Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008170.1 Hibiscus syriacus cultivar Beakdansim tig00110761_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: 686002
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:203128 original size:29 final size:30
Alignment explanation
Indices: 203094--203152 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
203084 GTACCAAAAA
*
203094 TATAATTTT-AT-TTTTATTTTTTATATACT
1 TATAATTTTAATATTTT-TTGTTTATATACT
203123 TATAATTTTAATATTTTTTGTTTATATACT
1 TATAATTTTAATATTTTTTGTTTATATACT
203153 AAAATTTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.33
30 14 0.52
31 4 0.15
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (30 bp):
TATAATTTTAATATTTTTTGTTTATATACT
Found at i:203158 original size:29 final size:29
Alignment explanation
Indices: 203097--203159 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
203087 CCAAAAATAT
* *
203097 AATTTTATTTTTATTTTTTATATACTTAT
1 AATTTTATTTTTATTGTTTATATACTTAA
203126 AATTTTAATATTTT-TTGTTTATATAC-TAA
1 AATTTT-AT-TTTTATTGTTTATATACTTAA
203155 AATTT
1 AATTT
203160 GTCAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 13 0.43
30 13 0.43
31 4 0.13
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (29 bp):
AATTTTATTTTTATTGTTTATATACTTAA
Found at i:203213 original size:15 final size:15
Alignment explanation
Indices: 203181--203214 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
203171 AACATTTTTG
*
203181 AAAAAAATATTATGT
1 AAAAAAATATTATAT
*
203196 AAAAAAATATTTTAT
1 AAAAAAATATTATAT
203211 AAAA
1 AAAA
203215 TATTATCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
AAAAAAATATTATAT
Found at i:204327 original size:59 final size:60
Alignment explanation
Indices: 204252--204412 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 60
204242 AATTTAAATC
* * * *
204252 CTAAATTAATCTTTAAACTTTTTGAATATTTTAATTTTATCCCCAACCTATGA-CTCATTT
1 CTAAATTAATCCTTAAACTTTTTAAATATTTTAATTTCATCCCCAAACTATGACCTC-TTT
* * * *
204312 -TAAATTAATCCTTAAA-TTTTTTAACATTCTAATTTCATCCCTAAACTATGACCCTCTTT
1 CTAAATTAATCCTTAAACTTTTTAAATATTTTAATTTCATCCCCAAACTATGA-CCTCTTT
* * * *
204371 CTAAACTAATTCTCAAAC-TTTTAAATATTTCAATTTCATCCC
1 CTAAATTAATCCTTAAACTTTTTAAATATTTTAATTTCATCCC
204413 AAATTAATCC
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
58 29 0.35
59 18 0.22
60 36 0.43
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (60 bp):
CTAAATTAATCCTTAAACTTTTTAAATATTTTAATTTCATCCCCAAACTATGACCTCTTT
Found at i:204361 original size:58 final size:59
Alignment explanation
Indices: 204253--204363 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 59
204243 ATTTAAATCC
* * * * *
204253 TAAATTAATCTTTAAACTTTTTGAATATTTTAATTTTATCCCCAACCTATGACTCATTT
1 TAAATTAATCCTTAAACTTTTTGAACATTCTAATTTCATCCCCAAACTATGACTCATTT
* *
204312 TAAATTAATCCTTAAA-TTTTTTAACATTCTAATTTCATCCCTAAACTATGAC
1 TAAATTAATCCTTAAACTTTTTGAACATTCTAATTTCATCCCCAAACTATGAC
204364 CCTCTTTCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 30 0.67
59 15 0.33
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.45
Consensus pattern (59 bp):
TAAATTAATCCTTAAACTTTTTGAACATTCTAATTTCATCCCCAAACTATGACTCATTT
Found at i:211752 original size:2 final size:2
Alignment explanation
Indices: 211747--211780 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
211737 TATATTTGTG
211747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
211781 GAGTCGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:215575 original size:21 final size:21
Alignment explanation
Indices: 215549--215590 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
215539 ATTTGAATAT
215549 TATGAAGGGGTA-TCGATTCCC
1 TATGAAGGGGTACT-GATTCCC
215570 TATGAAGGGGTACTGATTCCC
1 TATGAAGGGGTACTGATTCCC
215591 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACTGATTCCC
Found at i:222795 original size:29 final size:29
Alignment explanation
Indices: 222761--222819 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
222751 CCTAAATTAA
222761 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
222790 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
222819 T
1 T
222820 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:238525 original size:21 final size:21
Alignment explanation
Indices: 238501--238541 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
238491 CATGCAATAC
*
238501 CATGCGTAATTGTCAACAATT
1 CATGCGCAATTGTCAACAATT
*
238522 CATGTGCAATTGTCAACAAT
1 CATGCGCAATTGTCAACAAT
238542 CTCCCACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (21 bp):
CATGCGCAATTGTCAACAATT
Found at i:242919 original size:230 final size:232
Alignment explanation
Indices: 242516--242978 Score: 912
Period size: 230 Copynumber: 2.0 Consensus size: 232
242506 GTGAACCACC
242516 GTGTATTAGAACATCTCCGTCGACAAATTAATATCGCCGACAAATTTTTTTTACTATTCACAAAA
1 GTGTATTAGAACATCTCCGTCGACAAATTAATATCGCCGACAAATTTTTTTTACTATTCACAAAA
242581 TTTACTATTCACGTGAATAGTAACCTCACAAAAAATTGACAAAATTCACAACCAAAAGCTCTGAT
66 TTTACTATTCACGTGAATAGTAACCTCACAAAAAATTGACAAAATTCACAACCAAAAGCTCTGAT
242646 TACCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTTTCTATAACCAGATTAGTGATAATGCG
131 TACCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTTTCTATAACCAGATTAGTGATAATGCG
242711 AAATAAAAGCAG-AAAAAATACCCG-AATTGATAACG
196 AAATAAAAGCAGAAAAAAATACCCGAAATTGATAACG
242746 GTGTATTAGAACATCTCCGTCGACAAATTAATATCGCCGACAAATTTTTTTTACTATTCACAAAA
1 GTGTATTAGAACATCTCCGTCGACAAATTAATATCGCCGACAAATTTTTTTTACTATTCACAAAA
242811 TTTACTATTCACGTGAATAGTAACCTCACAAAAAATTGACAAAATTCACAACCAAAAGCTCTGAT
66 TTTACTATTCACGTGAATAGTAACCTCACAAAAAATTGACAAAATTCACAACCAAAAGCTCTGAT
242876 TACCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTTTCTATAACCAGATTAGTGATAATGCG
131 TACCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTTTCTATAACCAGATTAGTGATAATGCG
242941 AAATAAAAGCAGAAAAAAATACCCGAAATTGATAACG
196 AAATAAAAGCAGAAAAAAATACCCGAAATTGATAACG
242978 G
1 G
242979 AGTTAAGCCA
Statistics
Matches: 231, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
230 207 0.90
231 12 0.05
232 12 0.05
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (232 bp):
GTGTATTAGAACATCTCCGTCGACAAATTAATATCGCCGACAAATTTTTTTTACTATTCACAAAA
TTTACTATTCACGTGAATAGTAACCTCACAAAAAATTGACAAAATTCACAACCAAAAGCTCTGAT
TACCAGTTGTTGGGAAATAAACCGAGTACGAGTAATTTTTCTATAACCAGATTAGTGATAATGCG
AAATAAAAGCAGAAAAAAATACCCGAAATTGATAACG
Found at i:243355 original size:21 final size:22
Alignment explanation
Indices: 243326--243371 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
243316 GAATCCCATG
*
243326 CAATACCATGCGTAATTGTCAA
1 CAATACCATGCGCAATTGTCAA
243348 CAAT-CCATGCGCAATTGTCAA
1 CAATACCATGCGCAATTGTCAA
243369 CAA
1 CAA
243372 AAAACACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (22 bp):
CAATACCATGCGCAATTGTCAA
Found at i:250313 original size:24 final size:24
Alignment explanation
Indices: 250293--250408 Score: 99
Period size: 24 Copynumber: 4.7 Consensus size: 24
250283 ATTTGAAATA
250293 TGTTCTGATTTCTGATCTGAATTC
1 TGTTCTGATTTCTGATCTGAATTC
* * *
250317 TGTTCTCATTTCTGATTTGGATTC
1 TGTTCTGATTTCTGATCTGAATTC
* *
250341 TGTTCTGATATCTGATATCTG-ATATA
1 TGTTCTGATTTCTG--ATCTGAAT-TC
* * *
250367 TGATATCTGATATATGATATGAATTC
1 TG-T-TCTGATTTCTGATCTGAATTC
*
250393 TGTTTTGATTTCTGAT
1 TGTTCTGATTTCTGAT
250409 ATCTCCGTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
24 43 0.59
25 3 0.04
26 14 0.19
27 3 0.04
28 10 0.14
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (24 bp):
TGTTCTGATTTCTGATCTGAATTC
Found at i:250363 original size:14 final size:14
Alignment explanation
Indices: 250344--250386 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
250334 TGGATTCTGT
*
250344 TCTGATATCTGATA
1 TCTGATATATGATA
250358 TCTGATATATGATA
1 TCTGATATATGATA
250372 TCTGATATATGATA
1 TCTGATATATGATA
250386 T
1 T
250387 GAATTCTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (14 bp):
TCTGATATATGATA
Found at i:250378 original size:7 final size:7
Alignment explanation
Indices: 250344--250386 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
250334 TGGATTCTGT
250344 TCTGATA
1 TCTGATA
250351 TCTGATA
1 TCTGATA
250358 TCTGATA
1 TCTGATA
*
250365 TATGATA
1 TCTGATA
250372 TCTGATA
1 TCTGATA
*
250379 TATGATA
1 TCTGATA
250386 T
1 T
250387 GAATTCTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (7 bp):
TCTGATA
Found at i:251623 original size:60 final size:60
Alignment explanation
Indices: 251552--251668 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
251542 ATGAAATTGG
** ** *
251552 AATATTCAAAAGTTTGGGGATTAATTTAGAAA-GAGGGTCATAGTTTAGGGATGTAATTAA
1 AATATTCAAAAGTTTAAGGACCAATTTA-AAATGAGGGTCATAGTTTAGGGATATAATTAA
* * *
251612 AATATTTAAAAGTTTAAGGACCAATTTAAAATGAGGGTTATAGTTTGGGGATATAAT
