Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1435217 original size:13 final size:13
Alignment explanation
Indices: 1435199--1435223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1435189 GAGTGTAAAG
1435199 GGTGTCGTGTGAT
1 GGTGTCGTGTGAT
1435212 GGTGTCGTGTGA
1 GGTGTCGTGTGA
1435224 GGTTGTAATG
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:0.08, C:0.08, G:0.48, T:0.36
Consensus pattern (13 bp):
GGTGTCGTGTGAT
Found at i:1436915 original size:14 final size:14
Alignment explanation
Indices: 1436875--1436917 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1436865 TAATGATTAA
1436875 TAGTATCAAATCAT
1 TAGTATCAAATCAT
*
1436889 TATTAGT--AATCAT
1 TAGTA-TCAAATCAT
1436902 TAGTATCAAATCAT
1 TAGTATCAAATCAT
1436916 TA
1 TA
1436918 AATATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 10 0.42
14 12 0.50
15 1 0.04
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (14 bp):
TAGTATCAAATCAT
Found at i:1436947 original size:14 final size:14
Alignment explanation
Indices: 1436930--1437097 Score: 82
Period size: 14 Copynumber: 12.6 Consensus size: 14
1436920 TATTAATAAT
1436930 AAATCATTATTATC
1 AAATCATTATTATC
1436944 AAAT-A--ATTA-C
1 AAATCATTATTATC
1436954 TAAATCATTA-T-T-
1 -AAATCATTATTATC
1436966 -A-TCATTATTATC
1 AAATCATTATTATC
1436978 AAATCATTATTAT-
1 AAATCATTATTATC
* *
1436991 -AATGATTAGTA-C
1 AAATCATTATTATC
1437003 TAAATCATTATTAT-
1 -AAATCATTATTATC
*
1437017 -AATAATTATTATC
1 AAATCATTATTATC
1437030 AAATCATTACTAAATCATC
1 AAATCATTA-T---T-ATC
* * *
1437049 CAATCATTAAATATT
1 AAATCATT-ATTATC
*
1437064 AAA--ATCATTAT-
1 AAATCATTATTATC
1437075 AAATCATTATTATC
1 AAATCATTATTATC
1437089 AAATCATTA
1 AAATCATTA
1437098 CTAAATCATA
Statistics
Matches: 116, Mismatches: 13, Indels: 50
0.65 0.07 0.28
Matches are distributed among these distances:
9 6 0.05
10 3 0.03
11 12 0.10
12 25 0.22
13 12 0.10
14 40 0.34
15 5 0.04
16 1 0.01
18 1 0.01
19 10 0.09
20 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (14 bp):
AAATCATTATTATC
Found at i:1436998 original size:26 final size:25
Alignment explanation
Indices: 1436878--1437038 Score: 135
Period size: 26 Copynumber: 6.5 Consensus size: 25
1436868 TGATTAATAG
*
1436878 TATCAAATCATTATTAGTAATCATTAG
1 TATCAAATCATTATTA-TAAT-ATTAT
1436905 TATCAAATC---ATTA-AATATTAAT
1 TATCAAATCATTATTATAATATT-AT
* *
1436927 AAT-AAATCATTATTATCAA-ATAAT
1 TATCAAATCATTATTAT-AATATTAT
*
1436951 TA-CTAAATCATTATTAT--CATTAT
1 TATC-AAATCATTATTATAATATTAT
*
1436974 TATCAAATCATTATTATAATGATTAG
1 TATCAAATCATTATTATAAT-ATTAT
1437000 TA-CTAAATCATTATTATAATAATTAT
1 TATC-AAATCATTATTATAAT-ATTAT
1437026 TATCAAATCATTA
1 TATCAAATCATTA
1437039 CTAAATCATC
Statistics
Matches: 110, Mismatches: 9, Indels: 31
0.73 0.06 0.21
Matches are distributed among these distances:
21 8 0.07
22 6 0.05
23 19 0.17
24 12 0.11
25 16 0.15
26 39 0.35
27 10 0.09
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.42
Consensus pattern (25 bp):
TATCAAATCATTATTATAATATTAT
Found at i:1437117 original size:59 final size:61
Alignment explanation
Indices: 1437004--1437118 Score: 180
Period size: 59 Copynumber: 1.9 Consensus size: 61
1436994 GATTAGTACT
*
1437004 AAATCATTATTATAATAATTATTATCAAATCATTACTAAATCATCCAATCATTAAATATTA
1 AAATCATTATTATAATAATTATTATCAAATCATTACTAAATCATACAATCATTAAATATTA
* * *
1437065 AAATCATTA-TA-AATCATTATTATCAAATCATTACTAAATCATATAATTATTAAA
1 AAATCATTATTATAATAATTATTATCAAATCATTACTAAATCATACAATCATTAAA
1437119 AAAAATCCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 39 0.78
60 2 0.04
61 9 0.18
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (61 bp):
AAATCATTATTATAATAATTATTATCAAATCATTACTAAATCATACAATCATTAAATATTA
Found at i:1437220 original size:11 final size:11
Alignment explanation
Indices: 1437204--1437229 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1437194 AAAAAACTTG
1437204 ATTACTAAATC
1 ATTACTAAATC
1437215 ATTACTAAATC
1 ATTACTAAATC
1437226 ATTA
1 ATTA
1437230 GTATCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:1437388 original size:21 final size:20
Alignment explanation
Indices: 1437364--1437419 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1437354 AAATCATTAC
1437364 TTAATCATTAAT-ATCAAATCA
1 TTAAT-ATTAATAAT-AAATCA
1437385 TTAAATATTAATAATAAATCA
1 TT-AATATTAATAATAAATCA
* *
1437406 TTATTAATAATAAT
1 TTAATATTAATAAT
1437420 TACTAAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.32
21 16 0.52
22 5 0.16
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATATTAATAATAAATCA
Found at i:1437411 original size:24 final size:23
Alignment explanation
Indices: 1437353--1437441 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 23
1437343 TATTAATGTT
1437353 TAAATCATTACTTAATCATTAAT-A
1 TAAATCATTA-TTAAT-ATTAATAA
1437377 TCAAATCATTA--AATATTAATAA
1 T-AAATCATTATTAATATTAATAA
* *
1437399 TAAATCATTATTAATAATAATTAC
1 TAAATCATTATTAATATTAA-TAA
*
1437423 TAAATCATTATTATTATTA
1 TAAATCATTATTAATATTA
1437442 TTATTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
21 15 0.27
22 5 0.09
23 7 0.12
24 20 0.36
25 9 0.16
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAATCATTATTAATATTAATAA
Found at i:1437417 original size:26 final size:27
Alignment explanation
Indices: 1437388--1437489 Score: 72
Period size: 24 Copynumber: 3.9 Consensus size: 27
1437378 CAAATCATTA
1437388 AATATTAATAAT-AAATCATTATTAAT
1 AATATTAATAATCAAATCATTATTAAT
* * *
1437414 AATA--ATTACT-AAATCATTATTATT
1 AATATTAATAATCAAATCATTATTAAT
* * *
1437438 ATTATTATTATTATCAAATTATTATT-AT
1 AATATTA--ATAATCAAATCATTATTAAT
*
1437466 AATGATT-ATCATCAAATCATTATT
1 AAT-ATTAATAATCAAATCATTATT
1437490 TTCATTATCA
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
24 20 0.34
26 20 0.34
28 5 0.09
29 13 0.22
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (27 bp):
AATATTAATAATCAAATCATTATTAAT
Found at i:1437458 original size:23 final size:24
Alignment explanation
Indices: 1437435--1437510 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 24
1437425 AATCATTATT
* *
1437435 ATTATTATT-ATTATTATCAAATT
1 ATTATTATTCATTATCATCAAATC
*
1437458 ATTATTATAATGATTATCATCAAATC
1 ATTATTAT--TCATTATCATCAAATC
1437484 ATTATT-TTCATTATCATCAAATC
1 ATTATTATTCATTATCATCAAATC
1437507 ATTA
1 ATTA
1437511 CTAAATCATC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
23 27 0.57
25 2 0.04
26 18 0.38
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTATTATTCATTATCATCAAATC
Found at i:1437502 original size:26 final size:25
Alignment explanation
Indices: 1437432--1437510 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 25
1437422 CTAAATCATT
* *
1437432 ATTATTATTATTATTATTATCAAATT
1 ATTATT-TTATTATTATCATCAAATC
* *
1437458 ATTATTATAATGATTATCATCAAATC
1 ATTATT-TTATTATTATCATCAAATC
*
1437484 ATTA-TTT-TCATTATCATCAAATC
1 ATTATTTTATTATTATCATCAAATC
1437507 ATTA
1 ATTA
1437511 CTAAATCATC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 19 0.40
24 1 0.02
25 1 0.02
26 26 0.55
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (25 bp):
ATTATTTTATTATTATCATCAAATC
Found at i:1437769 original size:14 final size:14
Alignment explanation
Indices: 1437750--1437814 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
1437740 AATAATTATT
1437750 AAATCATTAATATC
1 AAATCATTAATATC
*
1437764 AAATCATTATTAT-
1 AAATCATTAATATC
* * *
1437777 AATTTTATTATTA-C
1 AA-ATCATTAATATC
* *
1437791 TAATCATTACTATC
1 AAATCATTAATATC
1437805 AAATCATTAA
1 AAATCATTAA
1437815 ATATTAATAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
13 9 0.23
14 30 0.77
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:1441800 original size:28 final size:29
Alignment explanation
Indices: 1441735--1441791 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
1441725 TTTATATAAT
1441735 ATAATATATAACTTAAACTAACAAACTAAC
1 ATAAT-TATAACTTAAACTAACAAACTAAC
1441765 ATAA-TATAACTTAAACTAACAAACTAA
1 ATAATTATAACTTAAACTAACAAACTAA
1441792 TAATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.85
30 4 0.15
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (29 bp):
ATAATTATAACTTAAACTAACAAACTAAC
Found at i:1442379 original size:29 final size:29
Alignment explanation
Indices: 1442346--1442401 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1442336 GGCTCATGCA
* * *
1442346 TAGCTCGCTCGGATGCCCTGGCGACCTCT
1 TAGCTCGCACGGATGCCATGGCAACCTCT
1442375 TAGCTCGCACGGATGCCATGGCAACCT
1 TAGCTCGCACGGATGCCATGGCAACCT
1442402 TCAACAGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.36, G:0.27, T:0.21
Consensus pattern (29 bp):
TAGCTCGCACGGATGCCATGGCAACCTCT
Found at i:1443439 original size:20 final size:21
Alignment explanation
Indices: 1443416--1443459 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1443406 AGAGAAAGAC
*
1443416 TAAAACATAATA-TGAAAATA
1 TAAAACAAAATACTGAAAATA
* *
1443436 TAAAATAAAATACTTAAAATA
1 TAAAACAAAATACTGAAAATA
1443457 TAA
1 TAA
1443460 GAGTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAACAAAATACTGAAAATA
Found at i:1443609 original size:20 final size:20
Alignment explanation
Indices: 1443584--1443629 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1443574 ATGAATCATG
1443584 GGGGTTTGATTAATTAAGAA
1 GGGGTTTGATTAATTAAGAA
1443604 GGGGTTTGATTAATTAAGAA
1 GGGGTTTGATTAATTAAGAA
*
1443624 GTGGTT
1 GGGGTT
1443630 GATGCATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (20 bp):
GGGGTTTGATTAATTAAGAA
Found at i:1452547 original size:20 final size:20
Alignment explanation
Indices: 1452519--1452556 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1452509 GTATGTTCAA
*
1452519 GGGGTATCGATTCCCCCTGG
1 GGGGGATCGATTCCCCCTGG
1452539 GGGGGATCGATTCCCCCT
1 GGGGGATCGATTCCCCCT
1452557 AAAGGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGATCGATTCCCCCTGG
Found at i:1453011 original size:46 final size:46
Alignment explanation
Indices: 1452960--1453064 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
1452950 TTATATGACT
* *
1452960 ATATGAAATGATATATGAATATGCAATACGTGATATATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
* *
1453006 ATATGAAATGGCATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
1453052 ATATGAAAT-ACAT
1 ATATGAAATGACAT
