Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003132.1 Hibiscus syriacus cultivar Beakdansim tig00006570_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: 1555756
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1147875 original size:19 final size:19
Alignment explanation
Indices: 1147837--1147875 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1147827 AACAACAAAA
*
1147837 TAAATAAAAAATTCATAAT
1 TAAATAAAAAATTCACAAT
* *
1147856 TAAATAAAAATTTTACAAT
1 TAAATAAAAAATTCACAAT
1147875 T
1 T
1147876 GCTGGTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATAAAAAATTCACAAT
Found at i:1148374 original size:21 final size:21
Alignment explanation
Indices: 1148327--1148374 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1148317 ACCCGGCTGC
** *
1148327 GGTGGCATCTGATATGGGTGT
1 GGTGGCATCTGATATGGAAGA
*
1148348 GATGGCATCTGATATGGAAGA
1 GGTGGCATCTGATATGGAAGA
1148369 GGTGGC
1 GGTGGC
1148375 GTCTAACTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.10, G:0.42, T:0.27
Consensus pattern (21 bp):
GGTGGCATCTGATATGGAAGA
Found at i:1148425 original size:21 final size:21
Alignment explanation
Indices: 1148399--1148441 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1148389 CGGTTGAAAT
1148399 GGTTGCAGTACCATCTGATAC
1 GGTTGCAGTACCATCTGATAC
*
1148420 GGTTGCGGTACCATCTGATAC
1 GGTTGCAGTACCATCTGATAC
1148441 G
1 G
1148442 ACTACAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
GGTTGCAGTACCATCTGATAC
Found at i:1161148 original size:22 final size:22
Alignment explanation
Indices: 1161122--1161191 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 22
1161112 GGATTCAAGA
1161122 TGAAAACCCGTAAAGGGCATCT
1 TGAAAACCCGTAAAGGGCATCT
* *
1161144 TG-AAACCAG-AGAAGGTC-TCAGGT
1 TGAAAACCCGTA-AAGGGCATC---T
*
1161167 TGAAAACCCGTAAAGGGCAGCT
1 TGAAAACCCGTAAAGGGCATCT
1161189 TGA
1 TGA
1161192 GAATTGTGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
20 3 0.08
21 11 0.31
22 6 0.17
23 3 0.08
24 11 0.31
25 2 0.06
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (22 bp):
TGAAAACCCGTAAAGGGCATCT
Found at i:1163651 original size:64 final size:63
Alignment explanation
Indices: 1163582--1163743 Score: 150
Period size: 64 Copynumber: 2.5 Consensus size: 63
1163572 TAATGAAGGT
* **
1163582 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCAATCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCAATCGATCGTTTTATT-TTAA-AA
1163645 G
63 G
* * * * * *
1163646 ATGCATCAATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCAATCGATCGTTTTATTTTAAAAG
** *
1163709 AGTGCATCGATGCACTACCAGTGCATCGATACACT
1 A-TGCATCGATGCACTACTTGTGCATCGATGCACT
1163744 TTCAAACACT
Statistics
Matches: 78, Mismatches: 15, Indels: 10
0.76 0.15 0.10
Matches are distributed among these distances:
63 3 0.04
64 66 0.85
65 9 0.12
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCAATCGATCGTTTTATTTTAAAAG
Found at i:1169578 original size:29 final size:28
Alignment explanation
Indices: 1169517--1169579 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
1169507 TTTCATATGT
* *
1169517 TCATGTACTCATGTCATTTCTCTTGTGA
1 TCATGTACTCATGTCATTTCTCATGTCA
1169545 TCATGTAGCTCATGTCATGTTCTCATGTCA
1 TCATGTA-CTCATGTCAT-TTCTCATGTCA
1169575 -CATGT
1 TCATGT
1169580 GTATTTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 7 0.23
29 15 0.48
30 9 0.29
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (28 bp):
TCATGTACTCATGTCATTTCTCATGTCA
Found at i:1170006 original size:64 final size:64
Alignment explanation
Indices: 1169937--1170056 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
1169927 GAAGGTATGC
* *
1169937 ATCGATGCACT-ACTTATGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGGGAT
1 ATCGATGCA-TGACTTATGCATCGATGCACT-AAATGCATTCGATCCTTTTATT-TTAATGGGAT
1169999 AT
63 AT
* *
1170001 ATCGATGCATGCCTTATGCATCGATGCACTAATTGCATTCGATCCTTTTATTTTAA
1 ATCGATGCATGACTTATGCATCGATGCACTAAATGCATTCGATCCTTTTATTTTAA
1170057 AAGAGTGCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
63 1 0.02
64 40 0.82
65 8 0.16
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (64 bp):
ATCGATGCATGACTTATGCATCGATGCACTAAATGCATTCGATCCTTTTATTTTAATGGGATAT
Found at i:1171123 original size:115 final size:115
Alignment explanation
Indices: 1170918--1171125 Score: 301
Period size: 115 Copynumber: 1.8 Consensus size: 115
1170908 CTCTCAGATT
* *
1170918 TGATAATCCCTTCAGAAGAAGCGGAATAAATCCATCTCCTTCAAGATTTGATATTCCCTGAGTGA
1 TGATAATCCCTTCAGAAGAAGCGGAATAAATCCATATCCTCCAAGATTTGATATTCCCTGAGTGA
* * *
1170983 AAGTGGAACAAATCTGCCCTAATTCAATGGATTACATTTCTTTCCATATA
66 AAGCGGAACAAATCTACCCCAATTCAATGGATTACATTTCTTTCCATATA
* * *
1171033 TGATATTCCCTTTAGAAGAAGCGGAATAAATTTC-TATCCTCCAAGATTTGATATTCCCTGAGTG
1 TGATAATCCCTTCAGAAGAAGCGGAATAAA-TCCATATCCTCCAAGATTTGATATTCCCTGAGTG
* * *
1171097 ACAGCGGAACAAGTCTACCCCGATTCAAT
65 AAAGCGGAACAAATCTACCCCAATTCAAT
1171126 CTTCCCTGAG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
115 79 0.98
116 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (115 bp):
TGATAATCCCTTCAGAAGAAGCGGAATAAATCCATATCCTCCAAGATTTGATATTCCCTGAGTGA
AAGCGGAACAAATCTACCCCAATTCAATGGATTACATTTCTTTCCATATA
Found at i:1171279 original size:137 final size:137
Alignment explanation
Indices: 1171033--1171382 Score: 576
Period size: 137 Copynumber: 2.6 Consensus size: 137
1171023 TTTCCATATA
* * ** *
1171033 TGATATTCCCTTTAGAAGAAGCGGAATAAATTTCTATCCTCCAAGATTTGATATTCCCTGAGTGA
1 TGATAATCCCTTTAGAAGAAGCGGAACAAATCCCTCTCCTCCAAGATTTGATATTCCCTGAGTGA
1171098 CAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATAAATCACCTCTCCTC
66 CAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATAAATCACCTCTCCTC
1171163 TCAGATC
131 TCAGATC
1171170 TGATAATCCCTTTAGAAGAAGCGGAACAAATCCCTCTCCTCCAAGATTTGATATTCCCTGAGTGA
1 TGATAATCCCTTTAGAAGAAGCGGAACAAATCCCTCTCCTCCAAGATTTGATATTCCCTGAGTGA
* * *
1171235 CAGCGGAACAAGTCTATCCTGATTCAATCTTCCCTGAGTGACAGCGGAATGAATCACCTCTCCTC
66 CAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATAAATCACCTCTCCTC
1171300 TCAGATC
131 TCAGATC
* * *
1171307 TGATAATCCCTTCAGAAGAAGTC-TAACAAATCCCTCTCCTTCAAGATTTGATATTCCCTGAGTG
1 TGATAATCCCTTTAGAAGAAG-CGGAACAAATCCCTCTCCTCCAAGATTTGATATTCCCTGAGTG
*
1171371 ACAGTGGAACAA
65 ACAGCGGAACAA
1171383 ATATGTCCTA
Statistics
Matches: 200, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
137 199 1.00
138 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (137 bp):
TGATAATCCCTTTAGAAGAAGCGGAACAAATCCCTCTCCTCCAAGATTTGATATTCCCTGAGTGA
CAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATAAATCACCTCTCCTC
TCAGATC
Found at i:1171750 original size:12 final size:12
Alignment explanation
Indices: 1171724--1171765 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
1171714 CATTTAATAT
1171724 TAATATTATTTAA
1 TAATATTA-TTAA
1171737 TAATATTATTAA
1 TAATATTATTAA
*
1171749 TAATATTATTAC
1 TAATATTATTAA
1171761 TAATA
1 TAATA
1171766 GTTTTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATATTATTAA
Found at i:1172165 original size:20 final size:20
Alignment explanation
Indices: 1172140--1172188 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1172130 ATCACGACTG
*
1172140 TCGACCATCCCACGTGAACC
1 TCGACCACCCCACGTGAACC
1172160 TCGACCACCCCACGTGAACC
1 TCGACCACCCCACGTGAACC
1172180 TCGACCACC
1 TCGACCACC
1172189 TACAATATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.49, G:0.14, T:0.12
Consensus pattern (20 bp):
TCGACCACCCCACGTGAACC
Found at i:1178577 original size:27 final size:27
Alignment explanation
Indices: 1178511--1178565 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1178501 GGGCAAAATG
1178511 TAAGGTTATTAATGCATCATTTTAGCA
1 TAAGGTTATTAATGCATCATTTTAGCA
1178538 TAAGGTTATTAATGCATCATTTTAGCA
1 TAAGGTTATTAATGCATCATTTTAGCA
1178565 T
1 T
1178566 TATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (27 bp):
TAAGGTTATTAATGCATCATTTTAGCA
Found at i:1181097 original size:16 final size:16
Alignment explanation
Indices: 1181076--1181115 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1181066 TTGACTTTTT
1181076 GTCAAAGTCAATGCTG
1 GTCAAAGTCAATGCTG
*
1181092 GTCAAAGTCAATGTTG
1 GTCAAAGTCAATGCTG
1181108 GTCAAAGT
1 GTCAAAGT
1181116 AAAAGTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (16 bp):
GTCAAAGTCAATGCTG
Found at i:1181120 original size:22 final size:22
Alignment explanation
Indices: 1181095--1181146 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1181085 AATGCTGGTC
1181095 AAAGTCAATGT-TGGTCAAAGTA
1 AAAGTCAAT-TCTGGTCAAAGTA
1181117 AAAGTCAATTCTGGTCAAAGTA
1 AAAGTCAATTCTGGTCAAAGTA
1181139 AAAGTCAA
1 AAAGTCAA
1181147 CGAGTTGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (22 bp):
AAAGTCAATTCTGGTCAAAGTA
Found at i:1182266 original size:14 final size:14
Alignment explanation
Indices: 1182247--1182290 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1182237 TAATCTAAAA
1182247 TTATAAAAATATAT
1 TTATAAAAATATAT
* *
1182261 TTATAATATTATAT
1 TTATAAAAATATAT
1182275 TT-TAAAGAATATAT
1 TTATAAA-AATATAT
1182289 TT
1 TT
1182291 TGAGGGTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 3 0.12
14 22 0.88
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTATAAAAATATAT
Found at i:1182266 original size:27 final size:28
Alignment explanation
Indices: 1182235--1182290 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1182225 TTATATCAAA
*
1182235 TATAATCTAAAATTATAAA-AATATATT
1 TATAATATAAAATTATAAAGAATATATT
* * *
1182262 TATAATATTATATTTTAAAGAATATATT
1 TATAATATAAAATTATAAAGAATATATT
1182290 T
1 T
1182291 TGAGGGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
TATAATATAAAATTATAAAGAATATATT
Found at i:1183667 original size:2 final size:2
Alignment explanation
Indices: 1183660--1183745 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
1183650 ATACTTCAAC
1183660 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
1183702 T- TA TA T- 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
1183742 TA TA
1 TA TA
1183746 AAACTGAATT
Statistics
Matches: 82, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.02
2 80 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1183929 original size:30 final size:32
Alignment explanation
Indices: 1183895--1183956 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
1183885 AGTTTGATAG
1183895 TGATTATTAACAT-ATAATTCA-GTTAAAATA
1 TGATTATTAACATGATAATTCACGTTAAAATA
*
1183925 TGATTATTAACATGATATTTCATCGTTAAAAT
1 TGATTATTAACATGATAATTCA-CGTTAAAAT
1183957 TGAAATCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 13 0.46
31 7 0.25
33 8 0.29
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (32 bp):
TGATTATTAACATGATAATTCACGTTAAAATA
Found at i:1185214 original size:200 final size:200
Alignment explanation
Indices: 1184871--1185270 Score: 784
Period size: 200 Copynumber: 2.0 Consensus size: 200
1184861 CGATACGGTA
1184871 TCCTTCATGCACGTGATTCTGCCATGCACCCATACAATATGCTTTTCAATATAATCCAAATTATT