1 AATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAGTTTAGGGATATAAT
251669 GCAATTAACT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 3 0.06
60 45 0.94
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.34
Consensus pattern (60 bp):
AATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAGTTTAGGGATATAATTAA
Found at i:251779 original size:60 final size:60
Alignment explanation
Indices: 251707--251824 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
251697 TAAATTATTC
** ** *
251707 AAATATTCAAAAGTTTGGGGATTAATTTAGAAA-GAGGGTCATAGTTTAGGGATGTAATTA
1 AAATATTCAAAAGTTTAAGGACCAATTTA-AAATGAGGGTCATAGTTTAGGGATATAATTA
* * *
251767 AAATATTTAAAAGTTTAAGGACCAATTTAAAATGAGGGTTATAGTTTGGGGATATAAT
1 AAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAGTTTAGGGATATAAT
251825 GCAATTAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 3 0.06
60 46 0.94
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (60 bp):
AAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAGTTTAGGGATATAATTA
Found at i:251836 original size:156 final size:156
Alignment explanation
Indices: 251552--251864 Score: 626
Period size: 156 Copynumber: 2.0 Consensus size: 156
251542 ATGAAATTGG
251552 AATATTCAAAAGTTTGGGGATTAATTTAGAAAGAGGGTCATAGTTTAGGGATGTAATTAAAATAT
1 AATATTCAAAAGTTTGGGGATTAATTTAGAAAGAGGGTCATAGTTTAGGGATGTAATTAAAATAT
251617 TTAAAAGTTTAAGGACCAATTTAAAATGAGGGTTATAGTTTGGGGATATAATGCAATTAACTCTT
66 TTAAAAGTTTAAGGACCAATTTAAAATGAGGGTTATAGTTTGGGGATATAATGCAATTAACTCTT
251682 TTTTGATATTATATCTAAATTATTCA
131 TTTTGATATTATATCTAAATTATTCA
251708 AATATTCAAAAGTTTGGGGATTAATTTAGAAAGAGGGTCATAGTTTAGGGATGTAATTAAAATAT
1 AATATTCAAAAGTTTGGGGATTAATTTAGAAAGAGGGTCATAGTTTAGGGATGTAATTAAAATAT
251773 TTAAAAGTTTAAGGACCAATTTAAAATGAGGGTTATAGTTTGGGGATATAATGCAATTAACTCTT
66 TTAAAAGTTTAAGGACCAATTTAAAATGAGGGTTATAGTTTGGGGATATAATGCAATTAACTCTT
251838 TTTTGATATTATATCTAAATTATTCA
131 TTTTGATATTATATCTAAATTATTCA
251864 A
1 A
251865 CAAAAATTAG
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 157 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (156 bp):
AATATTCAAAAGTTTGGGGATTAATTTAGAAAGAGGGTCATAGTTTAGGGATGTAATTAAAATAT
TTAAAAGTTTAAGGACCAATTTAAAATGAGGGTTATAGTTTGGGGATATAATGCAATTAACTCTT
TTTTGATATTATATCTAAATTATTCA
Found at i:256002 original size:32 final size:30
Alignment explanation
Indices: 255922--256012 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 30
255912 ATCATCGAAA
*
255922 TCTCAAAAATTATAAAATAGTGATTAAACT
1 TCTCAAAAATTATAAAATAGTCATTAAACT
255952 TCTCAAAAGATTATAAAAT-GATCATTAAACT
1 TCTCAAAA-ATTATAAAATAG-TCATTAAACT
*
255983 TTTCAAAAATATTATAAAATAGTCATTAAA
1 TCTC-AAAA-ATTATAAAATAGTCATTAAA
256013 TATTATCAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
30 9 0.17
31 22 0.41
32 22 0.41
33 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (30 bp):
TCTCAAAAATTATAAAATAGTCATTAAACT
Found at i:259599 original size:31 final size:28
Alignment explanation
Indices: 259570--259635 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
259560 TTTGTTCGGG
259570 TCGGGTC--GTTTTTTTAAGTT-TGATAT
1 TCGGGTCGGGTTTTTTTAA-TTGTGATAT
259596 TCGGGTCGGGTTTTTTTAATTGTGATAT
1 TCGGGTCGGGTTTTTTTAATTGTGATAT
*
259624 TCGGGTCAGGTT
1 TCGGGTCGGGTT
259636 CGGGTTTAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 7 0.19
27 2 0.06
28 27 0.75
ACGTcount: A:0.14, C:0.09, G:0.29, T:0.48
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAATTGTGATAT
Found at i:264430 original size:41 final size:41
Alignment explanation
Indices: 264296--264495 Score: 124
Period size: 41 Copynumber: 4.9 Consensus size: 41
264286 AGTTGTACTT
* * * *
264296 TAGCGGCGTTTTTATACAAACGCCGCAATAAGGATCGTTTA
1 TAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCGTTCA
** * * * * * * *
264337 TAATGGCGTTTTTCTAACAAATGCCACGATA-GATTAGTACTT
1 TAGCGGCGTTTTTAT-ACAAATGCCGCAATAGGGTTCGTTC-A
264379 TAGCGG-GTTTTTATACAAATGCCGCAATAGGGTTCGTTCA
1 TAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCGTTCA
* * * * * * *
264419 TAGTGGTGTTTTTCCA-ACAAATGTCGTGATAAAGAGTAC-TT--
1 TAGCGGCGTTTTT--ATACAAATGCCG-CA-ATAGGGTTCGTTCA
264460 TAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTC
1 TAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTC
264496 TTTAGCGATG
Statistics
Matches: 116, Mismatches: 34, Indels: 21
0.68 0.20 0.12
Matches are distributed among these distances:
38 6 0.05
39 2 0.02
40 27 0.23
41 46 0.40
42 25 0.22
43 4 0.03
44 6 0.05
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (41 bp):
TAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCGTTCA
Found at i:264430 original size:82 final size:82
Alignment explanation
Indices: 264258--264495 Score: 311
Period size: 82 Copynumber: 2.9 Consensus size: 82
264248 ATACTTTAGC
* *
264258 GGCGTTTCTTCAACAAACGCCGCGATAGAGTT-GTACTTTAGCGGCGTTTTTATACAAACGCCGC
1 GGCGTTT-TTCAACAAATGCCGCGATAGA-TTAGTACTTTAGCGGCGTTTTTATACAAATGCCGC
* * *
264322 AATAAGGATCGTTTATAAT
64 AATAGGGTTCGTTCATAAT
*
264341 GGCGTTTTTCTAACAAATGCCACGATAGATTAGTACTTTAGCGG-GTTTTTATACAAATGCCGCA
1 GGCGTTTTTC-AACAAATGCCGCGATAGATTAGTACTTTAGCGGCGTTTTTATACAAATGCCGCA
*
264405 ATAGGGTTCGTTCATAGT
65 ATAGGGTTCGTTCATAAT
* * * **
264423 GGTGTTTTTCCAACAAATGTCGTGATA-AAGAGTACTTTAGCGGCGTTTTTATACAAATGCCGCA
1 GGCGTTTTT-CAACAAATGCCGCGATAGATTAGTACTTTAGCGGCGTTTTTATACAAATGCCGCA
264487 ATAGGGTTC
65 ATAGGGTTC
264496 TTTAGCGATG
Statistics
Matches: 138, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
81 14 0.10
82 88 0.64
83 36 0.26
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (82 bp):
GGCGTTTTTCAACAAATGCCGCGATAGATTAGTACTTTAGCGGCGTTTTTATACAAATGCCGCAA
TAGGGTTCGTTCATAAT
Found at i:264529 original size:82 final size:82
Alignment explanation
Indices: 264290--264568 Score: 242
Period size: 82 Copynumber: 3.4 Consensus size: 82
264280 CGATAGAGTT
* * * ** * * *
264290 GTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAAGGATCGTTTATAATGGCGTTTTTCTAAC
1 GTACTTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCG-TTATAGCGGTGTTTTTCAAAA
** ** * * *
264355 AAATGCCACGATAGATTA
65 AAACACCGTGACAAAGTA
* * *
264373 GTACTTTAGCGG-GTTTTTATACAAATGCCGCAATAGGGTTCGTTCATAGTGGTGTTTTTCCAAC
1 GTACTTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCGTT-ATAGCGGTGTTTTTCAAAA
*** *
264437 AAATGTCGTGATAAAG-A
65 AAACACCGTGACAAAGTA
* *
264454 GTACTTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTC-TT-TAGCGATGTTTTTTTGTAA
1 GTACTTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCGTTATAGCG--GTGTTTTT-CAA
*
264517 AAAAACACCGTGACAACGTA
63 AAAAACACCGTGACAAAGTA
* *
264537 GTACTTTAGCGGCGTTTGTATAAAAATGCCGC
1 GTACTTTAGCGGCGTTTTTATACAAATGCCGC
264569 TATATACTTT
Statistics
Matches: 167, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
79 4 0.02
81 24 0.14
82 96 0.57
83 43 0.26
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (82 bp):
GTACTTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCGTTATAGCGGTGTTTTTCAAAAA
AACACCGTGACAAAGTA
Found at i:267753 original size:43 final size:43
Alignment explanation
Indices: 267705--268015 Score: 276
Period size: 43 Copynumber: 7.2 Consensus size: 43
267695 AAGGTAATTA
* * **
267705 GCGGCGTTTGTATCAAAAAATGCCGCTATAGATCTGATATTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
*
267748 GCGGCGTTTGTATCCAAAAACGCCGCCATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * ** * *
267791 GCGGCATTTGT-TCAAAAAATGCAACTATAGATTTTACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
267833 GCGGCGTTTGTATCCTAAAACGCCGCTATAGAAATC-AACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAG--ATCTGACCTTTT
* *
267877 GCGGCGTTTGT-TCCAAAAACGTCGCTATAGATATTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-CTGACCTTTT
** * * * * *
267920 GCATCGTTTGT-TACAAAAACACCGCAAGAAATAGC-GACCGTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT--CTGACC-TTTT
* *
267964 GCGGCGTTTGT-TCCAAAAACGCCG-TGATAGATCTTAACCTATT
1 GCGGCGTTTGTATCCAAAAACGCCGCT-ATAGATC-TGACCTTTT
268007 GCGGCGTTT
1 GCGGCGTTT
268016 TTTGTTCTCA
Statistics
Matches: 214, Mismatches: 44, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
41 2 0.01
42 35 0.16
43 126 0.59
44 49 0.23
45 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:267939 original size:86 final size:84
Alignment explanation
Indices: 267705--268015 Score: 299
Period size: 87 Copynumber: 3.6 Consensus size: 84
267695 AAGGTAATTA
* * **
267705 GCGGCGTTTGTATCAAAAAATGCCGCTATAGATCTGATATTTTGCGGCGTTTGTATCCAAAAACG
1 GCGGCGTTTGT-TCAAAAAACG-CGCTATAGATTTGACCTTTTGCGGCGTTTGTATCCAAAAACG
267770 CCGCCATAG--ATCTGACCTTTT
64 CCG-CATAGAAATC-GACCTTTT
* * * * *
267791 GCGGCATTTGTTCAAAAAATGCAACTATAGATTTTACCTTTTGCGGCGTTTGTATCCTAAAACGC
1 GCGGCGTTTGTTCAAAAAACGC-GCTATAGATTTGACCTTTTGCGGCGTTTGTATCCAAAAACGC
