGAATTT
1673942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1673977 CAAACATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1679541 original size:50 final size:50
Alignment explanation
Indices: 1679468--1679575 Score: 136
Period size: 50 Copynumber: 2.2 Consensus size: 50
1679458 ATATTTAAAT
*
1679468 TATT-ATTTAATAATAAATATTTTTA-TTTAAAT-TTAATTATAAAATATTAA
1 TATTAATTTAAAAATAAATATTTTTATTTTAAATATT--TTAT-AAATATTAA
1679518 TATTAATTTAAAAATAAAT-TTTTTATTTTTAAATATTTTATAAATATTAA
1 TATTAATTTAAAAATAAATATTTTTA-TTTTAAATATTTTATAAATATTAA
1679568 T-TTAATTT
1 TATTAATTT
1679576 TTTTTAATTG
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
49 7 0.13
50 20 0.38
51 17 0.32
52 7 0.13
53 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (50 bp):
TATTAATTTAAAAATAAATATTTTTATTTTAAATATTTTATAAATATTAA
Found at i:1680835 original size:2 final size:2
Alignment explanation
Indices: 1680828--1680853 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1680818 ATTTTGAGTT
1680828 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1680854 ACTCATTTCC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1692831 original size:36 final size:39
Alignment explanation
Indices: 1692756--1692832 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 39
1692746 ACTCAAAATA
* *
1692756 AATTTTACATATTAATATAAATATATTATATATTTTATT
1 AATTTTACATATTAATATAAATATATTATATAATATATT
*
1692795 AATTTTA-ATTATTTATA-AAATAT-TTA-ATAATATATT
1 AATTTTACA-TATTAATATAAATATATTATATAATATATT
1692831 AA
1 AA
1692833 AAATAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 10 0.29
37 3 0.09
38 7 0.21
39 14 0.41
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (39 bp):
AATTTTACATATTAATATAAATATATTATATAATATATT
Found at i:1693805 original size:3 final size:3
Alignment explanation
Indices: 1693790--1693822 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1693780 ATGGAAATAA
*
1693790 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1693823 TGTGAAGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1694625 original size:18 final size:17
Alignment explanation
Indices: 1694602--1694640 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1694592 TGCATTAAAA
1694602 ATTATGA-ATAATAATAAT
1 ATTATGATA-AATAAT-AT
1694620 ATTATGATAAATAATAT
1 ATTATGATAAATAATAT
1694637 ATTA
1 ATTA
1694641 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 13 0.65
19 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
ATTATGATAAATAATAT
Found at i:1695702 original size:11 final size:12
Alignment explanation
Indices: 1695679--1695728 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
1695669 CCTGCCTTAA
1695679 TAATTTCTTTTAT
1 TAATTT-TTTTAT
1695692 TAA-TTTTTTA-
1 TAATTTTTTTAT
*
1695702 TAATTTTTTTAA
1 TAATTTTTTTAT
1695714 TAATTTTTTTAT
1 TAATTTTTTTAT
1695726 TAA
1 TAA
1695729 AAAAATTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 3 0.09
11 12 0.35
12 16 0.47
13 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTTTTTTAT
Found at i:1695725 original size:23 final size:23
Alignment explanation
Indices: 1695678--1695722 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1695668 ACCTGCCTTA
*
1695678 ATAATTTCTTTTATTAATTTTTT
1 ATAATTTCTTTTAATAATTTTTT
1695701 ATAATTT-TTTTAATAATTTTTT
1 ATAATTTCTTTTAATAATTTTTT
1695723 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
ATAATTTCTTTTAATAATTTTTT
Found at i:1700906 original size:27 final size:27
Alignment explanation
Indices: 1700849--1700906 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1700839 ATCAATTTAT
* *
1700849 AAAAATATTAAAATTTTAATTATAAAT
1 AAAAATATTAAAATTTTAAGTATAAAC
* *
1700876 AAAACTATTAAAA-TTTAAGTATGGAAC
1 AAAAATATTAAAATTTTAAGTAT-AAAC
1700903 AAAA
1 AAAA
1700907 GTCATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (27 bp):
AAAAATATTAAAATTTTAAGTATAAAC
Found at i:1701027 original size:17 final size:17
Alignment explanation
Indices: 1700993--1701040 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1700983 TTTTAGCATT
1700993 AAATT-TATATTA-TAA
1 AAATTATATATTATTAA
1701008 AAATTATATATTATTAA
1 AAATTATATATTATTAA
* *
1701025 AAATTAAAAATTATTA
1 AAATTATATATTATTA
1701041 TATTATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 5 0.17
16 7 0.24
17 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTATATATTATTAA
Found at i:1701404 original size:44 final size:45
