Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008621.1 Hibiscus syriacus cultivar Beakdansim tig00111584_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: 1991651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1509095 original size:231 final size:224
Alignment explanation
Indices: 1508686--1509113 Score: 567
Period size: 231 Copynumber: 1.9 Consensus size: 224
1508676 GATATTCGGG
* * *
1508686 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATATTTTTACCTTAT
1 TCGGGTCGAGTTCAGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTAT
* *
1508751 ATATTTAGGATTAAATATAATAATACCCCTATATATATATATATATATATTTTTCAATTAAGTCA
66 ATATTTAGGAATAAATACAATAATACCCC---ATATATATATATATATATTTTTCAATTAAGTCA
* *
1508816 CTGTTTTTATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATA
128 ATGTTTTTATTGAATAAAAATAATTTTTTATTATTTCGGGTAGGGTCGGATTTCTAATTCATATA
1508881 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGT
193 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGT
* **
1508913 TCGGGTCGGGTTCAGGTTTAGGGTGAAAAAAATTGGGCCGACCCGAAAAAATATATAATTTTACC
1 TCGGGTCGAGTTCAGGTTTAGGGTG--AAAAA-T-ACCCGACCCGAAAAAATATATAATTTTACC
* *
1508978 TTATATATTTAGGAATAATTACAATAATACCCC-TCTATATATA-AT-T-TTTTTCAATTAAGTC
62 TTATATATTTAGGAATAAATACAATAATACCCCATATATATATATATATATTTTTCAATTAAGTC
* * *
1509039 AATGTTTTTATTGAATAAAAATATTTTTTTTATTATTTTTGTGACGTGTAGGGTCGGGTTTCTAA
127 AATGTTTTTATTGAATAAAAATA-ATTTTTTATTA---TT-T--CGGGTAGGGTCGGATTTCTAA
1509104 TTCATATATT
185 TTCATATATT
1509114 AAATAAAAAT
Statistics
Matches: 175, Mismatches: 15, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
224 37 0.21
225 11 0.06
226 2 0.01
227 32 0.18
228 2 0.01
229 6 0.03
230 1 0.01
231 84 0.48
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (224 bp):
TCGGGTCGAGTTCAGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTAT
ATATTTAGGAATAAATACAATAATACCCCATATATATATATATATATTTTTCAATTAAGTCAATG
TTTTTATTGAATAAAAATAATTTTTTATTATTTCGGGTAGGGTCGGATTTCTAATTCATATATTC
GGGTCGGGTCGGGTGAAACTTTATTTTGT
Found at i:1513258 original size:18 final size:17
Alignment explanation
Indices: 1513235--1513307 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 17
1513225 TAAAACAGCG
1513235 GTTGCGGCATCTGTCGCA
1 GTTGCGG-ATCTGTCGCA
*
1513253 GTTGCGG---TGTCGCG
1 GTTGCGGATCTGTCGCA
*
1513267 GTTGCTGTATCTGTCGCA
1 GTTGC-GGATCTGTCGCA
*
1513285 GTTGCGG---TGTCGCG
1 GTTGCGGATCTGTCGCA
1513299 GTTGCGGAT
1 GTTGCGGAT
1513308 GCTGCGGACG
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
14 24 0.55
15 1 0.02
17 1 0.02
18 18 0.41
ACGTcount: A:0.07, C:0.22, G:0.40, T:0.32
Consensus pattern (17 bp):
GTTGCGGATCTGTCGCA
Found at i:1513279 original size:32 final size:32
Alignment explanation
Indices: 1513232--1513305 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
1513222 GTATAAAACA
1513232 GCGGTTGCGGCATCTGTCGCAGTTGCGGTGTC
1 GCGGTTGCGGCATCTGTCGCAGTTGCGGTGTC
* *
1513264 GCGGTTGCTGTATCTGTCGCAGTTGCGGTGTC
1 GCGGTTGCGGCATCTGTCGCAGTTGCGGTGTC
1513296 GCGGTTGCGG
1 GCGGTTGCGG
1513306 ATGCTGCGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.05, C:0.23, G:0.42, T:0.30
Consensus pattern (32 bp):
GCGGTTGCGGCATCTGTCGCAGTTGCGGTGTC