1453065 GGTTACACAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 3 0.06
46 51 0.94
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
Found at i:1453264 original size:17 final size:17
Alignment explanation
Indices: 1453242--1453306 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 17
1453232 ACAGATTACA
1453242 TCCTTCGGGATGACAGG
1 TCCTTCGGGATGACAGG
1453259 TCCTTCTGGACACAGATGACA--
1 TCCTTC-GG-----GATGACAGG
*
1453280 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGACAGG
1453297 TCCTTCGGGA
1 TCCTTCGGGA
1453307 CATTTATACG
Statistics
Matches: 39, Mismatches: 1, Indels: 16
0.70 0.02 0.29
Matches are distributed among these distances:
15 6 0.15
17 16 0.41
18 2 0.05
20 2 0.05
21 6 0.15
23 7 0.18
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.26
Consensus pattern (17 bp):
TCCTTCGGGATGACAGG
Found at i:1453270 original size:38 final size:38
Alignment explanation
Indices: 1453213--1453308 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
1453203 TATAAGACAT
* *
1453213 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
* *
1453251 ATGACAGGTCCTTCTGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1453289 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
1453309 TTTATACGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:1459789 original size:23 final size:22
Alignment explanation
Indices: 1459762--1459836 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
1459752 TGATATATGA
1459762 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
1459785 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
1459807 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
1459831 ATATGA
1 ATATGA
1459837 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:1459795 original size:46 final size:46
Alignment explanation
Indices: 1459744--1459848 Score: 185
Period size: 46 Copynumber: 2.3 Consensus size: 46
1459734 CTATATGACT
*
1459744 ATATGAAATGATATATGAATATGCAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
*
1459790 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
1459836 ATATGAAAT-ACAT
1 ATATGAAATGACAT
1459849 GGTTACACAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 4 0.07
46 53 0.93
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
Found at i:1460065 original size:38 final size:38
Alignment explanation
Indices: 1459997--1460092 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
1459987 TATAAGATAC
* * * * *
1459997 ATGATAGGTCCTACGGGACACAGATTACATCTTTCGGG
1 ATGACAGGTCCTTCGGGACACAAATGACATCCTTCGGG
*
1460035 ATGACAGGTTCTTCGGGACACAAATGACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAAATGACATCCTTCGGG
*
1460073 ATGATAGGTCCTTCGGGACA
1 ATGACAGGTCCTTCGGGACA
1460093 TTTATACGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAAATGACATCCTTCGGG
Found at i:1460813 original size:43 final size:43
Alignment explanation
Indices: 1460740--1461158 Score: 183
Period size: 43 Copynumber: 9.8 Consensus size: 43
1460730 ATTTTATGAA
* * *
1460740 ATTGTAAAAAAT-TAGATGCCTTAATTATAAAGGTAGAAATTGAA
1 ATTGAAAAAAATAT-GA-GCCTCAATTATAAAGGTAGAAATTGAG
* *
1460784 ATTGAAAAAAATATGAGCCTCAATCATAAATGG-A-TAATTGAG
1 ATTGAAAAAAATATGAGCCTCAATTATAAA-GGTAGAAATTGAG
* * * * * *
1460826 A-T-AAAAAATTCTTAAGGGCCTCAATTAGAAAGTTAGAAAGTGAG
1 ATTGAAAAAA---ATATGAGCCTCAATTATAAAGGTAGAAATTGAG
* * * *
1460870 ATT-AAAAAAATTTAAGGGCCTCAATTATAAAGTTA-AAAGTGAG
1 ATTGAAAAAAA--TATGAGCCTCAATTATAAAGGTAGAAATTGAG
* * * *
1460913 ATT--AAAAATTAGGGGCCTCAATTATAAAAGTAGAAATTGAG
1 ATTGAAAAAAATATGAGCCTCAATTATAAAGGTAGAAATTGAG
* * *
1460954 ATTGAAAAAAACT-TAGAGGCCTTAATTGA-AAAGGTAGAAAATGAA
1 ATTGAAAAAAA-TAT-GA-GCCTCAATT-ATAAAGGTAGAAATTGAG
** ** * * *
1460999 ATTGAAAAACCTTAAAAGCTTCAATTATAAAGTTA-AAAGTGAG
1 ATTGAAAAA-AATATGAGCCTCAATTATAAAGGTAGAAATTGAG
* * *
1461042 ATT-ATAAAATTAGTG-GCCTCAATTATAAAGGTA-AAAATG-G
1 ATTGAAAAAAATA-TGAGCCTCAATTATAAAGGTAGAAATTGAG
** ** *
1461082 ATTGAAAAAAAT-TAGAGATTTCAATTATAAAAATAAAAAGTT-AG
1 ATTGAAAAAAATAT-GAG-CCTCAATTATAAAGGTAGAAA-TTGAG
* * *
1461126 ATTGAATAATATTAGGA-CCTCAATTATAAAGGT
1 ATTGAA-AAAAATATGAGCCTCAATTATAAAGGT
1461159 CAAAAATAAG
Statistics
Matches: 288, Mismatches: 57, Indels: 61
0.71 0.14 0.15
Matches are distributed among these distances:
39 1 0.00
40 31 0.11
41 42 0.15
42 30 0.10
43 70 0.24
44 67 0.23
45 46 0.16
46 1 0.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (43 bp):
ATTGAAAAAAATATGAGCCTCAATTATAAAGGTAGAAATTGAG
Found at i:1460877 original size:44 final size:44
Alignment explanation
Indices: 1460829--1461090 Score: 185
Period size: 44 Copynumber: 6.1 Consensus size: 44
1460819 AATTGAGATA
*
1460829 AAAAATTCTTAAGGGCCTCAATTAGAAAGTTAGAAAGTGAGATTAA
1 AAAAA-TCTTAAGGGCCTCAATTAGAAAGTTAGAAAGTGAGATT-G
*
1460875 AAAAAT-TTAAGGGCCTCAATTATAAAGTTA-AAAGTGAGATT-
1 AAAAATCTTAAGGGCCTCAATTAGAAAGTTAGAAAGTGAGATTG
* * *
1460916 AAAAA--TTAGGGGCCTCAATTATAAAAG-TAGAAATTGAGATTG
1 AAAAATCTTAAGGGCCTCAATTA-GAAAGTTAGAAAGTGAGATTG
* * * * *
1460958 AAAAAAACTT-AGAGGCCTTAATT-GAAAAGGTAGAAAATGAAATTG
1 -AAAAATCTTAAG-GGCCTCAATTAG-AAAGTTAGAAAGTGAGATTG
* ** * *
1461003 AAAAACCTTAAAAGCTTCAATTATAAAGTTA-AAAGTGAGATT-
1 AAAAATCTTAAGGGCCTCAATTAGAAAGTTAGAAAGTGAGATTG
* * *
1461045 ATAAAA--TT-AGTGGCCTCAATTATAAAGGTA-AAAATG-GATTG
1 A-AAAATCTTAAG-GGCCTCAATTAGAAAGTTAGAAAGTGAGATTG
1461086 AAAAA
1 AAAAA
1461091 AATTAGAGAT
Statistics
Matches: 179, Mismatches: 23, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
40 26 0.15
41 43 0.24
42 1 0.01
43 29 0.16
44 49 0.27
45 26 0.15
46 5 0.03
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (44 bp):
AAAAATCTTAAGGGCCTCAATTAGAAAGTTAGAAAGTGAGATTG
Found at i:1460992 original size:129 final size:127
Alignment explanation
Indices: 1460854--1461098 Score: 348
Period size: 129 Copynumber: 1.9 Consensus size: 127
1460844 CCTCAATTAG
* * * * **
1460854 AAAGTTAGAAAGTGAGATTAAAAAAATTTAAGGGCCTCAATTATAAAGTTAAAAGTGAGATTA-A
1 AAAGGTAGAAAATGAAATTAAAAAAACTTAAAAGCCTCAATTATAAAGTTAAAAGTGAGATTATA
*
1460918 AAATTAGGGGCCTCAATTATAAAAGTAGAAATTGAGATTGAAAAAAACTTAGAGGCCTTAATTGA
66 AAATTAGGGGCCTCAATTATAAAAGTA-AAAATG-GATTGAAAAAAA-TTAGAGGCCTTAATTGA
* * *
1460983 AAAGGTAGAAAATGAAATTGAAAAACCTTAAAAGCTTCAATTATAAAGTTAAAAGTGAGATTATA
1 AAAGGTAGAAAATGAAATTAAAAAAACTTAAAAGCCTCAATTATAAAGTTAAAAGTGAGATTATA
* *
1461048 AAATTAGTGGCCTCAATTATAAAGGTAAAAATGGATTGAAAAAAATTAGAG
66 AAATTAGGGGCCTCAATTATAAAAGTAAAAATGGATTGAAAAAAATTAGAG
1461099 ATTTCAATTA
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
127 6 0.06
128 12 0.12
129 59 0.57
130 26 0.25
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (127 bp):
AAAGGTAGAAAATGAAATTAAAAAAACTTAAAAGCCTCAATTATAAAGTTAAAAGTGAGATTATA
AAATTAGGGGCCTCAATTATAAAAGTAAAAATGGATTGAAAAAAATTAGAGGCCTTAATTGA
Found at i:1461074 original size:85 final size:85
Alignment explanation
Indices: 1460837--1461177 Score: 274
Period size: 85 Copynumber: 4.0 Consensus size: 85
1460827 TAAAAAATTC
* * * *
1460837 TTAAGGGCCTCAATTA-GAAAGTTAGAAAGTGAGATTAAAAAAATTTAAGGGCCTCAATTATAAA
1 TTAAGAGCTTCAATTATAAAAGTTAGAAAGTGAGATTAAAAAAACTT-AGGGCCTCAATTATAAA
* *
1460901 GTTAAAAGTGAGATT-AAAAA
65 GGTAAAAATGAGATTGAAAAA
* * * * *
1460921 TTAGGGGCCTCAATTATAAAAG-TAGAAATTGAGATTGAAAAAAACTTAGAGGCCTTAATTGA-A
1 TTAAGAGCTTCAATTATAAAAGTTAGAAAGTGAGATT-AAAAAAACTTAG-GGCCTCAATT-ATA
*
1460984 AAGGTAGAAAATGAAATTGAAAAA
63 AAGGTA-AAAATGAGATTGAAAAA
* *
1461008 CCTTAAAAGCTTCAATTAT-AAAGTTA-AAAGTGAGATT-ATAAAA-TTAGTGGCCTCAATTATA
1 --TTAAGAGCTTCAATTATAAAAGTTAGAAAGTGAGATTAAAAAAACTTAG-GGCCTCAATTATA
1461069 AAGGTAAAAATG-GATTGAAAAAAA
63 AAGGTAAAAATGAGATTG--AAAAA
* * * * * * *
1461093 TT-AGAGATTTCAATTATAAAA-ATAAAAAGTTAGATTGAATAATA-TTAGGACCTCAATTATAA
1 TTAAGAG-CTTCAATTATAAAAGTTAGAAAGTGAGATT-AAAAAAACTTAGGGCCTCAATTATAA
* *
1461155 AGGTCAAAAATAAGATTTAAAAA
64 AGGT-AAAAATGAGATTGAAAAA
1461178 AAAATTAAAG
Statistics
Matches: 213, Mismatches: 25, Indels: 37
0.77 0.09 0.13
Matches are distributed among these distances:
82 3 0.01
83 17 0.08
84 50 0.23
85 75 0.35
86 30 0.14
87 9 0.04
88 14 0.07
89 15 0.07
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (85 bp):
TTAAGAGCTTCAATTATAAAAGTTAGAAAGTGAGATTAAAAAAACTTAGGGCCTCAATTATAAAG
GTAAAAATGAGATTGAAAAA
Found at i:1461171 original size:43 final size:42
Alignment explanation
Indices: 1460888--1461208 Score: 176
Period size: 45 Copynumber: 7.5 Consensus size: 42
1460878 AATTTAAGGG
* * * *
1460888 CCTCAATTATAAAGTTAAAAGTGAGATT--A-AAAATTAGGGG
1 CCTCAATTATAAAGGTAAAAAT-AGATTGAATAAAATTAGAGA
* * * *
1460928 CCTCAATTATAAAAGTAGAAATTGAGATTGAAAAAAACTTAGAGG
1 CCTCAATTATAAAGGTA-AAAAT-AGATTGAATAAAA-TTAGAGA
* * * *
1460973 CCTTAATTGA-AAAGGTAGAAAATGAAATTGAA-AAACCTTA-AAA
1 CCTCAATT-ATAAAGGTA-AAAAT-AGATTGAATAAA-ATTAGAGA
* * * * *
1461016 GCTTCAATTATAAAGTTAAAAGTGAGATT--ATAAAATTAGTGG
1 -CCTCAATTATAAAGGTAAAAAT-AGATTGAATAAAATTAGAGA
* *
1461058 CCTCAATTATAAAGGTAAAAATGGATTGAAAAAAATTAGAGA
1 CCTCAATTATAAAGGTAAAAATAGATTGAATAAAATTAGAGA
** ** *
1461100 TTTCAATTATAAAAATAAAAAGTTAGATTGAATAATATTAG-GA
1 CCTCAATTATAAAGGTAAAAA--TAGATTGAATAAAATTAGAGA
* * *
1461143 CCTCAATTATAAAGGTCAAAAATAAGATTTAAAAAAAAATTAAAGA
1 CCTCAATTATAAAGGT-AAAAAT-AGA-TT-GAATAAAATTAGAGA
*
1461189 CCT-AATTATAAAGATAAAAA
1 CCTCAATTATAAAGGTAAAAA
1461209 AATGAAAACC
Statistics
Matches: 218, Mismatches: 43, Indels: 36
0.73 0.14 0.12
Matches are distributed among these distances:
40 19 0.09
41 33 0.15
42 31 0.14
43 29 0.13
44 49 0.22
45 51 0.23
46 6 0.03
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (42 bp):
CCTCAATTATAAAGGTAAAAATAGATTGAATAAAATTAGAGA
Found at i:1461224 original size:29 final size:30
Alignment explanation
Indices: 1461175--1461243 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
1461165 TAAGATTTAA
* * *
1461175 AAAAAAATTAAAGACCTAATTATAAAGAT-
1 AAAAAAATGAAAGACCCAATTACAAAGATG
* *
1461204 AAAAAAATGAAA-ACCCCAATTGCAAGGATG
1 AAAAAAATGAAAGA-CCCAATTACAAAGATG
1461234 AAAAAAATGA
1 AAAAAAATGA
1461244 GTGCTCAGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 1 0.03
29 22 0.67
30 10 0.30
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (30 bp):
AAAAAAATGAAAGACCCAATTACAAAGATG