Alignment explanation
Indices: 1701316--1701404 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 45
1701306 CCAAACATAT
* *
1701316 CTTTAATTAATTAAAAACTATTACTAACCAATGTCATTAGAACAC
1 CTTTAATTAATTAAAAACTATTACTAACCAATGTCATCAAAACAC
*
1701361 CTTTAATTAATTAAAAAC-ATTACTAACCAATGTTATCAAAACAC
1 CTTTAATTAATTAAAAACTATTACTAACCAATGTCATCAAAACAC
1701405 AATCTAAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 23 0.56
45 18 0.44
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (45 bp):
CTTTAATTAATTAAAAACTATTACTAACCAATGTCATCAAAACAC
Found at i:1701663 original size:2 final size:2
Alignment explanation
Indices: 1701656--1701687 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1701646 TTAAATATTG
*
1701656 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1701688 CCTGAAATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1711063 original size:2 final size:2
Alignment explanation
Indices: 1711046--1711086 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1711036 CACTCACCAT
* * *
1711046 TA TA TA TG TA TG TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1711087 TTATCGATCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1711375 original size:2 final size:2
Alignment explanation
Indices: 1711368--1711427 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1711358 GCAGTCGTCG
* **
1711368 AT AT AT AT AT AT AT GT AT GC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1711410 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1711428 TCCTTTTGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1711575 original size:2 final size:2
Alignment explanation
Indices: 1711568--1711595 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1711558 GAAATTATGA
1711568 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1711596 GATGCTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1713281 original size:2 final size:2
Alignment explanation
Indices: 1713274--1713299 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1713264 AATGAATTGT
1713274 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1713300 ATTAAATATT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1713368 original size:28 final size:27
Alignment explanation
Indices: 1713285--1713375 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 27
1713275 ATATATATAT
*
1713285 ATATATATATATATAATTAAATATTTGA
1 ATATATATATTTATAATTAAATA-TTGA
* *
1713313 ATA-ATAACTATGTTCATGAATGATATATTGA
1 ATATAT-A-TAT-TT-AT-AATTAAATATTGA
*
1713344 ATATATATATTTGATAATTACATATTGA
1 ATATATATATTT-ATAATTAAATATTGA
1713372 ATAT
1 ATAT
1713376 TAATTTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.04
28 19 0.37
29 7 0.14
30 4 0.08
31 10 0.20
32 9 0.18
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (27 bp):
ATATATATATTTATAATTAAATATTGA
Found at i:1713719 original size:16 final size:16
Alignment explanation
Indices: 1713672--1713719 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1713662 TTGTTCTTTT
*
1713672 TTATATTTTTTAA-ATC
1 TTAT-TTTTTTAATATA
1713688 TTATTTTTAATTAATATA
1 TTATTTTT--TTAATATA
1713706 TTATTTTTTTAATA
1 TTATTTTTTTAATA
1713720 CAGACTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 10 0.36
17 4 0.14
18 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTTTTTAATATA
Found at i:1715582 original size:3 final size:3
Alignment explanation
Indices: 1715574--1715605 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1715564 ATATATAAAA
1715574 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1715606 CATCAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1715939 original size:6 final size:6
Alignment explanation
Indices: 1715928--1715958 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1715918 TTATGAAATC
1715928 TATTTT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
1715959 TTCCTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:1717947 original size:2 final size:2
Alignment explanation
Indices: 1717940--1717964 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1717930 TTTTACATTT
1717940 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1717965 TAATTAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1720240 original size:2 final size:2
Alignment explanation
Indices: 1720233--1720268 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1720223 TTGTTTTTCA