*
267856 CGCTATAGAAATCAACCTTTT
65 CGC-ATAGAAATCGACCTTTT
* ** * *
267877 GCGGCGTTTGTTCCAAAAACGTCGCTATAGATATTGACCTTTTGCATCGTTTGT-TACAAAAACA
1 GCGGCGTTTGTTCAAAAAACG-CGCTATAGAT-TTGACCTTTTGCGGCGTTTGTATCCAAAAACG
267941 CCGCA-AGAAATAGCGACCGTTTT
64 CCGCATAGAAAT--CGACC-TTTT
* * *
267964 GCGGCGTTTGTTCCAAAAACGC-CGTGATAGATCTTAACCTATTGCGGCGTTT
1 GCGGCGTTTGTTCAAAAAACGCGC-T-ATAGAT-TTGACCTTTTGCGGCGTTT
268016 TTTGTTCTCA
Statistics
Matches: 190, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
84 8 0.04
85 54 0.28
86 60 0.32
87 68 0.36
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (84 bp):
GCGGCGTTTGTTCAAAAAACGCGCTATAGATTTGACCTTTTGCGGCGTTTGTATCCAAAAACGCC
GCATAGAAATCGACCTTTT
Found at i:270429 original size:153 final size:154
Alignment explanation
Indices: 270151--270461 Score: 597
Period size: 153 Copynumber: 2.0 Consensus size: 154
270141 ATATGTGATA
270151 TTTTTTATATTTTCTATTAGTAATCTATTTTATTTGTCTTTAAAATTAAGAAGTTCGTTTTTTCT
1 TTTTTTATATTTTCTATTAGTAATCTATTTTATTTGTCTTTAAAATTAAGAAGTTCGTTTTTTCT
270216 AATATAATATCTTGCATTTGTCCCTGAATTCAACATATATGTAAGTGCAGCCAGTATACCTAAAC
66 AATATAATATCTTGCATTTGTCCCTGAATTCAACATATATGTAAGTGCAGCCAGTATACCTAAAC
270281 -TATACCAGCAAATGCAAGAGATT
131 ATATACCAGCAAATGCAAGAGATT
270304 TTTTTTATATTTTCTATTAGTAATCTATTTTATTTGTCTTTAAAATTAAGAAGTTCGTTTTTTCT
1 TTTTTTATATTTTCTATTAGTAATCTATTTTATTTGTCTTTAAAATTAAGAAGTTCGTTTTTTCT
270369 AATATAATATCTTGCATTTGTCCCTGAATTCAACATATATGTAAGTGCAGCCAGTATACCTAAAC
66 AATATAATATCTTGCATTTGTCCCTGAATTCAACATATATGTAAGTGCAGCCAGTATACCTAAAC
270434 ATATATACCAGCAAATGCAAGAGATT
131 --ATATACCAGCAAATGCAAGAGATT
270460 TT
1 TT
270462 GAAGATAAAT
Statistics
Matches: 155, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
153 130 0.84
156 25 0.16
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (154 bp):
TTTTTTATATTTTCTATTAGTAATCTATTTTATTTGTCTTTAAAATTAAGAAGTTCGTTTTTTCT
AATATAATATCTTGCATTTGTCCCTGAATTCAACATATATGTAAGTGCAGCCAGTATACCTAAAC
ATATACCAGCAAATGCAAGAGATT
Found at i:277013 original size:14 final size:14
Alignment explanation
Indices: 276996--277036 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
276986 ACTGCTTACA
276996 ACATAACACTTAAT
1 ACATAACACTTAAT
*
277010 ACATAACACTTATT
1 ACATAACACTTAAT
*
277024 GCATAACACTTAA
1 ACATAACACTTAA
277037 ACCAGAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.29
Consensus pattern (14 bp):
ACATAACACTTAAT
Found at i:280119 original size:228 final size:227
Alignment explanation
Indices: 279681--280132 Score: 816
Period size: 227 Copynumber: 2.0 Consensus size: 227
279671 AAAATAGGAC
* *
279681 ATAATGGTATGTGAGGCCTCAATTTTTTAAAAAAAAATCAATATAGCTCTCAAATTACTTTTACA
1 ATAATGGTATATGAGGCCTCAACTTTTTAAAAAAAAATCAATATAGCTCTCAAATTACTTTTACA
*
279746 TTCAATGTAGTCCTCAAACTAAAAAAATTAATGTGGTCCTTTGACCAACAATTTCTTTAGTTAAC
66 TTCAATGTAGTCCTCAAACTAAAAAAATTAATGTGATCCTTTGACCAACAATTTCTTTAGTTAAC
* *
279811 TATTAGGATGATGATGTGGCAGTTATGGTACTAATGTAGTGATCTACAGTGGTTGATGATGTGGC
131 TATTAGGATGATGATGTGGCAGTTATGGTACTAATGTAGCGATCTACAATGGTTGATGATGTGGC
279876 TAATCAATGGTGGATTTAGAATTTTTTTAGGG
196 TAATCAATGGTGGATTTAGAATTTTTTTAGGG
279908 ATAATGGTATATGAGGCCTCAAACTTTTT-AAAAAAAATCAATATAGCTCTCAAATTACTTTTAC
1 ATAATGGTATATGAGGCCTC-AACTTTTTAAAAAAAAATCAATATAGCTCTCAAATTACTTTTAC
* *
279972 ATTCAATGTAGTCCTCAAACTAAAAAAATTAATGTGATCCTTTGACCAACAGTTTCTTTAGTTGA
65 ATTCAATGTAGTCCTCAAACTAAAAAAATTAATGTGATCCTTTGACCAACAATTTCTTTAGTTAA
280037 CTATTAGGATGATGATGTGGCAGTTCATGGTACTAATGTAGCGATCTACAATGGTTGATGATGTG
130 CTATTAGGATGATGATGTGGCAGTT-ATGGTACTAATGTAGCGATCTACAATGGTTGATGATGTG
280102 GCTAATCAATGGTGGATTTAGAATTTTTTTA
194 GCTAATCAATGGTGGATTTAGAATTTTTTTA
280133 AGGTGGGCAT
Statistics
Matches: 216, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
227 141 0.65
228 75 0.35
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (227 bp):
ATAATGGTATATGAGGCCTCAACTTTTTAAAAAAAAATCAATATAGCTCTCAAATTACTTTTACA
TTCAATGTAGTCCTCAAACTAAAAAAATTAATGTGATCCTTTGACCAACAATTTCTTTAGTTAAC
TATTAGGATGATGATGTGGCAGTTATGGTACTAATGTAGCGATCTACAATGGTTGATGATGTGGC
TAATCAATGGTGGATTTAGAATTTTTTTAGGG
Found at i:296446 original size:177 final size:176
Alignment explanation
Indices: 296113--296462 Score: 634
Period size: 177 Copynumber: 2.0 Consensus size: 176
296103 TAGTTTCAGT
296113 GGAAACATCCTCAACAAATGGAGTGGCAGAGCGAATGAAAAGAACCTTGTTAGAAAGAACAAGAG
1 GGAAACATCCTCAACAAATGGAGTGGCAGAGCGAATGAAAAGAACCTTGTTAGAAAGAACAAGAG
296178 CAATGTTGAGGGATGCAGGCCTAGAAAATCATTATGGGCAGAAGCATCAATACCGCCTGTTATTG
66 CAATGTTGAGGGATGCAGGCCTAGAAAATCATTATGGGCAGAAGCATCAATACCGCCTGTTATTG
296243 GTGAATCGAGCTCCATCAACTGTAATAGAGCTGAAAACACCAAGTG
131 GTGAATCGAGCTCCATCAACTGTAATAGAGCTGAAAACACCAAGTG
*
296289 GGAAACATCCTCAACAAAATGGAGTGGCAGAGCG-ATGAACAG-ACCTTGTTAGAAAGAACAAGA
1 GGAAACATCCTCAAC-AAATGGAGTGGCAGAGCGAATGAAAAGAACCTTGTTAGAAAGAACAAGA
296352 GCAATGTTGAGGGATGCAGGCCTAGAAAAATCATT-TGGGCAGAAGCAGTCAATACCGCCTGTTA
65 GCAATGTTGAGGGATGCAGGCCTAG-AAAATCATTATGGGCAGAAGCA-TCAATACCGCCTGTTA
296416 TTTGGTGAATCGAGCTCCATCAACTGTAATAGAGCTGAAAACACCAA
128 -TTGGTGAATCGAGCTCCATCAACTGTAATAGAGCTGAAAACACCAA
296463 TGAATGTGGA
Statistics
Matches: 169, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
175 58 0.34
176 47 0.28
177 64 0.38
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (176 bp):
GGAAACATCCTCAACAAATGGAGTGGCAGAGCGAATGAAAAGAACCTTGTTAGAAAGAACAAGAG
CAATGTTGAGGGATGCAGGCCTAGAAAATCATTATGGGCAGAAGCATCAATACCGCCTGTTATTG
GTGAATCGAGCTCCATCAACTGTAATAGAGCTGAAAACACCAAGTG
Found at i:298850 original size:57 final size:58
Alignment explanation
Indices: 298788--298905 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 58
298778 CAAGAGAATT
298788 ATTATTG-TTTCTCCTTGATAGATCGAGAGGTTGTAATT-CTATTTTTCTCATAGTGAA
1 ATTATTGTTTTCTCCTTGATAGATCGAGA-GTTGTAATTCCTATTTTTCTCATAGTGAA
298845 ATTATTGTTTTCTCCTTGATAGATCGAGAGTTGTAATTCCTATTTTTCTCATAGTGAA
1 ATTATTGTTTTCTCCTTGATAGATCGAGAGTTGTAATTCCTATTTTTCTCATAGTGAA
298903 ATT
1 ATT
298906 CTTCTATCGT
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
57 16 0.27
58 43 0.73
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.47
Consensus pattern (58 bp):
ATTATTGTTTTCTCCTTGATAGATCGAGAGTTGTAATTCCTATTTTTCTCATAGTGAA
Found at i:306632 original size:28 final size:28
Alignment explanation
Indices: 306570--306624 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
306560 ATGAAATGCT
306570 TTAGAATGAATGATTGTGATTGTGGTGC
1 TTAGAATGAATGATTGTGATTGTGGTGC
*
306598 TTAGAATGAATGATTGTGGTTGTGGTG
1 TTAGAATGAATGATTGTGATTGTGGTG
306625 TGTTGAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.02, G:0.35, T:0.40
Consensus pattern (28 bp):
TTAGAATGAATGATTGTGATTGTGGTGC
Found at i:307032 original size:71 final size:72
Alignment explanation
Indices: 306911--307053 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 72
306901 ATACGTCCGT
306911 GCATAACTCCCAAAAGGAGAGTGGAACGTGCACAGTTACTTCAAAGAGTGAGTGACATGAACCAC
1 GCATAACTCCCAAAAGGAGAGTGGAACGTGCACAGTTACTTCAAAGAGTGAGTGACATGAACCAC
306976 TCAATGC
66 TCAATGC
306983 GCAT-ACTCCCAAAAGGAGAGTGGAACGTGCACAGTTACTTCAAAGAGTGAGTGACATGAACCAC
1 GCATAACTCCCAAAAGGAGAGTGGAACGTGCACAGTTACTTCAAAGAGTGAGTGACATGAACCAC
307047 TCAATGC
66 TCAATGC
307054 AGCAGTTAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 67 0.94
72 4 0.06
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (72 bp):
GCATAACTCCCAAAAGGAGAGTGGAACGTGCACAGTTACTTCAAAGAGTGAGTGACATGAACCAC
TCAATGC
Found at i:315314 original size:21 final size:21
Alignment explanation
Indices: 315285--315324 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
315275 TTTTTATTAT
* *
315285 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
315306 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
315325 CATTTAGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:317466 original size:16 final size:16
Alignment explanation
Indices: 317427--317477 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
317417 AACATTAGAA
* *
317427 TAATAATAATAATAA-
1 TAATAAAAAAAATAAT
*
317442 TAATAAAAAAATTAAT
1 TAATAAAAAAAATAAT
*
317458 TAATTAAAAAAATAA-
1 TAATAAAAAAAATAAT
317473 TAATA
1 TAATA
317478 GTAAAAGGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATAAAAAAAATAAT
Found at i:318362 original size:123 final size:124
Alignment explanation
Indices: 318220--318467 Score: 455
Period size: 123 Copynumber: 2.0 Consensus size: 124
318210 AAATAAAAAA
* *
318220 AAAGAGTTAAAAAATCAAATAAGTTAATTAAATTAAAGAAACAAATCAAATAAAATAAAG-GAAT
1 AAAGAGTTAAAAAACCAAATAAGTTAATTAAATTAAAGAAACAAATCAAATAAAATAAAGAAAAT
318284 AATAATAAAAAAGAAACAAAACAAAAATAATTATAAAAAAAATAAAAAAATAG-AATGTT
66 AATAATAAAAAAGAAACAAAACAAAAATAATTAT-AAAAAAATAAAAAAATAGAAATGTT
318343 AAAGAGTTAAAAAACCAAATAAGTTAATTAAATTAAAGAAACAAATCAAATAAAATAAAGAAAAT