Found at i:1462477 original size:32 final size:32
Alignment explanation
Indices: 1462430--1462495 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1462420 GATAAACTAA
*
1462430 ATTCGGGTTGCTTTCAGTTC-GGATTACTTTCG
1 ATTCGAGTTGCTTTCAGTTCAGG-TTACTTTCG
* *
1462462 ATTCGAGTTGGTTTCAGTTCAGGTTGCTTTCG
1 ATTCGAGTTGCTTTCAGTTCAGGTTACTTTCG
1462494 AT
1 AT
1462496 CCAACTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.44
Consensus pattern (32 bp):
ATTCGAGTTGCTTTCAGTTCAGGTTACTTTCG
Found at i:1463121 original size:17 final size:17
Alignment explanation
Indices: 1463075--1463124 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 17
1463065 TAATTTGTTT
*
1463075 TTTAAATT-TTATTTTA
1 TTTAAATTATTATTTAA
*
1463091 TTTTAATTA--A-TTAA
1 TTTAAATTATTATTTAA
1463105 TTTAAATTATTATTTAA
1 TTTAAATTATTATTTAA
1463122 TTT
1 TTT
1463125 TAAGTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
14 11 0.41
15 1 0.04
16 8 0.30
17 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAAATTATTATTTAA
Found at i:1463125 original size:31 final size:31
Alignment explanation
Indices: 1463075--1463148 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1463065 TAATTTGTTT
*
1463075 TTTAAATTTTATTTTATTTTAA-TTAATTAA
1 TTTAAATTTTATTTAATTTTAAGTTAATTAA
**
1463105 TTTAAATTATTATTTAATTTTAAGTTAATTTT
1 TTTAAATT-TTATTTAATTTTAAGTTAATTAA
1463137 TATTAAATTTTA
1 T-TTAAATTTTA
1463149 ACCACATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 8 0.21
31 13 0.34
32 10 0.26
33 7 0.18
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (31 bp):
TTTAAATTTTATTTAATTTTAAGTTAATTAA
Found at i:1463825 original size:15 final size:14
Alignment explanation
Indices: 1463776--1463831 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
1463766 TGACCATAAC
1463776 ATTATATATAAATA
1 ATTATATATAAATA
*
1463790 ATT-TATACTAAAAA
1 ATTATATA-TAAATA
*
1463804 ATAATATTATAAATA
1 ATTATA-TATAAATA
1463819 ATTATATATAAAT
1 ATTATATATAAAT
1463832 TTAAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 4 0.11
14 17 0.49
15 12 0.34
16 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATATATAAATA
Found at i:1464097 original size:17 final size:18
Alignment explanation
Indices: 1464059--1464104 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1464049 GTTTCTGAGA
1464059 GAATTAGAATCTGTGAAG
1 GAATTAGAATCTGTGAAG
*
1464077 GAATTAGAATCTGT-CAG
1 GAATTAGAATCTGTGAAG
*
1464094 GAATTGGAATC
1 GAATTAGAATC
1464105 CAATTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (18 bp):
GAATTAGAATCTGTGAAG
Found at i:1473293 original size:29 final size:31
Alignment explanation
Indices: 1473215--1473293 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 31
1473205 ATAAATATTT
1473215 AAATTTATAAAGACTAAAATAGATAAAAACAA
1 AAATTT-TAAAGACTAAAATAGATAAAAACAA
* * * * *
1473247 AAATTTTAAGGA-TCAAATA-TTACAAACTA
1 AAATTTTAAAGACTAAAATAGATAAAAACAA
1473276 AAA-TTTAAAGACTAAAAT
1 AAATTTTAAAGACTAAAAT
1473294 GGCAAAAGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 7 0.18
29 15 0.38
30 6 0.15
31 5 0.13
32 6 0.15
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (31 bp):
AAATTTTAAAGACTAAAATAGATAAAAACAA
Found at i:1474867 original size:40 final size:40
Alignment explanation
Indices: 1474823--1474989 Score: 219
Period size: 40 Copynumber: 4.2 Consensus size: 40
1474813 TCTAAAAGAT
* * *
1474823 GATGACACATTTCCTACGTGATGAGGATACCTAGTCGAGG
1 GATGACATAGTTCCTACGTGATGAGGAGACCTAGTCGAGG
* * *
1474863 GATGACATAGTTCCTACGTAATAAGGAGACCTAGTCAAGG
1 GATGACATAGTTCCTACGTGATGAGGAGACCTAGTCGAGG
*
1474903 GATGACATGGTTCCTACGTGATGAGGAGACCTAGTCGAGG
1 GATGACATAGTTCCTACGTGATGAGGAGACCTAGTCGAGG
* * * *
1474943 GATGACATGGTTCATACGTGATGAGGAAATCTAGTCG-GTG
1 GATGACATAGTTCCTACGTGATGAGGAGACCTAGTCGAG-G
1474983 GATGACA
1 GATGACA
1474990 ATATTTGTTG
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (40 bp):
GATGACATAGTTCCTACGTGATGAGGAGACCTAGTCGAGG
Found at i:1475648 original size:169 final size:171
Alignment explanation
Indices: 1475303--1475705 Score: 542
Period size: 169 Copynumber: 2.3 Consensus size: 171
1475293 TCATTTGTTA
* * *
1475303 TGAAGTTGAGCTTTGAATTGTATATCATTCGTTGTGAAGTTGAAATCCAATCTTGTATTGTTGCT
1 TGAAGTTGAGCTTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAA---TG--TTG-T-CT
* * * * * *
1475368 TGTGGGCATGATATCCTTCGTCGTGAAGTTAAAATATTGGATGTTTCGAGTCCAATATCCTTCAC
59 TATGAGAACGATATCCTTCGTCGTGAAGTTAAAATAGTGGATATTTCGAGTCCAATATCCTTCAC
*
1475433 CGTGAAGTTGAAATTAGCTCTGAATGAAACTGGGAAACCCCTTCGCTG
124 CGGGAAGTTGAAATTAGCTCTGAATGAAACTGGGAAACCCCTTCGCTG
*
1475481 TGAAGTTGAGCTTTGAATTGGATATCCTTCACTGTGAAGTTGAAATCCAATGTTGT-TTATGAGA
1 TGAAGTTGAGCTTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAATGTTGTCTTATGAGA
* * * *
1475545 ACGATATCCTTCGTCGTGGAGTTGAAATCGTGGATATTTCGAGTCCAATATCCTTC-GCGGGAAG
66 ACGATATCCTTCGTCGTGAAGTTAAAATAGTGGATATTTCGAGTCCAATATCCTTCACCGGGAAG
*
1475609 TTGAAATTGGCTCTGAATGAAACT-GGAAAGCCCCTTCGCTG
131 TTGAAATTAGCTCTGAATGAAACTGGGAAA-CCCCTTCGCTG
* * *
1475650 TGAAGTTAAGCTTTGAATTGGATATCCTTCATTGTGAAGTTAAAATCCAATCTTGT
1 TGAAGTTGAGCTTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAATGTTGT
1475706 GTTGTTTCGC
Statistics
Matches: 204, Mismatches: 20, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
168 5 0.02
169 92 0.45
170 55 0.27
172 1 0.00
173 3 0.01
175 2 0.01
178 46 0.23
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (171 bp):
TGAAGTTGAGCTTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAATGTTGTCTTATGAGA
ACGATATCCTTCGTCGTGAAGTTAAAATAGTGGATATTTCGAGTCCAATATCCTTCACCGGGAAG
TTGAAATTAGCTCTGAATGAAACTGGGAAACCCCTTCGCTG
Found at i:1475760 original size:64 final size:62
Alignment explanation
Indices: 1475659--1475826 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 62
1475649 GTGAAGTTAA
* * * *
1475659 GCTTTGAATTGGATATCCTTCATTGTGAAGTTAAAATCCAATCTTGT-GTTGTTTCGCCAAATTG
1 GCTTTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATC--GTAG-TGCTTCACCAAATTG
1475723 GCTTTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAA--GTAGTGCTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATCGTAGTGCTTCACCAAATTG
*
1475783 GCTTTGAGTTGGATATCCTTCATTGTGAATTTGAAATCCAATCG
1 GCTTTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATCG
1475827 AGAATATTAT
Statistics
Matches: 96, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
60 55 0.57
61 1 0.01
62 1 0.01
64 39 0.41
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (62 bp):
GCTTTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAATCGTAGTGCTTCACCAAATTG
Found at i:1477509 original size:14 final size:14
Alignment explanation
Indices: 1477476--1477510 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1477466 GTAAGAGAAG
*
1477476 TGTATGTATTCCAG
1 TGTATGTATTCCAA
*
1477490 TATATGTATTCCAA
1 TGTATGTATTCCAA
1477504 TGTATGT
1 TGTATGT
1477511 TCTAGATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (14 bp):
TGTATGTATTCCAA
Found at i:1482409 original size:29 final size:28
Alignment explanation
Indices: 1482329--1482417 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 28
1482319 TTTAAATTTA
*
1482329 TAAAGACTAAAATAGATAAAAACAAAACTTT
1 TAAAGACTAAAATAG-CAAAAACAAAA--TT
* * * *
1482360 TAAGGA-TCAAATATCACAAACTAAAATT
1 TAAAGACTAAAATAGCAAAAAC-AAAATT
1482388 TAAAGACTAAAATAGCAAAAACAGAAATT
1 TAAAGACTAAAATAGCAAAAACA-AAATT
1482417 T
1 T
1482418 TAGGGACATA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
28 8 0.17
29 23 0.50
30 10 0.22
31 5 0.11
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.22
Consensus pattern (28 bp):
TAAAGACTAAAATAGCAAAAACAAAATT
Found at i:1494686 original size:29 final size:29
Alignment explanation
Indices: 1494608--1494705 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
1494598 ATAAATATTT
1494608 AAATTTATAAAGACTAAAATAGATAAAAACAA
1 AAATTT-TAAAGACTAAAAT--ATAAAAACAA
* * * *
1494640 AAATTTTAAGGA-TCAAATATCACAAACTA
1 AAATTTTAAAGACTAAAATAT-AAAAACAA
* *
1494669 AAA-TTTAAAGACTAAAATAGCAAAAACAG
1 AAATTTTAAAGACTAAAATA-TAAAAACAA
1494698 AAATTTTA
1 AAATTTTA
1494706 GGGACATAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
28 9 0.17
29 23 0.44
30 9 0.17
31 5 0.10
32 6 0.12
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.24
Consensus pattern (29 bp):
AAATTTTAAAGACTAAAATATAAAAACAA
Found at i:1499625 original size:96 final size:95
Alignment explanation
Indices: 1499284--1499675 Score: 359
Period size: 96 Copynumber: 4.1 Consensus size: 95
1499274 CCTCCTATTG
* * *
1499284 ATTTCTGTATTTCCGCTTTACTTAGTTTAATTTTTGGATTCGAAA-TGAGATTCATTATATGTTC
1 ATTTCTATATTTCCGC-TTACTTAGTTTAATTTTTGGATTC-AAAGTAAGATTCATAATATGTTC
* * *
1499348 TTTTTGTTTGATTAAATCACCGCATGGCTCTTC
64 -TTTTGTTTGATTAAATTACCTCATAGCTCTTC
* * * * **
1499381 ATTTCTTTATTTCCGCTGTACTTAGTTT-ATTCTTCGGATTCGAAGTAAGGTTCATAATATAATC
1 ATTTCTATATTTCCGCT-TACTTAGTTTAATT-TTTGGATTCAAAGTAAGATTCATAATATGTTC
* * * *
1499445 TTTTGATTGAATAAATTCCCTCATATCT-TTCC
64 TTTTGTTTGATTAAATTACCTCATAGCTCTT-C
* * * * * * * * *
1499477 ATTTTTGTATTTCTG-GT--TTACTTTAATTTTTGGATCCGAAGCAAGATGCATAATATGTTCTT
1 ATTTCTATATTTCCGCTTACTTAGTTTAATTTTTGGATTCAAAGTAAGATTCATAATATGTTCTT
* *
1499539 TTGTTTGATTAAGTTACCTCGTAGCTCTTC
66 TTGTTTGATTAAATTACCTCATAGCTCTTC
* * * *
1499569 ATTTCCATATTTCCGCTCTACCTAGTTTAATTTGTGGATTCAAAGTAAGATTCATAATATGTCCT
1 ATTTCTATATTTCCGCT-TACTTAGTTTAATTTTTGGATTCAAAGTAAGATTCATAATATGTTCT
**
1499634 TTTGTTTGATTAAATTACAGCATAGCTCGTT-
65 TTTGTTTGATTAAATTACCTCATAGCTC-TTC
1499665 ATTTCTA-ATTT
1 ATTTCTATATTT
1499676 TTTTATTCGA
Statistics
Matches: 233, Mismatches: 51, Indels: 24
0.76 0.17 0.08
Matches are distributed among these distances:
92 65 0.28
93 5 0.02
94 2 0.01
95 6 0.03
96 106 0.45
97 49 0.21
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.47
Consensus pattern (95 bp):
ATTTCTATATTTCCGCTTACTTAGTTTAATTTTTGGATTCAAAGTAAGATTCATAATATGTTCTT
TTGTTTGATTAAATTACCTCATAGCTCTTC
Found at i:1511951 original size:31 final size:31
Alignment explanation
Indices: 1511913--1512068 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
1511903 CCCGAAGGAC
* * *