1 TCCTTCATGCACGTGATTCTGCCATGCACCCATACAATATGCTTTTCAATATAATCCAAATTATT
1184936 GAAGAACCAACGCCAGCTTCCATAATGTCACTGTTCCTTTTCCATGGTTTGTTAGAAAAGTACTG
66 GAAGAACCAACGCCAGCTTCCATAATGTCACTGTTCCTTTTCCATGGTTTGTTAGAAAAGTACTG
1185001 CTGCAACACAGCATAGTTAGTATTGATTATCATATAATAATAAATGAATAAAAAATGATATAATT
131 CTGCAACACAGCATAGTTAGTATTGATTATCATATAATAATAAATGAATAAAAAATGATATAATT
1185066 ATTTT
196 ATTTT
1185071 TCCTTCATGCAC-TGATTCTGCCATGCAACCCATACAATATGCTTTTCAATATAATCCAAATTAT
1 TCCTTCATGCACGTGATTCTGCCATGC-ACCCATACAATATGCTTTTCAATATAATCCAAATTAT
1185135 TGAAGAACCAACGCCAGCTTCCATAATGTCACTGTTCCTTTTCCATGGTTTGTTAGAAAAGTACT
65 TGAAGAACCAACGCCAGCTTCCATAATGTCACTGTTCCTTTTCCATGGTTTGTTAGAAAAGTACT
1185200 GCTGCAACACAGCATAGTTAGTATTGATTATCATATAATAATAAATGAATAAAAAATGATATAAT
130 GCTGCAACACAGCATAGTTAGTATTGATTATCATATAATAATAAATGAATAAAAAATGATATAAT
1185265 TATTTT
195 TATTTT
1185271 CACGTGATAG
Statistics
Matches: 199, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
199 14 0.07
200 185 0.93
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (200 bp):
TCCTTCATGCACGTGATTCTGCCATGCACCCATACAATATGCTTTTCAATATAATCCAAATTATT
GAAGAACCAACGCCAGCTTCCATAATGTCACTGTTCCTTTTCCATGGTTTGTTAGAAAAGTACTG
CTGCAACACAGCATAGTTAGTATTGATTATCATATAATAATAAATGAATAAAAAATGATATAATT
ATTTT
Found at i:1185636 original size:17 final size:17
Alignment explanation
Indices: 1185616--1185653 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1185606 AAGGGCTTAG
1185616 TGAAGCCATCAGCAACC
1 TGAAGCCATCAGCAACC
1185633 TGAAGCCATCAGCAACC
1 TGAAGCCATCAGCAACC
1185650 TGAA
1 TGAA
1185654 ACCCAGCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.32, G:0.18, T:0.13
Consensus pattern (17 bp):
TGAAGCCATCAGCAACC
Found at i:1189002 original size:23 final size:23
Alignment explanation
Indices: 1188972--1189015 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1188962 ATTACATATA
1188972 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
1188995 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
1189016 CCCTCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:1189525 original size:16 final size:17
Alignment explanation
Indices: 1189487--1189526 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1189477 TCTTCACGTT
1189487 TGAGAG-AAGAAGAAGA
1 TGAGAGAAAGAAGAAGA
*
1189503 TTA-AGAAAGAAGAA-A
1 TGAGAGAAAGAAGAAGA
1189518 TGAGAGAAA
1 TGAGAGAAA
1189527 TTTGGAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (17 bp):
TGAGAGAAAGAAGAAGA
Found at i:1194207 original size:21 final size:22
Alignment explanation
Indices: 1194183--1194229 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1194173 CAGATTACAA
*
1194183 ACAGCGAACCGATT-CCCTGCT
1 ACAGCGAACCAATTCCCCTGCT
* *
1194204 ACAGGGTACCAATTCCCCTGCT
1 ACAGCGAACCAATTCCCCTGCT
1194226 ACAG
1 ACAG
1194230 TACTTCCGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.19
Consensus pattern (22 bp):
ACAGCGAACCAATTCCCCTGCT
Found at i:1194968 original size:21 final size:23
Alignment explanation
Indices: 1194944--1194987 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1194934 TCCACGGAAT
1194944 TACATA-AA-TGTCCCGAAGGAC
1 TACATAGAATTGTCCCGAAGGAC
1194965 TACATAGAATTGTCCCGAAGGAC
1 TACATAGAATTGTCCCGAAGGAC
1194988 CGCGTAGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 2 0.10
23 13 0.62
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (23 bp):
TACATAGAATTGTCCCGAAGGAC
Found at i:1195100 original size:22 final size:24
Alignment explanation
Indices: 1195068--1195120 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
1195058 CTTTATACTT
1195068 ATCA-TTTCACAT-AACACATA-G
1 ATCACTTTCACATGAACACATATG
* *
1195089 TTCACTTTCACATGTACACATATG
1 ATCACTTTCACATGAACACATATG
1195113 ATCACTTT
1 ATCACTTT
1195121 ATCTTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.12
22 8 0.31
23 7 0.27
24 8 0.31
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.36
Consensus pattern (24 bp):
ATCACTTTCACATGAACACATATG
Found at i:1197481 original size:36 final size:36
Alignment explanation
Indices: 1197424--1197498 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1197414 CTTGTAACTA
*
1197424 AACCTTCACACACACGTAATGCACTATGAACATTATT
1 AACCTTCACACACACGCAATGCACTATGAACA-TATT
*
1197461 AACCTT-ACATACACGCAATGCACTATGAACATATT
1 AACCTTCACACACACGCAATGCACTATGAACATATT
1197496 AAC
1 AAC
1197499 TAACACTTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 7 0.19
36 23 0.64
37 6 0.17
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (36 bp):
AACCTTCACACACACGCAATGCACTATGAACATATT
Found at i:1199182 original size:29 final size:29
Alignment explanation
Indices: 1199143--1199252 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
1199133 TATATGATAT
1199143 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1199173 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
* *
1199202 GAGAAATGACATGAACTACATGATTACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1199231 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1199253 ATATATAAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.09
29 65 0.84
30 5 0.06
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1201301 original size:6 final size:6
Alignment explanation
Indices: 1201282--1201326 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1201272 TACAGGCCAG
* * * *
1201282 AGAGGA AGATGA AGAGGA AGAGGT AGAGGC AGAGGC AGAGGA AGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGA
1201327 AGCCAATCGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.44, C:0.04, G:0.47, T:0.04
Consensus pattern (6 bp):
AGAGGA
Found at i:1205618 original size:64 final size:64
Alignment explanation
Indices: 1205550--1205702 Score: 152
Period size: 64 Copynumber: 2.4 Consensus size: 64
1205540 TTGAAGGTGT
* ** *
1205550 ATCGATGCACATGTAGTGCATCGATACA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACAAGTAGTGCATCGATACATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
1205612 GC
63 GC
* * * * *
1205614 ATCGATGTATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCACAA-GTAGTGCATCGATACATCCCATTAATAATAAAACATCGAATGCATATTATGC
*
1205678 ACCGATGCACAAGTAGTGCATCGAT
1 ATCGATGCACAAGTAGTGCATCGAT
1205703 GTATACCTTC
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
63 2 0.03
64 60 0.85
65 9 0.13
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATACATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:1206122 original size:29 final size:29
Alignment explanation
Indices: 1206083--1206192 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
1206073 TATATGATAT
1206083 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1206113 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
1206142 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1206171 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1206193 ACATATAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1206295 original size:15 final size:15
Alignment explanation
Indices: 1206277--1206310 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1206267 GAGGGTATAA
1206277 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
1206292 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
1206307 TAGT
1 TAGT
1206311 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:1207572 original size:7 final size:7
Alignment explanation
Indices: 1207560--1207595 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
1207550 ATACAAGCAA
1207560 GCAATTT
1 GCAATTT
1207567 GCAATTT
1 GCAATTT
1207574 GCAATTT
1 GCAATTT
1207581 GCAATTT
1 GCAATTT
1207588 GCAATTT
1 GCAATTT
1207595 G
1 G
1207596 GCAGTAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (7 bp):
GCAATTT
Found at i:1207958 original size:6 final size:6
Alignment explanation
Indices: 1207949--1208027 Score: 54
Period size: 6 Copynumber: 12.2 Consensus size: 6
1207939 TCCTTTTAAA
* *
1207949 ATTATT ATTATA AATATT ATTATT ATTA-T ATATATAT ATATATAT ATATATAT
1 ATTATT ATTATT ATTATT ATTATT ATTATT AT-TAT-T AT-TAT-T AT-TAT-T
1208002 ATATATAT ATTA-T ATTATT ATTATT A
1 AT-TAT-T ATTATT ATTATT ATTATT A
1208028 AATAAAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
5 8 0.12
6 28 0.43
7 2 0.03
8 27 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTATT
Found at i:1207968 original size:12 final size:13
Alignment explanation
Indices: 1207954--1208015 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 13
1207944 TTAAAATTAT
1207954 TATTATAAATAT-
1 TATTATAAATATA
*
1207966 TATTATTATTATATA
1 TATTA-TA-AATATA
*
1207981 TATATATATATATA
1 TAT-TATAAATATA
*
1207995 TATATATATATATA
1 TAT-TATAAATATA
1208009 TATTATA
1 TATTATA
1208016 TTATTATTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
12 5 0.11
13 6 0.13
14 27 0.60
15 5 0.11
16 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTATAAATATA
Found at i:1207972 original size:18 final size:18
Alignment explanation
Indices: 1207949--1208027 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
1207939 TCCTTTTAAA
1207949 ATTATTATTATAAATATT
1 ATTATTATTATAAATATT
*
1207967 ATTATTATTATATATA-T
1 ATTATTATTATAAATATT
*
1207984 A-TA-TATATATATATATAT
1 ATTATTAT-TATAAATAT-T
*
1208002 ATATATATATTAT-ATTATT
1 AT-TAT-TATTATAAATATT
1208021 ATTATTA
1 ATTATTA
1208028 AATAAAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
15 3 0.06
16 10 0.20
17 4 0.08
18 20 0.39
19 3 0.06
20 5 0.10
21 3 0.06
22 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTATTATAAATATT
Found at i:1207982 original size:2 final size:2
Alignment explanation
Indices: 1207975--1208016 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1207965 TTATTATTAT
1207975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1208016 T
1 T
1208017 TATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1212550 original size:7 final size:7
Alignment explanation
Indices: 1212534--1212573 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
1212524 TTTTCATACA
1212534 TGCA-TT
1 TGCATTT
1212540 TGCATTT
1 TGCATTT
1212547 TGCATCTT
1 TGCAT-TT
1212555 TGCATTT
1 TGCATTT
1212562 T-CATTT
1 TGCATTT
1212568 TGCATT
1 TGCATT
1212574 CATACTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.32
7 14 0.45
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:1212633 original size:13 final size:13
Alignment explanation
Indices: 1212591--1212637 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
1212581 TTATGTTTGC
*
1212591 ATTTGCATTTCTAT
1 ATTTTCATTT-TAT
*
1212605 ATTTTCA-TTTAC
1 ATTTTCATTTTAT
1212617 ATTTTCATTTTAT
1 ATTTTCATTTTAT
1212630 ATTTTCAT
1 ATTTTCAT
1212638 CTATGCATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 9 0.31
13 14 0.48
14 6 0.21
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (13 bp):
ATTTTCATTTTAT
Found at i:1215204 original size:11 final size:12
Alignment explanation
