Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 5 of 143
Found at i:1600556 original size:7 final size:7
Alignment explanation
Indices: 1600543--1600573 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1600533 CCCTACTCAG
1600543 TATTCAC
1 TATTCAC
*
1600550 GATTCAC
1 TATTCAC
1600557 TATTCAC
1 TATTCAC
1600564 TATTCAC
1 TATTCAC
1600571 TAT
1 TAT
1600574 CTGTCTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.42
Consensus pattern (7 bp):
TATTCAC
Found at i:1602243 original size:31 final size:29
Alignment explanation
Indices: 1602175--1602244 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
1602165 AATTTATATC
* *
1602175 TTTATTATTTTTTAAAAATTAAATTAAAT
1 TTTATTATTTTTGAAAAATTAAAGTAAAT
* *
1602204 TTTAATTATTTTTGAAGAAGTTAAAGTATACT
1 TTT-ATTATTTTTGAA-AAATTAAAGTA-AAT
1602236 TTTATTATT
1 TTTATTATT
1602245 AATTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 15 0.44
32 5 0.15
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (29 bp):
TTTATTATTTTTGAAAAATTAAAGTAAAT
Found at i:1602396 original size:15 final size:16
Alignment explanation
Indices: 1602366--1602400 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1602356 TGATTATAGT
*
1602366 TTAAATTTATAAAAAA
1 TTAAATTGATAAAAAA
1602382 TTAAATTGA-AAAAAA
1 TTAAATTGATAAAAAA
1602397 TTAA
1 TTAA
1602401 TGGTTACCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TTAAATTGATAAAAAA
Found at i:1602610 original size:3 final size:3
Alignment explanation
Indices: 1602602--1602629 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1602592 GAATTTACCC
1602602 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1602630 ATGGGTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1605138 original size:13 final size:13
Alignment explanation
Indices: 1605115--1605139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1605105 CATTTATAAA
1605115 TTTTATTTATTAT
1 TTTTATTTATTAT
1605128 TTTTATTTATTA
1 TTTTATTTATTA
1605140 AAAAATATTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTATTAT
Found at i:1611436 original size:2 final size:2
Alignment explanation
Indices: 1611429--1611459 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1611419 ATTGCCACTG
1611429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1611460 ACAAAACTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1611572 original size:3 final size:3
Alignment explanation
Indices: 1611564--1611596 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1611554 GCAACATGCT
1611564 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG- TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
1611597 CTCCCTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.30, G:0.33, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:1622627 original size:39 final size:39
Alignment explanation
Indices: 1622573--1622651 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1622563 GCCAAAAAAG
*
1622573 AAGAATGTGACGATTTCATATATGGCCTGAAAGAAACAA
1 AAGAATGTAACGATTTCATATATGGCCTGAAAGAAACAA
*
1622612 AAGAATGTAATGATTTCATATATGGCCTGAAAGAAACAA
1 AAGAATGTAACGATTTCATATATGGCCTGAAAGAAACAA
1622651 A
1 A
1622652 TGTTGTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (39 bp):
AAGAATGTAACGATTTCATATATGGCCTGAAAGAAACAA
Found at i:1626656 original size:18 final size:19
Alignment explanation
Indices: 1626630--1626666 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1626620 TTTCATTATA
*
1626630 TAACAAAATAGTCAAATAT
1 TAACAAAATAATCAAATAT
1626649 TAAC-AAATAATCAAATAT
1 TAACAAAATAATCAAATAT
1626667 CATTTTGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (19 bp):
TAACAAAATAATCAAATAT
Found at i:1627111 original size:30 final size:31
Alignment explanation
Indices: 1627053--1627113 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1627043 AAATTGAATA
*
1627053 AAAAATCAAAATGTCATGTATAAAATTGCAC
1 AAAAATCAAAATGTCATATATAAAATTGCAC
* *
1627084 AAAAATTAAAAT-TCATATATAACATTGCAC
1 AAAAATCAAAATGTCATATATAAAATTGCAC
1627114 TTCGAATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (31 bp):
AAAAATCAAAATGTCATATATAAAATTGCAC
Found at i:1627902 original size:2 final size:2
Alignment explanation
Indices: 1627895--1627923 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1627885 GAACCTTATG
1627895 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 T
1627924 TAAAGTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1633759 original size:3 final size:3
Alignment explanation
Indices: 1633751--1633777 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1633741 TTGATATTGC
1633751 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1633778 ATTTTTTGAA
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):
TTA
Found at i:1634146 original size:14 final size:16
Alignment explanation
Indices: 1634113--1634149 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1634103 AATTATTAAT
1634113 TAATTTTATATAAATA
1 TAATTTTATATAAATA
*
1634129 TAATTTTA-AT-ATTA
1 TAATTTTATATAAATA
1634143 TAATTTT
1 TAATTTT
1634150 CTTCTACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 10 0.50
15 2 0.10
16 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTTTATATAAATA
Found at i:1641141 original size:23 final size:20
Alignment explanation
Indices: 1641100--1641141 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
1641090 CTATATATAA
1641100 ATTTTCAAAAATAAAAATAT
1 ATTTTCAAAAATAAAAATAT
1641120 ATTTTCTAAATAATTAAAAATA
1 ATTTTC-AAA-AA-TAAAAATA
1641142 AAAGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 3 0.16
22 2 0.11
23 8 0.42
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTTCAAAAATAAAAATAT
Found at i:1642738 original size:30 final size:30
Alignment explanation
Indices: 1642698--1642759 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1642688 TGAGTTAATT
* *
1642698 TATAATAATTAGATC-AAATCAAAATTTCATG
1 TATAATAATTACA-CAAAATC-AAAGTTCATG
1642729 TATAA-AATTACACAAAATCAAAGTTCATG
1 TATAATAATTACACAAAATCAAAGTTCATG
1642758 TA
1 TA
1642760 CACAATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 12 0.43
30 11 0.39
31 5 0.18
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.32
Consensus pattern (30 bp):
TATAATAATTACACAAAATCAAAGTTCATG
Found at i:1642930 original size:16 final size:16
Alignment explanation
Indices: 1642909--1642949 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1642899 TCAATCTTTT
1642909 TTATAACAACAATTCG
1 TTATAACAACAATTCG
* * *
1642925 TTATAATAACATTTTG
1 TTATAACAACAATTCG
1642941 TTATAACAA
1 TTATAACAA
1642950 TTAATTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (16 bp):
TTATAACAACAATTCG
Found at i:1646394 original size:26 final size:24
Alignment explanation
Indices: 1646348--1646399 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
1646338 TTTTAAATCT
* *
1646348 TTAAAAAAAAACCTATTTAATCAA
1 TTAAAAAAAAACATATATAATCAA
*
1646372 TTAAAAAAAACGACATATATAATTAA
1 TTAAAAAAAA--ACATATATAATCAA
1646398 TT
1 TT
1646400 TAGTTGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
26 13 0.57
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (24 bp):
TTAAAAAAAAACATATATAATCAA
Found at i:1652172 original size:23 final size:24
Alignment explanation
Indices: 1652131--1652178 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1652121 CTTGGATGAA
1652131 CTTTAGCCTTAATACATTTAATCT
1 CTTTAGCCTTAATACATTTAATCT
**
1652155 CTTTAG-CTTAATGTATTTAATCT
1 CTTTAGCCTTAATACATTTAATCT
1652178 C
1 C
1652179 ATCCTTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (24 bp):
CTTTAGCCTTAATACATTTAATCT
Found at i:1653551 original size:18 final size:19
Alignment explanation
Indices: 1653529--1653572 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1653519 CAAATTTTAG
*
1653529 AAATTTT-ATAAATATTTT