1511913 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1511944 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1511975 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1512006 CAGTCCATATATCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1512037 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1512068 C
1 C
1512069 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1513841 original size:10 final size:10
Alignment explanation
Indices: 1513826--1513851 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1513816 AACTACCCTC
1513826 TTTTTTTCTT
1 TTTTTTTCTT
1513836 TTTTTTTCTT
1 TTTTTTTCTT
1513846 TTTTTT
1 TTTTTT
1513852 GCATCCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:1513935 original size:16 final size:16
Alignment explanation
Indices: 1513896--1513938 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1513886 AGCATCAGTT
*
1513896 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
1513912 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
1513929 CTTATCAATC
1 CTTATCAATC
1513939 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:1516788 original size:31 final size:31
Alignment explanation
Indices: 1516750--1516892 Score: 216
Period size: 31 Copynumber: 4.6 Consensus size: 31
1516740 TCCATAGATT
* *
1516750 CCGAAGAACCTAGGTAATCAGTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
* *
1516781 CCAAAGAACATAGGTAAATAGTAC-ATATGTC
1 CCGAAGAACATAGGTAAACAGT-CTATATGTC
1516812 CCGAAGAACATAGGTAAACAGTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
* *
1516843 CCGAAGAACATAGGTAAACATTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
1516874 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
1516893 CCTCGACCCT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
30 1 0.01
31 100 0.98
32 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCTATATGTC
Found at i:1517805 original size:23 final size:22
Alignment explanation
Indices: 1517779--1517836 Score: 84
Period size: 20 Copynumber: 2.7 Consensus size: 22
1517769 TTCGCTTGAG
*
1517779 GGGTATCGATTCCCCCATTGAAT
1 GGGTACCGATTCCCCC-TTGAAT
1517802 GGGTACCGATT--CCCTTGAAT
1 GGGTACCGATTCCCCCTTGAAT
1517822 GGGTACCGATTCCCC
1 GGGTACCGATTCCCC
1517837 TTGCCCAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 17 0.53
21 3 0.09
22 2 0.06
23 10 0.31
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.28
Consensus pattern (22 bp):
GGGTACCGATTCCCCCTTGAAT
Found at i:1519091 original size:15 final size:15
Alignment explanation
Indices: 1519071--1519099 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1519061 TTGATTGAAC
1519071 AATAAATTATATATT
1 AATAAATTATATATT
1519086 AATAAATTATATAT
1 AATAAATTATATAT
1519100 CAATGATTGA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATATATT
Found at i:1524318 original size:32 final size:32
Alignment explanation
Indices: 1524266--1524338 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
1524256 CATAAATCTT
*
1524266 TTGGTATTCGGGTCGAATTTTTTTTTAAAAAAA
1 TTGGGATTCGGGTCGAA-TTTTTTTTAAAAAAA
*
1524299 TTGGGATT-GGGTCGGATTTTTTTTAAAAAAA
1 TTGGGATTCGGGTCGAATTTTTTTTAAAAAAA
*
1524330 TCGGG-TTCG
1 TTGGGATTCG
1524339 ATTCGGGTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 2 0.06
31 20 0.56
32 7 0.19
33 7 0.19
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (32 bp):
TTGGGATTCGGGTCGAATTTTTTTTAAAAAAA
Found at i:1524329 original size:33 final size:33
Alignment explanation
Indices: 1524266--1524329 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1524256 CATAAATCTT
* *
1524266 TTGGTATTCGGGTCGAATTTTTTTTTAAAAAAA
1 TTGGGATTCGGGTCGAATTTTTTTTAAAAAAAA
*
1524299 TTGGGATT-GGGTCGGATTTTTTTTAAAAAAA
1 TTGGGATTCGGGTCGAATTTTTTTTAAAAAAA
1524330 TCGGGTTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGGGATTCGGGTCGAATTTTTTTTAAAAAAAA
Found at i:1524388 original size:32 final size:32
Alignment explanation
Indices: 1524344--1524479 Score: 145
Period size: 32 Copynumber: 4.3 Consensus size: 32
1524334 GTTCGATTCG
* *
1524344 GGTCGGGTTTTTTTAATTTTGATATTCGGGTC
1 GGTCGGGTTTTTTTAAGTATGATATTCGGGTC
* * *
1524376 GGTCGGGATTTTTAAAGTGTGATATTCGGGTC
1 GGTCGGGTTTTTTTAAGTATGATATTCGGGTC
1524408 GGTCGGGTTTTTTTAAGTATGATATTC--G--
1 GGTCGGGTTTTTTTAAGTATGATATTCGGGTC
* * * *
1524436 AGTCGGATTTTTTTAAGTTTGATATTCGGTTC
1 GGTCGGGTTTTTTTAAGTATGATATTCGGGTC
*
1524468 AGGTCGAGTTTT
1 -GGTCGGGTTTT
1524480 ACAATAATAC
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
28 24 0.28
30 1 0.01
32 52 0.61
33 8 0.09
ACGTcount: A:0.17, C:0.09, G:0.29, T:0.46
Consensus pattern (32 bp):
GGTCGGGTTTTTTTAAGTATGATATTCGGGTC
Found at i:1524441 original size:28 final size:28
Alignment explanation
Indices: 1524409--1524463 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1524399 ATTCGGGTCG
*
1524409 GTCGGGTTTTTTTAAGTATGATATTCGA
1 GTCGGATTTTTTTAAGTATGATATTCGA
*
1524437 GTCGGATTTTTTTAAGTTTGATATTCG
1 GTCGGATTTTTTTAAGTATGATATTCG
1524464 GTTCAGGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (28 bp):
GTCGGATTTTTTTAAGTATGATATTCGA
Found at i:1524925 original size:16 final size:16
Alignment explanation
Indices: 1524904--1524939 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1524894 AAGTTTCAGA
* *
1524904 TTCAGATTTCAATTCC
1 TTCAGATTCCAAATCC
1524920 TTCAGATTCCAAATCC
1 TTCAGATTCCAAATCC
1524936 TTCA
1 TTCA
1524940 CAGATTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (16 bp):
TTCAGATTCCAAATCC
Found at i:1535595 original size:3 final size:3
Alignment explanation
Indices: 1535587--1535622 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1535577 ATTCCCACAT
1535587 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1535623 CTCGGTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1536102 original size:3 final size:3
Alignment explanation
Indices: 1536094--1536138 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
1536084 ATTTATTTAT
* * * *
1536094 TTA TTA TTA TAA TTA TAA TAA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1536139 AAATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1537768 original size:19 final size:21
Alignment explanation
Indices: 1537740--1537778 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1537730 CTGATATTAC
1537740 TAAATAAATA-A-ATATTTTA
1 TAAATAAATATATATATTTTA
*
1537759 TAAATTAATATATATATTTT
1 TAAATAAATATATATATTTT
1537779 TTTAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATAAATATATATATTTTA
Found at i:1541607 original size:15 final size:15
Alignment explanation
Indices: 1541587--1541618 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1541577 TCAATACCTT
1541587 TTTTGCATACATACA
1 TTTTGCATACATACA
*
1541602 TTTTGCATACATTCA
1 TTTTGCATACATACA
1541617 TT
1 TT
1541619 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:1550398 original size:93 final size:93
Alignment explanation
Indices: 1550239--1550520 Score: 489
Period size: 93 Copynumber: 3.0 Consensus size: 93
1550229 GATCATAGTA
*
1550239 GAAAT-AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAATAAAGAA-ACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1550303 TGAACCCCGAAAAACCAATCATTGGATTT
65 TGAACCCCGAAAAACCAATCATTGGATTT
1550332 GAAATAAAGAAACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
1 GAAATAAAGAAACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
1550397 GAACCCCGAAAAACCAATCATTGGATTT
66 GAACCCCGAAAAACCAATCATTGGATTT
1550425 GAAATAAAGAAACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
1 GAAATAAAGAAACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
* * *
1550490 GAA-ACC-ACAGAACCAATCATTGAATTT
66 GAACCCCGA-AAAACCAATCATTGGATTT
1550517 GAAA
1 GAAA
1550521 GATGAATGTG
Statistics
Matches: 183, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
91 1 0.01
92 23 0.13
93 154 0.84
94 5 0.03
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (93 bp):
GAAATAAAGAAACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
GAACCCCGAAAAACCAATCATTGGATTT
Found at i:1550627 original size:115 final size:115
Alignment explanation
Indices: 1550425--1550755 Score: 569
Period size: 115 Copynumber: 2.9 Consensus size: 115
1550415 CATTGGATTT
*
1550425 GAAATAAAGAA-ACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAT-AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1550489 TGAAACCACAGAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGTA
65 TGAAACCACAGAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGTA
1550540 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
1 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
1550605 GAAACCACAGAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGTA
66 GAAACCACAGAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGTA
* * *
1550655 TAAATAAGAGGACCCAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-
1 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
* *
1550719 GGAACCACAGAACCAATCATTGGAA-TTAAAAGATGAA
66 GAAACCACAGAACCAATCATT-GAATTTGAAAGATGAA
1550756 CTGCATGATC
Statistics
Matches: 208, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
114 36 0.17
115 172 0.83
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (115 bp):
GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT
GAAACCACAGAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGTA
Found at i:1551662 original size:116 final size:116
Alignment explanation
Indices: 1551444--1552108 Score: 860
Period size: 116 Copynumber: 5.8 Consensus size: 116
1551434 GCAAAGATTC
* * * * * *
1551444 AAATTCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCT
1 AAATTCATTATTTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCT
* *
1551505 GAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* *
1551557 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAATTCATAATAAGAAGAACTCATCATCTG
1 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
*
1551622 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTGTTT
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
1551673 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1551738 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
1551789 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
* * *
1551854 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * * * * * * * *
1551905 AAATCCATCACTTGATGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTG
1 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
* * * *
1551967 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTTGCTC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * * *** *
1552018 AAATCCATCACTTGATGGATCGGT-TTTTTTCCA-G-AGATGTTCATAATGAGAAGAA--C-TCA
1 AAATTCATTATTTGATGGAT---TAACATTGCCAGGTAGA-GTTCATAATGAGAAGAACTCATCA
1552077 TCT---GAA-GAAGAAGAAGTTCATAATGAGAAGAA
62 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1552109 CTCATCTGAA
Statistics
Matches: 510, Mismatches: 34, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
110 25 0.05
111 3 0.01
112 1 0.00
113 121 0.24
114 25 0.05
115 9 0.02
116 326 0.64
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (116 bp):
AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
Found at i:1552103 original size:36 final size:36
Alignment explanation
Indices: 1552056--1552141 Score: 154
Period size: 36 Copynumber: 2.4 Consensus size: 36
1552046 TTCCAGAGAT
*
1552056 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAA
1552092 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAA
*
1552128 GTTCACAATGAGAA
1 GTTCATAATGAGAA
1552142 TAGCTTATTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.20
Consensus pattern (36 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAA
Found at i:1552227 original size:120 final size:119
Alignment explanation
Indices: 1552090--1552369 Score: 341
Period size: 124 Copynumber: 2.3 Consensus size: 119
1552080 GAAGAAGAAG
*
1552090 AAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAAAAGTTCACAATGAGAATAGCTTATTCAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAA
* * * * *
1552154 CCTTTTGCATAATTCTATCACAG-AAGCAGATAGATTAGCATCAACCTTTCCAG-AGA
66 CCTTTTGAATAACTCTATCACAGAAAG-AAATAGATCAACATCAACC---CCAGTAGA
* *
1552210 AAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATT
1 AAGTTCATAATGAGAAGAACTCATCTG-A--AGAAAGAAAAAGTTCACAATGAGAAGAGCTTATT
* * * * *
1552275 CAATCTTTTGAATGACTCTATCACAGAAAGAAATAGGTCAACATCATCCCCAGTGGA
63 CAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACCCCAGTAGA
* *
1552332 AAGTTCATAATGAGAAGAACTCGTCTAAAGAAAGAAAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAAA
1552370 GGATTTATTC
Statistics
Matches: 138, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
119 9 0.07
120 27 0.20
121 6 0.04
122 27 0.20
123 2 0.01
124 64 0.46
125 3 0.02
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (119 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAA
CCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACCCCAGTAGA
Found at i:1552529 original size:3 final size:3
Alignment explanation
Indices: 1552521--1552559 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1552511 ATTTATTTAT
* *
1552521 TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1552560 ATATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1553869 original size:12 final size:12
Alignment explanation
Indices: 1553848--1553882 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1553838 TTTTATATGT
*
1553848 TTACTTTTATTA
1 TTACTATTATTA
1553860 TTACTATTATTA
1 TTACTATTATTA
*
1553872 TTATTATTATT
1 TTACTATTATT
1553883 TAACCATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (12 bp):
TTACTATTATTA
Found at i:1554182 original size:2 final size:2
Alignment explanation
Indices: 1554175--1554200 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1554165 TTATAAATTA
1554175 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
1554201 TTAAAATAAT
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):
AT
Found at i:1555957 original size:24 final size:23
Alignment explanation
Indices: 1555901--1555963 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
1555891 ATGTTCAAAC
*
1555901 AAGTTCGCTTATCAACTGTTTAT
1 AAGTTCGTTTATCAACTGTTTAT
*
1555924 AAGCTT-GTTTATCGACTTGTTTAT
1 AAG-TTCGTTTATCAAC-TGTTTAT
*
1555948 GAGTTCGTTTACTCAA
1 AAGTTCGTTTA-TCAA
1555964 TTCTTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 13 0.41
24 16 0.50
25 3 0.09
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (23 bp):
AAGTTCGTTTATCAACTGTTTAT
Found at i:1560788 original size:58 final size:61
Alignment explanation
Indices: 1560679--1560823 Score: 165
Period size: 58 Copynumber: 2.4 Consensus size: 61
1560669 TGTTAAGTTT
* * *
1560679 TCAACTATTAAAAGTTACAAAATGAT-CTTCTAATTATAGGAGGTTGATTTGTTAAGTC-C
1 TCAACTATTAAAAGTTACAAAATGATCCCTCTAAATATAGGAGATTGATTTGTTAAGTCAC
* * *
1560738 -CAACTTTTAAAAGTTACAAAATGATCCCTC-AAATATAGG-GCATTGCTTTGTTGAGTCAC
1 TCAACTATTAAAAGTTACAAAATGATCCCTCTAAATATAGGAG-ATTGATTTGTTAAGTCAC
** *
1560797 TTGACTATTAAAAGTTATAAAATGATC
1 TCAACTATTAAAAGTTACAAAATGATC
1560824 ATTCGACTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
57 1 0.01
58 45 0.62
59 4 0.06
60 22 0.31
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (61 bp):
TCAACTATTAAAAGTTACAAAATGATCCCTCTAAATATAGGAGATTGATTTGTTAAGTCAC
Found at i:1566025 original size:33 final size:33
Alignment explanation
Indices: 1565983--1566060 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
1565973 AGTCCTACTT
* *
1565983 GGACTCAAATGC-TTCGGTTTTAGTGTTTTAATA
1 GGACTCAAATACGTT-GGTTTTAGTGTTTCAATA
*
1566016 GGACCCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
*
1566049 AGACTCAAATAC
1 GGACTCAAATAC
1566061 ATTGATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (33 bp):
GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
Found at i:1566139 original size:14 final size:14
Alignment explanation
Indices: 1566120--1566172 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1566110 CCTGCAAAAA
1566120 TAATAAAGA-AATAT
1 TAATAAA-ATAATAT
1566134 TAATAATAATAATAT
1 TAATAA-AATAATAT
1566149 TAAATAAATATAATA-
1 T-AATAAA-ATAATAT
1566164 TAATAAAAT
1 TAATAAAAT
1566173 GTTTTTGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.06
14 13 0.37
15 9 0.26
16 11 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
TAATAAAATAATAT
Found at i:1566152 original size:26 final size:24
Alignment explanation
Indices: 1566118--1566169 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
1566108 GGCCTGCAAA
1566118 AATAATAAAGAAATATTAATAATAAT
1 AATAATAAAGAAATA-TAAT-ATAAT
* *
1566144 AATATTAAATAAATATAATATAAT
1 AATAATAAAGAAATATAATATAAT
1566168 AA
1 AA
1566170 AATGTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 4 0.17
26 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAATAAAGAAATATAATATAAT
Found at i:1567014 original size:32 final size:32
Alignment explanation
Indices: 1566971--1567053 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
1566961 GTGCACGATT
*
1566971 CCCTTCATCGTGAAGTTGAAACCGCGAGTAGC
1 CCCTTCGTCGTGAAGTTGAAACCGCGAGTAGC
* * *
1567003 CCCTTCGTCGTGAAGTTAAAACCGCGGGTGGC
1 CCCTTCGTCGTGAAGTTGAAACCGCGAGTAGC
1567035 CCCTTCGTCGTGAAGTTGA
1 CCCTTCGTCGTGAAGTTGA
1567054 GCATGTAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.24
Consensus pattern (32 bp):
CCCTTCGTCGTGAAGTTGAAACCGCGAGTAGC
Found at i:1567316 original size:110 final size:108
Alignment explanation
Indices: 1567112--1567369 Score: 367
Period size: 110 Copynumber: 2.4 Consensus size: 108
1567102 GTATTGCTCC
* *** * *
1567112 GAGTCCAATATCCTCCACCGTGAAGTTGAAATTGGCTCTG--GAACTGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGAAATGGAAAATTGTTTGTTGAC
* *
1567175 AATCTGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
66 AATCAGCCACCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
* * *
1567218 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-GAAATGGAAAA-TTGTTTGTTG
*
1567283 ACAATCAGTCACCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
64 ACAATCAGCCACCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
*
1567328 GGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
1567370 ATTGGGAAAT
Statistics
Matches: 133, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
106 34 0.26
109 8 0.06
110 91 0.68
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (108 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGAAATGGAAAATTGTTTGTTGAC
AATCAGCCACCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:1571028 original size:4 final size:4
Alignment explanation
Indices: 1571010--1571055 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
1571000 AAAAATGAAT
1571010 AATA AAT- AATAA AATA AAT- AATA AATA AATA AAT- AAT- AATA AATA
1 AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA AATA
1571055 A
1 A
1571056 TGTATTATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.32
4 23 0.61
5 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1571029 original size:19 final size:18
Alignment explanation
Indices: 1571001--1571056 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 18
1570991 CAAAAAAGAA
1571001 AAAATGAATAATAAATAAT
1 AAAAT-AATAATAAATAAT
1571020 AAAATAAATAATAAATAA-
1 AAAAT-AATAATAAATAAT
1571038 ATAAATAATAATAAATAAT
1 A-AAATAATAATAAATAAT
1571057 GTATTATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
18 13 0.38
19 21 0.62
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAATAATAATAAATAAT
Found at i:1571032 original size:15 final size:15
Alignment explanation
Indices: 1571014--1571052 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
1571004 ATGAATAATA
1571014 AATAATAAAATAAAT
1 AATAATAAAATAAAT
1571029 AATAA-ATAAATAAAT
1 AATAATA-AAATAAAT
1571044 AATAATAAA
1 AATAATAAA
1571053 TAATGTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATAAAATAAAT
Found at i:1571056 original size:7 final size:7
Alignment explanation
Indices: 1571007--1571048 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
1570997 AGAAAAAATG
1571007 AATAATA
1 AATAATA
1571014 AATAAT-
1 AATAATA
1571020 AA-AATA
1 AATAATA
1571026 AATAATA
1 AATAATA
1571033 AATAAATA
1 AAT-AATA
1571041 AATAATA
1 AATAATA
1571048 A
1 A
1571049 TAAATAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 3 0.09
6 4 0.12
7 18 0.56
8 7 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:1571582 original size:33 final size:33
Alignment explanation