Indices: 1215188--1215222 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
1215178 TCAGTCATCT
1215188 GAAAAAAAAAA-
1 GAAAAAAAAAAG
1215199 GAAAAAAAAAAG
1 GAAAAAAAAAAG
1215211 GAAAGAAAAAAA
1 GAAA-AAAAAAA
1215223 TTGAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 4 0.18
13 7 0.32
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAG
Found at i:1215206 original size:12 final size:12
Alignment explanation
Indices: 1215189--1215222 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1215179 CAGTCATCTG
1215189 AAAAAAAAAAGA
1 AAAAAAAAAAGA
*
1215201 AAAAAAAAAGGA
1 AAAAAAAAAAGA
1215213 AAGAAAAAAA
1 AA-AAAAAAA
1215223 TTGAATTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1217566 original size:42 final size:42
Alignment explanation
Indices: 1217519--1217705 Score: 124
Period size: 42 Copynumber: 4.6 Consensus size: 42
1217509 AAGCAAATAT
*
1217519 TGGGGCATCTCGAAAGCCTATTTCATACAGAAATGATCCATG
1 TGGGGCATCTTGAAAGCCTATTTCATACAGAAATGATCCATG
* * * *
1217561 TGGGGCATTTTGAAGGTCC-A----ATTCAGACA-GATCCATG
1 TGGGGCATCTTGAAAG-CCTATTTCATACAGAAATGATCCATG
* * *
1217598 TGGGACATCTTGAAAGTCTATTTCA-ACAAGAAAT-AT-AATG
1 TGGGGCATCTTGAAAGCCTATTTCATAC-AGAAATGATCCATG
* * * * * * *
1217638 TTGGGGCATTTTGAATGTCTAATTAAAACAGAAATGATTCATG
1 -TGGGGCATCTTGAAAGCCTATTTCATACAGAAATGATCCATG
*
1217681 TGGGGCATGC-TGAAAGCCCATTTCA
1 TGGGGCAT-CTTGAAAGCCTATTTCA
1217706 ATCAAAAATT
Statistics
Matches: 108, Mismatches: 24, Indels: 26
0.68 0.15 0.16
Matches are distributed among these distances:
36 1 0.01
37 22 0.20
38 7 0.06
40 4 0.04
41 33 0.31
42 36 0.33
43 5 0.05
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (42 bp):
TGGGGCATCTTGAAAGCCTATTTCATACAGAAATGATCCATG
Found at i:1219148 original size:22 final size:22
Alignment explanation
Indices: 1219120--1219198 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
1219110 ACATCAACAT
1219120 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
1219142 TCTTCAAAGATAATAGATTTTA
1 TCTTCAAAGATGATAGATTCTC
*
1219164 TCTTCAAAGATGAAAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
1219186 TTTTCAAATATGA
1 TCTTCAAAGATGA
1219199 AAGCTTTATT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1219971 original size:45 final size:45
Alignment explanation
Indices: 1219922--1220504 Score: 950
Period size: 45 Copynumber: 13.0 Consensus size: 45
1219912 GGGAGCTTTT
*
1219922 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1219967 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGGA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1220012 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1220057 TGATGTTTTCAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1220102 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1220147 TTATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1220192 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1220237 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1220282 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1220327 TGATGTTTTCAAAGCCTTCGGGTCATATGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1220372 TGATGTTTTCAAAGCCTTCGGCTCATCTGTAATCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * * * *
1220417 TGATATTTTCAAAACCTTTGGGTCATCTGTAAGACCTTTAATGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1220462 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGACCTACAGTG
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTG
1220505 TAAGATGATA
Statistics
Matches: 498, Mismatches: 40, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 498 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1220695 original size:3 final size:3
Alignment explanation
Indices: 1220687--1220751 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
1220677 TCCTTTTTAA
* * *
1220687 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT AAT ATT A-T ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
1220732 ATT ATAT ATT ATT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT A
1220752 AATAAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1224979 original size:18 final size:19
Alignment explanation
Indices: 1224958--1225003 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
1224948 ACTAACAATC
1224958 TATTTAAAAAGTAATTT-T
1 TATTTAAAAAGTAATTTAT
* *
1224976 TA-TTAAAAATTATTTTAT
1 TATTTAAAAAGTAATTTAT
*
1224994 TCTTTAAAAA
1 TATTTAAAAA
1225004 AGATTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 12 0.52
18 4 0.17
19 7 0.30
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTTAAAAAGTAATTTAT
Found at i:1225936 original size:17 final size:17
Alignment explanation
Indices: 1225914--1225948 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1225904 GGAGATTAAC
1225914 TATTTTAGAAACCATGA
1 TATTTTAGAAACCATGA
*
1225931 TATTTTAGAAATCATGA
1 TATTTTAGAAACCATGA
1225948 T
1 T
1225949 GCGGTCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (17 bp):
TATTTTAGAAACCATGA
Found at i:1229866 original size:90 final size:90
Alignment explanation
Indices: 1229713--1229890 Score: 356
Period size: 90 Copynumber: 2.0 Consensus size: 90
1229703 TCTTTTTTTT
1229713 CATTTCTTGTTTCCCCGCACTCTCTCATCATTATCAACTCTCTTCCTTCTCTATAAATCTTCCCA
1 CATTTCTTGTTTCCCCGCACTCTCTCATCATTATCAACTCTCTTCCTTCTCTATAAATCTTCCCA
1229778 GAATCTGGCAGGAGCCCAGCCGCGG
66 GAATCTGGCAGGAGCCCAGCCGCGG
1229803 CATTTCTTGTTTCCCCGCACTCTCTCATCATTATCAACTCTCTTCCTTCTCTATAAATCTTCCCA
1 CATTTCTTGTTTCCCCGCACTCTCTCATCATTATCAACTCTCTTCCTTCTCTATAAATCTTCCCA
1229868 GAATCTGGCAGGAGCCCAGCCGC
66 GAATCTGGCAGGAGCCCAGCCGC
1229891 CGGCCGTCGT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.19, C:0.36, G:0.12, T:0.33
Consensus pattern (90 bp):
CATTTCTTGTTTCCCCGCACTCTCTCATCATTATCAACTCTCTTCCTTCTCTATAAATCTTCCCA
GAATCTGGCAGGAGCCCAGCCGCGG
Found at i:1230621 original size:3 final size:3
Alignment explanation
Indices: 1230613--1230647 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1230603 GTTTGGCTTT
1230613 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1230648 GGTTGAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1231178 original size:52 final size:50
Alignment explanation
Indices: 1231116--1231216 Score: 175
Period size: 52 Copynumber: 2.0 Consensus size: 50
1231106 AAATTGGACA
1231116 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTA--GGATTACAACTAATTACAAGG
*
1231168 CATAGAAATAGGAGACTAGCCTAGAGTTAGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGATTACAACTAATTACAAG
1231217 AATATTATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 20 0.42
52 28 0.58
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (50 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGATTACAACTAATTACAAGG
Found at i:1235632 original size:52 final size:52
Alignment explanation
Indices: 1235570--1235672 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
1235560 AAATTGGACA
*
1235570 CATAGAAATAGGAAATTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
* *
1235622 CATAGAAATAGGAGACTAGCCTAGGGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1235673 AATATTATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:1240940 original size:17 final size:17
Alignment explanation
Indices: 1240870--1240943 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
1240860 TTGGGCTTTG
* *
1240870 TAATAAATAATAATATTTT
1 TAAT-AATAATAATA-ATA
1240889 TAA-AATAATAATAAT-
1 TAATAATAATAATAATA
*
1240904 TAATAGTAATACTATAAATA
1 TAATAATAATA--AT-AATA
1240924 TAATAATAATAATAATA
1 TAATAATAATAATAATA
1240941 TAA
1 TAA
1240944 GGTAATGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
15 3 0.06
16 7 0.15
17 17 0.36
18 4 0.09
19 6 0.13
20 10 0.21
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
TAATAATAATAATAATA
Found at i:1241407 original size:22 final size:20
Alignment explanation
Indices: 1241373--1241419 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1241363 ATAATTATTT
1241373 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAA-ACC
* *
1241394 AAAAATATTTAATAAAAAACT
1 AAAAA-ATTAAATAAAAAACC
1241415 AAAAA
1 AAAAA
1241420 CATCCCCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAACC
Found at i:1243213 original size:15 final size:15
Alignment explanation
Indices: 1243193--1243226 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1243183 AATTCAATTT
1243193 CAAACATATAGATTA
1 CAAACATATAGATTA
*
1243208 CAAACATATGGATTA
1 CAAACATATAGATTA
1243223 CAAA
1 CAAA
1243227 AGCGATCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.24
Consensus pattern (15 bp):
CAAACATATAGATTA
Found at i:1244113 original size:33 final size:33
Alignment explanation
Indices: 1244071--1244144 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
1244061 AATGATATTT
1244071 TATTATTTGGATCAAATCAAACTATTTTAAAAA
1 TATTATTTGGATCAAATCAAACTATTTTAAAAA
1244104 TATTATTTGGATCAAATCAAACTATTTTAAAAA
1 TATTATTTGGATCAAATCAAACTATTTTAAAAA
1244137 TATTATTT
1 TATTATTT
1244145 TAGATAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (33 bp):
TATTATTTGGATCAAATCAAACTATTTTAAAAA
Found at i:1245099 original size:22 final size:21
Alignment explanation
Indices: 1245074--1245120 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1245064 TAATTATAGG
1245074 TAATATAATT-TAAAATTAAAAT
1 TAATAT-ATTATAAAATT-AAAT
*
1245096 TAATATATTATTAAATTAAAT
1 TAATATATTATAAAATTAAAT
1245117 TAAT
1 TAAT
1245121 GATTATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATATATTATAAAATTAAAT
Found at i:1245134 original size:25 final size:23
Alignment explanation
Indices: 1245086--1245151 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 23
1245076 ATATAATTTA
1245086 AAATTAAAATT-AA-TATATTATT
1 AAATT-AAATTAAATTATATTATT
*
1245108 AAATTAAATTAATGATTATATTCTT
1 AAATTAAATTAA--ATTATATTATT
*
1245133 AAATTAATTTAAATTATAT
1 AAATTAAATTAAATTATAT
1245152 CAAAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 5 0.13
22 6 0.16
23 7 0.18
24 1 0.03
25 19 0.50
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATTAAATTAAATTATATTATT
Found at i:1245181 original size:11 final size:11
Alignment explanation
Indices: 1245131--1245207 Score: 55
Period size: 10 Copynumber: 7.8 Consensus size: 11
1245121 GATTATATTC
1245131 TTAAATTA-AT
1 TTAAATTATAT
1245141 TTAAATTATA-
1 TTAAATTATAT
*
1245151 TCAAA--AT-T
1 TTAAATTATAT
*
1245159 TTAGATTA-AT
1 TTAAATTATAT
1245169 TTAAATTATAT
1 TTAAATTATAT
1245180 TT--A-TATAT
1 TTAAATTATAT
*
1245188 TTAAATTAGAT
1 TTAAATTATAT
*
1245199 TTAATTTAT
1 TTAAATTAT
1245208 TAAGCTTAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
8 12 0.24
9 1 0.02
10 22 0.43
11 16 0.31
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (11 bp):
TTAAATTATAT
Found at i:1246696 original size:2 final size:2
Alignment explanation
Indices: 1246691--1246726 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1246681 GTGTTGTGTG
1246691 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