1 AAATTTTGAAAAATATTTT
*
1653547 GAATTTTGAAAAATATTTT
1 AAATTTTGAAAAATATTTT
1653566 AAATTTT
1 AAATTTT
1653573 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
AAATTTTGAAAAATATTTT
Found at i:1660116 original size:3 final size:3
Alignment explanation
Indices: 1660108--1660132 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1660098 GAATTAGTGG
1660108 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1660133 CAATTATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1667712 original size:3 final size:3
Alignment explanation
Indices: 1667704--1667734 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1667694 TCAGTTTTTA
1667704 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1667735 TAGAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1668267 original size:15 final size:16
Alignment explanation
Indices: 1668219--1668283 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
1668209 AGTGTCAAAT
1668219 TATATTTCTAATATTTTTA
1 TATATTT-TAA-A-TTTTA
* *
1668238 TAAATTTATAAATTTTT
1 TATATTT-TAAATTTTA
*
1668255 TAT-TTTTAGATTTTA
1 TATATTTTAAATTTTA
1668270 TATATTTTAAATTT
1 TATATTTTAAATTT
1668284 CAAAAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 10 0.26
16 12 0.32
17 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TATATTTTAAATTTTA
Found at i:1670908 original size:29 final size:29
Alignment explanation
Indices: 1670876--1670961 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
1670866 AATCGAGGTT
*
1670876 AAAATAGAATTTTGGAAAGTTCGGGAGCG
1 AAAATAGAATTTTGGAAAGTTCGGGAGCA
* * *
1670905 AAAATATAATTTTTGGTGAAA--TCAGGATCA
1 AAAATAGAA-TTTT-G-GAAAGTTCGGGAGCA
*
1670935 AAAATAGAATTTTGGAAAGTTTGGGAG
1 AAAATAGAATTTTGGAAAGTTCGGGAG
1670962 GGTCAAAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
27 4 0.09
28 1 0.02
29 16 0.36
30 18 0.41
31 1 0.02
32 4 0.09
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.29
Consensus pattern (29 bp):
AAAATAGAATTTTGGAAAGTTCGGGAGCA
Found at i:1670948 original size:59 final size:59
Alignment explanation
Indices: 1670846--1670979 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 59
1670836 TTTCGGGGGT
*
1670846 AAAATGATAATTTTTGATAAAATCGAGGTTAAAATAGAATTTTGGAAAGTTCGGGAGCG-
1 AAAAT-ATAATTTTTGATAAAATCGAGGTAAAAATAGAATTTTGGAAAGTTCGGGAGCGC
* * * *
1670905 AAAATATAATTTTTGGTGAAATC-AGGATCAAAAATAGAATTTTGGAAAGTTTGGGAGGGTC
1 AAAATATAATTTTTGATAAAATCGAGG-T-AAAAATAGAATTTTGGAAAGTTCGGGAGCG-C
*
1670966 AAAATGTAATTTTT
1 AAAATATAATTTTT
1670980 AGAAAGTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
57 3 0.05
58 17 0.26
59 32 0.49
61 13 0.20
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (59 bp):
AAAATATAATTTTTGATAAAATCGAGGTAAAAATAGAATTTTGGAAAGTTCGGGAGCGC
Found at i:1671023 original size:29 final size:29
Alignment explanation
Indices: 1670942--1671155 Score: 207
Period size: 30 Copynumber: 7.2 Consensus size: 29
1670932 TCAAAAATAG
* * *
1670942 AATTTTGGAAAGTTTGGGAGGGTCAAAATGT
1 AATTTTGAAAAGTTT-TG-GGGTTAAAATGT
* * *
1670973 AATTTTTAGAAAGTTTTAGGGTTAAAATAT
1 AATTTTGA-AAAGTTTTGGGGTTAAAATGT
*
1671003 AATTTTGGAAAAG-TATGGGGTTAAAATGT
1 AATTTT-GAAAAGTTTTGGGGTTAAAATGT
* *
1671032 AATTTTCAAAAGTTTTGGGGTCAAAATGT
1 AATTTTGAAAAGTTTTGGGGTTAAAATGT
* * *
1671061 AATTTTCAAAAAGTTTTAGGGTTAAAATAT
1 AATTTT-GAAAAGTTTTGGGGTTAAAATGT
* * *
1671091 AATTTTAGAAAAG-TATGAGGTCAAAATGT
1 AATTTT-GAAAAGTTTTGGGGTTAAAATGT
*
1671120 AATTTTTAGAAAGTTTTGGGGTTAAAATGT
1 AATTTTGA-AAAGTTTTGGGGTTAAAATGT
1671150 AATTTT
1 AATTTT
1671156 TGGATAGTCT
Statistics
Matches: 149, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
28 6 0.04
29 60 0.40
30 69 0.46
31 7 0.05
32 7 0.05
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (29 bp):
AATTTTGAAAAGTTTTGGGGTTAAAATGT
Found at i:1671084 original size:59 final size:59
Alignment explanation
Indices: 1670960--1671155 Score: 216
Period size: 59 Copynumber: 3.3 Consensus size: 59
1670950 AAAGTTTGGG
* * * * * ** *
1670960 AGGGTCAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAG-TAT
1 AGGGTTAAAATGTAATTTTCA-AAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGTTTT
*
1671019 GGGGTTAAAATGTAATTTTCAAAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGTTTT
1 AGGGTTAAAATGTAATTTTCAAAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGTTTT
* * * * * *
1671078 AGGGTTAAAATATAATTTTAGAAAAG-TATGAGGTCAAAATGTAATTTTTAGAAAGTTTT
1 AGGGTTAAAATGTAATTTT-CAAAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGTTTT
*
1671137 GGGGTTAAAATGTAATTTT
1 AGGGTTAAAATGTAATTTT
1671156 TGGATAGTCT
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
58 29 0.25
59 83 0.71
60 5 0.04
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (59 bp):
AGGGTTAAAATGTAATTTTCAAAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGTTTT
Found at i:1671169 original size:88 final size:88
Alignment explanation
Indices: 1670961--1671156 Score: 320
Period size: 88 Copynumber: 2.2 Consensus size: 88
1670951 AAGTTTGGGA
* * *
1670961 GGGTCAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGTATGGGGTTA
1 GGGTCAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTAGAAAAGTATGAGGTCA
1671026 AAATGTAATTTTCAAAAGTTTTG
66 AAATGTAATTTTCAAAAGTTTTG
* *
1671049 GGGTCAAAATGTAATTTTCAAAAAGTTTTAGGGTTAAAATATAATTTTAGAAAAGTATGAGGTCA
1 GGGTCAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTAGAAAAGTATGAGGTCA
*
1671114 AAATGTAATTTTTAGAAAGTTTTG
66 AAATGTAATTTTCA-AAAGTTTTG
*
1671138 GGGTTAAAATGTAATTTTT
1 GGGTCAAAATGTAATTTTT
1671157 GGATAGTCTA
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 73 0.74
89 26 0.26
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (88 bp):
GGGTCAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTAGAAAAGTATGAGGTCA
AAATGTAATTTTCAAAAGTTTTG
Found at i:1672158 original size:19 final size:21
Alignment explanation
Indices: 1672134--1672179 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
1672124 ACCTTTCTTT
*
1672134 TTATTATTTAAT-AATATT-A
1 TTATTATTAAATAAATATTAA
1672153 TTATTATTAAATAAATATTAA
1 TTATTATTAAATAAATATTAA
1672174 TTATTA
1 TTATTA
1672180 CTATTTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.46
20 6 0.25
21 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTATTAAATAAATATTAA
Found at i:1672949 original size:12 final size:12
Alignment explanation
Indices: 1672932--1673021 Score: 84
Period size: 11 Copynumber: 7.9 Consensus size: 12
1672922 TGAAAATTGA
*
1672932 TTAAATTTAATT
1 TTAAATTTAAAT
1672944 TTAAATTTTAAA-
1 TTAAA-TTTAAAT
*
1672956 TTAAATCTAAAT
1 TTAAATTTAAAT
*
1672968 TTGAA-TTAAAT
1 TTAAATTTAAAT
1672979 TTAAATTT-AA-
1 TTAAATTTAAAT
*
1672989 -TAAACTTAAAT
1 TTAAATTTAAAT
*
1673000 TTAAA-ATAAAT
1 TTAAATTTAAAT
1673011 TTAAATTTAAA
1 TTAAATTTAAA
1673022 ATGGATTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
9 6 0.10
10 2 0.03
11 26 0.41
12 24 0.38
13 5 0.08
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:1672977 original size:11 final size:11
Alignment explanation
Indices: 1672932--1673048 Score: 71
Period size: 11 Copynumber: 10.5 Consensus size: 11
1672922 TGAAAATTGA
*
1672932 TTAAATTTAATT
1 TTAAA-TTAAAT
1672944 TTAAATTTTAAA-
1 TTAAA--TTAAAT
1672956 TTAAATCTAAAT
1 TTAAAT-TAAAT
*
1672968 TTGAATTAAAT
1 TTAAATTAAAT
*
1672979 TTAAATTTAA-
1 TTAAATTAAAT
1672989 -TAAACTTAAAT
1 TTAAA-TTAAAT
*
1673000 TTAAAATAAAT
1 TTAAATTAAAT
*
1673011 TTAAATTTAAAA
1 TTAAA-TTAAAT
** *
1673023 TGGATTTAAAT
1 TTAAATTAAAT
*
1673034 TTAAA-CAAAT
1 TTAAATTAAAT
1673044 TTAAA
1 TTAAA
1673049 ATGGTTTGGT
Statistics
Matches: 82, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
9 4 0.05
10 14 0.17
11 34 0.41
12 25 0.30
13 5 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:1673021 original size:17 final size:17