Indices: 1571545--1571609 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1571535 TGCTTCACTT
*
1571545 TTAGTGTTTCAATAGGACTCAAATATGTTGATG
1 TTAGTGTTTCAATAAGACTCAAATATGTTGATG
*
1571578 TTAGTGTTTTAATAAGACTCAAATATGTTGAT
1 TTAGTGTTTCAATAAGACTCAAATATGTTGAT
1571610 TTATTTTCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (33 bp):
TTAGTGTTTCAATAAGACTCAAATATGTTGATG
Found at i:1572787 original size:17 final size:17
Alignment explanation
Indices: 1572762--1572801 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1572752 AGGTAAAATT
*
1572762 ATTAATATTTTAATATA
1 ATTATTATTTTAATATA
1572779 ATTATTATTTTAATATA
1 ATTATTATTTTAATATA
*
1572796 AATATT
1 ATTATT
1572802 TATATCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTATTTTAATATA
Found at i:1575081 original size:19 final size:19
Alignment explanation
Indices: 1575053--1575136 Score: 159
Period size: 19 Copynumber: 4.4 Consensus size: 19
1575043 AGAGAAACGA
1575053 AAAAGGAAATTCGAGATCG
1 AAAAGGAAATTCGAGATCG
*
1575072 AAAAGAAAATTCGAGATCG
1 AAAAGGAAATTCGAGATCG
1575091 AAAAGGAAATTCGAGATCG
1 AAAAGGAAATTCGAGATCG
1575110 AAAAGGAAATTCGAGATCG
1 AAAAGGAAATTCGAGATCG
1575129 AAAAGGAA
1 AAAAGGAA
1575137 TTTGGGGTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.51, C:0.10, G:0.25, T:0.14
Consensus pattern (19 bp):
AAAAGGAAATTCGAGATCG
Found at i:1576402 original size:32 final size:31
Alignment explanation
Indices: 1576361--1576434 Score: 107
Period size: 29 Copynumber: 2.4 Consensus size: 31
1576351 TTGTTTAAAA
*
1576361 AATAATTATTTTATAATAATTTAATAAATTTT
1 AATAATTATTTT-TAAGAATTTAATAAATTTT
1576393 AATAATTA--TTTAAGAATTTAATAAATTTT
1 AATAATTATTTTTAAGAATTTAATAAATTTT
*
1576422 AATGATTATTTTT
1 AATAATTATTTTT
1576435 GTAACAACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 25 0.66
30 2 0.05
31 3 0.08
32 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
AATAATTATTTTTAAGAATTTAATAAATTTT
Found at i:1576663 original size:60 final size:59
Alignment explanation
Indices: 1576578--1576712 Score: 139
Period size: 60 Copynumber: 2.3 Consensus size: 59
1576568 ATTATTACCC
* * * * * *
1576578 TTATTTTAAATT-GATCTTTATAATTTTGAACACAT-CAATTTTATCCCTATATTATGAATA
1 TTATTTTAAATTAG-TCATTAAAATTTTGAACA-ATGCAATTTCATCCCAAAACTAT-AATA
* *
1576638 TTATTTTAAATTAGTCATTAAAATTTTTAACATTGCAATTTCATCCCAAAACTATAATA
1 TTATTTTAAATTAGTCATTAAAATTTTGAACAATGCAATTTCATCCCAAAACTATAATA
*
1576697 TTCATTCTAAATTAGT
1 TT-ATTTTAAATTAGT
1576713 TCCTAATTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
59 7 0.11
60 55 0.87
61 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (59 bp):
TTATTTTAAATTAGTCATTAAAATTTTGAACAATGCAATTTCATCCCAAAACTATAATA
Found at i:1579165 original size:2 final size:2
Alignment explanation
Indices: 1579154--1579186 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1579144 TTTTCCATAA
*
1579154 AT AT AA 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 AT A
1579187 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1581671 original size:2 final size:2
Alignment explanation
Indices: 1581664--1581689 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1581654 TAATAATAAT
1581664 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
1581690 TATATATATG
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1585446 original size:1 final size:1
Alignment explanation
Indices: 1585440--1585465 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1585430 TTATGTATTT
1585440 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1585466 GGAGGAGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1586687 original size:13 final size:13
Alignment explanation
Indices: 1586665--1586697 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1586655 CTTACTTTTT
*
1586665 TTTA-TTTATTTG
1 TTTATTTTATTTA
1586677 TTTATTTTATTTA
1 TTTATTTTATTTA
1586690 TTTATTTT
1 TTTATTTT
1586698 TCTTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:1597489 original size:17 final size:19
Alignment explanation
Indices: 1597463--1597511 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
1597453 AATTTAATAA
1597463 AAAAATAAAATG-AAT-TAT
1 AAAAA-AAAATGCAATCTAT
1597481 AAAAAAAAATGACCAATCTAT
1 AAAAAAAAATG--CAATCTAT
1597502 AAAAAAAAAT
1 AAAAAAAAAT
1597512 TAAAGAACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.22
18 5 0.19
20 3 0.11
21 13 0.48
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAAAAAAATGCAATCTAT
Found at i:1597838 original size:2 final size:2
Alignment explanation
Indices: 1597784--1597818 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1597774 ACAAACACCT
*
1597784 TA TA TA TA TA CA 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
1597819 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1600343 original size:25 final size:25
Alignment explanation
Indices: 1600319--1600366 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1600309 ACTAGGTAAG
*
1600319 GAAAATCC-AAGTAGATAAAGCTAA
1 GAAAATCCTAACTAGATAAAGCTAA
*
1600343 GTAAATCCTAACTAGATAAAGCTA
1 GAAAATCCTAACTAGATAAAGCTA
1600367 GCATGTGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (25 bp):
GAAAATCCTAACTAGATAAAGCTAA
Found at i:1603964 original size:21 final size:21
Alignment explanation
Indices: 1603938--1604011 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
1603928 ATTATGACTA
1603938 TCGCAATGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
1603959 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
**
1603980 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
1604001 TCGCAATGCGA
1 TCGCAATGCGA
1604012 ATAAGTAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.09
21 39 0.83
22 4 0.09
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:1604088 original size:20 final size:20
Alignment explanation
Indices: 1604001--1604074 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
1603991 TTTTCCCAAT
*
1604001 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1604021 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1604042 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1604062 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1604075 CTTACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 31 0.63
21 18 0.37
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1604651 original size:19 final size:20
Alignment explanation
Indices: 1604602--1604661 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1604592 TAGTTTCGAG
*
1604602 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGAA
*
1604622 AAT-AACTATCGCAACGC-AA
1 AATGAA-AATCGCAACGCGAA
*
1604641 AATGAAAATCGCAATGCGAA
1 AATGAAAATCGCAACGCGAA
1604661 A
1 A
1604662 CCAAAATCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGAA
Found at i:1607951 original size:2 final size:2
Alignment explanation
Indices: 1607946--1608014 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1607936 TTTATTTGAT
1607946 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
1607988 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 T
1608015 GTGTGTGTGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1608150 original size:39 final size:38
Alignment explanation
Indices: 1608068--1608174 Score: 99
Period size: 39 Copynumber: 2.7 Consensus size: 38
1608058 TTTTGACAAA
* *
1608068 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTT
1 ATATAATATATAATTTT-TGAAAAT-ATTTTCGAAAATAT
* *
1608108 ATATATTATATAATTTTTGAAAATATTTT-TAAAATACAT
1 ATATAATATATAATTTTTGAAAATATTTTCGAAAAT--AT
* * * *
1608147 ATATAATATTTTAGTTTTGAAAACATTT
1 ATATAATATATAATTTTTGAAAATATTT
1608175 ATATATTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
37 5 0.09
38 5 0.09
39 30 0.54
40 16 0.29
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (38 bp):
ATATAATATATAATTTTTGAAAATATTTTCGAAAATAT
Found at i:1608177 original size:28 final size:27
Alignment explanation
Indices: 1608146--1608201 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1608136 TTAAAATACA
*
1608146 TATATAATATTTTAGTTTTGAAAACATT
1 TATATAATA-TATAGTTTTGAAAACATT
* *
1608174 TATATATTATATAGTTTTTAAAACATT
1 TATATAATATATAGTTTTGAAAACATT
1608201 T
1 T
1608202 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (27 bp):
TATATAATATATAGTTTTGAAAACATT
Found at i:1608182 original size:67 final size:63
Alignment explanation
Indices: 1608095--1608237 Score: 180
Period size: 66 Copynumber: 2.2 Consensus size: 63
1608085 CAGAAAATGA
* * *
1608095 TTTTCGAAA-ATTTATATATTATATAATTTTTGAAAATATTTTTAAAATACATATATAATATTTT
1 TTTTCAAAACATTTATATATTATATAATTTTT-AAAACATTTTTAAAA-A-ATATATAATA-TAT
1608159 AG
62 AG
* * * *
1608161 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTTAAAAATTATATAATATATGG
1 TTTTCAAAACATTTATATATTATATAATTTTTAAAACATTTTTAAAAAATATATAATATATAG
1608224 TTTTCAAAACATTT
1 TTTTCAAAACATTT
1608238 TTGAAAAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 16 0.24
64 9 0.13
65 1 0.01
66 21 0.31
67 21 0.31
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (63 bp):
TTTTCAAAACATTTATATATTATATAATTTTTAAAACATTTTTAAAAAATATATAATATATAG
Found at i:1608214 original size:29 final size:27
Alignment explanation
Indices: 1608158--1608215 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1608148 TATAATATTT
* *
1608158 TAGTTTTGAAAACATTTATATATTATA
1 TAGTTTTGAAAACATTTAAAAATTATA
*
1608185 TAGTTTTTAAAACATTTTTAAAAATTATA
1 TAGTTTTGAAAACA--TTTAAAAATTATA
1608214 TA
1 TA
1608216 ATATATGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.50
29 13 0.50
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
TAGTTTTGAAAACATTTAAAAATTATA
Found at i:1608221 original size:36 final size:37
Alignment explanation
Indices: 1608161--1608318 Score: 187
Period size: 38 Copynumber: 4.2 Consensus size: 37
1608151 AATATTTTAG
*
1608161 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACAT
1 TTTTGAAAA-A-TTATATAATATATAGTTTTTAAAACAT
* *
1608200 TTTT-AAAAATTATATAATATATGGTTTTCAAAACAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
* *
1608236 TTTTGAAAAAATTATATAATATATAATTTTAAAAACATT
1 TTTTG-AAAAATTATATAATATATAGTTTTTAAAACA-T
* * *
1608275 TTTTGAAAACTTATATAATAT-T-TTTTTTAAATCAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