1246727 GAACTTAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1247871 original size:22 final size:21
Alignment explanation
Indices: 1247829--1247872 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1247819 TATACTAGTA
*
1247829 CTGTAGCAGGGTATCGATTCC
1 CTGTAGCAGGGAATCGATTCC
*
1247850 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCA-GGGAATCGATTCC
1247872 C
1 C
1247873 CTATGACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (21 bp):
CTGTAGCAGGGAATCGATTCC
Found at i:1248082 original size:13 final size:14
Alignment explanation
Indices: 1248054--1248087 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1248044 AAAAAATCTA
*
1248054 AATAAAAGTTAAAT
1 AATAAAAGTAAAAT
1248068 AATAAAA-TAAAAT
1 AATAAAAGTAAAAT
1248081 AATAAAA
1 AATAAAA
1248088 AGTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
AATAAAAGTAAAAT
Found at i:1248088 original size:28 final size:28
Alignment explanation
Indices: 1248057--1248117 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1248047 AAATCTAAAT
*
1248057 AAAAGT-TA-AATAATAAAATAAAATAATA
1 AAAAGTATATAATAAT-AAATAAAACAA-A
*
1248085 AAAAGTATATTATAATAAATAAAACAAA
1 AAAAGTATATAATAATAAATAAAACAAA
1248113 AAAAG
1 AAAAG
1248118 AATTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.41
29 12 0.41
30 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (28 bp):
AAAAGTATATAATAATAAATAAAACAAA
Found at i:1249589 original size:37 final size:36
Alignment explanation
Indices: 1249477--1249736 Score: 308
Period size: 37 Copynumber: 7.1 Consensus size: 36
1249467 CAATATATGC
* * *
1249477 TTTCAAAGATGTTTTAAAAACTATATTATATATATATGT
1 TTTCAAA-ATATTTTCAAAACTATA-TAT-TATATACGT
* * *
1249516 TTTCAAAAAAATTTAAAAACTATATA-T-TATACGT
1 TTTCAAAATATTTTCAAAACTATATATTATATACGT
* *
1249550 TTTCAACAATTTTTTCAAAACTATATATTATATATGT
1 TTTCAA-AATATTTTCAAAACTATATATTATATACGT
* *
1249587 TTTCAAAAATATTTTCAAAATTATATATTATATACATT
1 TTTC-AAAATATTTTCAAAACTATATATTATATAC-GT
* * *
1249625 TTTAAAAATGTTTTCAAAACTATATGTTATATACGT
1 TTTCAAAATATTTTCAAAACTATATATTATATACGT
1249661 TTTCAAACATATTTTCAAAACTATATATTATATACGT
1 TTTCAAA-ATATTTTCAAAACTATATATTATATACGT
*
1249698 TTTCAAACATATTTTCAAAATTATATATTATATACGT
1 TTTCAAA-ATATTTTCAAAACTATATATTATATACGT
1249735 TT
1 TT
1249737 AAAAATGTTG
Statistics
Matches: 193, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
34 12 0.06
35 17 0.09
36 8 0.04
37 129 0.67
38 20 0.10
39 7 0.04
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTCAAAATATTTTCAAAACTATATATTATATACGT
Found at i:1249642 original size:74 final size:74
Alignment explanation
Indices: 1249422--1249736 Score: 340
Period size: 74 Copynumber: 4.3 Consensus size: 74
1249412 AAAATTTTAA
* * * * * *
1249422 AAAATTATATATTATATA--TTTTCAAAAAT-TGTTTTACAAACTGTACA--ATATATGCTTTCA
1 AAAACTATATATTATATACGTTTTCAAAAATAT-TTTCA-AAACTATATATTATATACGTTTTCA
* *
1249482 AAGATGTTTTA
64 AAAATGTTTTC
* * *
1249493 AAAACTATATTATATATATATGTTTTCAAAAA-AATTTAAAAACTATATA-T-TATACGTTTTCA
1 AAAACTATA-TAT-TATATACGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTCA
* *
1249555 ACAATTTTTTC
64 AAAATGTTTTC
* * * *
1249566 AAAACTATATATTATATATGTTTTCAAAAATATTTTCAAAATTATATATTATATACATTTTTAAA
1 AAAACTATATATTATATACGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTCAAA
1249631 AATGTTTTC
66 AATGTTTTC
* *
1249640 AAAACTATATGTTATATACGTTTTCAAACATATTTTCAAAACTATATATTATATACGTTTTCAAA
1 AAAACTATATATTATATACGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTCAAA
* *
1249705 CATATTTTC
66 AATGTTTTC
*
1249714 AAAATTATATATTATATACGTTT
1 AAAACTATATATTATATACGTTT
1249737 AAAAATGTTG
Statistics
Matches: 207, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
71 26 0.13
72 20 0.10
73 41 0.20
74 110 0.53
75 10 0.05
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (74 bp):
AAAACTATATATTATATACGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTCAAA
AATGTTTTC
Found at i:1249683 original size:111 final size:109
Alignment explanation
Indices: 1249469--1249750 Score: 340
Period size: 111 Copynumber: 2.6 Consensus size: 109
1249459 AAACTGTACA
* * * * * * ** *
1249469 ATATATGCTTTCAAAGATGTTTTAAAAACTATAT-TATATATATATGTTTTCAAAAA-AATTTAA
1 ATATATGTTTTCAAAAATATTTTCAAAATTATATAT-TATATACAT-TTTT-AAAAATGTTTTCA
*
1249532 AAACTATATATTATACGTTTTCAACAATTTTTTCAAAACTATATATT
63 AAACTATATATTATACGTTTTCAACAATATTTTCAAAACTATATATT
1249579 ATATATGTTTTCAAAAATATTTTCAAAATTATATATTATATACATTTTTAAAAATGTTTTCAAAA
1 ATATATGTTTTCAAAAATATTTTCAAAATTATATATTATATACATTTTTAAAAATGTTTTCAAAA
*
1249644 CTATATGTTATATACGTTTTCAA-ACATATTTTCAAAACTATATATT
66 CTATAT-AT-TATACGTTTTCAACA-ATATTTTCAAAACTATATATT
* * * *
1249690 ATATACGTTTTCAAACATATTTTCAAAATTATATATTATATAC--GTTTAAAAATGTTGTCAA
1 ATATATGTTTTCAAAAATATTTTCAAAATTATATATTATATACATTTTTAAAAATGTTTTCAA
1249751 TTTATATTTT
Statistics
Matches: 152, Mismatches: 15, Indels: 11
0.85 0.08 0.06
Matches are distributed among these distances:
108 5 0.03
109 33 0.22
110 39 0.26
111 75 0.49
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (109 bp):
ATATATGTTTTCAAAAATATTTTCAAAATTATATATTATATACATTTTTAAAAATGTTTTCAAAA
CTATATATTATACGTTTTCAACAATATTTTCAAAACTATATATT
Found at i:1249763 original size:34 final size:37
Alignment explanation
Indices: 1249493--1249765 Score: 261
Period size: 37 Copynumber: 7.5 Consensus size: 37
1249483 AGATGTTTTA
* * * *
1249493 AAAACTATATTATATATATATGTTTTCAAAAAAATT-TA
1 AAAATTATA-TAT-TATATACGTTTTCAAAAATATTGTC
* * * *
1249531 AAAACTATATA-T-TATACGTTTTCAACAATTTTTTC
1 AAAATTATATATTATATACGTTTTCAAAAATATTGTC
* * *
1249566 AAAACTATATATTATATATGTTTTCAAAAATATTTTC
1 AAAATTATATATTATATACGTTTTCAAAAATATTGTC
* * * *
1249603 AAAATTATATATTATATACATTTTTAAAAATGTTTTC
1 AAAATTATATATTATATACGTTTTCAAAAATATTGTC
* * * *
1249640 AAAACTATATGTTATATACGTTTTCAAACATATTTTC
1 AAAATTATATATTATATACGTTTTCAAAAATATTGTC
* * *
1249677 AAAACTATATATTATATACGTTTTCAAACATATTTTC
1 AAAATTATATATTATATACGTTTTCAAAAATATTGTC
*
1249714 AAAATTATATATTATATACG-TTT-AAAAATGTTGTC
1 AAAATTATATATTATATACGTTTTCAAAAATATTGTC
* *
1249749 -AATTTATATTTTATATA
1 AAAATTATATATTATATA
1249766 TATATATATA
Statistics
Matches: 206, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
34 31 0.15
35 22 0.11
36 4 0.02
37 140 0.68
38 9 0.04
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (37 bp):
AAAATTATATATTATATACGTTTTCAAAAATATTGTC
Found at i:1249767 original size:2 final size:2
Alignment explanation
Indices: 1249760--1249792 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1249750 ATTTATATTT
1249760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1249793 TTAAAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1250340 original size:53 final size:53
Alignment explanation
Indices: 1250277--1250378 Score: 195
Period size: 53 Copynumber: 1.9 Consensus size: 53
1250267 TAATCTCAAC
*
1250277 CATTCATTTTCAATAATTCAACGATCATAAAATTATTTGAAATTTAAAAATTT
1 CATTCATTTTCAATAATTCAACGATCACAAAATTATTTGAAATTTAAAAATTT
1250330 CATTCATTTTCAATAATTCAACGATCACAAAATTATTTGAAATTTAAAA
1 CATTCATTTTCAATAATTCAACGATCACAAAATTATTTGAAATTTAAAA
1250379 GTTTTATGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (53 bp):
CATTCATTTTCAATAATTCAACGATCACAAAATTATTTGAAATTTAAAAATTT
Found at i:1250796 original size:2 final size:2
Alignment explanation
Indices: 1250789--1250815 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1250779 AACTTAACCG
1250789 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
1250816 TAACATCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1251530 original size:16 final size:17
Alignment explanation
Indices: 1251493--1251530 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1251483 GGATAAAAAA
*
1251493 TTAAACAAATTATTTGT
1 TTAAACAAATTATTTAT
1251510 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
1251526 TTAAA
1 TTAAA
1251531 TTAATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:1251845 original size:80 final size:80
Alignment explanation
Indices: 1251749--1251917 Score: 223
Period size: 80 Copynumber: 2.1 Consensus size: 80
1251739 TTTGGTTCAA
* * * * *
1251749 TTAAATGAACCTAATTTTTGCTTCGATTAATTCGATTAA-TAATTTAAAAAAATTGGTTAATTCG
1 TTAAATTAACCGAATTTTTGCTTCGATTAATTCGATTAATTAATTTAAAAAAA-CGATTAATTAG
*
1251813 GTTCGGTTAATAATTT
65 GTTCGGCTAATAATTT
* * ** *
1251829 TTAAATTAACCGAATTTTTTCTTCGATTAATTCGGTTAATTTTTTTTAAAAAACGATTAATTAGG
1 TTAAATTAACCGAATTTTTGCTTCGATTAATTCGATTAATTAATTTAAAAAAACGATTAATTAGG
1251894 TTCGGCTAATAATTT
66 TTCGGCTAATAATTT
1251909 TTAAATTAA
1 TTAAATTAA
1251918 TTTGGTTCGG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 67 0.87
81 10 0.13
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (80 bp):
TTAAATTAACCGAATTTTTGCTTCGATTAATTCGATTAATTAATTTAAAAAAACGATTAATTAGG
TTCGGCTAATAATTT
Found at i:1251926 original size:29 final size:29
Alignment explanation
Indices: 1251884--1251954 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
1251874 TTAAAAAACG
* *
1251884 ATTAATTAGGTTCGGCTAATAATTTTTAA
1 ATTAATTTGGTTCGGCTAATAATTTTCAA
*
1251913 ATTAATTTGGTTCGGTTAATAATTTTCAA
1 ATTAATTTGGTTCGGCTAATAATTTTCAA
*
1251942 ATAAATTTTGGTT
1 ATTAA-TTTGGTT
1251955 TGATTAACTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (29 bp):
ATTAATTTGGTTCGGCTAATAATTTTCAA
Found at i:1251984 original size:138 final size:138
Alignment explanation
Indices: 1251831--1252099 Score: 389
Period size: 138 Copynumber: 1.9 Consensus size: 138
1251821 AATAATTTTT
* * **
1251831 AAATTAACCGAATTTTTTCTTCGATTAATTCGGTTAATTTTTTTTAAAAAA-C-GATTAATTAGG
1 AAATTAACCAAATTTTTGCTTCGATTAATTCGGTTAA--TAATTTAAAAAATCTGATTAATTAGG
* * * * *
1251894 TTCGGCTAATAATTTTTAAATTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTTGAT
64 TTCGACTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGAT
1251959 TAACTGAAAC
129 TAACTGAAAC
* * *
1251969 AAATTAACCAAATTTTTGCTTCGATTAATTCGTTTAATAATTTAAAAAATCTGGTTAATTCGGTT
1 AAATTAACCAAATTTTTGCTTCGATTAATTCGGTTAATAATTTAAAAAATCTGATTAATTAGGTT
*
1252034 CGATTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTA
66 CGACTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTA
1252099 A
131 A
1252100 TCGAACCAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
136 10 0.09
137 1 0.01
138 105 0.91
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (138 bp):
AAATTAACCAAATTTTTGCTTCGATTAATTCGGTTAATAATTTAAAAAATCTGATTAATTAGGTT
CGACTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTA
ACTGAAAC
Found at i:1252059 original size:29 final size:29
Alignment explanation
Indices: 1252023--1252100 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
1252013 AAAAATCTGG
1252023 TTAATTCGGTTCGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
1252052 TTAATTCGGTTC-AGTTAATAATTTTCAAA
1 TTAATTCGGTTCGA-TTAATAATTTTCAAA
* *
1252081 TAAATTTTGGTTCGATTAAT
1 TTAA-TTCGGTTCGATTAAT
1252101 CGAACCAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 1 0.02