Found at i:1514943 original size:100 final size:100
Alignment explanation
Indices: 1514770--1514969 Score: 384
Period size: 100 Copynumber: 2.0 Consensus size: 100
1514760 TTCTTATTTT
1514770 GGTCACCAATCATAAAAATTTAACATTTTCTCTTGACTAATACAAAGCAAATTGATATTGCTTTG
1 GGTCACCAATCATAAAAATTTAACATTTTCTCTTGACTAATACAAAGCAAATTGATATTGCTTTG
1514835 AGTGTAGGGAGAGGATATGAACTTTGGTTCAGGCC
66 AGTGTAGGGAGAGGATATGAACTTTGGTTCAGGCC
1514870 GGTCACCAATCATTAAAAA-TTAACATTTTCTCTTGACTAATACAAAGCAAATTGATATTGCTTT
1 GGTCACCAATCA-TAAAAATTTAACATTTTCTCTTGACTAATACAAAGCAAATTGATATTGCTTT
1514934 GAGTGTAGGGAGAGGATATGAACTTTGGTTCAGGCC
65 GAGTGTAGGGAGAGGATATGAACTTTGGTTCAGGCC
1514970 CTCCACTCGC
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
100 93 0.94
101 6 0.06
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (100 bp):
GGTCACCAATCATAAAAATTTAACATTTTCTCTTGACTAATACAAAGCAAATTGATATTGCTTTG
AGTGTAGGGAGAGGATATGAACTTTGGTTCAGGCC
Found at i:1516192 original size:36 final size:36
Alignment explanation
Indices: 1516145--1516220 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
1516135 ATATTTGATA
1516145 TTAAAAAATA-TTAAAATTATTGTATTTGAATCCCAG
1 TTAAAAAATATTTAAAA-TATTGTATTTGAATCCCAG
1516181 TTAAAAAATATTTAAAATATTGTATTTGAATCCCAG
1 TTAAAAAATATTTAAAATATTGTATTTGAATCCCAG
1516217 TTAA
1 TTAA
1516221 TTTAGTAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 33 0.85
37 6 0.15
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (36 bp):
TTAAAAAATATTTAAAATATTGTATTTGAATCCCAG
Found at i:1518164 original size:34 final size:34
Alignment explanation
Indices: 1518126--1518194 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
1518116 GAAATAAGCA
* *
1518126 ATAATTTTAGAATAATTAAATAT-AGTATAAATAT
1 ATAATTTTAGAACAATGAAAT-TCAGTATAAATAT
1518160 ATAATTTTAGAACAATGAAATTCAGTATAAATAT
1 ATAATTTTAGAACAATGAAATTCAGTATAAATAT
1518194 A
1 A
1518195 AAAATGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (34 bp):
ATAATTTTAGAACAATGAAATTCAGTATAAATAT
Found at i:1518824 original size:3 final size:3
Alignment explanation
Indices: 1518816--1518869 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
1518806 TGAATATTAG
* *
1518816 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1518864 ATT ATT
1 ATT ATT
1518870 GAATAAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1522554 original size:22 final size:21
Alignment explanation
Indices: 1522520--1522561 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1522510 ATAATTATTT
1522520 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
1522541 AAAAATATTTAATAAAAATAC
1 AAAAA-ATTAAATAAAAATAC
1522562 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:1534536 original size:2 final size:2
Alignment explanation
Indices: 1534529--1534578 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1534519 AAGACAATTC
1534529 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
1534571 AT AT AT AT
1 AT AT AT AT
1534579 TGAATTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1541411 original size:27 final size:27
Alignment explanation
Indices: 1541370--1541422 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1541360 AACAACGTAA
*