1720233 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1720269 ACACACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1723323 original size:2 final size:2
Alignment explanation
Indices: 1723316--1723356 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1723306 TTTGCATTAT
1723316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1723357 TCTTCCACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1723406 original size:7 final size:7
Alignment explanation
Indices: 1723393--1723439 Score: 76
Period size: 7 Copynumber: 6.6 Consensus size: 7
1723383 AGCAACAGGA
1723393 AATTTTT
1 AATTTTT
*
1723400 TATTTTT
1 AATTTTT
1723407 AATTTTT
1 AATTTTT
1723414 AATTTTT
1 AATTTTT
1723421 AATTTTT
1 AATTTTT
1723428 AATTTTTT
1 AA-TTTTT
1723436 AATT
1 AATT
1723440 AGGAGAGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 30 0.81
8 7 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
AATTTTT
Found at i:1725276 original size:10 final size:10
Alignment explanation
Indices: 1725255--1725304 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
1725245 ATATGTATCC
1725255 ATATTTT-T-
1 ATATTTTATA
1725263 ATATTTTATA
1 ATATTTTATA
*
1725273 ATATTTTATT
1 ATATTTTATA
*
1725283 ATTTTTTATA
1 ATATTTTATA
1725293 AT-TATTTATA
1 ATAT-TTTATA
1725303 AT
1 AT
1725305 TTATTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 7 0.19
9 2 0.06
10 27 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATATTTTATA
Found at i:1725284 original size:20 final size:21
Alignment explanation
Indices: 1725261--1725299 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1725251 ATCCATATTT
1725261 TTATATTTTATAA-TATTTTA
1 TTATATTTTATAATTATTTTA
*
1725281 TTATTTTTTATAATTATTT
1 TTATATTTTATAATTATTT
1725300 ATAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATATTTTATAATTATTTTA
Found at i:1725300 original size:20 final size:18
Alignment explanation
Indices: 1725255--1725331 Score: 59
Period size: 20 Copynumber: 4.1 Consensus size: 18
1725245 ATATGTATCC
*
1725255 ATATTT-TTATATTTTATA
1 ATATTTATTATTTTTTA-A
1725273 ATATTTTATTATTTTTTATA
1 ATA-TTTATTATTTTTTA-A
* *
1725293 ATTATTTATAATTTATTAA
1 A-TATTTATTATTTTTTAA
*
1725312 AAATTTA-TATATTTTTAA
1 ATATTTATTAT-TTTTTAA
1725330 AT
1 AT
1725332 TATTATCTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 2 0.04
18 15 0.31
19 5 0.10
20 24 0.50
21 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTATTATTTTTTAA
Found at i:1725319 original size:18 final size:18
Alignment explanation
Indices: 1725296--1725330 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1725286 TTTTATAATT
1725296 ATTTATA-ATTTATTAAAA
1 ATTTATATATTT-TTAAAA
1725314 ATTTATATATTTTTAAA
1 ATTTATATATTTTTAAA
1725331 TTATTATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTATATATTTTTAAAA
Found at i:1725333 original size:37 final size:37
Alignment explanation
Indices: 1725260--1725335 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
1725250 TATCCATATT
* * *
1725260 TTTATATTTTATAATATTTTATTATTTTTTATAATTA
1 TTTATAATTTATAAAAATTTATTATTTTTTATAATTA
1725297 TTTATAATTTATTAAAAATTTA-TATATTTTTA-AATTA
1 TTTATAATTTA-TAAAAATTTATTAT-TTTTTATAATTA
1725334 TT
1 TT
1725336 ATCTCATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (37 bp):
TTTATAATTTATAAAAATTTATTATTTTTTATAATTA
Found at i:1725337 original size:18 final size:18
Alignment explanation
Indices: 1725262--1725337 Score: 52
Period size: 19 Copynumber: 4.1 Consensus size: 18
1725252 TCCATATTTT
1725262 TATATTTTATAATATT-TTA
1 TATATTTT-TAA-ATTATTA
1725281 T-TATTTTTTATAATTATT-
1 TATA-TTTTTA-AATTATTA
*
1725299 TATAATTTATTAAA-AATTTA
1 TAT-ATTT-TTAAATTA-TTA
1725319 TATATTTTTAAATTATTA
1 TATATTTTTAAATTATTA
1725337 T
1 T
1725338 CTCATATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 19
0.69 0.03 0.28
Matches are distributed among these distances:
18 18 0.39
19 21 0.46
20 7 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTTAAATTATTA
Found at i:1725756 original size:21 final size:23
Alignment explanation
Indices: 1725730--1725773 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1725720 AAATATATTA
1725730 ATAAATTA-AAATTTA-TATAAT
1 ATAAATTATAAATTTATTATAAT
*
1725751 ATAAATTATTAATTTATTATAAT
1 ATAAATTATAAATTTATTATAAT
1725774 TTATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAATTATAAATTTATTATAAT
Found at i:1725775 original size:32 final size:33