29 30 0.68
30 12 0.27
31 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Found at i:1252581 original size:17 final size:18
Alignment explanation
Indices: 1252551--1252589 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1252541 AAATTGTCCT
* *
1252551 TATTATATATTTGTATAA
1 TATTACATATTTGTAAAA
1252569 TATTACATA-TTGTAAAA
1 TATTACATATTTGTAAAA
1252586 TATT
1 TATT
1252590 TATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATTACATATTTGTAAAA
Found at i:1252596 original size:18 final size:17
Alignment explanation
Indices: 1252551--1252597 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1252541 AAATTGTCCT
*
1252551 TATTATATATTTGTATAA
1 TATTATATA-TTGTAAAA
*
1252569 TATTACATATTGTAAAA
1 TATTATATATTGTAAAA
1252586 TATTTATATATT
1 TA-TTATATATT
1252598 TTCTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
TATTATATATTGTAAAA
Found at i:1257419 original size:24 final size:24
Alignment explanation
Indices: 1257379--1257424 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1257369 TCAAATTTTT
*
1257379 TAATATATATAACTTTATTTTAAA
1 TAATATATATAACTTTAATTTAAA
*
1257403 TAATATA-ATATAGTTTAATTTA
1 TAATATATATA-ACTTTAATTTA
1257425 CTAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TAATATATATAACTTTAATTTAAA
Found at i:1262159 original size:13 final size:13
Alignment explanation
Indices: 1262141--1262170 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1262131 AATCTTAGAT
*
1262141 ACAACTTTGAGAG
1 ACAACTTTGAGAC
1262154 ACAACTTTGAGAC
1 ACAACTTTGAGAC
1262167 ACAA
1 ACAA
1262171 TTCACAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (13 bp):
ACAACTTTGAGAC
Found at i:1262529 original size:3 final size:3
Alignment explanation
Indices: 1262523--1262552 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1262513 ATTTATTTAT
1262523 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1262553 CTTGGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1268564 original size:4 final size:4
Alignment explanation
Indices: 1268557--1268601 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
1268547 AGGAAGGTAT
1268557 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1268602 CATATAGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:1273180 original size:20 final size:20
Alignment explanation
Indices: 1273152--1273199 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1273142 TATCCGTATT
*
1273152 TCTCAGCTTTTAAACTTTTC
1 TCTCGGCTTTTAAACTTTTC
1273172 TCTCGGCTTTTAAACTTTTC
1 TCTCGGCTTTTAAACTTTTC
1273192 TCTCGGCT
1 TCTCGGCT
1273200 ATAAATACGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.27, G:0.10, T:0.48
Consensus pattern (20 bp):
TCTCGGCTTTTAAACTTTTC
Found at i:1273381 original size:8 final size:8
Alignment explanation
Indices: 1273368--1273434 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
1273358 AACATATTTA
1273368 AATAAAAT
1 AATAAAAT
1273376 AATAAAAAT
1 AAT-AAAAT
*
1273385 AATTAAAT
1 AATAAAAT
*
1273393 AATTAAAT
1 AATAAAAT
*
1273401 AA-AATACT
1 AATAA-AAT
*
1273409 AACAAAAT
1 AATAAAAT
*
1273417 ATTAAATAT
1 AATAAA-AT
1273426 AATAAAAT
1 AATAAAAT
1273434 A
1 A
1273435 TACCTTATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
7 1 0.02
8 30 0.62
9 17 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAAAAT
Found at i:1273401 original size:30 final size:31
Alignment explanation
Indices: 1273365--1273424 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1273355 AATAACATAT
1273365 TTAAATAAAATAAT-A-AAAATAATTAAATAA
1 TTAAATAAAATAATAACAAAAT-ATTAAATAA
*
1273395 TTAAATAAAATACTAACAAAATATTAAATA
1 TTAAATAAAATAATAACAAAATATTAAATA
1273425 TAATAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 13 0.48
31 9 0.33
32 5 0.19
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (31 bp):
TTAAATAAAATAATAACAAAATATTAAATAA
Found at i:1279878 original size:39 final size:39
Alignment explanation
Indices: 1279811--1279910 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 39
1279801 ACATAGCATA
* * * *
1279811 AGGA-CCTGCGGTAAGAACTTACCTTGAGCACAATCCTG
1 AGGAGCCTACGGTAAGGACTTACCCTGAGCACAAACCTG
* ** **
1279849 AGGAGCTTGTGGTAAGGACTTACCCTGAGCACAAAGTTG
1 AGGAGCCTACGGTAAGGACTTACCCTGAGCACAAACCTG
1279888 AGGAGCCTACGGTAAGGACTTAC
1 AGGAGCCTACGGTAAGGACTTAC
1279911 AAGTCATAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 4 0.08
39 47 0.92
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (39 bp):
AGGAGCCTACGGTAAGGACTTACCCTGAGCACAAACCTG
Found at i:1287289 original size:39 final size:39
Alignment explanation
Indices: 1287230--1287323 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
1287220 CATAAGGACT
* *** *
1287230 TGCGATAAGGACTTACCCTGAGCACAAAGTTGAGGAGCC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCCAAAGAGCC
1287269 TGCGGTAAGGACTTACCCTGAGCACAAAGCCAAAGAGCC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCCAAAGAGCC
*
1287308 TGTGGTAAGGACTTAC
1 TGCGGTAAGGACTTAC
1287324 AAGTCATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (39 bp):
TGCGGTAAGGACTTACCCTGAGCACAAAGCCAAAGAGCC
Found at i:1289541 original size:48 final size:48
Alignment explanation
Indices: 1289443--1289544 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 48
1289433 TACTTTTGAG
* * *
1289443 TAAATTGTCAATTAAAAAACTTTCTCCTCCATTTTTCAATTTAGATTT
1 TAAATTGTCAATTAAAAAACTTTCTCCTCCATTTTCCAATTTACAATT
* ** * *
1289491 TAAATTGTCAATTAAAAAATTTTCCTTTTCC-TTTTCCATTTTTCAATT
1 TAAATTGTCAATTAAAAAACTTT-CTCCTCCATTTTCCAATTTACAATT
1289539 TAAATT
1 TAAATT
1289545 TTAAAAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
48 40 0.89
49 5 0.11
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (48 bp):
TAAATTGTCAATTAAAAAACTTTCTCCTCCATTTTCCAATTTACAATT
Found at i:1291365 original size:16 final size:16
Alignment explanation
Indices: 1291346--1291447 Score: 114
Period size: 16 Copynumber: 6.2 Consensus size: 16
1291336 AACAAGCAAT
*
1291346 GAGCATCGACCTTAAC
1 GAGCATCGAGCTTAAC
* **
1291362 GAGCAACGAGGCAAGCAAC
1 GAGCATCGA-GC--TTAAC
1291381 GAGCATCGAGCTTAAC
1 GAGCATCGAGCTTAAC
1291397 GAGCATCGAGCTTAAC
1 GAGCATCGAGCTTAAC
* *
1291413 GAGCATCGAACTTAAT
1 GAGCATCGAGCTTAAC
*
1291429 GAGCAACGAGCTTAAC
1 GAGCATCGAGCTTAAC
1291445 GAG
1 GAG
1291448 TAACGAGTTG
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
16 57 0.80
17 1 0.01
18 2 0.03
19 11 0.15
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (16 bp):
GAGCATCGAGCTTAAC
Found at i:1291385 original size:35 final size:35
Alignment explanation
Indices: 1291338--1291438 Score: 118
Period size: 35 Copynumber: 3.0 Consensus size: 35
1291328 GTGAGCTTAA
* *
1291338 CAAGCAATGAGCATCGACCTTAACGAGCAACGAGG
1 CAAGCAACGAGCATCGAACTTAACGAGCAACGAGG
* *
1291373 CAAGCAACGAGCATCGAGCTTAACGAGCATCGA-G
1 CAAGCAACGAGCATCGAACTTAACGAGCAACGAGG
** *
1291407 C--TTAACGAGCATCGAACTTAATGAGCAACGAG
1 CAAGCAACGAGCATCGAACTTAACGAGCAACGAG
1291439 CTTAACGAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
32 25 0.44
34 2 0.04
35 30 0.53
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.14
Consensus pattern (35 bp):
CAAGCAACGAGCATCGAACTTAACGAGCAACGAGG
Found at i:1298403 original size:43 final size:43
Alignment explanation
Indices: 1298355--1298454 Score: 173
Period size: 43 Copynumber: 2.3 Consensus size: 43
1298345 CGAATGTTAA
*
1298355 ATGAATTATGTGAACATATGCTTATGAGGTAAGACCCATGACT
1 ATGAATTATGTGAACATATGCTTATGAGATAAGACCCATGACT
1298398 ATGAATTATGTGAACATATGCTTATGAGATAAGACCCATGACT
1 ATGAATTATGTGAACATATGCTTATGAGATAAGACCCATGACT
**
1298441 ATGAGCTATGTGAA
1 ATGAATTATGTGAA
1298455 AAAGAATACA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (43 bp):
ATGAATTATGTGAACATATGCTTATGAGATAAGACCCATGACT
Found at i:1298423 original size:23 final size:23
Alignment explanation
Indices: 1298355--1298424 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
1298345 CGAATGTTAA
1298355 ATGAATTATGTGAACATATGCTT
1 ATGAATTATGTGAACATATGCTT
** * **
1298378 ATGAGGTA--AG-ACCCATGAC-T
1 ATGAATTATGTGAACATATG-CTT
1298398 ATGAATTATGTGAACATATGCTT
1 ATGAATTATGTGAACATATGCTT
1298421 ATGA
1 ATGA
1298425 GATAAGACCC
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 2 0.06
23 16 0.50
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (23 bp):
ATGAATTATGTGAACATATGCTT
Found at i:1306670 original size:21 final size:21
Alignment explanation
Indices: 1306644--1306686 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1306634 AATATATAAG
1306644 TCAGTTTCTGAATTACATTCT
1 TCAGTTTCTGAATTACATTCT
1306665 TCAGTTTCTGAATTACATTCT
1 TCAGTTTCTGAATTACATTCT
1306686 T
1 T
1306687 TCTGTTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (21 bp):
TCAGTTTCTGAATTACATTCT
Found at i:1318269 original size:23 final size:23
Alignment explanation
Indices: 1318222--1318271 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1318212 AATAACATAT
**
1318222 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
1318245 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
1318268 TAGG
1 TAGG
1318272 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:1318331 original size:87 final size:86
Alignment explanation
Indices: 1318185--1318357 Score: 301
Period size: 87 Copynumber: 2.0 Consensus size: 86
1318175 TATGTTATAT
* * *
1318185 CATTTAACCGGAAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACACATTAAGTAGCGCTTATATAATGTAATAGGT
1318250 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATAT-ATAAAATAGG
1318272 CATTTAACCGGAAATATTATCAAGTACAATAACACATTAAGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACACATTAAGTAGCGCTTATATAATGTAATAGGT
*
1318337 AGCGCTTATATATATAATAGG
66 AGCGCTTATATATAAAATAGG
1318358 TAGCGCTTAT
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 9 0.11
87 73 0.89
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (86 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACACATTAAGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATATAAAATAGG
Found at i:1318357 original size:22 final size:23
Alignment explanation
Indices: 1318312--1318369 Score: 100
Period size: 22 Copynumber: 2.6 Consensus size: 23
1318302 AACACATTAA
*
1318312 GTAGCGCTTATATAATGTAATAG
1 GTAGCGCTTATATAATATAATAG
1318335 GTAGCGCTTATAT-ATATAATAG
1 GTAGCGCTTATATAATATAATAG
1318357 GTAGCGCTTATAT
1 GTAGCGCTTATAT
1318370 TGACTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (23 bp):
GTAGCGCTTATATAATATAATAG
Found at i:1319228 original size:200 final size:199
Alignment explanation
Indices: 1318364--1319292 Score: 1068
Period size: 201 Copynumber: 4.6 Consensus size: 199
1318354 TAGGTAGCGC
* ** * *
1318364 TTATATTGACTTATTTT-ATAAGT-AAACATGTATATTTATACCGGTAACATTGCAAATTTACCT
1 TTATGTTGACTTATTTTCATAA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCT
* *
1318427 ATTACATTATAATTATCGGTTTCGATGTTTTTTGGATCGATACAATTTT--AAATGTATCGACAC
65 ATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATAC--TTTTAAAAATGTATCGACAC