Alignment explanation
Indices: 1672943--1673048 Score: 110
Period size: 17 Copynumber: 6.4 Consensus size: 17
1672933 TAAATTTAAT
*
1672943 TTTAAATTTTAAATTAAA
1 TTTAAA-TTTAAAATAAA
* * *
1672961 TCTAAATTTGAATTAAA
1 TTTAAATTTAAAATAAA
1672978 TTTAAATTT--AATAAA
1 TTTAAATTTAAAATAAA
*
1672993 CTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
**
1673010 TTTAAATTTAAAATGGA
1 TTTAAATTTAAAATAAA
*
1673027 TTTAAATTT-AAACAAA
1 TTTAAATTTAAAATAAA
1673043 TTTAAA
1 TTTAAA
1673049 ATGGTTTGGT
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
15 13 0.17
16 10 0.13
17 47 0.63
18 5 0.07
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1673038 original size:6 final size:6
Alignment explanation
Indices: 1672932--1673021 Score: 84
Period size: 6 Copynumber: 15.8 Consensus size: 6
1672922 TGAAAATTGA
* * *
1672932 TTAAAT TTAATT TTAAATT TTAAA- TTAAAT CTAAAT TTGAA- TTAAAT
1 TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
1672979 TTAAAT TT-AA- -TAAAC TTAAAT TTAAA- ATAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
1673022 ATGGATTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 15 0.22
6 44 0.65
7 6 0.09
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (6 bp):
TTAAAT
Found at i:1674372 original size:67 final size:67
Alignment explanation
Indices: 1674231--1674363 Score: 169
Period size: 67 Copynumber: 2.0 Consensus size: 67
1674221 CTAAACATCA
* * * * * * *
1674231 AAATGTATAATGTGAATATAGATATTTATTTAGAATCTTGTAATATAATATATATATATATATAT
1 AAATTTATAATGTGAACATAAATATTTATTTACAATCTTATAATATAATATATATAAAGATATAT
1674296 AT
66 AT
*
1674298 AAATTTATAATGTGAACATAAATATTTATTTACAA-CTTTATAATATAATATGTATAAAAGATAT
1 AAATTTATAATGTGAACATAAATATTTATTTACAATC-TTATAATATAATATATAT-AAAGATAT
1674362 AT
64 AT
1674364 TCACTTTATC
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
66 1 0.02
67 47 0.84
68 8 0.14
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (67 bp):
AAATTTATAATGTGAACATAAATATTTATTTACAATCTTATAATATAATATATATAAAGATATAT
AT
Found at i:1676060 original size:21 final size:21
Alignment explanation
Indices: 1676003--1676090 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
1675993 AGGTTTAGGG
* *
1676003 TTAAGGATTTAGGTTTTAG-GG
1 TTAA-GATTTAGGATTTAGAGT
* *
1676024 TTAGAGTTTTATGATTTAGAGT
1 TTA-AGATTTAGGATTTAGAGT
* *
1676046 TTAAGATTTGGGATTTAAAGT
1 TTAAGATTTAGGATTTAGAGT
* * *
1676067 TTAAGGTTTAGGATTCAGGGT
1 TTAAGATTTAGGATTTAGAGT
1676088 TTA
1 TTA
1676091 GGTTAAAAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 47 0.90
22 5 0.10
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.44
Consensus pattern (21 bp):
TTAAGATTTAGGATTTAGAGT
Found at i:1680180 original size:21 final size:21
Alignment explanation
Indices: 1680133--1680186 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1680123 ACCTAAATTT
*
1680133 TTTAAAGAATAACAT--AATA
1 TTTAAAGAATAAAATAAAATA
1680152 -TT-AA-AATAAAATAAAATA
1 TTTAAAGAATAAAATAAAATA
*
1680170 TTTAAAGAATAATATAA
1 TTTAAAGAATAAAATAA
1680187 TAAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 7 0.25
17 2 0.07
18 6 0.21
19 2 0.07
20 2 0.07
21 9 0.32
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
TTTAAAGAATAAAATAAAATA
Found at i:1680183 original size:19 final size:19
Alignment explanation
Indices: 1680133--1680188 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
1680123 ACCTAAATTT
*
1680133 TTTAAAGAATAACATAATA
1 TTTAAAGAATAATATAATA
* * *
1680152 TTAAAATAA-AATAAAATA
1 TTTAAAGAATAATATAATA
1680170 TTTAAAGAATAATATAATA
1 TTTAAAGAATAATATAATA
1680189 AAAATAATTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
TTTAAAGAATAATATAATA
Found at i:1681990 original size:20 final size:20
Alignment explanation
Indices: 1681965--1682015 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 20
1681955 GTGGACTAGT
1681965 TTTAATATAAAATTGTATAC
1 TTTAATATAAAATTGTATAC
*
1681985 TTTAATCT-AAA----ATAC
1 TTTAATATAAAATTGTATAC
1682000 TTTAATATAAAATTGT
1 TTTAATATAAAATTGT
1682016 TATAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
19 3 0.12
20 7 0.29
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (20 bp):
TTTAATATAAAATTGTATAC
Found at i:1682287 original size:21 final size:21
Alignment explanation
Indices: 1682248--1682286 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1682238 TTAATTGTAA
*
1682248 TTTTGATTTATTTTTAAAATG
1 TTTTAATTTATTTTTAAAATG
1682269 TTTTAATTT-TTTTTAAAA
1 TTTTAATTTATTTTTAAAA
1682287 AATTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTAATTTATTTTTAAAATG
Found at i:1685343 original size:26 final size:26
Alignment explanation
Indices: 1685314--1685367 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1685304 AACCATGCAC
1685314 ATACCAATCGAATTAAGACTCAACCG
1 ATACCAATCGAATTAAGACTCAACCG
1685340 ATACCAATCGAATTAAGACTCAACCG
1 ATACCAATCGAATTAAGACTCAACCG
1685366 AT
1 AT
1685368 TAATCTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (26 bp):
ATACCAATCGAATTAAGACTCAACCG
Found at i:1686560 original size:69 final size:69
Alignment explanation
Indices: 1686446--1686574 Score: 231
Period size: 69 Copynumber: 1.9 Consensus size: 69
1686436 CCCCCTATTT
1686446 ATGGATTGGGGAGGAGCTATGGATAGTTTTAGACATTGTGACAAAAAGAACAAATATAATAATAT
1 ATGGATTGGGGAGGAGCTATGGATAGTTTTAGACATTGTGACAAAAAGAACAAATATAATAATAT
1686511 TTTG
66 TTTG
* * *
1686515 ATGGATTGGGGAGGAGCTATGGATAGTTTTAGTCATTGTGTCAAAAAGAACAGATATAAT
1 ATGGATTGGGGAGGAGCTATGGATAGTTTTAGACATTGTGACAAAAAGAACAAATATAAT
1686575 GTTGATTGAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.30
Consensus pattern (69 bp):
ATGGATTGGGGAGGAGCTATGGATAGTTTTAGACATTGTGACAAAAAGAACAAATATAATAATAT
TTTG
Found at i:1689440 original size:18 final size:18
Alignment explanation
Indices: 1689400--1689442 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1689390 GTTAAAGGTA
1689400 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
1689418 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
1689436 TAATTAA
1 TAATTAA
1689443 AAATCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:1689732 original size:17 final size:18
Alignment explanation
Indices: 1689695--1689733 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1689685 AAATTAGTCT
1689695 ATATAAACAATAAGACAG
1 ATATAAACAATAAGACAG
* *
1689713 ATATAAAGAA-AAGACGG
1 ATATAAACAATAAGACAG
1689730 ATAT
1 ATAT
1689734 GAAGGGATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (18 bp):
ATATAAACAATAAGACAG
Found at i:1691007 original size:12 final size:13
Alignment explanation
Indices: 1690962--1691017 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 13
1690952 TTAAATTCAT
1690962 TTTAAATTAAAATA
1 TTTAAATTAAAA-A
*
1690976 TTTGAAATAAATTTAAA
1 TTT-AAATTAA---AAA
1690993 TTT-AATTAAAAA
1 TTTAAATTAAAAA
1691005 TTTAAATTAAAAA
1 TTTAAATTAAAAA
1691018 AGTCCAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
12 6 0.17
13 9 0.26
14 3 0.09
15 11 0.31
17 4 0.11
18 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
TTTAAATTAAAAA
Found at i:1691857 original size:3 final size:3
Alignment explanation
Indices: 1691798--1691843 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1691788 CAACAGCCAT
*
1691798 TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1691844 GGTTTAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1692927 original size:29 final size:29
Alignment explanation
Indices: 1692895--1693004 Score: 129
Period size: 29 Copynumber: 3.8 Consensus size: 29
1692885 AAACAGTCCA
*
1692895 AAAATTTCCA-TTTTACCCCCGAACTTTCC
1 AAAA-TTCCATTTTTAACCCCGAACTTTCC
1692924 AAAATTCCATTTTTAACCCCG-A-TTTCACC
1 AAAATTCCATTTTTAACCCCGAACTTT--CC
*
1692953 AAAAATTACCA-TTTTACCCCCGAACTTTCC
1 -AAAATT-CCATTTTTAACCCCGAACTTTCC
1692983 AAAATTCCATTTTTAACCCCGA