1541370 GATGACATTATTGTTACCTGAAAATAG
1 GATGACATTACTGTTACCTGAAAATAG
*
1541397 GATGTCATTACTGTTACCTGAAAATA
1 GATGACATTACTGTTACCTGAAAATA
1541423 TTCCTTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (27 bp):
GATGACATTACTGTTACCTGAAAATAG
Found at i:1541904 original size:30 final size:30
Alignment explanation
Indices: 1541832--1541909 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
1541822 TACACTGAGC
*
1541832 GTCCTTATACACTACAGTATTGTACTAAGT
1 GTCCTTATACACTATAGTATTGTACTAAGT
*
1541862 GT-CTTCACACACTATAGTATTGTACTAAGT
1 GTCCTT-ATACACTATAGTATTGTACTAAGT
1541892 GTCCTTATACACTATAGT
1 GTCCTTATACACTATAGT
1541910 GCTAATCCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 3 0.07
30 37 0.86
31 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (30 bp):
GTCCTTATACACTATAGTATTGTACTAAGT
Found at i:1553253 original size:21 final size:21
Alignment explanation
Indices: 1553227--1553276 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1553217 CCAATCTCCT
1553227 TCGATCCACCCCACTAATCCC
1 TCGATCCACCCCACTAATCCC
1553248 TCGATCCACCCCACTAATCCC
1 TCGATCCACCCCACTAATCCC
1553269 TCGATCCA
1 TCGATCCA
1553277 TCATATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.50, G:0.06, T:0.20
Consensus pattern (21 bp):
TCGATCCACCCCACTAATCCC
Found at i:1554538 original size:43 final size:43
Alignment explanation
Indices: 1554484--1554709 Score: 389
Period size: 43 Copynumber: 5.3 Consensus size: 43
1554474 TGGTAACAAA
* *
1554484 AAACGCTGCAATAGGTGTTGAGATTTAGCGACGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1554527 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
1554570 AAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
1554613 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* *
1554656 AAACGCCGCAATAGGTCTTGAGATTTAACGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
1554699 AAACACCGCAA
1 AAACGCCGCAA
1554710 AAGATCTAGT
Statistics
Matches: 174, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 174 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:1554736 original size:43 final size:43
Alignment explanation
Indices: 1554484--1554735 Score: 348
Period size: 43 Copynumber: 5.9 Consensus size: 43
1554474 TGGTAACAAA
* * *
1554484 AAACGCTGCAATAGGTGTTGAGATTTAGCGACGTTTTTCCCAC
1 AAACGCCGCAATAGGTGCTGAGATTTAGCGGCGTTTTTCCCAC
*
1554527 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGCTGAGATTTAGCGGCGTTTTTCCCAC
* *
1554570 AAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGCTGAGATTTAGCGGCGTTTTTCCCAC
* *
1554613 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCAATAGGTGCTGAGATTTAGCGGCGTTTTTCCCAC
*
1554656 AAACGCCGCAATAGGT-CTTGAGATTTAACGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGC-TGAGATTTAGCGGCGTTTTTCCCAC
* * * *
1554699 AAACACCGCAAAAGAT-CT-AGTATATAGCGGCGTTTTT
1 AAACGCCGCAATAGGTGCTGAG-ATTTAGCGGCGTTTTT
1554736 TAGAACAAAC
Statistics
Matches: 194, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
41 2 0.01
42 15 0.08
43 177 0.91
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGCTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:1554787 original size:129 final size:129
Alignment explanation