Alignment explanation
Indices: 1725711--1725781 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 33
1725701 CGTGAAATAA
1725711 ATATAATATAAATATATTAATAAATTAAAATTT
1 ATATAATATAAATATATTAATAAATTAAAATTT
** *
1725744 ATATAATATAAAT-TATTAATTTATTATAATTT
1 ATATAATATAAATATATTAATAAATTAAAATTT
1725776 ATATAA
1 ATATAA
1725782 AAATTGTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAAATATATTAATAAATTAAAATTT
Found at i:1725944 original size:2 final size:2
Alignment explanation
Indices: 1725937--1725964 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1725927 TACATTCTAG
1725937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1725965 CCCACTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1728325 original size:24 final size:24
Alignment explanation
Indices: 1728293--1728340 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1728283 AGACACAGCC
1728293 TTGCAAGAAACGACACATCAGTGA
1 TTGCAAGAAACGACACATCAGTGA
*
1728317 TTGCAAGAAACGGCACATCAGTGA
1 TTGCAAGAAACGACACATCAGTGA
1728341 ATCTGCTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.17
Consensus pattern (24 bp):
TTGCAAGAAACGACACATCAGTGA
Found at i:1738316 original size:12 final size:13
Alignment explanation
Indices: 1738289--1738318 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1738279 TATTTAAAGA
1738289 TTAAATAATATTT
1 TTAAATAATATTT
1738302 TTAAATAAT-TTT
1 TTAAATAATATTT
1738314 TTAAA
1 TTAAA
1738319 AAAGTGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAAATAATATTT
Found at i:1747111 original size:18 final size:16
Alignment explanation
Indices: 1747079--1747113 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1747069 ATTTTAAAAT
1747079 TTTATATATTAAATAA
1 TTTATATATTAAATAA
1747095 TTTATATCATATAAATAA
1 TTTATAT-AT-TAAATAA
1747113 T
1 T
1747114 AAATATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 2 0.12
18 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTATATATTAAATAA
Found at i:1747147 original size:14 final size:13
Alignment explanation
Indices: 1747103--1747157 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 13
1747093 AATTTATATC
*
1747103 ATATAAATAATAA
1 ATATAAATATTAA
*
1747116 ATATATAATATTTTA
1 ATATA-AATA-TTAA
1747131 ATATAAATATTAA
1 ATATAAATATTAA
*
1747144 A-ATATATATTAA
1 ATATAAATATTAA
1747156 AT
1 AT
1747158 TATTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 11 0.31
13 9 0.26
14 8 0.23
15 7 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAAATATTAA
Found at i:1748355 original size:16 final size:17
Alignment explanation
Indices: 1748323--1748355 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1748313 GCTTAAATTT
1748323 ATATTTTATAATTAAAA
1 ATATTTTATAATTAAAA
*
1748340 ATATTTT-TATTTAAAA
1 ATATTTTATAATTAAAA
1748356 TTAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTTTATAATTAAAA
Found at i:1748814 original size:15 final size:14
Alignment explanation
Indices: 1748796--1748831 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
1748786 TTTAGAAATA
1748796 TTATATTTATATTTT
1 TTATATTT-TATTTT
1748811 TTATTATTTTATTTT
1 TTA-TATTTTATTTT
1748826 TTATAT
1 TTATAT
1748832 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 12 0.60
16 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATATTTTATTTT
Found at i:1748848 original size:15 final size:16
Alignment explanation
Indices: 1748825--1748904 Score: 60
Period size: 16 Copynumber: 5.0 Consensus size: 16
1748815 TATTTTATTT
1748825 TTTATATAAATTTTAA
1 TTTATATAAATTTTAA
* *
1748841 TTTA-AT-AATAATTCA
1 TTTATATAAAT-TTTAA
1748856 TATTATATAAATTTTAA
1 T-TTATATAAATTTTAA
*
1748873 TTTA-ATAATAATTT-A
1 TTTATATAA-ATTTTAA
*
1748888 TATTATATAAATATTAA
1 T-TTATATAAATTTTAA
1748905 AATATTATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
14 3 0.06
15 12 0.24
16 20 0.41
17 11 0.22
18 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTATATAAATTTTAA
Found at i:1748862 original size:32 final size:32
Alignment explanation
Indices: 1748826--1748904 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
1748816 ATTTTATTTT
1748826 TTATATAAATTTTAATTTAATAATAATTCATA
1 TTATATAAATTTTAATTTAATAATAATTCATA
*
1748858 TTATATAAATTTTAATTTAATAATAATTTATA
1 TTATATAAATTTTAATTTAATAATAATTCATA
*
1748890 TTATATAAATATTAA
1 TTATATAAATTTTAA
1748905 AATATTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TTATATAAATTTTAATTTAATAATAATTCATA
Done.