1 AAAATTCCATTTTTAACCCCGA
1693005 TTTCACCAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
27 3 0.04
28 9 0.13
29 33 0.47
30 18 0.26
31 4 0.06
32 3 0.04
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATTCCATTTTTAACCCCGAACTTTCC
Found at i:1692984 original size:59 final size:59
Alignment explanation
Indices: 1692892--1693100 Score: 267
Period size: 59 Copynumber: 3.4 Consensus size: 59
1692882 CCCAAACAGT
*
1692892 CCAAAAATTTCCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1692951 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * **
1693010 CCAAAAATCACCAAAATTACCATTTTACCCCC-AAATTTACTAAAATTCCATTTTCGACCCCGAT
1 -C------CA--AAAATTACCATTTTACCCCCGAACTTT-CCAAAATTCCATTTTTAACCCCGAT
1693074 TTCA
56 TTCA
*
1693078 CCAAAAATTACCATTTTTCCCCC
1 CCAAAAATTACCATTTTACCCCC
1693101 CGGATATCCA
Statistics
Matches: 134, Mismatches: 6, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
59 77 0.57
60 1 0.01
61 2 0.01
66 2 0.01
67 6 0.04
68 46 0.34
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.32
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:1693013 original size:29 final size:29
Alignment explanation
Indices: 1692922--1693015 Score: 122
Period size: 29 Copynumber: 3.2 Consensus size: 29
1692912 CCCGAACTTT
1692922 CCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAATTCCATTTTTAACCCCGATTTCA
*
1692951 CCAAAAATTACCA-TTTTACCCCCGAACTTT--
1 CC-AAAATT-CCATTTTTAACCCCG-A-TTTCA
1692981 CCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAATTCCATTTTTAACCCCGATTTCA
1693010 CCAAAA
1 CCAAAA
1693016 ATCACCAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
27 3 0.05
28 4 0.07
29 24 0.43
30 18 0.32
31 4 0.07
32 3 0.05
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (29 bp):
CCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:1693030 original size:68 final size:68
Alignment explanation
Indices: 1692948--1693090 Score: 216
Period size: 68 Copynumber: 2.1 Consensus size: 68
1692938 AACCCCGATT
* *
1692948 TCACCAAAAATTACCATTTTACCCCCGAACTTT-CCAAAATTCCATTTTTAACCCCGATTTCACC
1 TCACC-AAAATTACCATTTTACCCCC-AAATTTACCAAAATTCCATTTTCAACCCCGATTTCACC
1693012 AAAAA
64 AAAAA
* *
1693017 TCACCAAAATTACCATTTTACCCCCAAATTTACTAAAATTCCATTTTCGACCCCGATTTCACCAA
1 TCACCAAAATTACCATTTTACCCCCAAATTTACCAAAATTCCATTTTCAACCCCGATTTCACCAA
1693082 AAA
66 AAA
*
1693085 TTACCA
1 TCACCA
1693091 TTTTTCCCCC
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
67 5 0.07
68 58 0.85
69 5 0.07
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.29
Consensus pattern (68 bp):
TCACCAAAATTACCATTTTACCCCCAAATTTACCAAAATTCCATTTTCAACCCCGATTTCACCAA
AAA
Found at i:1693083 original size:29 final size:30
Alignment explanation
Indices: 1693017--1693100 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 30
1693007 TCACCAAAAA
1693017 TCACCAAAATTACCATTTTACCCCCAAATT
1 TCACCAAAATTACCATTTTACCCCCAAATT
* *
1693047 T-ACTAAAATT-CCATTTT-CGACCCC-GATT
1 TCACCAAAATTACCATTTTAC--CCCCAAATT
*
1693075 TCACCAAAAATTACCATTTTTCCCCC
1 TCACC-AAAATTACCATTTTACCCCC
1693101 CGGATATCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 1 0.02
28 11 0.24
29 14 0.31
30 11 0.24
31 7 0.16
32 1 0.02
ACGTcount: A:0.32, C:0.33, G:0.02, T:0.32
Consensus pattern (30 bp):
TCACCAAAATTACCATTTTACCCCCAAATT
Found at i:1693111 original size:127 final size:128
Alignment explanation
Indices: 1692895--1693135 Score: 335
Period size: 127 Copynumber: 1.9 Consensus size: 128
1692885 AAACAGTCCA
* * *
1692895 AAAATTTCCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCCGAAATTTCCAAAATTCCATTTTCAACCCCGATTTCACCAAAAATT
* * *
1692960 ACCATTTTACCCCCGAACTTTCCAAA-ATTCCATTTTTAACCCCGATTTCACCAAAAATCACC
66 ACCATTTTACCCCCGAACTATCCAAAGATCCCATTTTCAACCCCGATTTCACCAAAAATCACC
* *
1693022 AAAATTACCATTTTACCCCC-AAATTTACTAAAATTCCATTTTCGACCCCGATTTCACCAAAAAT
1 AAAATTACCATTTTACCCCCGAAATTT-CCAAAATTCCATTTTCAACCCCGATTTCACCAAAAAT
* * * *
1693086 TACCATTTTTCCCCCCGGA-TATCCAAAGGTCCCGTTTTCAACCCCGATTT
65 TACCA-TTTTACCCCCGAACTATCCAAAGATCCCATTTTCAACCCCGATTT
1693136 TGTCGTTTCT
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
126 5 0.05
127 65 0.66
128 29 0.29
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (128 bp):
AAAATTACCATTTTACCCCCGAAATTTCCAAAATTCCATTTTCAACCCCGATTTCACCAAAAATT
ACCATTTTACCCCCGAACTATCCAAAGATCCCATTTTCAACCCCGATTTCACCAAAAATCACC
Found at i:1695104 original size:21 final size:19
Alignment explanation
Indices: 1695076--1695135 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
1695066 TTCGACCTTG
1695076 TTTTTAATATTTTTATTAA
1 TTTTTAATATTTTTATTAA
*
1695095 -TTTTAATAATTTTTTAGTAAA
1 TTTTTAAT-A-TTTTTA-TTAA
*
1695116 TTTTTTATATTTTTA-TAA
1 TTTTTAATATTTTTATTAA
1695134 TT
1 TT
1695136 AATGGTTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 11 0.32
19 1 0.03
20 12 0.35
21 4 0.12
22 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTAATATTTTTATTAA
Found at i:1702317 original size:21 final size:21
Alignment explanation
Indices: 1702293--1702415 Score: 192
Period size: 21 Copynumber: 5.9 Consensus size: 21
1702283 CTTCTATGGC
* *
1702293 AATGAACCTGACCCAGGCAGA
1 AATGAACCCGACCCAGGAAGA
1702314 AATGAACCCGACCCAGGAAGA
1 AATGAACCCGACCCAGGAAGA
* *
1702335 AATGAACCTGACCCAGGTAGA
1 AATGAACCCGACCCAGGAAGA
* *
1702356 AATGAACCCGACCCTGGCAGA
1 AATGAACCCGACCCAGGAAGA
1702377 AATGAACCCGACCCAGGAAGA
1 AATGAACCCGACCCAGGAAGA
1702398 AATGAACCCGACCCAGGA
1 AATGAACCCGACCCAGGA
1702416 CGCAAAATTA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 93 1.00
ACGTcount: A:0.39, C:0.29, G:0.24, T:0.08
Consensus pattern (21 bp):
AATGAACCCGACCCAGGAAGA
Found at i:1702392 original size:63 final size:63
Alignment explanation
Indices: 1702293--1702414 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 63
1702283 CTTCTATGGC
* *
1702293 AATGAACCTGACCCAGGCAGAAATGAACCCGACCCAGGAAGAAATGAACCTGACCCAGGTAGA
1 AATGAACCCGACCCAGGCAGAAATGAACCCGACCCAGGAAGAAATGAACCCGACCCAGGTAGA
*
1702356 AATGAACCCGACCCTGGCAGAAATGAACCCGACCCAGGAAGAAATGAACCCGACCCAGG
1 AATGAACCCGACCCAGGCAGAAATGAACCCGACCCAGGAAGAAATGAACCCGACCCAGG
1702415 ACGCAAAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.39, C:0.30, G:0.24, T:0.08
Consensus pattern (63 bp):
AATGAACCCGACCCAGGCAGAAATGAACCCGACCCAGGAAGAAATGAACCCGACCCAGGTAGA
Found at i:1708988 original size:20 final size:20
Alignment explanation
Indices: 1708965--1709005 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1708955 AAGATATCTC
1708965 ACTATCTCCCTCTACAAAAA
1 ACTATCTCCCTCTACAAAAA
1708985 ACTATCTCCCTCTACAAAAA
1 ACTATCTCCCTCTACAAAAA
1709005 A
1 A
1709006 TTGGCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.24
Consensus pattern (20 bp):
ACTATCTCCCTCTACAAAAA
Found at i:1710994 original size:29 final size:29
Alignment explanation
Indices: 1710913--1710996 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
1710903 AAAATGTCAA
* *
1710913 AATTCAAAAAGTATAGATATTAAAATTGACC
1 AATT-AAAAA-TATAAATACTAAAATTGACC
* *
1710944 AATTCGAAAAATACAAACACTAAAATTGATCC
1 AATT--AAAAATATAAATACTAAAATTGA-CC
1710976 AATT-AAAATATAAATACTAAA
1 AATTAAAAATATAAATACTAAA
1710997 TCCACAACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 15 0.34
31 18 0.41
32 11 0.25
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (29 bp):
AATTAAAAATATAAATACTAAAATTGACC
Found at i:1711333 original size:15 final size:15
Alignment explanation
Indices: 1711310--1711347 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1711300 ATGTTTTTTT
*
1711310 TTTATAATTTTGA-TA
1 TTTAAAATTTT-ATTA
1711325 TTTAAAATTTTATTA
1 TTTAAAATTTTATTA
1711340 TTTAAAAT
1 TTTAAAAT
1711348 ACTACATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTAAAATTTTATTA
Found at i:1714093 original size:2 final size:2