1608310 TTTTGAAAA
1 TTTTGAAAA
1608319 CTTTTTAAAG
Statistics
Matches: 106, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
35 10 0.09
36 37 0.35
37 2 0.02
38 47 0.44
39 10 0.09
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
Found at i:1608251 original size:74 final size:75
Alignment explanation
Indices: 1608161--1608319 Score: 207
Period size: 74 Copynumber: 2.1 Consensus size: 75
1608151 AATATTTTAG
* * * *
1608161 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACA-TTTTT-AAAAATTATATAATATATGG
1 TTTTGAAAACAATTATATAATATATAATTTTAAAAACATTTTTTGAAAAATTATATAATAT-T-G
1608224 TTTTCAAAACAT
64 TTTTCAAAACAT
* *
1608236 TTTTGAAAA-AATTATATAATATATAATTTTAAAAACATTTTTTGAAAACTTATATAATATTTTT
1 TTTTGAAAACAATTATATAATATATAATTTTAAAAACATTTTTTGAAAAATTATATAATATTGTT
* *
1608300 TTTAAATCAT
66 TTCAAAACAT
1608310 TTTTGAAAAC
1 TTTTGAAAAC
1608320 TTTTTAAAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
74 43 0.59
75 15 0.21
76 15 0.21
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (75 bp):
TTTTGAAAACAATTATATAATATATAATTTTAAAAACATTTTTTGAAAAATTATATAATATTGTT
TTCAAAACAT
Found at i:1608386 original size:3 final size:3
Alignment explanation
Indices: 1608378--1608432 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
1608368 ATATAGGTTA
* *
1608378 TAT TAT TAT TAG TAT T-G TATT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
1608423 TAT TAT TAT T
1 TAT TAT TAT T
1608433 TTGTTTACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 43 0.93
4 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1609882 original size:25 final size:23
Alignment explanation
Indices: 1609854--1609905 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
1609844 TTTTGTTCTC
* *
1609854 TTTAATATTTTTTTTTATTTATTTA
1 TTTAACATTTATTTTTA-TTA-TTA
1609879 TTTAACATTTATTTTTATTATTA
1 TTTAACATTTATTTTTATTATTA
1609902 TTTA
1 TTTA
1609906 GTTTTTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 3 0.12
25 15 0.60
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTAACATTTATTTTTATTATTA
Found at i:1610388 original size:21 final size:21
Alignment explanation
Indices: 1610358--1610424 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
1610348 CTGAATAAAA
1610358 TTTTATAAATAAATTTAAATAT
1 TTTTA-AAATAAATTTAAATAT
* * *
1610380 TTTTAAAATATATATATAATAAA
1 TTTTAAAATAAATTTA-AAT-AT
*
1610403 TTTTAATATAAATATT-AATAT
1 TTTTAAAATAAAT-TTAAATAT
1610424 T
1 T
1610425 ATACGATCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
21 11 0.31
22 11 0.31
23 12 0.34
24 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAATAAATTTAAATAT
Found at i:1610404 original size:32 final size:30
Alignment explanation
Indices: 1610353--1610411 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
1610343 TTTATCTGAA
*
1610353 TAAAATTTTATAAATAAATTTAAATATTTT
1 TAAAATTATATAAATAAATTTAAATATTTT
*
1610383 TAAAATATATATATAATAAATTTTAATAT
1 TAAAAT-TATATA-AATAAATTTAAATAT
1610412 AAATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 5 0.20
32 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAATTATATAAATAAATTTAAATATTTT
Found at i:1610407 original size:23 final size:23
Alignment explanation
Indices: 1610355--1610422 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
1610345 TATCTGAATA
*
1610355 AAATTTTATAAATAAATTTA-AAT
1 AAATTTTA-AAATAAATATATAAT
* *
1610378 -ATTTTTAAAATATATATATAAT
1 AAATTTTAAAATAAATATATAAT
*
1610400 AAATTTTAATATAAATAT-TAAT
1 AAATTTTAAAATAAATATATAAT
1610422 A
1 A
1610423 TTATACGATC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
21 9 0.24
22 14 0.38
23 14 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATTTTAAAATAAATATATAAT
Found at i:1614012 original size:17 final size:17
Alignment explanation
Indices: 1613990--1614028 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1613980 CGAGCTCGAA
*
1613990 TAATTTAAATTCAAAAT
1 TAATTTAAATCCAAAAT
* *
1614007 TAATTTGAATCCAATAT
1 TAATTTAAATCCAAAAT
1614024 TAATT
1 TAATT
1614029 CTAACCTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATTTAAATCCAAAAT
Found at i:1618297 original size:37 final size:37
Alignment explanation
Indices: 1618247--1618374 Score: 142
Period size: 37 Copynumber: 3.6 Consensus size: 37
1618237 TTTTAAAATA
1618247 ATTTATTTTAAAATAATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTATAAAATATGGATTG
* *
1618284 ATTTATTTTAAAATAATTTATT-TTAAATA---ATTT
1 ATTTATTTTAAAATAATTTATTATAAAATATGGATTG
* * * * * *
1618317 A-TTAGTATAGATTTATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTATAAAATATGGATTG
1618353 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
1618375 GTATAAATTG
Statistics
Matches: 71, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
32 15 0.21
33 10 0.14
36 19 0.27
37 27 0.38
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (37 bp):
ATTTATTTTAAAATAATTTATTATAAAATATGGATTG
Found at i:1618313 original size:14 final size:15
Alignment explanation
Indices: 1618204--1618319 Score: 153
Period size: 15 Copynumber: 7.3 Consensus size: 15
1618194 ATAAGGTTAA
1618204 TTATTTTAAAATAAT
1 TTATTTTAAAATAAT
1618219 TTATTTTAAAATAAT
1 TTATTTTAAAATAAT
1618234 TTATTTTAAAATAAT
1 TTATTTTAAAATAAT
1618249 TTATTTTAAAATAAT
1 TTATTTTAAAATAAT
*
1618264 TTATTATAAAATATGGATTGAT
1 TTATT-TTAAA-AT--A---AT
1618286 TTATTTTAAAATAAT
1 TTATTTTAAAATAAT
1618301 TTATTTT-AAATAAT
1 TTATTTTAAAATAAT
1618315 TTATT
1 TTATT
1618320 AGTATAGATT
Statistics
Matches: 92, Mismatches: 2, Indels: 15
0.84 0.02 0.14
Matches are distributed among these distances:
14 12 0.13
15 59 0.64
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 7 0.08
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATTTTAAAATAAT
Found at i:1618338 original size:32 final size:32
Alignment explanation
Indices: 1618299--1618616 Score: 163
Period size: 32 Copynumber: 10.4 Consensus size: 32
1618289 TTTTAAAATA
*
1618299 ATTTATTTTAAATAATTTATTAGTATAGATTT
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
1618331 ATTTATTTT-AA-AA--TA-T-G----GATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
1618353 ATTTATTTTAAATAATTTATTAGTATAAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
1618385 ATTTATTTT-AA-AA--TA-T-G----GATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
1618407 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
* *
1618439 ATTTATTTTAAA-ATATTGATTA--ATATATT-
1 ATTTATTTTAAATA-ATTTATTAGTATAGATTG
* * * *
1618468 ATTGTAGTTGTATAGATTGATTTATT--T-TA-AATA
1 ATT-TA-TT-T-TA-AATAATTTATTAGTATAGATTG
* * * * *
1618501 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATT--T-T-AAATAATTTA--TT--AGTATAGATTG
1618541 ATTTATTTTAAATAATTTATTAGTAT-GAATTG
1 ATTTATTTTAAATAATTTATTAGTATAG-ATTG
*
1618573 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
1618605 ATTTATTTTAAA
1 ATTTATTTTAAA
1618617 ATATGGATTG
Statistics
Matches: 227, Mismatches: 18, Indels: 82
0.69 0.06 0.25
Matches are distributed among these distances:
22 26 0.11
23 4 0.02
24 4 0.02
26 6 0.03
27 4 0.02
28 6 0.03
29 3 0.01
30 11 0.05
31 10 0.04
32 114 0.50
33 8 0.04
34 11 0.05
36 7 0.03
37 1 0.00
38 2 0.01
39 1 0.00
40 9 0.04
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTG
Found at i:1618365 original size:54 final size:54
Alignment explanation
Indices: 1618299--1618745 Score: 337
Period size: 54 Copynumber: 8.1 Consensus size: 54
1618289 TTTTAAAATA
*
1618299 ATTTATTTTAAATAATTTATTAGTATAGATTTATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
*
1618353 ATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* * *
1618407 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* * * * * * *
1618461 ATATATTATT--GTAGTTGTA-TAG-ATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATT-TTAAATAATT-TATTAGTATAGATTGA-TTT--AT--TTTA-AAATATGGATTG
** * * * ** * * * *
1618519 ATTTATTTTAAA-ATATGGATT-GATTTA-TTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATA-ATTTATTAG-TATAGATTGATTTATTTTA-AAATATGGATTG
*
1618573 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* * * * *
1618627 ATTTA--TT--AT--TGTATTTGCATGGATTGATTTATTTTAAATAATTTATTAGTATGGTATG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT-AA-AA--TA-T-G---GAT-TG
1618685 ATTTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATATGGATTG
1618739 ATTTATT
1 ATTTATT
1618746 ATTGTAGTTG
Statistics
Matches: 312, Mismatches: 47, Indels: 68
0.73 0.11 0.16
Matches are distributed among these distances:
48 23 0.07
49 2 0.01
50 4 0.01
52 11 0.04
53 11 0.04
54 169 0.54
55 17 0.05
56 1 0.00
57 8 0.03
58 26 0.08
59 7 0.02
60 5 0.02
62 4 0.01
63 3 0.01
64 21 0.07
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
Found at i:1618412 original size:80 final size:84
Alignment explanation
Indices: 1618344--1618840 Score: 397
Period size: 80 Copynumber: 6.0 Consensus size: 84
1618334 TATTTTAAAA
*
1618344 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATATATTGATTAGTATAAATTGATTTATTTTAAAATATGGATTGA
1618408 TTTATTTTAAATAATTTATTAG
66 TTTA-TTT-AAT-ATTTATTAG
* *
1618430 TATGGATTGATTTATTTTAAA-ATATTGATTA--ATATATT-ATTGTAGTTGT---ATA--GATT
1 TATGGATTGATTTATTTTAAATATATTGATTAGTATAAATTGATT-TA-TTTTAAAATATGGATT
1618486 GATTTATTTTAAATAATTTATTAG
64 GATTTA-TTT-AAT-ATTTATTAG
* * * * *
1618510 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA-TAATTTA--TT--AGTATGAA
1 TATGGATTGATTTATTTT-AAATAT--ATTGA-TTAGTATAAATTGATTTATTTTAAAATATGGA
1618570 TTGATTTATTTTAAATAATTTATTAG
62 TTGATTTA-TTT-AAT-ATTTATTAG
* ** **
1618596 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATT-ATTGTA-TTT---GCATGGATTG
1 TATGGATTGATTTATTTTAAATATATTGATTAGTATAAATTGATT-TATTTTAAAATATGGATTG
1618653 ATTTATTTTAAATAATTTATTAG
65 ATTTA-TTT-AAT-ATTTATTAG
* *
1618676 TATGG-TATGATTTATTTTAAATA-ATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 TATGGAT-TGATTTATTTTAAATATATTGATTAGTATAAATTGATTTATTTTAAAATATGGATTG
*
1618739 ATTTA-TT-AT-TGTAGTT-G
65 ATTTATTTAATATTTA-TTAG
* **
1618756 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATATATTGATTAGTATAAATTGATTTATTTTAAAATATGGATTGA
1618820 TTTATTTTAAATAATTTATTA
66 TTTA-TTT-AAT-ATTTATTA
1618841 TTGTAGTTAT
Statistics