* * * * *
1318490 TTTATGCGTGCACCTCG-TTGGGTATTCATTCT-GAAAACAAGTAACAACATAAACTTAAAGAGT
128 TTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAA-AAGTATCGACACAAACTTAAA-AGT
1318553 GTCGATACA
191 GTCGATACA
* * * * * *
1318562 TTAT-TTAGACCTTTTTTCTTCTTCATAAAACCGGTATATTTCTATCGGGTACATTGTAAATTTA
1 TTATGTT-GA-C-TTATT-TTCATAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTA
* * *
1318626 CCTATAACATTGTAATTATCGGTTTCGATATTTTTGGGATCGATAGTTTTAATAAATGTATCGAC
62 CCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTAA-AAATGTATCGAC
* * *
1318691 ACTTTATGCGTGCACCT-GTTT-GGCATTCATTATGGACAAAATGTATCGAAACAAATTTAATAA
126 ACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAA-GTATCGACACAAACTTAA-AA
*
1318754 GTGTCGATACT
189 GTGTCGATACA
* * * * * *
1318765 TTATGATGACCTATTTTC-TCATAAAACGGGTATATTTATACCAGTTACATTGTAAATTTACATA
1 TTATGTTGACTTATTTTCATAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
*
1318829 TTACATTATAATTATCGGTTTCGATATTTTTTGGATCGATACTTTTTAAAACATGTATCGACACT
66 TTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATAC-TTTTAAAA-ATGTATCGACACT
* * *
1318894 TTATGCGTGCAACTC-TTTTGGCATTCATTTTGGACAAAAAGTATCGACACAAA-TATAAAACGT
129 TTATGCGTGCACCTCGTTTGGGCATTCATTCTGGAC-AAAAGTATCGACACAAACT-TAAAA-GT
1318957 GTCGATACA
191 GTCGATACA
* * *
1318966 TTATGTTCACATATTTT-A-ACATAAAATCGGTATATTTATACCGGTTACATTGTAAATTTACCT
1 TTATGTTGACTTATTTTCATA-ATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCT
* * *
1319029 ATTACATTATAATTATCGGTTTTGAT-TTTATTGGGATTGATACTTTTAATAATTGTATCGACAC
65 ATTACATTATAATTATCGGTTTCGATATTT-TTGGGATCGATACTTTTAA-AAATGTATCGACAC
* *
1319093 TTTATGCGTGCACCTCGTTTGGGAATTCATTCTAGACAATAAGTATCGACACAAA-TTACACAAG
128 TTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAA-AAGTATCGACACAAACTTA-A-AAG
1319157 TGTCGATACA
190 TGTCGATACA
* * *
1319167 TTATGTTGACTTGTTTTC-TAAT-TAACCGGTATATTTATACCGGTTACATTGTTAATTTACCTA
1 TTATGTTGACTTATTTTCATAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* *
1319230 TTACATTATAATTATTGGTTTCGATGTTTTTTGGG-TCGATACTTTTAGAAAATGTATCGACAC
66 TTACATTATAATTATCGGTTTCGAT-ATTTTTGGGATCGATACTTTTA-AAAATGTATCGACAC
1319293 ATATTTAGGT
Statistics
Matches: 629, Mismatches: 68, Indels: 66
0.82 0.09 0.09
Matches are distributed among these distances:
197 2 0.00
198 6 0.01
199 81 0.13
200 173 0.28
201 203 0.32
202 97 0.15
203 65 0.10
204 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (199 bp):
TTATGTTGACTTATTTTCATAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
TTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTAAAAATGTATCGACACTTT
ATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAAAAGTATCGACACAAACTTAAAAGTGTCGA
TACA
Found at i:1319253 original size:401 final size:401
Alignment explanation
Indices: 1318393--1319292 Score: 1180
Period size: 401 Copynumber: 2.2 Consensus size: 401
1318383 AAGTAAACAT
* *
1318393 GTATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* *
1318458 TTGGATCGATACAATTTT--AAATGTATCGACACTTTATGCGTGCACCTCGTTGGGTATTCATTC
66 TTGGATCGATAC--TTTTAAAAATGTATCGACACTTTATGCGTGCAACTCGTTGGGCATTCATTC
* * * * **
1318521 TGAAAACAAGTAACAACATAAACTTAAAGAGTGTCGATACATTATTTAGACCTTTTTTCTTCTTC
129 TGAAAACAAGTAACAACACAAACTTAAAGAGTGTCGATACATTATTTACACCTATATTCTTCAAC
* * *
1318586 ATAAAACCGGTATATTTCTATCGGGTACATTGTAAATTTACCTATAACATTGTAATTATCGGTTT
194 ATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATAACATTATAATTATCGGTTT
* *
1318651 CGATATTTTTGGGATCGATAGTTTTAATAAATGTATCGACACTTTATGCGTGCACCTGTTTGGCA
259 CGATATTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTGTTTGGAA
* * *
1318716 TTCATTATGGACAAAATGTATCGAAACAAATTTAATAAGTGTCGATACTTTATGATGACCTATTT
324 TTCATTATAGACAAAATGTATCGAAACAAATTTAACAAGTGTCGATACATTATGATGACCTATTT
* *
1318781 TCTCATAAAACGG
389 TCTAATAAAACCG
* * *
1318794 GTATATTTATACCAGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGATATTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * *
1318859 TTGGATCGATACTTTTTAAAACATGTATCGACACTTTATGCGTGCAACTCTTTTGGCATTCATTT
66 TTGGATCGATAC-TTTTAAAA-ATGTATCGACACTTTATGCGTGCAACTCGTTGGGCATTCATTC
* *
1318924 TGGACAAA-AAGTATCGACACAAA-TATAAA-ACGTGTCGATACATTATGTT-CA-C-ATATT-T
129 T-GA-AAACAAGTAACAACACAAACT-TAAAGA-GTGTCGATACATTAT-TTACACCTATATTCT
* * *
1318982 T-AACATAAAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATC
189 TCAACATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATAACATTATAATTATC
* * *
1319046 GGTTTTGAT-TTTATTGGGATTGATACTTTTAATAATTGTATCGACACTTTATGCGTGCACCTCG
254 GGTTTCGATATTT-TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCT-G
* * *
1319110 TTTGGGAATTCATTCTAGACAATAA-GTATCGACACAAA-TTACACAAGTGTCGATACATTATGT
317 TTT-GGAATTCATTATAGACAA-AATGTATCGAAACAAATTTA-ACAAGTGTCGATACATTATGA
* * *
1319173 TGACTTGTTTTCTAAT-TAACCG
379 TGACCTATTTTCTAATAAAACCG
* *
1319195 GTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
*
1319260 TTGGGTCGATACTTTTAGAAAATGTATCGACAC
66 TTGGATCGATACTTTTA-AAAATGTATCGACAC
1319293 ATATTTAGGT
Statistics
Matches: 438, Mismatches: 47, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
399 3 0.01
400 130 0.30
401 159 0.36
402 63 0.14
403 44 0.10
404 34 0.08
405 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (401 bp):
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TTGGATCGATACTTTTAAAAATGTATCGACACTTTATGCGTGCAACTCGTTGGGCATTCATTCTG
AAAACAAGTAACAACACAAACTTAAAGAGTGTCGATACATTATTTACACCTATATTCTTCAACAT
AAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATAACATTATAATTATCGGTTTCG
ATATTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTGTTTGGAATT
CATTATAGACAAAATGTATCGAAACAAATTTAACAAGTGTCGATACATTATGATGACCTATTTTC
TAATAAAACCG
Found at i:1323763 original size:201 final size:198
Alignment explanation
Indices: 1323399--1324168 Score: 882
Period size: 201 Copynumber: 3.8 Consensus size: 198
1323389 CGTTATTTAT
* * * *
1323399 AAGTATCGATACAAATCTAAAACGTGTCGATACATTATGCTAACCTATTTTCTCATAAAACCGGT
1 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATG-TAAACTATTCTCACATAAAACCGGT
* * *
1323464 ACATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTT
65 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* * * *
1323529 GGATCGATACTTTTTAAAACATGTATTGACACTTTATGCGTGCAACCCTTTTGGCATTCATTTTG
130 GGATCGATACTTTTTAAAA-ATGTATCGACACTTTATGCATAC-ACCCTTTTGGCATTCATTCTG
1323594 GACAAA
193 GACAAA
* * *
1323600 AAGTATTGACACAAATCTAAAACGTGTCGATACATTATGTTAAACTATTTTAACATAAAACCGGT
1 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATG-TAAACTATTCTCACATAAAACCGGT
* *
1323665 ATATTTATACCTGTTACATTGTAAATTTACCTACTACATTATAATTATCGGTTTCGATGTTTTTG
65 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* * * * * *
1323730 GAATTGATACTTTTTTATAAATTTATCGACACTTTATGCCTTCACCCTTTTGGGCATTCATTCTG
130 GGATCGATAC-TTTTTAAAAATGTATCGACACTTTATGCATACACCCTTTT-GGCATTCATTCTG
* *
1323795 TACAAC
193 GACAAA
* * * * * *
1323801 AAGTATCGACACAACAT-TAAAAAGTGTTGACATATTATGTAGACCTATTCTCACATAAAACCAG
1 AAGTATCGACACAA-ATCTAAAACGTGTCGATACATTATGTA-AACTATTCTCACATAAAACCGG
* * ** * * *
1323865 TATATTTATATCGGTTATATTACAAAATTACCTATTATATTATAATTATAGGTTTCGATGTTTTT
64 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* * * * * *
1323930 GGGATCGATACGTTTTAAAAATGTTTCAACACTTTATGAATACACCCTTTATGGATATTCCTTCT
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCATACACCCTTT-TGG-CATTCATTCT
1323995 GGACAAA
192 GGACAAA
* * * * * *
1324002 CAA-TAACGACACAAATTCCAGAA-GTGTCGATAAATTATGTAGACTTATTCTCTCATAAAACCG
1 -AAGTATCGACACAAA-TCTAAAACGTGTCGATACATTATGTAAAC-TATTCTCACATAAAACCG
* * * *
1324065 GTTTAGTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTTAT-GGATTTTGATGTTT
63 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGG-TTTCGATGTTT
* * *
1324129 CTGGGATTGATACTTTTTAAAACTGTATCGACACTTTATG
127 TTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATG
1324169 AGAAACTTTA
Statistics
Matches: 479, Mismatches: 79, Indels: 22
0.83 0.14 0.04
Matches are distributed among these distances:
200 47 0.10
201 417 0.87
202 15 0.03
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (198 bp):
AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTAAACTATTCTCACATAAAACCGGTA
TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
GATCGATACTTTTTAAAAATGTATCGACACTTTATGCATACACCCTTTTGGCATTCATTCTGGAC
AAA
Found at i:1324143 original size:402 final size:401
Alignment explanation
Indices: 1323399--1324168 Score: 975
Period size: 402 Copynumber: 1.9 Consensus size: 401
1323389 CGTTATTTAT
* * * * * *
1323399 AAGTATCGATACAAATCTAAAACGTGTCGATACATTATGCTAACCTATTTTCTCATAAAACCGGT
1 AAGTATCGACACAAATCTAAAAAGTGTCGACACATTATGCTAACCTATTCTCACATAAAACCAGT
** * * *
1323464 ACATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTT
66 ACATTTATACCGATTACATTACAAAATTACCTATTACATTATAATTATAGGTTTCGATGTTTTTG
* * ** * *
1323529 GGATCGATACTTTTTAAAACATGTATTGACACTTTATGCGTGCAACCCTTTTGGCATTCATTTTG
131 GGATCGATACGTTTTAAAACATGTATTAACACTTTATGAATACAACCCTTTTGGCATTCATTCTG
** * * *
1323594 GACAAAAAGTATTGACACAAATCTAAAACGTGTCGATACATTATGTTAAACTATTTTAACATAAA
196 GACAAAAAGTAACGACACAAATCCAAAACGTGTCGATAAATTATGTTAAACTATTCTAACATAAA
* *
1323659 ACCGGTATATTTATACCTGTTACATTGTAAATTTACCTACTACATTATAATTATCGGTTTCGATG
261 ACCGGTATAGTTATACCGGTTACATTGTAAATTTACCTACTACATTATAATTATCGGTTTCGATG
* *
1323724 TTTTTGGAATTGATACTTTTTTATAAA-TTTATCGACACTTTATGCCTTCACCCTTTTGGGCATT
326 TTTCTGGAATTGATAC-TTTTTA-AAACTGTATCGACACTTTATGCCTTCACCCTTTTGGGCATT
1323788 CATTCTGTACAAC
389 CATTCTGTACAAC
* *
1323801 AAGTATCGACACAACAT-TAAAAAGTGTTGACATATTATG-TAGACCTATTCTCACATAAAACCA
1 AAGTATCGACACAA-ATCTAAAAAGTGTCGACACATTATGCTA-ACCTATTCTCACATAAAACCA
* * * * *
1323864 GTATATTTATATCGGTTATATTACAAAATTACCTATTATATTATAATTATAGGTTTCGATGTTTT
64 GTACATTTATACCGATTACATTACAAAATTACCTATTACATTATAATTATAGGTTTCGATGTTTT
* *
1323929 TGGGATCGATACGTTTTAAAA-ATGT-TTCAACACTTTATGAATAC-ACCCTTTATGGATATTCC
129 TGGGATCGATACGTTTTAAAACATGTATT-AACACTTTATGAATACAACCCTTT-TGG-CATTCA
* *
1323991 TTCTGGACAAACAA-TAACGACACAAATTCCAGAA-GTGTCGATAAATTATG-TAGACTTATTCT
191 TTCTGGACAAA-AAGTAACGACACAAA-TCCAAAACGTGTCGATAAATTATGTTAAAC-TATTCT
** * * *
1324053 CTCATAAAACCGGTTTAGTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTTAT-GG
253 AACATAAAACCGGTATAGTTATACCGGTTACATTGTAAATTTACCTACTACATTATAATTATCGG
* *
1324117 ATTTTGATGTTTCTGGGATTGATACTTTTTAAAACTGTATCGACACTTTATG
318 -TTTCGATGTTTCTGGAATTGATACTTTTTAAAACTGTATCGACACTTTATG
1324169 AGAAACTTTA
Statistics
Matches: 314, Mismatches: 44, Indels: 21
0.83 0.12 0.06
Matches are distributed among these distances:
400 12 0.04
401 49 0.16
402 244 0.78
403 9 0.03
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (401 bp):
AAGTATCGACACAAATCTAAAAAGTGTCGACACATTATGCTAACCTATTCTCACATAAAACCAGT
ACATTTATACCGATTACATTACAAAATTACCTATTACATTATAATTATAGGTTTCGATGTTTTTG
GGATCGATACGTTTTAAAACATGTATTAACACTTTATGAATACAACCCTTTTGGCATTCATTCTG
GACAAAAAGTAACGACACAAATCCAAAACGTGTCGATAAATTATGTTAAACTATTCTAACATAAA