Alignment explanation
Indices: 1714086--1714120 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1714076 CACTTTCCAT
1714086 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1714121 GAAAGAGGTA
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:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1718597 original size:16 final size:16
Alignment explanation
Indices: 1718548--1718597 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
1718538 TATGTTTTCT
*
1718548 TATACTTTGATAAATC
1 TATATTTTGATAAATC
*
1718564 T-TTTTTTGA-ATAAT-
1 TATATTTTGATA-AATC
1718578 TATATTTTGATAAATC
1 TATATTTTGATAAATC
1718594 TATA
1 TATA
1718598 GTATACATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 2 0.07
15 19 0.70
16 6 0.22
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
TATATTTTGATAAATC
Found at i:1718758 original size:31 final size:30
Alignment explanation
Indices: 1718717--1718795 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
1718707 AAGATCATTT
* **
1718717 ATATGTTTTTATATTTTTGTAAAATTCAGAA
1 ATATATTTTTATATTTTTAAAAAATTCA-AA
1718748 ATATATTTTTATATCATTTTAAAAAATTCAAA
1 ATATATTTTTATAT--TTTTAAAAAATTCAAA
*
1718780 A-ATA-TTATATATTTTT
1 ATATATTTTTATATTTTT
1718796 TCACCTACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.10
30 7 0.17
31 16 0.38
32 3 0.07
33 12 0.29
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (30 bp):
ATATATTTTTATATTTTTAAAAAATTCAAA
Found at i:1719096 original size:17 final size:17
Alignment explanation
Indices: 1719058--1719097 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1719048 TAAAATCTAT
* *
1719058 AAAAATATATTTAAAAC
1 AAAAATAAATTTAAAAA
*
1719075 CAAAATAAATTTAAAAA
1 AAAAATAAATTTAAAAA
1719092 AAAAAT
1 AAAAAT
1719098 TCACACATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAATAAATTTAAAAA
Found at i:1720258 original size:23 final size:21
Alignment explanation
Indices: 1720207--1720259 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 21
1720197 GTGCTGGGGA
1720207 AACAGTAGGCACACACAGTGC
1 AACAGTAGGCACACACAGTGC
1720228 AATTCAGTAGGCACACACAGTGC
1 AA--CAGTAGGCACACACAGTGC
1720251 TGAACAGTA
1 --AACAGTA
1720260 AGCGCGCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.07
23 24 0.86
25 2 0.07
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (21 bp):
AACAGTAGGCACACACAGTGC
Found at i:1728843 original size:7 final size:7
Alignment explanation
Indices: 1728831--1728862 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1728821 CAAGCTTTGA
1728831 AATTTTC
1 AATTTTC
1728838 AATTTTC
1 AATTTTC
1728845 AATTTTC
1 AATTTTC
1728852 AATTTTC
1 AATTTTC
1728859 AATT
1 AATT
1728863 CTATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTC
Found at i:1732242 original size:18 final size:18
Alignment explanation
Indices: 1732199--1732244 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1732189 TAATATCACC
1732199 TAATAA-AAACTAAAATA
1 TAATAATAAACTAAAATA
*
1732216 TTATAAATAAA-TAAATATA
1 TAAT-AATAAACTAAA-ATA
1732235 TAATAATAAA
1 TAATAATAAA
1732245 ATATGTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATAATAAACTAAAATA
Found at i:1732246 original size:19 final size:17
Alignment explanation
Indices: 1732199--1732247 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1732189 TAATATCACC
*
1732199 TAATAAAAACTAAAATA
1 TAATAAAAAATAAAATA
*
1732216 TTATAAATAAATAAATATA
1 TAATAAA-AAATAAA-ATA
1732235 TAATAATAAAATA
1 TAATAA-AAAATA
1732248 TGTTATACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.23
18 6 0.23
19 13 0.50
20 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAAAAAATAAAATA
Found at i:1736404 original size:14 final size:13
Alignment explanation
Indices: 1736378--1736420 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1736368 CGATTTGTTT
*
1736378 TTTTAAAATTATA
1 TTTTAAAAATATA
1736391 TTTTAAATAATATA
1 TTTTAAA-AATATA
*
1736405 -TTAAAAAATATA
1 TTTTAAAAATATA
1736417 TTTT
1 TTTT
1736421 TTAATTACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 6 0.24
13 14 0.56
14 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTTAAAAATATA
Found at i:1737146 original size:2 final size:2
Alignment explanation
Indices: 1737139--1737181 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1737129 TTAGATAACA
1737139 AT AT AT AT AT 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 AT AT AT AT AT
1737181 A
1 A
1737182 GATGAATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1750792 original size:30 final size:28
Alignment explanation
Indices: 1750729--1750792 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
1750719 TTCTCATTAA
*
1750729 AAATGTAATCACAATAAATATTATATAT
1 AAATTTAATCACAATAAATATTATATAT
* *
1750757 --TTTTAATCACTATTAAATATTATCATAT
1 AAATTTAATCAC-AATAAATATTAT-ATAT
1750785 AAATTTAA
1 AAATTTAA
1750793 CATGTTAGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
26 8 0.29
27 11 0.39
28 4 0.14
30 5 0.18
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (28 bp):
AAATTTAATCACAATAAATATTATATAT
Found at i:1754505 original size:19 final size:20
Alignment explanation
Indices: 1754469--1754506 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1754459 TAAAAATTTT
1754469 AAATTTTGAAATCCAAATCC
1 AAATTTTGAAATCCAAATCC
*
1754489 AAATTTTTAAA-CCAAATC
1 AAATTTTGAAATCCAAATC
1754507 ATAGTTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATTTTGAAATCCAAATCC
Found at i:1756291 original size:55 final size:55
Alignment explanation
Indices: 1756228--1756335 Score: 164
Period size: 55 Copynumber: 2.0 Consensus size: 55
1756218 CAATTTTCTA
* * * *
1756228 AAAATATTACTTCTTTTGGATCGATTGTTTTTATGTTTAAA-TCGATTGTTATGCT
1 AAAATATTACTTCTTTTGAATCAATCGTTTATATGTTTAAATTC-ATTGTTATGCT
1756283 AAAATATTACTTCTTTTGAATCAATCGTTTATATGTTTAAATTCATTGTTATG
1 AAAATATTACTTCTTTTGAATCAATCGTTTATATGTTTAAATTCATTGTTATG
1756336 TAACACGTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 46 0.96
56 2 0.04
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (55 bp):
AAAATATTACTTCTTTTGAATCAATCGTTTATATGTTTAAATTCATTGTTATGCT
Found at i:1758149 original size:14 final size:14
Alignment explanation
Indices: 1758127--1758159 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1758117 GTCAATTCAC
*
1758127 TATTATATTGTTAT
1 TATTTTATTGTTAT
1758141 TATTTTATTGTTAT
1 TATTTTATTGTTAT
1758155 TATTT
1 TATTT
1758160 GGATTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (14 bp):
TATTTTATTGTTAT
Found at i:1758674 original size:19 final size:20
Alignment explanation
Indices: 1758640--1758679 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1758630 AGATTTTTTT
**
1758640 ATCAAAATAAGTTTAA-AAA
1 ATCAAAATAAAATTAATAAA
1758659 ATCAAAATAAAATTAATAAA
1 ATCAAAATAAAATTAATAAA
1758679 A
1 A
1758680 AAAACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (20 bp):
ATCAAAATAAAATTAATAAA
Found at i:1763685 original size:22 final size:23
Alignment explanation
Indices: 1763659--1763701 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1763649 ACCTAAAATT
*
1763659 TTAAATTC-GAAAAATAAAAGGA
1 TTAAATCCTGAAAAATAAAAGGA
*
1763681 TTAAATCCTTAAAAATAAAAG
1 TTAAATCCTGAAAAATAAAAG
1763702 TATGAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (23 bp):
TTAAATCCTGAAAAATAAAAGGA
Found at i:1767714 original size:2 final size:2
Alignment explanation
Indices: 1767707--1767752 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1767697 AGCACAGCAC
1767707 AT AT AT AT AT 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 AT AT AT AT AT
1767749 AT AT
1 AT AT
1767753 TGAGGGTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1770633 original size:2 final size:2
Alignment explanation
Indices: 1770626--1770654 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1770616 AACAAGTACC