1 AAAGAGTTAAAAAACCAAATAAGTTAATTAAATTAAAGAAACAAATCAAATAAAATAAAGAAAAT
318408 AATAATAAAAAAGAAACAAAACAAAAATAATTATAAAAAAATAAAAAAATAGAAATGTT
66 AATAATAAAAAAGAAACAAAACAAAAATAATTATAAAAAAATAAAAAAATAGAAATGTT
318467 A
1 A
318468 GCTAAAATAT
Statistics
Matches: 121, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
123 77 0.64
124 44 0.36
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (124 bp):
AAAGAGTTAAAAAACCAAATAAGTTAATTAAATTAAAGAAACAAATCAAATAAAATAAAGAAAAT
AATAATAAAAAAGAAACAAAACAAAAATAATTATAAAAAAATAAAAAAATAGAAATGTT
Found at i:318401 original size:22 final size:22
Alignment explanation
Indices: 318371--318432 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
318361 ATAAGTTAAT
*
318371 TAAATTAAAGAAACAAATCAAA
1 TAAAATAAAGAAACAAATCAAA
318393 TAAAATAAAGAAA-ATAAT--AA
1 TAAAATAAAGAAACA-AATCAAA
*
318413 T-AAA-AAAGAAACAAAACAAA
1 TAAAATAAAGAAACAAATCAAA
318433 AATAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 5 0.15
21 1 0.03
22 15 0.44
ACGTcount: A:0.74, C:0.06, G:0.05, T:0.15
Consensus pattern (22 bp):
TAAAATAAAGAAACAAATCAAA
Found at i:318456 original size:28 final size:27
Alignment explanation
Indices: 318390--318456 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
318380 GAAACAAATC
*
318390 AAATAAAATAAAGAAAATAATAATAAAA
1 AAATAAAA-AAAAAAAATAATAATAAAA
* *
318418 AAGA-AACAAAACAAAAATAATTATAAAA
1 AA-ATAA-AAAAAAAAAATAATAATAAAA
318446 AAATAAAAAAA
1 AAATAAAAAAA
318457 TAGAAATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
27 5 0.16
28 24 0.75
29 3 0.09
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (27 bp):
AAATAAAAAAAAAAAATAATAATAAAA
Found at i:319817 original size:22 final size:21
Alignment explanation
Indices: 319772--319834 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
319762 GGTGTTAGAT
*
319772 AAAAAAAATAAATAATAAGAA
1 AAAAAAAATAAAGAATAAGAA
319793 AAAAAGAAATAAAGAA-AAGAGA
1 AAAAA-AAATAAAGAATAAGA-A
*
319815 AAATAATAATAAATGAATAA
1 AAA-AAAAATAAA-GAATAA
319835 ATACAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 9 0.26
22 19 0.54
23 5 0.14
24 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAAAAAATAAAGAATAAGAA
Found at i:321123 original size:24 final size:24
Alignment explanation
Indices: 321093--321139 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
321083 AACAAAAACG
321093 AAAAGAAAGAAAATA-AATAAATAA
1 AAAAGAAAGAAAATATAA-AAATAA
*
321117 AAAAGAATGAAAATATAAAAATA
1 AAAAGAAAGAAAATATAAAAATA
321140 TATATGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.15
Consensus pattern (24 bp):
AAAAGAAAGAAAATATAAAAATAA
Found at i:322007 original size:20 final size:18
Alignment explanation
Indices: 321942--321991 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
321932 CAAAATCAAA
* *
321942 AAATAAAGAATAAA-AAAG
1 AAATAAA-AAAAAAGAAAC
321960 AAAT-AAAAAAAAGAAAC
1 AAATAAAAAAAAAGAAAC
321977 AAATAATAAAAAAAG
1 AAATAA-AAAAAAAG
321992 GAAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 5 0.19
19 8 0.30
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (18 bp):
AAATAAAAAAAAAGAAAC
Found at i:322910 original size:11 final size:11
Alignment explanation
Indices: 322894--322919 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
322884 CTTAAAATAA
322894 TTTTTAGGAAT
1 TTTTTAGGAAT
322905 TTTTTAGGAAT
1 TTTTTAGGAAT
322916 TTTT
1 TTTT
322920 CCAACACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
TTTTTAGGAAT
Found at i:326138 original size:103 final size:103
Alignment explanation
Indices: 325913--326130 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
325903 GTCGAGGGTC
325913 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
* *
325978 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
326016 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
*
326081 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
326119 TATGTGATCCTT
1 TATGTGGTCCTT
326131 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:326178 original size:23 final size:23
Alignment explanation
Indices: 326147--326229 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
326137 ATTATTATAT
* *
326147 GGCATTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
326170 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
326193 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
326216 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
326230 TTTATATGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:328567 original size:24 final size:24
Alignment explanation
Indices: 328522--328586 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
328512 GATTCATTAC
* * *
328522 CTGAATTCTGTTCTAATTTCTGAT
1 CTGAATTATGTTCTGATATCTGAT
*
328546 CTGGATTATGTTCTGATATCTGAT
1 CTGAATTATGTTCTGATATCTGAT
*
328570 CTGAATTATGTTTTGAT
1 CTGAATTATGTTCTGAT
328587 TTCAGATATC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
CTGAATTATGTTCTGATATCTGAT
Found at i:329517 original size:17 final size:18
Alignment explanation
Indices: 329497--329535 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
329487 GGTGTTAGAT
*
329497 AAAAAAATAAAAAT-AAG
1 AAAAAAACAAAAATAAAG
*
329514 AAAAAAACAGAAATAAAG
1 AAAAAAACAAAAATAAAG
329532 AAAA
1 AAAA
329536 GAGAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAAAAACAAAAATAAAG
Found at i:329670 original size:3 final size:3
Alignment explanation
Indices: 329597--329648 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
329587 AAAACATTGG
*
329597 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA A-A AAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
329642 A-A ATA AT
1 ATA ATA AT
329649 TAATTAATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
2 8 0.18
3 37 0.82
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:330270 original size:2 final size:2
Alignment explanation
Indices: 330263--330299 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
330253 ATGTTAGGTA
330263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
330300 GTATTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:330347 original size:2 final size:2
Alignment explanation
Indices: 330342--330383 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
330332 AAGAAAAAAA
330342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
330384 GAAACAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:330502 original size:25 final size:25
Alignment explanation
Indices: 330474--330535 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
330464 TTAGATAAAA
330474 AAATAAATAATAAGA-AAAAAA-ACAT
1 AAATAAATAA-AAGAGAAAAAATA-AT
*
330499 AAATAAAGAAAAGAGAAAAAATAAT
1 AAATAAATAAAAGAGAAAAAATAAT
330524 AAATGAAATAAA
1 AAAT-AAATAAA
330536 TAGAATCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.12
25 21 0.66
26 7 0.22
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.15
Consensus pattern (25 bp):
AAATAAATAAAAGAGAAAAAATAAT
Found at i:332875 original size:29 final size:29
Alignment explanation
Indices: 332829--332884 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
332819 TATTATCTTA
*
332829 TAATTATTTTAGATTATTTCATA-AATTAT
1 TAATTATTTTACATTATTT-ATATAATTAT
332858 TAATTATTTTCACA-TATTTATATAATT
1 TAATTATTTT-ACATTATTTATATAATT
332885 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.12
29 19 0.79
30 2 0.08
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (29 bp):
TAATTATTTTACATTATTTATATAATTAT
Found at i:336993 original size:82 final size:81
Alignment explanation
Indices: 336792--337177 Score: 470
Period size: 82 Copynumber: 4.7 Consensus size: 81
336782 AACATTGATG
*
336792 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCACATCA
1 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCACGTCA
*
336857 TTT-TTTTCATTGATA
66 TTTGTTTTCATTGACA
* * * * *
336872 TATCACATCAAATCAGATAAAC-AAAATTATTTTAGAGAATCATATAATCTACAATATTCACGTC
1 TATCACATCAACTCAGATAAACTGAAA-TATTTTAGAGAATCAGAGAATCTACACTATTCACGTC
* *
336936 ATTTGATTTTCCTCGACA
65 ATTTG-TTTTCATTGACA
* * * * * * *
336954 TATCACATCAACTCATATAAATTGAAACATTTTAGAGAATCGGAGAATCTACAATATTCATGTCC
1 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCACGTCA
337019 TTTGTTTTTCATTGACA
66 TTTG-TTTTCATTGACA
* * * * * * * *
337036 CATCGCATCAACTCAGATAAATTGAAAAATTTTAGAGAATCAAATAATCTATACTATTCACGTCC
1 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCACGTCA
337101 TTTGCTTTTCATTGACA
66 TTTG-TTTTCATTGACA
* ** *
337118 TATCACATCAACTAAGATAAACTGAAATATTTTTTAGAATTAGAGAATCTACACTATTCA
1 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCA
337178 TGTCCACATC
Statistics
Matches: 258, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
79 3 0.01
80 58 0.22
82 194 0.75
83 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (81 bp):
TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCACGTCA
TTTGTTTTCATTGACA
Found at i:337085 original size:164 final size:162
Alignment explanation
Indices: 336792--337183 Score: 518
Period size: 164 Copynumber: 2.4 Consensus size: 162
336782 AACATTGATG
**
336792 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCACAT-C
1 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCATGTCC
* * *
336856 ATTTTTTTCATTGATATATCACATCAAATCAGATAAACAAAATTATTTTAGAGAATCATATAATC
66 ATTTTTTTCATTGACACATCACATCAAATCAGATAAACAAAA-TATTTTAGAGAATCAAATAATC
*
336921 TACAATATTCACGTCATTTGATTTTCCTCGACA
130 TACAATATTCACGTCATTTGATTTTCATCGACA
* * * * *
336954 TATCACATCAACTCATATAAATTGAAACATTTTAGAGAATCGGAGAATCTACAATATTCATGTCC
1 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCATGTCC
* * * *
337019 TTTGTTTTTCATTGACACATCGCATCAACTCAGATAAATTGAAAA-ATTTTAGAGAATCAAATAA
66 ATT-TTTTTCATTGACACATCACATCAAATCAGATAAA--CAAAATATTTTAGAGAATCAAATAA
* * * * *
337083 TCTATACTATTCACGTCCTTTGCTTTTCATTGACA
128 TCTACAATATTCACGTCATTTGATTTTCATCGACA
* ** *
337118 TATCACATCAACTAAGATAAACTGAAATATTTTTTAGAATTAGAGAATCTACACTATTCATGTCC
1 TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCATGTCC
337183 A
66 A
337184 CATCAACTCA
Statistics
Matches: 196, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
162 56 0.29
163 3 0.02
164 133 0.68
166 4 0.02
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (162 bp):
TATCACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGAGAATCTACACTATTCATGTCC
ATTTTTTTCATTGACACATCACATCAAATCAGATAAACAAAATATTTTAGAGAATCAAATAATCT
ACAATATTCACGTCATTTGATTTTCATCGACA
Found at i:337191 original size:61 final size:61
Alignment explanation
Indices: 337121--337243 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
337111 ATTGACATAT
** * *
337121 CACATCAACTAAGATAAACTGAAATATTTTTTAGAATTAGAGAATCTACACTATTCATGTC
1 CACATCAACTAAGATAAACTGAAATATTTTAGAGAATCAGAGAATATACACTATTCATGTC
* * *
337182 CACATCAACTCAGATAAACTGAAATATTTTAGAGAATCAGATAATATATACTATTCATGTC
1 CACATCAACTAAGATAAACTGAAATATTTTAGAGAATCAGAGAATATACACTATTCATGTC
337243 C
1 C
337244 TTTGCTTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (61 bp):
CACATCAACTAAGATAAACTGAAATATTTTAGAGAATCAGAGAATATACACTATTCATGTC
Found at i:340877 original size:5 final size:5
Alignment explanation
Indices: 340867--340907 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
340857 GTTAATTCAC
* *
340867 ACGCA ACGCA ACGCA AGGCA ACGCA AGGCA ACGCA ACGCA A
1 ACGCA ACGCA ACGCA ACGCA ACGCA ACGCA ACGCA ACGCA A
340908 AGCATTCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.34, G:0.24, T:0.00
Consensus pattern (5 bp):
ACGCA
Found at i:344393 original size:25 final size:25
Alignment explanation
Indices: 344365--344426 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
344355 TTGATTTTGA
344365 ATTTAGTTGTTGTTATCCTTATTCG
1 ATTTAGTTGTTGTTATCCTTATTCG
344390 ATTTAGTTGTTGTTATCCTTATTCG
1 ATTTAGTTGTTGTTATCCTTATTCG
344415 ATTTAGTTGTTG
1 ATTTAGTTGTTG
344427 AGTTTAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.16, C:0.10, G:0.18, T:0.56
Consensus pattern (25 bp):
ATTTAGTTGTTGTTATCCTTATTCG
Found at i:345816 original size:17 final size:17
Alignment explanation
Indices: 345791--345825 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
345781 ACGTCGAAAA
*
345791 TTCATAAAATATGACTT
1 TTCAGAAAATATGACTT
*
345808 TTCAGAAAATTTGACTT
1 TTCAGAAAATATGACTT
345825 T
1 T
345826 ATGGCTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (17 bp):
TTCAGAAAATATGACTT
Found at i:345877 original size:22 final size:22
Alignment explanation
Indices: 345835--345877 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
345825 TATGGCTAAA
*
345835 GTCAAAGTCAACTTTGATCAAG
1 GTCAAAGTCAACTTAGATCAAG
345857 GTCAAAGTCAACTCTAG-TCAA
1 GTCAAAGTCAACT-TAGATCAA
345878 AATCAACGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (22 bp):
GTCAAAGTCAACTTAGATCAAG
Found at i:345883 original size:22 final size:22
Alignment explanation
Indices: 345836--345883 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
345826 ATGGCTAAAG
* **
345836 TCAAAGTCAACTTTGATCAAGG
1 TCAAAGTCAACTTAGATCAAAA
345858 TCAAAGTCAACTCTAG-TCAAAA
1 TCAAAGTCAACT-TAGATCAAAA
345880 TCAA
1 TCAA
345884 CGGTCAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (22 bp):
TCAAAGTCAACTTAGATCAAAA
Found at i:350861 original size:27 final size:28
Alignment explanation
Indices: 350831--350883 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
350821 AAGATAAATT
350831 TATAAAATTTTAAAAATG-AAACAAACA
1 TATAAAATTTTAAAAATGAAAACAAACA
*
350858 TATAAAGTTTTAAAAATGAAAACAAA
1 TATAAAATTTTAAAAATGAAAACAAA
350884 TTATTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (28 bp):
TATAAAATTTTAAAAATGAAAACAAACA
Found at i:351623 original size:17 final size:19
Alignment explanation
Indices: 351603--351643 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
351593 ATTGTAGTTA
351603 TTTATATTAA-TTTAAT-T
1 TTTATATTAATTTTAATAT
351620 TTTAT-TTAATTTTAATAT
1 TTTATATTAATTTTAATAT
351638 TTTATA
1 TTTATA
351644 ATATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATTAATTTTAATAT
Found at i:352529 original size:2 final size:2
Alignment explanation
Indices: 352524--352548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
352514 ATAATTTAAG
352524 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
352549 AATCACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:355649 original size:31 final size:31
Alignment explanation
Indices: 355602--355685 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
355592 GGTTCAAATG
* * *
355602 TTAAATTAAAAATTTATCTGAAGTTTAATGA-
1 TTAAATTAATACTTTATCTAAAGTTTAA-GAT
* *
355633 TTAAATTGATATTTTATCTAAAGTTTAAGAT
1 TTAAATTAATACTTTATCTAAAGTTTAAGAT
355664 TTAAATTAATACTTTATCTAAA
1 TTAAATTAATACTTTATCTAAA
355686 TTTCAGGGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 2 0.04
31 44 0.96
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (31 bp):
TTAAATTAATACTTTATCTAAAGTTTAAGAT
Found at i:356178 original size:24 final size:24
Alignment explanation
Indices: 356151--356223 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
356141 CGTTCATTTA
356151 CGTTCG-TGAACGTTCGGTTATGTT
1 CGTTCGAT-AACGTTCGGTTATGTT
* * *
356175 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATAACGTTCGGTTATGTT
* * *
356199 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATAACGTTCGGTTATGTT
356223 C
1 C
356224 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 44 0.98
25 1 0.02
ACGTcount: A:0.12, C:0.15, G:0.23, T:0.49
Consensus pattern (24 bp):
CGTTCGATAACGTTCGGTTATGTT
Found at i:356180 original size:14 final size:14
Alignment explanation
Indices: 356161--356216 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
356151 CGTTCGTGAA
*
356161 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
356175 CGTTCGATTATGTT
1 CGTTCGATTATGTT
356189 CG-T---TTATGTT
1 CGTTCGATTATGTT
356199 CGTTCGATTATGTT
1 CGTTCGATTATGTT
356213 CGTT
1 CGTT
356217 TATGTTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.11, C:0.14, G:0.23, T:0.52
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:356233 original size:24 final size:24
Alignment explanation
Indices: 356162--356236 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
356152 GTTCGTGAAC
*
356162 GTTCGGTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
356186 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
356210 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
356234 GTT
1 GTT
356237 TAACCCAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.13, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:357307 original size:16 final size:16
Alignment explanation
Indices: 357286--357352 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
357276 GTCTCCAACG
357286 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
357302 TTTATGTTCGCGTTCG
1 TTTATGTTCGTGTTCA
*
357318 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
357334 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
357348 TTTAT
1 TTTAT
357353 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:357427 original size:10 final size:10
Alignment explanation
Indices: 357412--357464 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
357402 CAAAAAAAAT
357412 TGTTCGTTTA
1 TGTTCGTTTA
357422 TGTTCG----
1 TGTTCGTTTA
357428 TGTTCGTTTA
1 TGTTCGTTTA
357438 TGTTC----A
1 TGTTCGTTTA
357444 TGTTCGTTTA
1 TGTTCGTTTA
357454 TGTTCGTTTA
1 TGTTCGTTTA
357464 T
1 T
357465 TTATTAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
6 12 0.34
10 23 0.66
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:357433 original size:16 final size:16
Alignment explanation