ACCGGTATAGTTATACCGGTTACATTGTAAATTTACCTACTACATTATAATTATCGGTTTCGATG
TTTCTGGAATTGATACTTTTTAAAACTGTATCGACACTTTATGCCTTCACCCTTTTGGGCATTCA
TTCTGTACAAC
Found at i:1324494 original size:25 final size:25
Alignment explanation
Indices: 1324465--1324517 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
1324455 ATACACAAGA
1324465 AATTTATACATAACAA-TGTTCAAAT
1 AATTTATACATAA-AATTGTTCAAAT
1324490 AATTTATACATAAAATTGTTCAAAT
1 AATTTATACATAAAATTGTTCAAAT
1324515 AAT
1 AAT
1324518 GTACCCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTTATACATAAAATTGTTCAAAT
Found at i:1325505 original size:3 final size:3
Alignment explanation
Indices: 1325497--1325540 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1325487 ACGTGTTTGG
* * * *
1325497 ATC ATC ATC ATC ATC ATC ATC TTC ATC GTC ATC TTC ATC TTC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1325541 TGACCTCTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (3 bp):
ATC
Found at i:1325514 original size:12 final size:12
Alignment explanation
Indices: 1325497--1325540 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1325487 ACGTGTTTGG
*
1325497 ATCATCATCATC
1 ATCATCATCTTC
1325509 ATCATCATCTTC
1 ATCATCATCTTC
*
1325521 ATCGTCATCTTC
1 ATCATCATCTTC
*
1325533 ATCTTCAT
1 ATCATCAT
1325541 TGACCTCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:1327518 original size:200 final size:198
Alignment explanation
Indices: 1327021--1328377 Score: 1511
Period size: 200 Copynumber: 6.8 Consensus size: 198
1327011 ATTTAAAATG
* * * * * *
1327021 GTATCGACACAAATTTAATAATTGTCGATACTTTATG-ATGACCTATTTTCTCATAAAACCGGTA
1 GTATCGACACAAATTAAACAAGTGTCGATACATTATGTA-GACCTATTCTCACATAAAACCGGTA
* ** * *
1327085 TATCTATACCGGTTACATTGGAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTCTTGG
65 TATTTATACCGGTTACATTAAAAATTT-CCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* * * * * *
1327150 GATTGACACTTTTTAAAAAAGTATCGACACTTTATGCATGCAACC-CTTT-GGCATTCCTTTTGG
129 GATCGACACTTTTTATAAATGTATCGACACTTTATGCGTGC-ACCATTTTGGGCATTCCTTCTGG
1327213 ACAAAAA
193 AC-AAAA
* ** *
1327220 GTATCGACACCAATTCCACAAGTGTCGATACATGT-TATAGACCTATTCT-ATCATAAAACCGGT
1 GTATCGACACAAATTAAACAAGTGTCGATACAT-TATGTAGACCTATTCTCA-CATAAAACCGGT
* *** * *
1327283 ATAGTTATACCGGTTACATCGTAAATTTACCTATTATATTATATTTATGGGTTTCGATGTTTTTG
64 ATATTTATACCGGTTACATTAAAAATTT-CCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* * ** * *
1327348 GTATCGACACTTTTTATAAATATATCGACACTTTATGCGTTTATCATTTTGGGCATTCATTCTGG
128 GGATCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCCTTCTGG
1327413 ACAAAA
193 ACAAAA
* * * *
1327419 CGTATCGACACAAAATAAAAAAGTGTTGATATATTATGTAGACCTATTCTCACATAAAACCGGTA
1 -GTATCGACACAAATTAAACAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTA
* *
1327484 TATTTATACCGGTTATATTACAAAATTTCCTATTACATTATAATTATGGGTTTCGATGTTTTTAG
65 TATTTATACCGGTTACATTA-AAAATTTCCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* * * *
1327549 GATCGACACTTTGTATAAATGTATTGACAC-TTAGTG-GTGTACCCTTTTTGGGCATTCCTTCTG
129 GATCGACACTTTTTATAAATGTATCGACACTTTA-TGCGTGCA-CCATTTTGGGCATTCCTTCTG
1327612 GACCAAAA
192 GA-CAAAA
* * * * *
1327620 GTATCGATACAAATTACACAAGTGTCGATACA-TATTGTACACCTATTCTCTCATAAAATCGGTA
1 GTATCGACACAAATTAAACAAGTGTCGATACATTA-TGTAGACCTATTCTCACATAAAACCGGTA
** * * * *
1327684 TAAGTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATGGTTTTCGATGTTTCTGG
65 TATTTATACCGGTTACATT-AAAAATTTCCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* *
1327749 GATCGACACTTCTTATAAATGTATCGACAC-TTAGTG-GTGCACCCTTTTTGGGCATTCCTTCTG
129 GATCGACACTTTTTATAAATGTATCGACACTTTA-TGCGTGCA-CCATTTTGGGCATTCCTTCTG
1327812 GACCAAAA
192 GA-CAAAA
* * * *
1327820 GTATCGACACAAATTACACAAGTTTCGATACA-TATTGTACACCTATTCTCTCATAAAACCGGTA
1 GTATCGACACAAATTAAACAAGTGTCGATACATTA-TGTAGACCTATTCTCACATAAAACCGGTA
* * * * *
1327884 TATGTATACCGGCTACATTGAAAAATTTCCTATTACATTATAATTATGGGTTTCAATGTTTCTAG
65 TATTTATACCGGTTACATT-AAAAATTTCCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* *
1327949 GATCGATACTTGTTTATAAATGTATCGACACTCTT-TGCGTGCACCCTTTTGGGCATTCCTTCTG
129 GATCGACACTT-TTTATAAATGTATCGACACT-TTATGCGTGCACCATTTTGGGCATTCCTTCTG
*
1328013 GAGAAACA
192 GACAAA-A
** * * * *
1328021 GTATCGACACAAATTCTAGAAGTGTCGATACATTATGTAGACCTATTCTCCCATAAAATCGGTTT
1 GTATCGACACAAATTAAACAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * * *
1328086 AGTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGG
66 ATTTATACCGGTTACATT-AAAAATTTCCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
** * * * * *
1328151 ATCGACACTTTCAATAAATGTATCGACACGTTATGCGTTCATCATTTTGGGCAATCATTCTGGAC
130 ATCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCCTTCTGGAC
1328216 AAAAA
195 -AAAA
* * *
1328221 GTATCGACACATAATGAAA-AAGTGTCGATACATTATGTAAACCTATTCTCACATAAAACTGGTA
1 GTATCGACACA-AATTAAACAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTA
* * * *
1328285 TATTTATACCAGTTATATTACAAAATTACTTATTACATTATAATTATGGGATTT--ACTGTTTTT
65 TATTTATACCGGTTACATTA-AAAATTTCCTATTACATTATAATTATGGG-TTTCGA-TGTTTTT
* *
1328348 GGGATCGACAGTTTTTATAAACGTATCGAC
127 GGGATCGACACTTTTTATAAATGTATCGAC
1328378 TCATATGCTT
Statistics
Matches: 1001, Mismatches: 131, Indels: 51
0.85 0.11 0.04
Matches are distributed among these distances:
198 2 0.00
199 161 0.16
200 644 0.64
201 185 0.18
202 7 0.01
203 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (198 bp):
GTATCGACACAAATTAAACAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
ATTTATACCGGTTACATTAAAAATTTCCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGA
TCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCCTTCTGGACA
AAA
Found at i:1328141 original size:601 final size:598
Alignment explanation
Indices: 1327021--1328377 Score: 1642
Period size: 601 Copynumber: 2.3 Consensus size: 598
1327011 ATTTAAAATG
* * * * * *
1327021 GTATCGACACA-AATTTAATAATTGTCGATACTTTATG-ATGACCTATTTTCTCATAAAACCGGT
1 GTATCGACACATAA-TGAAAAAGTGTCGATACATTATGTA-AACCTATTCTCTCATAAAA-CGGT
* * *
1327084 ATATCTATACCGGTTACATTGGAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTCTT
63 ATATCTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTC-T
* * *
1327148 GGGATTGACACTTTTTAAAAAAGTATCGACACTTTATGCATGCAACCCTTTGGCATTCCTTTTGG
127 GGGATCGACACTTTTTATAAAAGTATCGACACTTTATGCATGCAACCCTTTGGCATTCCTTCTGG
* * * *
1327213 ACAAAAAGTATCGACACCAATTCCACAAGTGTCGATACATGTTATAGACCTATTCTATCATAAAA
192 ACAAAAAGTATCGACACAAATTACACAAGTGTCGATACATATTATACACCTATTCTATCATAAAA
* * * * *
1327278 CCGGTATAGTTATACCGGTTACATCGTAAATTTACCTATTATATTATATTTATGGGTTTCGATGT
257 CCGGTATAGTTATACCGGCTACATCGAAAATTTACCTATTACATTATAATTATGGGTTTCAATGT
* ** *
1327343 TTTTGGTATCGACACTTTTTATAAATATATCGACACTTTATGCGTTTATCATTTTGGGCATTCAT
322 TTTAGGTATCGACACTTTTTATAAATATATCGACACTTTATGCGTGCACCATTTTGGGCATTCAT
* *
1327408 TCTGGACAAAACGTATCGACACAAAATAAAAAAGTGTTGATATATTATGTAGACCTATTCTCACA
387 TCTGGACAAAACGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACA
* * * *
1327473 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTTCCTATTACATTATAATTATGGGTTTC
452 TAAAACCGGTATAGTTATACCAGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTC
* ** * *
1327538 GATGTTTTTAGGATCGACACTTTGTATAAATGTATTGACAC-TTAGTG-GTGT-ACCCTTTTTGG
517 GATATTTTTAGGATCGACACTTTCAATAAATGTATCGACACGTTA-TGCGT-TCA-CCATTTTGG
* * *
1327600 GCATTCCTTCTGGACCAAAA
579 GCAATCATTCTGGACAAAAA
* * * *
1327620 GTATCGATACA-AATTACACAAGTGTCGATACA-TATTGTACACCTATTCTCTCATAAAATCGGT
1 GTATCGACACATAATGA-AAAAGTGTCGATACATTA-TGTAAACCTATTCTCTCATAAAA-CGGT
**
1327683 ATAAGTATACCGATTACATTGAAAAATTACCTATTACATTATAATTAT-GGTTTTCGATGTTTCT
63 ATATCTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATCGG-TTTCGATGTTTCT
* * *
1327747 GGGATCGACACTTCTTATAAATGTATCGACAC-TTAGTG-GTGC-ACCCTTTTTGGGCATTCCTT
127 GGGATCGACACTTTTTATAAAAGTATCGACACTTTA-TGCATGCAACCC--TTT-GGCATTCCTT
* * * *
1327809 CTGGACCAAAAGTATCGACACAAATTACACAAGTTTCGATACATATTGTACACCTATTCTCTCAT
188 CTGGACAAAAAGTATCGACACAAATTACACAAGTGTCGATACATATTATACACCTATTCTATCAT
*
1327874 AAAACCGGTATA-TGTATACCGGCTACATTGAAAAATTT-CCTATTACATTATAATTATGGGTTT
253 AAAACCGGTATAGT-TATACCGGCTACATCG-AAAATTTACCTATTACATTATAATTATGGGTTT
* * *
1327937 CAATGTTTCTAGG-ATCGATACTTGTTTATAAATGTATCGACACTCTT-TGCGTGCACCCTTTTG
316 CAATGTTT-TAGGTATCGACACTT-TTTATAAATATATCGACACT-TTATGCGTGCACCATTTTG
* * * ** *
1328000 GGCATTCCTTCTGGA-GAAACAGTATCGACACAAATTCTAGAAGTGTCGATACATTATGTAGACC
378 GGCATTCATTCTGGACAAAAC-GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACC
* * *
1328064 TATTCTCCCATAAAATCGGTTTAGTTATACCAGTTACATTGA-AAAATTACCTATTACATTATAA
442 TATTCTCACATAAAACCGGTATAGTTATACCAGTTACATT-ACAAAATTACCTATTACATTATAA
* *
1328128 TTATGGGTTTCGATATTTTTGGGATCGACACTTTCAATAAATGTATCGACACGTTATGCGTTCAT
506 TTATGGGTTTCGATATTTTTAGGATCGACACTTTCAATAAATGTATCGACACGTTATGCGTTCAC
1328193 CATTTTGGGCAATCATTCTGGACAAAAA
571 CATTTTGGGCAATCATTCTGGACAAAAA
*
1328221 GTATCGACACATAATGAAAAAGTGTCGATACATTATGTAAACCTATTCTCACATAAAACTGGTAT
1 GTATCGACACATAATGAAAAAGTGTCGATACATTATGTAAACCTATTCTCTCATAAAAC-GGTAT
* * * * *
1328286 ATTTATACC-AGTTATATT-ACAAAATTACTTATTACATTATAATTATGGGATTT--ACTGTTTT
65 ATCTATACCGA-TTACATTGA-AAAATTACCTATTACATTATAATTATCGG-TTTCGA-TGTTTC
* *
1328347 TGGGATCGACAGTTTTTATAAACGTATCGAC
126 TGGGATCGACACTTTTTATAAAAGTATCGAC
1328378 TCATATGCTT
Statistics
Matches: 654, Mismatches: 78, Indels: 50
0.84 0.10 0.06
Matches are distributed among these distances:
597 4 0.01
598 13 0.02
599 133 0.20
600 143 0.22
601 341 0.52
602 20 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (598 bp):
GTATCGACACATAATGAAAAAGTGTCGATACATTATGTAAACCTATTCTCTCATAAAACGGTATA
TCTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTCTGGGA
TCGACACTTTTTATAAAAGTATCGACACTTTATGCATGCAACCCTTTGGCATTCCTTCTGGACAA
AAAGTATCGACACAAATTACACAAGTGTCGATACATATTATACACCTATTCTATCATAAAACCGG
TATAGTTATACCGGCTACATCGAAAATTTACCTATTACATTATAATTATGGGTTTCAATGTTTTA
GGTATCGACACTTTTTATAAATATATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTG
GACAAAACGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAA
ACCGGTATAGTTATACCAGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATA
TTTTTAGGATCGACACTTTCAATAAATGTATCGACACGTTATGCGTTCACCATTTTGGGCAATCA
TTCTGGACAAAAA
Found at i:1328753 original size:19 final size:19
Alignment explanation
Indices: 1328729--1328796 Score: 127
Period size: 19 Copynumber: 3.6 Consensus size: 19
1328719 TTACATCCAC
*
1328729 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCTT
1328748 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
1328767 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
1328786 ATACAAAATTA
1 ATACAAAATTA
1328797 ACTCTACATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:1330375 original size:18 final size:18
Alignment explanation
Indices: 1330352--1330408 Score: 114
Period size: 18 Copynumber: 3.2 Consensus size: 18
1330342 TCCTCCTTAT
1330352 TTCCTCCCTCTTTTCTTC