1770626 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 A
1770655 AGGGAATGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1772441 original size:36 final size:37
Alignment explanation
Indices: 1772401--1772478 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
1772391 TTCTCTTTTT
1772401 TTTATAATTGT-CACAG-AATTTTTTGCATATTTACAA
1 TTTATAATTGTCCACAGAAATTTTTT-CATATTTACAA
* *
1772437 TTTATACTTGTGCCACAGAAATTTTTTTATATTTACAA
1 TTTATAATTGT-CCACAGAAATTTTTTCATATTTACAA
1772475 TTTA
1 TTTA
1772479 ATCCCTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 10 0.27
38 19 0.51
39 8 0.22
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (37 bp):
TTTATAATTGTCCACAGAAATTTTTTCATATTTACAA
Found at i:1772602 original size:97 final size:97
Alignment explanation
Indices: 1772436--1772624 Score: 306
Period size: 97 Copynumber: 1.9 Consensus size: 97
1772426 CATATTTACA
** *
1772436 ATTTATACTTGTGCCACAGAAATTTTTTTATATTTACAATTTAATCCCTTTCTTAATTTAATACA
1 ATTTATACTTGTGCCACAGAAATTTTTGCATATTTACAATTTAATCCCTTCCTTAATTTAATACA
*
1772501 TCATGTCATACTTTTTGATTTAACTTTTCCAT
66 TCATGTAATACTTTTTGATTTAACTTTTCCAT
* * *
1772533 ATTTATATTTGTGCCACAGAACTTTTTGCATATTTACAATTTGATCCCTTCCTTAATTTAATACA
1 ATTTATACTTGTGCCACAGAAATTTTTGCATATTTACAATTTAATCCCTTCCTTAATTTAATACA
*
1772598 TCATGTAATGCTTTTTGATTTAACTTT
66 TCATGTAATACTTTTTGATTTAACTTT
1772625 CTTTTGATGT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (97 bp):
ATTTATACTTGTGCCACAGAAATTTTTGCATATTTACAATTTAATCCCTTCCTTAATTTAATACA
TCATGTAATACTTTTTGATTTAACTTTTCCAT
Found at i:1774531 original size:27 final size:27
Alignment explanation
Indices: 1774496--1774549 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1774486 CTGAAATTGA
1774496 TTTAGTTTGCTAAATTAAATCAATAAG
1 TTTAGTTTGCTAAATTAAATCAATAAG
* *
1774523 TTTATTTTGCTGAATTAAATCAATAAG
1 TTTAGTTTGCTAAATTAAATCAATAAG
1774550 GAAATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (27 bp):
TTTAGTTTGCTAAATTAAATCAATAAG
Found at i:1774556 original size:27 final size:27
Alignment explanation
Indices: 1774501--1774557 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1774491 ATTGATTTAG
***
1774501 TTTGCTAAATTAAATCAATAAGTTTAT
1 TTTGCTAAATTAAATCAATAAGGAAAT
*
1774528 TTTGCTGAATTAAATCAATAAGGAAAT
1 TTTGCTAAATTAAATCAATAAGGAAAT
1774555 TTT
1 TTT
1774558 TTATCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (27 bp):
TTTGCTAAATTAAATCAATAAGGAAAT
Found at i:1790181 original size:2 final size:2
Alignment explanation
Indices: 1790174--1790238 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1790164 GAAAATTTTA
1790174 AT AT AT AT AT 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 AT AT AT AT AT
1790216 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1790239 ATTATCTAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1803424 original size:21 final size:21
Alignment explanation
Indices: 1803399--1803447 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1803389 ATTTATTAAG
1803399 TATATATGGTAAGATTTAAAT
1 TATATATGGTAAGATTTAAAT
*
1803420 TATATTTGGTAAGATTTAAAT
1 TATATATGGTAAGATTTAAAT
*
1803441 TGTATAT
1 TATATAT
1803448 AATACATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
TATATATGGTAAGATTTAAAT
Found at i:1817908 original size:20 final size:20
Alignment explanation
Indices: 1817872--1817910 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1817862 ACACCACACG
*
1817872 GCCATGAAGAAGGAAAAGAA
1 GCCATGAAGAAGAAAAAGAA
1817892 GCCAT-AAGAGAGAAAAAGA
1 GCCATGAAGA-AGAAAAAGA
1817911 GTATGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.10, G:0.28, T:0.05
Consensus pattern (20 bp):
GCCATGAAGAAGAAAAAGAA
Found at i:1820874 original size:22 final size:24
Alignment explanation
Indices: 1820831--1820874 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1820821 TTATTAGTTT
*
1820831 TTTTTATTTTTGATGGATTAAATA
1 TTTTTATTTTTGATGGAGTAAATA
*
1820855 TTTTT-TTTTTGA-GGGGTAAA
1 TTTTTATTTTTGATGGAGTAAA
1820875 AATGTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 7 0.39
24 5 0.28
ACGTcount: A:0.25, C:0.00, G:0.18, T:0.57
Consensus pattern (24 bp):
TTTTTATTTTTGATGGAGTAAATA
Found at i:1821711 original size:35 final size:35
Alignment explanation
Indices: 1821659--1821734 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1821649 ATGTGTGACT
* * *
1821659 CAAATTCTAAGAGATTGTTTGCAAGTCAAATTAAA
1 CAAAATCTAAGAAATTGTTTACAAGTCAAATTAAA
*
1821694 CAAAATCTAAGAAATTGTTTACAAGTCAAGTTAAA
1 CAAAATCTAAGAAATTGTTTACAAGTCAAATTAAA
*
1821729 TAAAAT
1 CAAAAT
1821735 ATATGATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (35 bp):
CAAAATCTAAGAAATTGTTTACAAGTCAAATTAAA
Found at i:1821803 original size:24 final size:24
Alignment explanation
Indices: 1821763--1821809 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1821753 ATCTAGTTGT
*
1821763 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
1821787 ATAATATATTTTA-CATTGATTAG
1 ATAATATA-TTTAGCATTGATTAG
1821810 AATTAAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:1829562 original size:21 final size:22
Alignment explanation
Indices: 1829522--1829563 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1829512 TAATATCTTC
1829522 TTTATTTATAATTTTAATTTTT
1 TTTATTTATAATTTTAATTTTT
*
1829544 TTTATTTAT-ATTTTTATTTT
1 TTTATTTATAATTTTAATTTT
1829564 CACTTAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTATAATTTTAATTTTT
Found at i:1847845 original size:109 final size:104
Alignment explanation
Indices: 1847692--1847902 Score: 269
Period size: 109 Copynumber: 2.0 Consensus size: 104
1847682 GGGGAACGGA
* ***
1847692 TTTGCATGATATTAACTTAAATTCTCATACTTACAATATAATACTCGTACCACTAAATCGGTAAA
1 TTTGCATGAGATTAACTTAAATTCTCATACTTACAATATAATACTCGTACCACTAAATCAACAAA
*
1847757 ACTTCTCATATATAAATTGATAATTTGGGGTGAGAAATGGG
66 ACTTCTCATA-A-AAATTGATAATTTGGGGTGAAAAATGGG
* * * * * *
1847798 TTTGCATGAGATTAACTACTCAAGTTCTCTTACTTACAGTATAATACTCTTGCCACTAAGTCAAC
1 TTTGCATGAGATTAACT--T-AAATTCTCATACTTACAATATAATACTCGTACCACTAAATCAAC
*
1847863 AAAACTTCTCATAAATATTGATAATTTGGGGTGAAAAATG
63 AAAACTTCTCATAAAAATTGATAATTTGGGGTGAAAAATG
1847903 AGATTAATTC
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
106 16 0.18
107 24 0.27
108 2 0.02
109 48 0.53
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (104 bp):
TTTGCATGAGATTAACTTAAATTCTCATACTTACAATATAATACTCGTACCACTAAATCAACAAA
ACTTCTCATAAAAATTGATAATTTGGGGTGAAAAATGGG
Found at i:1850838 original size:18 final size:18
Alignment explanation
Indices: 1850811--1850852 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1850801 TGGGAAACAT
1850811 TTATTTTGATGT-TTTTA
1 TTATTTTGATGTATTTTA
1850828 TTATATTTGATGTATTTTA
1 TTAT-TTTGATGTATTTTA
1850847 TT-TTTT
1 TTATTTT
1850853 AAATTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.30
18 9 0.39
19 7 0.30
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (18 bp):
TTATTTTGATGTATTTTA
Found at i:1853987 original size:29 final size:31
Alignment explanation
Indices: 1853918--1853987 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 31
1853908 TTAACGACGG
*
1853918 GTGACCAAAATAATAACAAATTTAAACGTTA
1 GTGACCAAATTAATAACAAATTTAAACGTTA
* *
1853949 GTGTCTAAATTAA-AA-AAATTTAAA-GTTGA
1 GTGACCAAATTAATAACAAATTTAAACGTT-A
1853978 GTGACCAAAT
1 GTGACCAAAT
1853988 CAAGAATGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 3 0.09
29 18 0.55
30 2 0.06
31 10 0.30
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.29
Consensus pattern (31 bp):
GTGACCAAATTAATAACAAATTTAAACGTTA
Found at i:1855267 original size:2 final size:2
Alignment explanation
Indices: 1855262--1855317 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1855252 ACCAATCTCT
1855262 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1855304 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