Indices: 357412--357460 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
357402 CAAAAAAAAT
357412 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
357428 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCG
357444 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
357460 T
1 T
357461 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:357645 original size:27 final size:28
Alignment explanation
Indices: 357596--357665 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 28
357586 TAATTTCTTT
*
357596 AAAGTAAAATATTTTGAATATATATTTAA
1 AAAGTAAAATATTTTGAATATATA-TAAA
357625 AAAGTAAAATATTTTGAATATATA-AAA
1 AAAGTAAAATATTTTGAATATATATAAA
357652 AAA-TAAAATATTTT
1 AAAGTAAAATATTTT
357666 TATTTTTGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 11 0.28
27 5 0.12
29 24 0.60
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (28 bp):
AAAGTAAAATATTTTGAATATATATAAA
Found at i:361936 original size:35 final size:36
Alignment explanation
Indices: 361872--361945 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 36
361862 AATTAGGTAC
361872 AACTAGTAAAATCACATCTTTATAAAAAGAAAAACTT
1 AACTAGTAAAAT-ACATCTTTATAAAAAGAAAAACTT
* *
361909 AACTAGTAAAAT-CATCTTTTTAGAAAGAAAAACTT
1 AACTAGTAAAATACATCTTTATAAAAAGAAAAACTT
361944 AA
1 AA
361946 TGAGTTGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 23 0.66
37 12 0.34
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (36 bp):
AACTAGTAAAATACATCTTTATAAAAAGAAAAACTT
Found at i:367215 original size:31 final size:31
Alignment explanation
Indices: 367177--367235 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
367167 AGTTGTATAG
367177 ATTATTTAAATTTCAGCATTGTAAAACTAAA
1 ATTATTTAAATTTCAGCATTGTAAAACTAAA
*
367208 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAGCATTGTAAAACT
367236 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGCATTGTAAAACTAAA
Found at i:376761 original size:3 final size:3
Alignment explanation
Indices: 376753--376790 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
376743 GACAAAGAAC
376753 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
376791 GGTGTTAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:380847 original size:12 final size:12
Alignment explanation
Indices: 380830--380856 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
380820 AAAATATATA
380830 TTATATAGAATT
1 TTATATAGAATT
380842 TTATATAGAATT
1 TTATATAGAATT
380854 TTA
1 TTA
380857 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TTATATAGAATT
Found at i:399165 original size:32 final size:33
Alignment explanation
Indices: 399127--399196 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 33
399117 AATTTGATTT
*
399127 AAAATGGTAAGTAATTTGGGAT-AAATGGGTTA
1 AAAATGGAAAGTAATTTGGGATAAAATGGGTTA
** * *
399159 AAAATGGAAAGTTTTTTGGGTTAAAATTGGTTA
1 AAAATGGAAAGTAATTTGGGATAAAATGGGTTA
399192 AAAAT
1 AAAAT
399197 AGTATCAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34
Consensus pattern (33 bp):
AAAATGGAAAGTAATTTGGGATAAAATGGGTTA
Found at i:400031 original size:19 final size:18
Alignment explanation
Indices: 400007--400050 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
399997 ATACCATTGA
*
400007 TATTTTTTATCGTCTTTTT
1 TATTTTCTATCGT-TTTTT
* *
400026 TATTTTCTCTTGTTTTTT
1 TATTTTCTATCGTTTTTT
400044 TATTTTC
1 TATTTTC
400051 AATAAGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (18 bp):
TATTTTCTATCGTTTTTT
Found at i:401094 original size:28 final size:27
Alignment explanation
Indices: 401046--401098 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
401036 TATCCATTTC
*
401046 TAAAATTTTATAAGTTTATTTTATAATA
1 TAAAATTTTATAAG-TTAATTTATAATA
401074 TAAAATTTTACTAA-TTAATTTATAA
1 TAAAATTTTA-TAAGTTAATTTATAA
401099 CTTAATAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 10 0.43
29 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TAAAATTTTATAAGTTAATTTATAATA
Found at i:416550 original size:2 final size:2
Alignment explanation
Indices: 416543--416567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
416533 TAATATACAT
416543 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
416568 TAATAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:416604 original size:5 final size:5
Alignment explanation
Indices: 416594--416626 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
416584 TCTTAAATGA
416594 ATATT ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATA
416627 GTTACAGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:417219 original size:28 final size:28
Alignment explanation
Indices: 417178--417238 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
417168 AAAATATCTT
417178 ATAGTCGATAATTATTTTATAACTTTTA
1 ATAGTCGATAATTATTTTATAACTTTTA
*
417206 ATAGTC-ATACATTATTTTATAATTTTTA
1 ATAGTCGATA-ATTATTTTATAACTTTTA
417234 ATAGT
1 ATAGT
417239 TGTAAAACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 3 0.10
28 28 0.90
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (28 bp):
ATAGTCGATAATTATTTTATAACTTTTA
Found at i:417775 original size:20 final size:20
Alignment explanation
Indices: 417750--417787 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
417740 AGTAGCAGGG
417750 AATTTTAAATTATTATATAT
1 AATTTTAAATTATTATATAT
* *
417770 AATTTTAATTTTTTATAT
1 AATTTTAAATTATTATAT
417788 TTTTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTAAATTATTATATAT
Found at i:417858 original size:24 final size:24
Alignment explanation
Indices: 417813--417858 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
417803 TGTCTTTTTC
* * *
417813 CTCTTAAAATTTTATAAGTTCATA
1 CTCTTAAAAATTTAGAAATTCATA
417837 CTCTTAAAAATTTAGAAATTCA
1 CTCTTAAAAATTTAGAAATTCA
417859 CCCTAAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (24 bp):
CTCTTAAAAATTTAGAAATTCATA
Found at i:426469 original size:21 final size:23
Alignment explanation
Indices: 426431--426475 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
426421 ATTATCCATC
426431 TCCGAGAAGAAGAAAAAAGTTTA
1 TCCGAGAAGAAGAAAAAAGTTTA
426454 TCCGAGAAG-A-AAAAAAGTTTA
1 TCCGAGAAGAAGAAAAAAGTTTA
426475 T
1 T
426476 TCATTCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.55
22 1 0.05
23 9 0.41
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (23 bp):
TCCGAGAAGAAGAAAAAAGTTTA
Found at i:428431 original size:21 final size:21
Alignment explanation
Indices: 428394--428438 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
428384 TTTATATGGG
*
428394 CAAGGGGAATCAGTACCCATT
1 CAAGGGGAACCAGTACCCATT
*
428415 CAAGGGGAACC-GATACCCCTT
1 CAAGGGGAACCAG-TACCCATT
428436 CAA
1 CAA
428439 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCAGTACCCATT
Found at i:429952 original size:23 final size:23
Alignment explanation
Indices: 429861--429944 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
429851 CATTATTATA
*
429861 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
429884 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
429907 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
429930 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
429945 TTTATACGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:432422 original size:169 final size:171
Alignment explanation
Indices: 432125--432461 Score: 635
Period size: 169 Copynumber: 2.0 Consensus size: 171
432115 GCATGCACAA
432125 AGCCACCACAGTTGTCAATCATTACTGAATACATGGAGATGGGATCATTGTACTTTTTAAGTCAT
1 AGCCACCACAGTTGTCAATCATTACTGAATACATGGAGATGGGATCATTGTACTTTTTAAGTCAT
432190 TCAAGTGGTAAATTGATTAAAACATGTTGAAATTTGGTGTGATTCTTAATTTCCATGATGAAAGA
66 TCAAGTGGTAAATTGATTAAAACATGTTGAAATTTGGTGTGATTCTTAATTTCCATGATGAAAGA
*
432255 -GA-TTTTTGAGGATATAGAGGTGTTAAATGCATAAAATTG
131 TGAGATTTTGAGGATATAGAGGTGTTAAATGCATAAAATTG
432294 AGCCACCACAGTTGTCAATCATTACTGAATACATGGAGATGGGATCATTGTACTTTTTAAGTCAT
1 AGCCACCACAGTTGTCAATCATTACTGAATACATGGAGATGGGATCATTGTACTTTTTAAGTCAT
432359 TCAAGTGGTAAATTGATTAAAACATGTTGAAAATTTGGTGTGATTCTTAATTTCCAT-ATGAAAG
66 TCAAGTGGTAAATTGATTAAAACATGTTG-AAATTTGGTGTGATTCTTAATTTCCATGATGAAAG
432423 ATGAGATTTTGAGGATATAGAGGTGTTAAATGCATAAAA
130 ATGAGATTTTGAGGATATAGAGGTGTTAAATGCATAAAA
432462 AATTGCTTTG
Statistics
Matches: 164, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
169 102 0.62
170 29 0.18
171 33 0.20
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (171 bp):
AGCCACCACAGTTGTCAATCATTACTGAATACATGGAGATGGGATCATTGTACTTTTTAAGTCAT
TCAAGTGGTAAATTGATTAAAACATGTTGAAATTTGGTGTGATTCTTAATTTCCATGATGAAAGA
TGAGATTTTGAGGATATAGAGGTGTTAAATGCATAAAATTG
Found at i:436526 original size:3 final size:3
Alignment explanation
Indices: 436518--436542 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
436508 AGTTGCTGAC
436518 CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT C