Indices: 1554479--1554793 Score: 294
Period size: 129 Copynumber: 2.4 Consensus size: 129
1554469 GCGTTTGGTA
* * * ** * * *** *
1554479 ACAAAAAACGCTGCAATAGGTGTTGAGATTTAGCGACGTTTTTCCCACAAACGCCGCAATAGGTG
1 ACAACAAACGCCGCAAAAGGTCATGAGATATAGCGGCGTTTTAGACACAAACGCCGCAATAGGTC
* * * * * * *
1554544 TTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTT
66 TTGAGATTTAACGGCGTTTTTCCCACAAACACCGCAAAAGATGCTGAGATATAGCGGCGTTTTT
* * * ** * ***
1554608 CCCACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTC
1 ACAACAAACGCCGCAAAAGGTCATGAGATATAGCGGCGTTTTAGACACAAACGCCGCAATAGGTC
1554673 TTGAGATTTAACGGCGTTTTTCCCACAAACACCGCAAAAGAT-CT-AGTATATAGCGGCGTTTTT
66 TTGAGATTTAACGGCGTTTTTCCCACAAACACCGCAAAAGATGCTGAG-ATATAGCGGCG-TTTT
1554736 T
129 T
* * ** *
1554737 AGAACAAACGCTGCAAAAGGTCAT-ATCTATAGCGGCGTTTTAAGATACAAACGCCGC
1 ACAACAAACGCCGCAAAAGGTCATGAGATATAGCGGCGTTTT-AGACACAAACGCCGC
1554794 TAATTACCTC
Statistics
Matches: 155, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
127 2 0.01
128 25 0.16
129 128 0.83
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (129 bp):
ACAACAAACGCCGCAAAAGGTCATGAGATATAGCGGCGTTTTAGACACAAACGCCGCAATAGGTC
TTGAGATTTAACGGCGTTTTTCCCACAAACACCGCAAAAGATGCTGAGATATAGCGGCGTTTTT
Found at i:1554931 original size:21 final size:21
Alignment explanation
Indices: 1554905--1554963 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1554895 ATTTTCCAAT
* *
1554905 AAACTTTACATCCATAACAAC
1 AAACTTAAAATCCATAACAAC
*
1554926 AAACTTAAAATCCATAACAAG
1 AAACTTAAAATCCATAACAAC
** *
1554947 AAAAATGAAATCCATAA
1 AAACTTAAAATCCATAA
1554964 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.03, T:0.20
Consensus pattern (21 bp):
AAACTTAAAATCCATAACAAC
Found at i:1556370 original size:16 final size:16
Alignment explanation
Indices: 1556307--1556374 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
1556297 CAACCAACAG
1556307 TTCCAAACATCACAAT
1 TTCCAAACATCACAAT
*
1556323 TTCC--ATATCACAAT
1 TTCCAAACATCACAAT
*
1556337 TTACC--TCATC-CAACAT
1 TT-CCAAACATCAC-A-AT
1556353 TTCCAAACATCACAAT
1 TTCCAAACATCACAAT
1556369 TTCCAA
1 TTCCAA
1556375 CAGTTCCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
14 12 0.29
15 8 0.19
16 16 0.38
17 5 0.12
18 1 0.02
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
TTCCAAACATCACAAT
Found at i:1559223 original size:41 final size:41
Alignment explanation
Indices: 1559172--1559513 Score: 340
Period size: 41 Copynumber: 8.3 Consensus size: 41
1559162 TGTTTGTTCA
*
1559172 AAAAATGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
* * * ** *
1559213 AAAAATGCCACGAAAGTACTAGT-CTATAAAGGCGTTTGTTT
1 AAAAACGCCACTAAAGTAC-AGTACTTTAGCGGCGTTTGTAT
1559254 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
** * *
1559295 AAAAACGTAACAAAAGTACTAGT-CTATAGCGGCGTTTGT-T
1 AAAAACGCCACTAAAGTAC-AGTACTTTAGCGGCGTTTGTAT
* * *
1559335 CAAAAAACGCCACTAAAGTACTAATA-TATAGCGGCGTTTGTTTT
1 --AAAAACGCCACTAAAGTAC-AGTACTTTAGCGGCGTTTG-TAT
* ** * * *
1559379 GAAAACGCCACTAAAG-ATTGTATTTTGGCGGCGTTTGTAG
1 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1559419 AAAAACGCCACTAAAGTACAGT-CTTTAGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
* * *