1 TTCCTCCCTCTTTTCTTC
1330370 TTCCTCCCTCTTTTCTTC
1 TTCCTCCCTCTTTTCTTC
1330388 TTCCTCCCTCTTTTCTTC
1 TTCCTCCCTCTTTTCTTC
1330406 TTC
1 TTC
1330409 ATATTTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCCTCTTTTCTTC
Found at i:1330602 original size:66 final size:67
Alignment explanation
Indices: 1330508--1330637 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 67
1330498 CATCAACCAC
* * **
1330508 CCCCTCCACCCTCGTAAGTTCACTCCTCAATTCCACAACCTCCTTCACCACTCCATCAATTTTTT
1 CCCCTCCACCATCGTAAGTTCACCCCTCAACACCACAACCTCCTTCACCACTCCATCAATTTTTT
1330573 CA
66 CA
* ** * * *
1330575 CCCCT-CACCATCTTAAGTTCACCCCTCAACACGTCAACTTCTTTCACCACTCCATCTATTTTT
1 CCCCTCCACCATCGTAAGTTCACCCCTCAACACCACAACCTCCTTCACCACTCCATCAATTTTT
1330638 CTTTCCACTT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
66 48 0.91
67 5 0.09
ACGTcount: A:0.22, C:0.43, G:0.03, T:0.32
Consensus pattern (67 bp):
CCCCTCCACCATCGTAAGTTCACCCCTCAACACCACAACCTCCTTCACCACTCCATCAATTTTTT
CA
Found at i:1330684 original size:21 final size:21
Alignment explanation
Indices: 1330659--1330702 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1330649 CCCCTTATGC
1330659 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
*
1330680 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
1330701 CT
1 CT
1330703 TAATTGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCGACT
Found at i:1331118 original size:22 final size:23
Alignment explanation
Indices: 1331090--1331145 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1331080 AACATGCATT
1331090 TATAATAAAAT-TTATAATTTTA
1 TATAATAAAATATTATAATTTTA
* *
1331112 TATAATAACTATATTATCATTTTA
1 TATAATAA-AATATTATAATTTTA
*
1331136 TATAAAAAAA
1 TATAATAAAA
1331146 CAAAAACGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATAAAATATTATAATTTTA
Found at i:1333713 original size:18 final size:17
Alignment explanation
Indices: 1333684--1333727 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1333674 TTATTTAAGA
*
1333684 TATTTTTTATTTTGTTT
1 TATTTTTTATTTTATTT
1333701 TATTTTCTTATTTTATTT
1 TATTTT-TTATTTTATTT
1333719 TATATTTTT
1 TAT-TTTTT
1333728 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 15 0.62
19 3 0.12
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (17 bp):
TATTTTTTATTTTATTT
Found at i:1333721 original size:10 final size:9
Alignment explanation
Indices: 1333686--1333737 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
1333676 ATTTAAGATA
1333686 TTTTTTATT
1 TTTTTTATT
1333695 TTGTTTTA-T
1 TT-TTTTATT
*
1333704 TTTCTTATT
1 TTTTTTATT
1333713 TTATTTTATAT
1 TT-TTTTAT-T
*
1333724 TTTTTAATT
1 TTTTTTATT
1333733 TTTTT
1 TTTTT
1333738 CCATTGATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 4 0.11
9 14 0.39
10 15 0.42
11 3 0.08
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTATT
Found at i:1333733 original size:8 final size:9
Alignment explanation
Indices: 1333683--1333736 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
1333673 GTTATTTAAG
1333683 ATATTTTTT
1 ATATTTTTT
1333692 AT-TTTGTTT
1 ATATTT-TTT
1333701 -TATTTTCTT
1 ATATTTT-TT
*
1333710 ATTTTATTTT
1 ATATT-TTTT
1333720 ATATTTTTT
1 ATATTTTTT
1333729 A-ATTTTTT
1 ATATTTTTT
1333737 TCCATTGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
8 12 0.32
9 15 0.39
10 9 0.24
11 2 0.05
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (9 bp):
ATATTTTTT
Found at i:1333737 original size:18 final size:18
Alignment explanation
Indices: 1333683--1333737 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
1333673 GTTATTTAAG
1333683 ATATTTTTT-ATTTTGTTT
1 ATATTTTTTAATTTT-TTT
*
1333701 -TATTTTCTTATTTTATTTT
1 ATATTTT-TTAATTT-TTTT
1333720 ATATTTTTTAATTTTTTT
1 ATATTTTTTAATTTTTTT
1333738 CCATTGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 12 0.39
20 7 0.23
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (18 bp):
ATATTTTTTAATTTTTTT
Found at i:1335216 original size:182 final size:181
Alignment explanation
Indices: 1334909--1335398 Score: 621
Period size: 182 Copynumber: 2.7 Consensus size: 181
1334899 TACGCGTACT
* * * * * * *
1334909 TATTAAAGTCTCGACACTTTCAATATATCTGGTAGCGCTTTACTGATTTTGTCATTT-AGAGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAACTCTTTACCGATTTTGTCTTTTCATA-ACC
* * * *
1334973 GGTTTTATCATAATTTTACCTT-TTATATCGTTATGGATAGATACATTTTTATAAAGAATCGACA
65 GGTTTTGTCAT-ATTTTA-TTTGTTATATCGTTGTGGATCGATACATTTTTATAAAGAATCGACA
* *
1335037 CTTTATAGGCGCTAAAATTGCTTCTCCTTTAAATTTACAATGTGTCGATACTTA
128 CTTTATAGGCGCTAAAATTGATTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * *
1335091 TATTAAAGTATCGACACTTTCAATATATCCGGTATCTCTTTACCGATTTTGTCTTTTCCTAACTG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAACTCTTTACCGATTTTGTCTTTTCATAACCG
* *
1335156 GTTTTGTCATATTATTATTTGTTATGTCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
66 GTTTTGTCATATT-TTATTTGTTATATCGTTGTGGATCGATACATTTTTATAAAGAATCGACACT
*
1335221 TTATAGGCGCTAAAATTGATTCTCCTTTAAATTCACTATGTGTCGATACTTA
130 TTATAGGCGCTAAAATTGATTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * *
1335273 TATTAAAGTAGCGACA-TTTGCAATATATCCGGTAACGT-TTTACCGATTTTATCTTTTCGTGAC
1 TATTAAAGTATCGACACTTT-CAATATATCCGGTAAC-TCTTTACCGATTTTGTCTTTTCATAAC
* * * * *
1335336 CGGTTTTGTCATATTTT-TTCATGTTATATTGATGTAGATCGATATATTTTTATAAAGTATCGA
64 CGGTTTTGTCATATTTTATT--TGTTATATCGTTGTGGATCGATACATTTTTATAAAGAATCGA
1335399 TATAAACCGA
Statistics
Matches: 270, Mismatches: 31, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
180 2 0.01
181 10 0.04
182 256 0.95
183 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAACTCTTTACCGATTTTGTCTTTTCATAACCG
GTTTTGTCATATTTTATTTGTTATATCGTTGTGGATCGATACATTTTTATAAAGAATCGACACTT
TATAGGCGCTAAAATTGATTCTCCTTTAAATTCACAATGTGTCGATACTTA
Found at i:1335926 original size:49 final size:49
Alignment explanation
Indices: 1335873--1335971 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
1335863 CTAACTATCA
1335873 TATATTAATTAAATATTATTCATAAAAAACCATTAATTATAATATTATT
1 TATATTAATTAAATATTATTCATAAAAAACCATTAATTATAATATTATT
*
1335922 TATATTAATTAAATATTATTCATCAAAAACCATTAATTATAATATTATT
1 TATATTAATTAAATATTATTCATAAAAAACCATTAATTATAATATTATT
1335971 T
1 T
1335972 TTTAAAACAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (49 bp):
TATATTAATTAAATATTATTCATAAAAAACCATTAATTATAATATTATT
Found at i:1343262 original size:29 final size:27
Alignment explanation
Indices: 1343229--1343284 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1343219 TATATTTTTA
1343229 ATTTTGTAAAAAAAAATTATATAAATATT
1 ATTTT-TAAAAAAAAA-TATATAAATATT
* *
1343258 ATTTTTTAAAGAAAATATATAAATATT
1 ATTTTTAAAAAAAAATATATAAATATT
1343285 TTACAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.48
28 8 0.32
29 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
ATTTTTAAAAAAAAATATATAAATATT
Found at i:1343840 original size:22 final size:21
Alignment explanation
Indices: 1343812--1343863 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
1343802 TAAATCACTG
*
1343812 TTTTTATTGAATAAAAATAATT
1 TTTTTATTAAAT-AAAATAATT
1343834 TTTTTATTAAATAAAATAATT
1 TTTTTATTAAATAAAATAATT
1343855 TTTTTATTA
1 TTTTTATTA
1343864 TTTCAGGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTATTAAATAAAATAATT
Found at i:1347630 original size:40 final size:40
Alignment explanation
Indices: 1347586--1347705 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
1347576 TTTATGACAC
1347586 ATTTTCTTCTACCTTTTGATTTTTCGATTGGTTGACCATT
1 ATTTTCTTCTACCTTTTGATTTTTCGATTGGTTGACCATT
* * *** * *
1347626 ATTTT-TGCTTATCTTTT--TTTAAGGATT-GATGA-CA-C
1 ATTTTCTTC-TACCTTTTGATTTTTCGATTGGTTGACCATT
*
1347661 ATTTTCTTCTACCTTTTGATTTTTCGATTGTTTGACCATT
1 ATTTTCTTCTACCTTTTGATTTTTCGATTGGTTGACCATT
1347701 ATTTT
1 ATTTT
1347706 TGCTTATCTT
Statistics
Matches: 58, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
35 12 0.21
36 4 0.07
37 11 0.19
38 10 0.17
39 4 0.07
40 17 0.29
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (40 bp):
ATTTTCTTCTACCTTTTGATTTTTCGATTGGTTGACCATT
Found at i:1347664 original size:75 final size:75
Alignment explanation
Indices: 1347579--1347730 Score: 295
Period size: 75 Copynumber: 2.0 Consensus size: 75
1347569 ATTTGCCTTT
1347579 ATGACACATTTTCTTCTACCTTTTGATTTTTCGATTGGTTGACCATTATTTTTGCTTATCTTTTT
1 ATGACACATTTTCTTCTACCTTTTGATTTTTCGATTGGTTGACCATTATTTTTGCTTATCTTTTT
1347644 TTAAGGATTG
66 TTAAGGATTG
*
1347654 ATGACACATTTTCTTCTACCTTTTGATTTTTCGATTGTTTGACCATTATTTTTGCTTATCTTTTT
1 ATGACACATTTTCTTCTACCTTTTGATTTTTCGATTGGTTGACCATTATTTTTGCTTATCTTTTT
1347719 TTAAGGATTG
66 TTAAGGATTG
1347729 AT
1 AT
1347731 TTGACATCGC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.54
Consensus pattern (75 bp):
ATGACACATTTTCTTCTACCTTTTGATTTTTCGATTGGTTGACCATTATTTTTGCTTATCTTTTT
TTAAGGATTG
Found at i:1347665 original size:35 final size:37
Alignment explanation
Indices: 1347618--1347730 Score: 97
Period size: 35 Copynumber: 3.0 Consensus size: 37
1347608 TTCGATTGGT
*
1347618 TGACCATTATTTTTGCTTATCTTTTTTTAAGGATTGA
1 TGACCATCATTTTTGCTTATCTTTTTTTAAGGATTGA
* * *** *
1347655 TGA-CA-CATTTTCTTC-TACCTTTTGATTTTTCGATTGTT
1 TGACCATCATTTT-TGCTTATCTTTT--TTTAAGGATTG-A
*
1347693 TGACCATTATTTTTGCTTATCTTTTTTTAAGGATTGA
1 TGACCATCATTTTTGCTTATCTTTTTTTAAGGATTGA
1347730 T
1 T
1347731 TTGACATCGC
Statistics
Matches: 55, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
35 12 0.22
36 4 0.07
37 12 0.22
38 11 0.20
39 4 0.07
40 12 0.22
ACGTcount: A:0.19, C:0.13, G:0.12, T:0.55
Consensus pattern (37 bp):
TGACCATCATTTTTGCTTATCTTTTTTTAAGGATTGA
Found at i:1347717 original size:40 final size:39
Alignment explanation
Indices: 1347598--1347717 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 39
1347588 TTTCTTCTAC
1347598 CTTTTGATTTTTCGATTGGTTGACCATTATTTTTGCTTAT
1 CTTTTGATTTTTCGATT-GTTGACCATTATTTTTGCTTAT
*** * * *
1347638 CTTTT--TTTAAGGATTGATGACACATT-TTCTT-C-TAC
1 CTTTTGATTTTTCGATTGTTGAC-CATTATTTTTGCTTAT
1347673 CTTTTGATTTTTCGATTGTTTGACCATTATTTTTGCTTAT
1 CTTTTGATTTTTCGATTG-TTGACCATTATTTTTGCTTAT
1347713 CTTTT
1 CTTTT
1347718 TTTAAGGATT
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
35 7 0.11
36 1 0.02
37 21 0.34
38 19 0.31
39 1 0.02
40 12 0.20
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (39 bp):
CTTTTGATTTTTCGATTGTTGACCATTATTTTTGCTTAT
Found at i:1348564 original size:65 final size:65
Alignment explanation
Indices: 1348469--1348598 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
1348459 AGCTATTTCC
1348469 TCCTCTCACTCAAAATAAATAGGTGAGTATTATAAATGTAAGCTCAATTTAACTCCTTTCCCCAA
1 TCCTCTCACTCAAAATAAATAGGTGAGTATTATAAATGTAAGCTCAATTTAACTCCTTTCCCCAA
1348534 TCCTCTCACTCAAAATAAATAGGTGAGTATTATAAATGTAAGCTCAATTTAACTCCTTTCCCCAA
1 TCCTCTCACTCAAAATAAATAGGTGAGTATTATAAATGTAAGCTCAATTTAACTCCTTTCCCCAA
1348599 AATTAAATGC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (65 bp):
TCCTCTCACTCAAAATAAATAGGTGAGTATTATAAATGTAAGCTCAATTTAACTCCTTTCCCCAA
Done.