1855318 TATATATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1855850 original size:22 final size:22
Alignment explanation
Indices: 1855824--1855886 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
1855814 ATATTCAAAT
1855824 AATAACAACAAAATAATAGCAA
1 AATAACAACAAAATAATAGCAA
* ** * **
1855846 TATAATTACGAAAGGATAGCAA
1 AATAACAACAAAATAATAGCAA
*
1855868 AACAACAACAAAAATAATA
1 AATAACAAC-AAAATAATA
1855887 TATATATTTT
Statistics
Matches: 27, Mismatches: 13, Indels: 1
0.66 0.32 0.02
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.16
Consensus pattern (22 bp):
AATAACAACAAAATAATAGCAA
Found at i:1858018 original size:2 final size:2
Alignment explanation
Indices: 1858013--1858038 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1858003 ATATATATAT
1858013 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
1858039 TATAGATGGC
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:1859147 original size:30 final size:30
Alignment explanation
Indices: 1859080--1859147 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
1859070 TGTGATTGAA
1859080 TATAA-ATATAATTATATATAATTATTATT
1 TATAATATATAATTATATATAATTATTATT
1859109 TA-ACATATATAATTAATATAATAATT-TT-TT
1 TATA-ATATATAATT-ATAT-ATAATTATTATT
1859139 TATAATATA
1 TATAATATA
1859148 ATATATTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
28 1 0.03
29 3 0.09
30 17 0.50
31 7 0.21
32 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (30 bp):
TATAATATATAATTATATATAATTATTATT
Found at i:1860122 original size:15 final size:15
Alignment explanation
Indices: 1860102--1860130 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1860092 TTCTTTTGAG
1860102 TCAATTAAAAAACAA
1 TCAATTAAAAAACAA
1860117 TCAATTAAAAAACA
1 TCAATTAAAAAACA
1860131 CATGAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.21
Consensus pattern (15 bp):
TCAATTAAAAAACAA
Found at i:1861840 original size:56 final size:56
Alignment explanation
Indices: 1861754--1861872 Score: 202
Period size: 56 Copynumber: 2.1 Consensus size: 56
1861744 CAATTCGCTT
* *
1861754 AGAATTTGTATTATAATAAATCACATCTACCTTTACACTCAACTTCAATCAACTTC
1 AGAATTTATATTATAATAAATCACATCTACCTTTACACTCAACCTCAATCAACTTC
* *
1861810 AGAATTTATATTATAATAGATCACATCTACCTTTGCACTCAACCTCAATCAACTTC
1 AGAATTTATATTATAATAAATCACATCTACCTTTACACTCAACCTCAATCAACTTC
1861866 AGAATTT
1 AGAATTT
1861873 TTCCATTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (56 bp):
AGAATTTATATTATAATAAATCACATCTACCTTTACACTCAACCTCAATCAACTTC
Found at i:1862767 original size:24 final size:24
Alignment explanation
Indices: 1862738--1862786 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1862728 CCACTAACTA
1862738 AAATTCACTAAACCAAATTTTAGG
1 AAATTCACTAAACCAAATTTTAGG
1862762 AAATTCACTAAACCAAATTTTAGG
1 AAATTCACTAAACCAAATTTTAGG
1862786 A
1 A
1862787 TGTGACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (24 bp):
AAATTCACTAAACCAAATTTTAGG
Found at i:1866890 original size:17 final size:18
Alignment explanation
Indices: 1866868--1866908 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1866858 TAAGATAGAA
1866868 TAATTTTT-TATATTATG
1 TAATTTTTATATATTATG
*
1866885 TTATTTTTATATATTATG
1 TAATTTTTATATATTATG
1866903 TAATTT
1 TAATTT
1866909 ACAACATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TAATTTTTATATATTATG
Found at i:1866981 original size:24 final size:21
Alignment explanation
Indices: 1866942--1866995 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1866932 AAAAATATAT
*
1866942 AAAATTAT-TAAATATTAAATTA
1 AAAATAATATAAATATTAAA--A
*
1866964 AAAATAATATAAATTATTTAAA
1 AAAATAATATAAA-TATTAAAA
1866986 AAAATAATAT
1 AAAATAATAT
1866996 GAACTGGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 18 0.64
23 4 0.14
24 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATAATATAAATATTAAAA
Found at i:1874287 original size:22 final size:24
Alignment explanation
Indices: 1874234--1874290 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
1874224 GATATTTTAA
*
1874234 ATTATTTTAAATATATAATATAGG
1 ATTATTTTTAATATATAATATAGG
* *
1874258 ATT-GTTTTAA-ATATAATATATG
1 ATTATTTTTAATATATAATATAGG
1874280 -TTATTTTTAAT
1 ATTATTTTTAAT
1874291 TTATTCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 2 0.07
22 17 0.63
23 5 0.19
24 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
ATTATTTTTAATATATAATATAGG
Found at i:1874799 original size:19 final size:19
Alignment explanation
Indices: 1874728--1874799 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 19
1874718 TTTATTTACC
1874728 TTTTAATTATTTAATGATGAT
1 TTTTAATTATTTAAT--TGAT
1874749 TTAATTAATT-TTTAATT-AT
1 TT--TTAATTATTTAATTGAT
*
1874768 TTTATGAA-GATTTAATTGAT
1 TTT-T-AATTATTTAATTGAT
1874788 TTTTAATTATTT
1 TTTTAATTATTT
1874800 TTTAGTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
17 1 0.02
18 3 0.07
19 18 0.43
20 6 0.14
21 2 0.05
22 6 0.14
23 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTAATTATTTAATTGAT
Found at i:1874800 original size:30 final size:30
Alignment explanation
Indices: 1874728--1874800 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1874718 TTTATTTACC
* *
1874728 TTTTAATTATTTAATGATGATTTAATTAAT
1 TTTTAATTATTTTATGAAGATTTAATTAAT
*
1874758 TTTTAATTATTTTATGAAGATTTAATTGAT
1 TTTTAATTATTTTATGAAGATTTAATTAAT
1874788 TTTTAATTATTTT
1 TTTTAATTATTTT
1874801 TTAGTTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (30 bp):
TTTTAATTATTTTATGAAGATTTAATTAAT
Found at i:1884688 original size:30 final size:31
Alignment explanation
Indices: 1884646--1884708 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1884636 GCTTACATTT
*
1884646 CAGTCTCCCAAC-TTTGAAAATGTGATAAAA
1 CAGTCTCCCAACTTTTGAAAATGTGACAAAA
1884676 CAGTC-CCTCAACTTTTGAAAATGTGACAAAA
1 CAGTCTCC-CAACTTTTGAAAATGTGACAAAA
1884707 CA
1 CA
1884709 ATCTTTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 2 0.07
30 9 0.30
31 19 0.63
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (31 bp):
CAGTCTCCCAACTTTTGAAAATGTGACAAAA
Found at i:1884867 original size:31 final size:30
Alignment explanation
Indices: 1884802--1884873 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
1884792 ATTACGTTTA
* * ** *
1884802 ACAAAACAGTCACTCAACTTTGGAAATGTG
1 ACAAAACAGTCACTAAAATTTCAAAAAGTG
1884832 ACAAAACAGTCACTAAAATTATCAAAAAGTG
1 ACAAAACAGTCACTAAAATT-TCAAAAAGTG
*
1884863 ACAAAATAGTC
1 ACAAAACAGTC
1884874 CTCTTATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (30 bp):
ACAAAACAGTCACTAAAATTTCAAAAAGTG
Found at i:1891391 original size:19 final size:20
Alignment explanation
Indices: 1891363--1891401 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1891353 TCGAACCAAA
*
1891363 TTTAAGGTTTGA-ATTCGAG
1 TTTAAAGTTTGAGATTCGAG
1891382 TTTAAAGTTTGAGATTCGAG
1 TTTAAAGTTTGAGATTCGAG
1891402 ATTCGAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (20 bp):
TTTAAAGTTTGAGATTCGAG
Found at i:1898332 original size:4 final size:4
Alignment explanation
Indices: 1898323--1898361 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1898313 CGTCTCGAAA
* * *
1898323 ATAC ATAC ATGC ATGC ATGC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1898362 AATGCATGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1898343 original size:8 final size:8
Alignment explanation
Indices: 1898326--1898379 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
1898316 CTCGAAAATA
1898326 CATACATG
1 CATACATG
*
1898334 CATGCATG
1 CATACATG
*
1898342 CATACATA
1 CATACATG
*
1898350 CATACATA
1 CATACATG
*
1898358 CATAAATG
1 CATACATG
*
1898366 CATGCATG
1 CATACATG
*
1898374 TATACA
1 CATACA
1898380 CAACATTGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (8 bp):
CATACATG