436543 TTCTCTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:436594 original size:40 final size:40
Alignment explanation
Indices: 436544--436624 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
436534 CTCCTCCTCT
436544 TCTCTAAACTAAAACCCCTTCACCACC-CTTCTTCTTCTTC
1 TCTCTAAACTAAAACCCCTTCACCACCTC-TCTTCTTCTTC
*
436584 TCTCTAAACTAAAACCCTTTCACCACCTCTCTTCTTCTTC
1 TCTCTAAACTAAAACCCCTTCACCACCTCTCTTCTTCTTC
436624 T
1 T
436625 TTTACGTACT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (40 bp):
TCTCTAAACTAAAACCCCTTCACCACCTCTCTTCTTCTTC
Found at i:437295 original size:3 final size:3
Alignment explanation
Indices: 437289--437317 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
437279 ATTTGGTAGT
437289 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
437318 GGTTGACGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:443984 original size:16 final size:17
Alignment explanation
Indices: 443942--443985 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
443932 CGTTTAAAGG
443942 ATCTTTAATTTTCTTAT
1 ATCTTTAATTTTCTTAT
*
443959 ATCTTAAATTTTCTT-T
1 ATCTTTAATTTTCTTAT
443975 CAT-TTTAATTT
1 -ATCTTTAATTT
443986 ATTTTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (17 bp):
ATCTTTAATTTTCTTAT
Found at i:444481 original size:20 final size:21
Alignment explanation
Indices: 444456--444507 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
444446 TTTTCCCAAT
*
444456 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
444476 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
444497 TCGCAATGCGA
1 TCGCAATGCGA
444508 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:444586 original size:20 final size:20
Alignment explanation
Indices: 444538--444590 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
444528 TAATACAAAA
* *
444538 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
444558 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
444578 TCGCAACGCGATT
1 TCGCAACGCGATT
444591 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:445193 original size:19 final size:19
Alignment explanation
Indices: 445149--445187 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
445139 AGAGAATCGT
*
445149 AACGCGAAATAAAAAACGC
1 AACGCGAAACAAAAAACGC
*
445168 AACGCGAAACAAAAATCGC
1 AACGCGAAACAAAAAACGC
445187 A
1 A
445188 TTGCGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.23, G:0.15, T:0.05
Consensus pattern (19 bp):
AACGCGAAACAAAAAACGC
Found at i:445205 original size:19 final size:19
Alignment explanation
Indices: 445183--445314 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
445173 GAAACAAAAA
*
445183 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
445202 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
445221 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
445235 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
445254 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
445273 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
445293 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
445313 TC
1 TC
445315 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 9 0.09
16 2 0.02
17 3 0.03
19 49 0.51
20 32 0.33
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:445432 original size:25 final size:24
Alignment explanation
Indices: 445378--445432 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
445368 TTATGTTTAT
* *
445378 TGTTTTTGGTATATCTTGACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
445402 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
445428 TGTTT
1 TGTTT
445433 ATTGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:447822 original size:19 final size:19
Alignment explanation
Indices: 447798--447837 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
447788 TAGTTTCTGA
447798 AAATGAAAATCGCAACACG
1 AAATGAAAATCGCAACACG
** *
447817 AAATGACTATCGCAACGCG
1 AAATGAAAATCGCAACACG
447836 AA
1 AA
447838 TTTGACTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACACG
Found at i:447845 original size:20 final size:20
Alignment explanation
Indices: 447806--447858 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
447796 GAAAATGAAA
*
447806 ATCGCAACACGAA-ATGACT
1 ATCGCAACGCGAATATGACT
*
447825 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
*
447845 ATCGCAACGAGAAT
1 ATCGCAACGCGAAT
447859 CGCAACGCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:448141 original size:22 final size:22
Alignment explanation
Indices: 448114--448157 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
448104 GATGGAGATA
*
448114 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
448136 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
448158 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:448486 original size:20 final size:20
Alignment explanation
Indices: 448352--448485 Score: 162
Period size: 20 Copynumber: 6.7 Consensus size: 20
448342 GATTATGTAT
448352 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
448372 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
448392 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
448412 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
448432 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
448453 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
448473 TATCGCATTGCGA
1 TATCGCGTTGCGA
448486 TTTTCCCAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
19 3 0.03
20 83 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:448504 original size:21 final size:21
Alignment explanation
Indices: 448475--448550 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
448465 ATAGTCAGTA
448475 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
448496 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
448516 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
448537 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
448551 ACTTATTTGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:448505 original size:41 final size:41
Alignment explanation
Indices: 448373--448548 Score: 137
Period size: 41 Copynumber: 4.3 Consensus size: 41
448363 GAAAGTCAGA
* * *** *
448373 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGT-CAGT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
* * * * ** *
448413 ATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
448454 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
* *
448496 -TCGCGTTGCGAT--TTACTTATTCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCA-GTA-TCGCATTGCGATTTT-CCAAT
448537 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
448549 TTACTTATTT
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.02
40 33 0.29
41 77 0.68
42 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:448519 original size:20 final size:20
Alignment explanation
Indices: 448475--448567 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
448465 ATAGTCAGTA
* **
448475 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
448496 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
448516 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
448537 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
*
448557 TTGCATTGCGA
1 TCGCATTGCGA
448568 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.54
21 26 0.46
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:448549 original size:41 final size:41
Alignment explanation
Indices: 448475--448567 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
448465 ATAGTCAGTA
448475 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
448516 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
448557 TTGCATTGCGA
1 TCGCATTGCGA
448568 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:449092 original size:48 final size:48
Alignment explanation
Indices: 449021--449112 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
449011 ATCGTGTTTT
449021 CAATTAATAAAAAGATGAATGACTTTATTCTATCTTTATTGACTAAAA
1 CAATTAATAAAAAGATGAATGACTTTATTCTATCTTTATTGACTAAAA
449069 CAATTAATAAAAAGATGAATGACTTTATTCTATCTTTATTGACT
1 CAATTAATAAAAAGATGAATGACTTTATTCTATCTTTATTGACT
449113 TTCTACACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (48 bp):
CAATTAATAAAAAGATGAATGACTTTATTCTATCTTTATTGACTAAAA
Found at i:450448 original size:25 final size:24
Alignment explanation
Indices: 450420--450487 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
450410 GATGATATCT
* *
450420 TTTTAAATTTAATAATAAAATATTA
1 TTTTATATTTAATAATAAAAT-TAA
* *
450445 TTTTATTATTT-AT-TTTAAATTAA
1 TTTTA-TATTTAATAATAAAATTAA
450468 TTTTATATTTAATAATAAAA
1 TTTTATATTTAATAATAAAA