Matches: 352, Mismatches: 24, Indels: 70
0.79 0.05 0.16
Matches are distributed among these distances:
79 6 0.02
80 173 0.49
81 12 0.03
82 20 0.06
83 10 0.03
84 21 0.06
85 12 0.03
86 92 0.26
87 6 0.02
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (84 bp):
TATGGATTGATTTATTTTAAATATATTGATTAGTATAAATTGATTTATTTTAAAATATGGATTGA
TTTATTTAATATTTATTAG
Found at i:1618496 original size:134 final size:134
Alignment explanation
Indices: 1618348--1618840 Score: 640
Period size: 134 Copynumber: 3.6 Consensus size: 134
1618338 TTAAAATATG
**
1618348 GATTGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
*
1618413 TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTAATATATTATTGTAGTTG
66 TTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATTGATTAATATATTATTGTAGTTG
1618478 TATA
131 TATA
1618482 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
* *
1618547 TTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAATAATTTATTAGTATGGATTGATT-TA
66 TTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT-ATTGATTAATAT--ATT-ATTGTA
*
1618610 -TTTTA-A
127 GTTGTATA
* * * * *
1618616 AATATGGATTGA-TTT--ATTATTGTATTTGCATGGATTGATTTATTTTAAATAATTTATTAGTA
1 GAT-T-GATTTATTTTAAATAATT-TATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G--
* * * *
1618678 TGGTATGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTT
55 -GAT-TGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATTGATTAATAT
*
1618743 ATTATTGTAGTTGTATG
118 ATTATTGTAGTTGTATA
1618760 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1618825 TTTAAATAATTTATTA
66 TTTAAATAATTTATTA
1618841 TTGTAGTTAT
Statistics
Matches: 310, Mismatches: 25, Indels: 48
0.81 0.07 0.13
Matches are distributed among these distances:
133 9 0.03
134 156 0.50
135 12 0.04
136 12 0.04
137 3 0.01
138 3 0.01
139 2 0.01
140 3 0.01
141 3 0.01
142 12 0.04
143 12 0.04
144 74 0.24
145 9 0.03
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (134 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATTGATTAATATATTATTGTAGTTG
TATA
Found at i:1618535 original size:22 final size:22
Alignment explanation
Indices: 1618510--1618552 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1618500 AATTTATTAG
1618510 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1618532 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1618553 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1618560 original size:14 final size:14
Alignment explanation
Indices: 1618541--1618593 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1618531 ATATGGATTG
1618541 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1618555 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
1618573 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1618587 ATTTATT
1 ATTTATT
1618594 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1618692 original size:32 final size:32
Alignment explanation
Indices: 1618649--1618728 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
1618639 ATTTGCATGG
1618649 ATTGATTTATTTTAAATAATTTATTAGTATG-
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
*
1618680 GTATGATTTATTTTAAATAATTTATTAGTATGA
1 AT-TGATTTATTTTAAATAATTTATTAGTATGA
1618713 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
1618729 ATATGGATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
31 1 0.02
32 43 0.96
33 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (32 bp):
ATTGATTTATTTTAAATAATTTATTAGTATGA
Found at i:1618741 original size:166 final size:166
Alignment explanation
Indices: 1618344--1618745 Score: 591
Period size: 166 Copynumber: 2.4 Consensus size: 166
1618334 TATTTTAAAA
1618344 TATGGATTGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGAT
*
1618409 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTAATATATTATTGTA
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATATATTATTGTA
*
1618474 GTTGTATAGATTGATTTATTTTAAATAATTTATTAG
131 GTTGCATAGATTGATTTATTTTAAATAATTTATTAG
* * * * * *
1618510 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA-TAATTTA--TT--AGTATGAA
1 TATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATAAATTGATTTATTTTAAAATATGGA
* *
1618570 TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTA
61 TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATATATTA
* *
1618635 TTGTATTTGCATGGATTGATTTATTTTAAATAATTTATTAG
126 TTGTAGTTGCATAGATTGATTTATTTTAAATAATTTATTAG
*
1618676 TATGG-TATGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 TATGGAT-TGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGA
1618740 TTTATT
65 TTTATT
1618746 ATTGTAGTTG
Statistics
Matches: 206, Mismatches: 19, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
161 7 0.03
162 10 0.05
164 2 0.01
165 6 0.03
166 156 0.76
167 5 0.02
168 2 0.01
170 10 0.05
171 8 0.04
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (166 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATATATTATTGTA
GTTGCATAGATTGATTTATTTTAAATAATTTATTAG
Found at i:1618799 original size:112 final size:111
Alignment explanation
Indices: 1618344--1618808 Score: 539
Period size: 112 Copynumber: 4.2 Consensus size: 111
1618334 TATTTTAAAA
*
1618344 TATGGATTGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
* * *
1618409 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA-ATATTGATTAA
66 TTA--TT--AT--TGTATT-GTATGGATTGATTTATTTTAAATA-ATTTATTAG
* * * * *
1618462 TAT--ATT-ATTGTAGTTGTATAGATTGATTTATT--T-T-AAATAATTTA--TT--AGTATGGA
1 TATGGATTGATT-TA-TT-T-TA-AATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGA
***
1618516 TTGATTTA-T-TT-TAAAATATGGATTGATTTATTTTAAATAATTTATTAG
61 TTGATTTATTATTGTATTGTATGGATTGATTTATTTTAAATAATTTATTAG
* *
1618564 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
*
1618629 TTATTATTGTATTTGCATGGATTGATTTATTTTAAATAATTTATTAG
66 TTATTATTGTA-TTGTATGGATTGATTTATTTTAAATAATTTATTAG
1618676 TATGG-TATGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 TATGGAT-TGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1618740 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
65 TTTATTATTGTA-TTGTATGGATTGATTTATTTTAAATAATTTATTAG
1618788 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1618809 ATATGGATTG
Statistics
Matches: 300, Mismatches: 24, Indels: 52
0.80 0.06 0.14
Matches are distributed among these distances:
100 9 0.03
101 2 0.01
102 33 0.11
103 6 0.02
104 13 0.04
105 3 0.01
106 3 0.01
108 15 0.05
109 2 0.01
110 2 0.01
111 3 0.01
112 171 0.57
113 1 0.00
114 2 0.01
115 3 0.01
116 13 0.04
117 3 0.01
118 5 0.02
119 2 0.01
120 9 0.03
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (111 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTATTGTATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1618813 original size:22 final size:22
Alignment explanation
Indices: 1618788--1618830 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1618778 AATTTATTAG
1618788 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1618810 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1618831 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1618817 original size:166 final size:160
Alignment explanation
Indices: 1618344--1618840 Score: 512
Period size: 166 Copynumber: 3.0 Consensus size: 160
1618334 TATTTTAAAA
1618344 TATGGATTGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGAT
*
1618409 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTAATATATTATTGTA
66 TTA---T---T-ATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTAGTATATTATTGTA
*
1618474 GTTGTATA--GATTGATTTATTTTAAATAATTTATTAG
124 -TTTTATATGGATTGATTTATTTTAAATAATTTATTAG
* * * * * *
1618510 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA-TAATTTATTAGTATGAAT-T-
1 TATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATAAATTGATTTATT-TTA-AAATATG
* * * *
1618572 GATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATT-GATTTATTAT
59 GATTGA-TTT--ATTATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTAG-TATATTAT
**
1618636 TGTA-TTTGCATGGATTGATTTATTTTAAATAATTTATTAG
120 TGTATTTTATATGGATTGATTTATTTTAAATAATTTATTAG
*
1618676 TATGG-TATGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 TATGGAT-TGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGA
*
1618740 TTTATTATTGTAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAGTATGGATTGATT-TA
65 TTTATTATT-TA-TTAGTATGGATTGATTTATTTTAAAAT-ATTGATTAGTAT--ATT-ATTGTA
1618802 TTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
124 TTTT---ATATGGATTGATTTATTTTAAATAATTTATTA
1618841 TTGTAGTTAT
Statistics
Matches: 275, Mismatches: 28, Indels: 56
0.77 0.08 0.16
Matches are distributed among these distances:
159 9 0.03
160 31 0.11
161 16 0.06
162 22 0.08
163 6 0.02
164 3 0.01
165 6 0.02
166 141 0.51
167 5 0.02
170 18 0.07
171 14 0.05
172 3 0.01
173 1 0.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (160 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTAGTATATTATTGTATTTTATA
TGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1624767 original size:2 final size:2
Alignment explanation
Indices: 1624760--1624785 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1624750 TAATTTACTA
1624760 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
1624786 TAATATTAGT
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):
AT
Found at i:1625319 original size:18 final size:18
Alignment explanation
Indices: 1625296--1625330 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1625286 TTTCTTTAAT
*
1625296 TTTTGTTTTTTATATTCC
1 TTTTGTCTTTTATATTCC
*
1625314 TTTTGTCTTTTGTATTC
1 TTTTGTCTTTTATATTC
1625331 TTATTTGGGA
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:0.09, C:0.11, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTGTCTTTTATATTCC
Found at i:1629937 original size:17 final size:17
Alignment explanation
Indices: 1629911--1629945 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1629901 ATTAGTGAAC
*
1629911 AATAACTATATCTAATG
1 AATAACTATATATAATG
*
1629928 AATAATTATATATAATG
1 AATAACTATATATAATG
1629945 A
1 A
1629946 GGGGACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (17 bp):
AATAACTATATATAATG
Done.