Found at i:1902699 original size:16 final size:16
Alignment explanation
Indices: 1902678--1902709 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1902668 TTAACTATAT
1902678 AAAAATACAAAAATCG
1 AAAAATACAAAAATCG
1902694 AAAAATACAAAAATCG
1 AAAAATACAAAAATCG
1902710 TCAAAGTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAATACAAAAATCG
Found at i:1904054 original size:15 final size:15
Alignment explanation
Indices: 1904034--1904072 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1904024 GCACATCAAA
*
1904034 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
1904049 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
1904063 CAAGAATTAA
1 CAAGAATTAA
1904073 GCACACACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:1905666 original size:55 final size:55
Alignment explanation
Indices: 1905579--1905706 Score: 177
Period size: 55 Copynumber: 2.3 Consensus size: 55
1905569 TTTTTTTCAA
* * * *
1905579 AATATTGCTTTTTTTGGA-TAATTGTTTTTATGTTTAAATCGATTATCATATTGG
1 AATATTGCTTTTTTTGAATTAATTATTTGTATGTTTAAATCAATTATCATATTGG
* * *
1905633 AATATTACTTTTTTTGAATTAATTATTTGTATGTTTAAATCAATTGTCATGTTGG
1 AATATTGCTTTTTTTGAATTAATTATTTGTATGTTTAAATCAATTATCATATTGG
*
1905688 AATATTGCTTCTTTTGAAT
1 AATATTGCTTTTTTTGAAT
1905707 CGATTGCTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
54 16 0.25
55 48 0.75
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.53
Consensus pattern (55 bp):
AATATTGCTTTTTTTGAATTAATTATTTGTATGTTTAAATCAATTATCATATTGG
Found at i:1905773 original size:37 final size:37
Alignment explanation
Indices: 1905670--1905825 Score: 180
Period size: 34 Copynumber: 4.3 Consensus size: 37
1905660 TGTATGTTTA
* *
1905670 AATCAATTGTCATGTTGGAATATTG---CTTCTTTTG
1 AATCGATTGTTATGTTGGAATATTGCTTCTTCTTTTG
* * * *
1905704 AATCGATTGCTATGGTGGAATACTACTTCTTCTTCCTTTG
1 AATCGATTGTTATGTTGGAATA-T--TGCTTCTTCTTTTG
*
1905744 AATCGATTGTTATATTGGAATATTGCTTCTTCTTTTG
1 AATCGATTGTTATGTTGGAATATTGCTTCTTCTTTTG
1905781 AATCGATTGTTATGTTGGAATATTG--T-TTCTTTTG
1 AATCGATTGTTATGTTGGAATATTGCTTCTTCTTTTG
1905815 AATCGATTGTT
1 AATCGATTGTT
1905826 TATATGTTTA
Statistics
Matches: 104, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
34 37 0.36
35 2 0.02
37 37 0.36
39 1 0.01
40 27 0.26
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (37 bp):
AATCGATTGTTATGTTGGAATATTGCTTCTTCTTTTG
Found at i:1905825 original size:18 final size:18
Alignment explanation
Indices: 1905773--1905826 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1905763 ATATTGCTTC
1905773 TTCTTTTGAATCGATTGT
1 TTCTTTTGAATCGATTGT
* *
1905791 TAT-GTTGGAAT--ATTGT
1 T-TCTTTTGAATCGATTGT
1905807 TTCTTTTGAATCGATTGT
1 TTCTTTTGAATCGATTGT
1905825 TT
1 TT
1905827 ATATGTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 1 0.04
16 12 0.43
18 14 0.50
19 1 0.04
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (18 bp):
TTCTTTTGAATCGATTGT
Found at i:1905832 original size:37 final size:36
Alignment explanation
Indices: 1905681--1905833 Score: 147
Period size: 37 Copynumber: 4.1 Consensus size: 36
1905671 ATCAATTGTC
*
1905681 ATGTTGGAATATTG-CTTCTTTTGAATCGATTG-CT
1 ATGTTGGAATATTGTCTTCTTTTGAATCGATTGTAT
*
1905715 ATGGTGGAATACTACT-TCTTCTTCCTTTGAATCGATTGT-T
1 ATGTTGGAATA-T--TGTCTTC-T--TTTGAATCGATTGTAT
*
1905755 ATATTGGAATATTGCTTCTTCTTTTGAATCGATTGT-T
1 ATGTTGGAATATTG--TCTTCTTTTGAATCGATTGTAT
1905792 ATGTTGGAATATTGT-TTCTTTTGAATCGATTGTTTAT
1 ATGTTGGAATATTGTCTTCTTTTGAATCGATTG--TAT
1905829 ATGTT
1 ATGTT
1905834 TAAATTGATT
Statistics
Matches: 101, Mismatches: 4, Indels: 25
0.78 0.03 0.19
Matches are distributed among these distances:
34 27 0.27
35 2 0.02
36 1 0.01
37 40 0.40
38 1 0.01
39 2 0.02
40 28 0.28
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (36 bp):
ATGTTGGAATATTGTCTTCTTTTGAATCGATTGTAT
Found at i:1906733 original size:28 final size:29
Alignment explanation
Indices: 1906697--1906754 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1906687 AATTTTAAAA
* *
1906697 ACACGTGAACTTTGATT-TATATAAATAT
1 ACACATGAAATTTGATTATATATAAATAT
*
1906725 ACACATGAAATTTGATTATATATATATAT
1 ACACATGAAATTTGATTATATATAAATAT
1906754 A
1 A
1906755 TAAAACTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (29 bp):
ACACATGAAATTTGATTATATATAAATAT
Found at i:1914684 original size:18 final size:19
Alignment explanation
Indices: 1914652--1914691 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
1914642 TTTGAATTGA
1914652 TAATTTAATATAATTAAAT
1 TAATTTAATATAATTAAAT
1914671 TAATTTAA-ATAATTAAAT
1 TAATTTAATATAATTAAAT
1914689 TAA
1 TAA
1914692 AAAATTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATTTAATATAATTAAAT
Found at i:1916990 original size:14 final size:15
Alignment explanation
Indices: 1916961--1916998 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
1916951 CTTTCAACTA
1916961 AAATAAAATGAAAATG
1 AAAT-AAATGAAAATG
1916977 AAATAAAT-AAAATG
1 AAATAAATGAAAATG
1916991 AAATAAAT
1 AAATAAAT
1916999 CTTGATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 4 0.18
16 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (15 bp):
AAATAAATGAAAATG
Found at i:1921543 original size:15 final size:16
Alignment explanation
Indices: 1921518--1921552 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1921508 TCGCGCTCAT
1921518 TGAACTGTAACAAATA
1 TGAACTGTAACAAATA
*
1921534 TGAA-TGTAACAACTA
1 TGAACTGTAACAAATA
1921549 TGAA
1 TGAA
1921553 AATCATATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (16 bp):
TGAACTGTAACAAATA
Found at i:1925210 original size:10 final size:10
Alignment explanation
Indices: 1925191--1925230 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1925181 GAGGTGGTTG
1925191 AAAT-TTAAA
1 AAATATTAAA
1925200 AAATATTAAA
1 AAATATTAAA
1925210 AAATA-T-AA
1 AAATATTAAA
1925218 AAATCATTAAA
1 AAAT-ATTAAA
1925229 AA
1 AA
1925231 TTAAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 6 0.22
9 6 0.22
10 11 0.41
11 4 0.15
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATATTAAA
Found at i:1925218 original size:19 final size:18
Alignment explanation
Indices: 1925195--1925239 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1925185 TGGTTGAAAT
1925195 TTAAAAAAT-ATTAAAAA
1 TTAAAAAATCATTAAAAA
*
1925212 ATATAAAAATCATTAAAAA
1 TTA-AAAAATCATTAAAAA
1925231 TTAAAAAAT
1 TTAAAAAAT
1925240 TAAAATTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 12 0.50
19 10 0.42
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAAATCATTAAAAA
Found at i:1925238 original size:8 final size:8
Alignment explanation
Indices: 1925198--1925244 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 8
1925188 TTGAAATTTA
1925198 AAAAATATT
1 AAAAA-ATT
1925207 AAAAAATAT
1 AAAAAAT-T
1925216 AAAAATCATT
1 AAAAA--ATT
1925226 -AAAAATT
1 AAAAAATT
1925233 AAAAAATT
1 AAAAAATT
1925241 AAAA
1 AAAA
1925245 TTGTATAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
7 3 0.09
8 13 0.38
9 15 0.44
10 1 0.03
11 2 0.06
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAAATT
Found at i:1932093 original size:15 final size:14
Alignment explanation
Indices: 1932068--1932098 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1932058 GATTAAAAAG
1932068 TTAATTTAATTCAA
1 TTAATTTAATTCAA
1932082 TTAATATTAATTCAA
1 TTAAT-TTAATTCAA
1932097 TT
1 TT
1932099 TGGTTAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAATTTAATTCAA
Found at i:1932732 original size:15 final size:16
Alignment explanation
Indices: 1932700--1932738 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1932690 AGCATCTTTA
*
1932700 AAATTTATAAAAACTT
1 AAATTAATAAAAACTT
1932716 AAATTAATAAAAA-TT
1 AAATTAATAAAAACTT
*
1932731 AATTTAAT
1 AAATTAAT
1932739 TTTTTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAATAAAAACTT
Done.