450488 AATATCACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
22 5 0.15
23 9 0.26
24 9 0.26
25 7 0.21
26 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTATATTTAATAATAAAATTAA
Found at i:450755 original size:8 final size:8
Alignment explanation
Indices: 450739--450783 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
450729 CCTAATATAG
450739 AAAAGAAA
1 AAAAGAAA
*
450747 AAAATAAA
1 AAAAGAAA
450755 AAAAGAAA
1 AAAAGAAA
*
450763 GAAAGAAA
1 AAAAGAAA
*
450771 GAAAGAAA
1 AAAAGAAA
450779 TAAAA
1 -AAAA
450784 AATCAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
8 29 0.91
9 3 0.09
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (8 bp):
AAAAGAAA
Found at i:450765 original size:4 final size:4
Alignment explanation
Indices: 450740--450778 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
450730 CTAATATAGA
* * *
450740 AAAG AAAA AAAT AAAA AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
450779 TAAAAAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:450797 original size:28 final size:28
Alignment explanation
Indices: 450740--450793 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
450730 CTAATATAGA
*
450740 AAAGAAAAAAATAAAAAAAGAAAGAAAG
1 AAAGAAAAAAATAAAAAAACAAAGAAAG
* *
450768 AAAGAAAGAAATAAAAAATC-AAGAAA
1 AAAGAAAAAAATAAAAAAACAAAGAAA
450794 AGAATCACAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.06
Consensus pattern (28 bp):
AAAGAAAAAAATAAAAAAACAAAGAAAG
Found at i:452526 original size:34 final size:34
Alignment explanation
Indices: 452483--452552 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
452473 CCTTTGTCAA
452483 CATTGAGTTTAACCACAAACATTTACTTAAGTCC
1 CATTGAGTTTAACCACAAACATTTACTTAAGTCC
* *
452517 CATTGAGTTTAACTACAAACATTTGCTTAAGTCC
1 CATTGAGTTTAACCACAAACATTTACTTAAGTCC
452551 CA
1 CA
452553 AAGACCTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (34 bp):
CATTGAGTTTAACCACAAACATTTACTTAAGTCC
Found at i:452577 original size:29 final size:29
Alignment explanation
Indices: 452539--452599 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
452529 CTACAAACAT
*
452539 TTGCTTAAGTCCCAAAGACCTCAAATTTA
1 TTGCTCAAGTCCCAAAGACCTCAAATTTA
* * *
452568 TTGCTCAAGTCCTAATGACTTCAAATTTA
1 TTGCTCAAGTCCCAAAGACCTCAAATTTA
452597 TTG
1 TTG
452600 AGTGGTCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (29 bp):
TTGCTCAAGTCCCAAAGACCTCAAATTTA
Found at i:458864 original size:23 final size:23
Alignment explanation
Indices: 458793--458865 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
458783 TTCATAAATA
*
458793 TTAAATGAATATGTTCGTGAACA
1 TTAAATGAATATGTTCGTGAACG
* * * *** *
458816 TGAAA-CAGATATATTCACCAAAG
1 TTAAATGA-ATATGTTCGTGAACG
458839 TTAAATGAATATGTTCGTGAACG
1 TTAAATGAATATGTTCGTGAACG
458862 TTAA
1 TTAA
458866 GCGAACATGT
Statistics
Matches: 33, Mismatches: 15, Indels: 4
0.63 0.29 0.08
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (23 bp):
TTAAATGAATATGTTCGTGAACG
Found at i:465508 original size:9 final size:9
Alignment explanation
Indices: 465494--465569 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
465484 ATATGTTGGC
*
465494 ATGTAATAA
1 ATGTAAGAA
465503 ATGTAAGAA
1 ATGTAAGAA
*
465512 ATATAAGAA
1 ATGTAAGAA
465521 ATGTAAGAA
1 ATGTAAGAA
*
465530 ATATAAGAA
1 ATGTAAGAA
*
465539 ATGTAATAA
1 ATGTAAGAA
465548 ATGTAAGAA
1 ATGTAAGAA
*
465557 ATATAAGAA
1 ATGTAAGAA
465566 ATGT
1 ATGT
465570 TTTAGTACGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (9 bp):
ATGTAAGAA
Found at i:466143 original size:19 final size:19
Alignment explanation
Indices: 466105--466144 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
466095 ACAAACAAAA
*
466105 TAAATAAAAATTTCATAAT
1 TAAATAAAAATTTCACAAT
466124 TAAATAAAAACTTT-ACAAT
1 TAAATAAAAA-TTTCACAAT
466143 TA
1 TA
466145 CCGGCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATAAAAATTTCACAAT
Found at i:468320 original size:35 final size:35
Alignment explanation
Indices: 468281--468351 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
468271 GATAGAATGA
468281 AGTGTCAAATATTAAAGGCCAAACTTCGCTTATAC
1 AGTGTCAAATATTAAAGGCCAAACTTCGCTTATAC
468316 AGTGTCAAATATTAAAGGCCAAACTTCGCTTATAC
1 AGTGTCAAATATTAAAGGCCAAACTTCGCTTATAC
468351 A
1 A
468352 TGTATACACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (35 bp):
AGTGTCAAATATTAAAGGCCAAACTTCGCTTATAC
Found at i:468957 original size:27 final size:28
Alignment explanation
Indices: 468894--468968 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
468884 TATTTCTTAA
* * *
468894 TCTTTCTAATAAATTAGTTATTAAATTTG
1 TCTTTCAAACAAATTA-TTCTTAAATTTG
468923 TCTTTCAAACAAATTATTCTTAAA-TTG
1 TCTTTCAAACAAATTATTCTTAAATTTG
468950 TCTTTCAAACAAATTATTC
1 TCTTTCAAACAAATTATTC
468969 CCTAAATAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 22 0.51
28 7 0.16
29 14 0.33
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (28 bp):
TCTTTCAAACAAATTATTCTTAAATTTG
Found at i:468974 original size:28 final size:27
Alignment explanation
Indices: 468915--468975 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
468905 AATTAGTTAT
*
468915 TAAATTTGTCTTTCAAACAAATTATTCT
1 TAAA-TTGTCTTTCAAACAAATTATTCC
468943 TAAATTGTCTTTCAAACAAATTATTCCC
1 TAAATTGTCTTTCAAACAAATTATT-CC
468971 TAAAT
1 TAAAT
468976 AAGATTAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.43
Consensus pattern (27 bp):
TAAATTGTCTTTCAAACAAATTATTCC
Found at i:470609 original size:16 final size:16
Alignment explanation
Indices: 470588--470618 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
470578 GTTTCAGATC
470588 CATATTCCAATTCCTA
1 CATATTCCAATTCCTA
*
470604 CATATTCTAATTCCT
1 CATATTCCAATTCCT
470619 TCACAGATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (16 bp):
CATATTCCAATTCCTA
Found at i:473934 original size:35 final size:35
Alignment explanation
Indices: 473888--473963 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
473878 AAAACAGACC
* * *
473888 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCAAAAATAAT
*
473923 TCAATTTCATTCTAAACCCTAAATTCAAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCAAAAATAAT
473958 TCAATT
1 TCAATT
473964 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCAAAAATAAT
Found at i:474501 original size:130 final size:130
Alignment explanation
Indices: 474360--474607 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
474350 TATTTATATA
* * **
474360 ATCAATTTGGTCCTAATTTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
474425 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
474490 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
474555 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
474608 GAATAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:474638 original size:130 final size:129
Alignment explanation
Indices: 474377--474638 Score: 312
Period size: 130 Copynumber: 2.0 Consensus size: 129
474367 TGGTCCTAAT
* ** *
474377 TTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCATGA
1 TTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCATGA
* * * * * **** *
474442 CACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCTAAA
66 CACATGTCATTGGTGACACATGTCACCACCTAATTAATAAAATAAGCTATCAAAGAAGT-CAAAA
474507 TTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCATGA
1 TTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCATGA
* * * *
474572 TATATGTTATTGGTGACACATGTCACCACCTAATTAGAATAAAATTAAGTTA-CAAAGAAGT-AA
66 CACATGTCATTGGTGACACATGTCACCACCTAATT--AATAAAA-TAAGCTATCAAAGAAGTCAA
474635 AA
128 AA
474637 TT
1 TT
474639 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
130 97 0.87
132 9 0.08
133 5 0.05
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
TTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCATGA
CACATGTCATTGGTGACACATGTCACCACCTAATTAATAAAATAAGCTATCAAAGAAGTCAAAA
Found at i:474875 original size:25 final size:25
Alignment explanation
Indices: 474846--474908 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
474836 TAAATGATGG
474846 GAAAATATTATATTTTTTTACAATA
1 GAAAATATTATATTTTTTTACAATA
474871 GAAAATATTATATTTTTTTACAATA
1 GAAAATATTATATTTTTTTACAATA
474896 -AAAA-ATTATATTT
1 GAAAATATTATATTT
474909 GATAATTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 9 0.24
24 4 0.11
25 25 0.66
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
GAAAATATTATATTTTTTTACAATA
Found at i:474989 original size:28 final size:27
Alignment explanation
Indices: 474958--475020 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
474948 AGTTGATACA
*
474958 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
474986 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
475014 ATATTTT
1 ATATTTT
475021 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Done.