1559459 AAAAGCGCCACAAAAGTATTAGTA-TTTAGCGGCGTTTGT-T
1 AAAAACGCCACTAAAGTA-CAGTACTTTAGCGGCGTTTGTAT
1559499 CAAAAAACGCCACTA
1 --AAAAACGCCACTA
1559514 GAAATGCCGC
Statistics
Matches: 249, Mismatches: 38, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
40 54 0.22
41 128 0.51
42 65 0.26
43 1 0.00
44 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
Found at i:1559286 original size:82 final size:83
Alignment explanation
Indices: 1559148--1559513 Score: 440
Period size: 82 Copynumber: 4.4 Consensus size: 83
1559138 TCTGTCATTC
* * *
1559148 CTAGTCTATAGCAGTGTTTGTTCAAAAAATGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
* *
1559213 AAAAATGCCACGAAAGTA
66 AAAAACGCCACAAAAGTA
** *
1559231 CTAGTCTATAAAGGCGTTTGTT-TAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
**
1559295 AAAAACGTAACAAAAGTA
66 AAAAACGCCACAAAAGTA
* *
1559313 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACTAATA-TATAGCGGCGTTTGTT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTAC-AGTACTTTAGCGGCGTTTG-T
* * *
1559377 TTGAAAACGCCACTAAAG-A
64 ATAAAAACGCCACAAAAGTA
* * * *
1559396 -TTGTATTTTGGCGGCGTTTG-T-AGAAAAACGCCACTAAAGTACAGT-CTTTAGCGGCGTTTGT
1 CTAGT-CTATAGCGGCGTTTGTTCA-AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGT
*
1559457 ATAAAAGCGCCACAAAAGTA
64 ATAAAAACGCCACAAAAGTA
* * *
1559477 TTAGTATTTAGCGGCGTTTGTTCAAAAAACGCCACTA
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTA
1559514 GAAATGCCGC
Statistics
Matches: 240, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
80 15 0.06
81 30 0.12
82 114 0.47
83 64 0.27
84 17 0.07
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (83 bp):
CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
AAAAACGCCACAAAAGTA
Found at i:1559425 original size:165 final size:164
Alignment explanation
Indices: 1559148--1559513 Score: 468
Period size: 165 Copynumber: 2.2 Consensus size: 164
1559138 TCTGTCATTC
* * * * *
1559148 CTAGTCTATAGCAGTGTTTGTTCAAAAAATGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAATACTATAGCGGCGTTTGTAT
* **
1559213 AAAAATGCCACGAAAGTACTAGTCTATAAAGGCGTTTGTTTAAAAACGCCACTAAAGTACAGTAC
66 AAAAACGCCACGAAAGTACTAGTCTATAAAGGCGTTTGTAGAAAAACGCCACTAAAGTACAGT-C
*
1559278 TTTAGCGGCGTTTGTATAAAAACGTAACAAAAGTA
130 TTTAGCGGCGTTTGTATAAAAACGCAACAAAAGTA
1559313 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACTAATA-TATAGCGGCGTTTGTT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTAC-AATACTATAGCGGCGTTTG-T
* * * * * * ***
1559377 TTGAAAACGCCACTAAAG-A-TTGTATTTTGGCGGCGTTTGTAGAAAAACGCCACTAAAGTACAG
64 ATAAAAACGCCACGAAAGTACTAGT-CTATAAAGGCGTTTGTAGAAAAACGCCACTAAAGTACAG
* *
1559440 TCTTTAGCGGCGTTTGTATAAAAGCGCCACAAAAGTA
128 TCTTTAGCGGCGTTTGTATAAAAACGCAACAAAAGTA
* * *
1559477 TTAGTATTTAGCGGCGTTTGTTCAAAAAACGCCACTA
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTA
1559514 GAAATGCCGC
Statistics
Matches: 175, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
164 70 0.40
165 87 0.50
166 18 0.10
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (164 bp):
CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAATACTATAGCGGCGTTTGTAT
AAAAACGCCACGAAAGTACTAGTCTATAAAGGCGTTTGTAGAAAAACGCCACTAAAGTACAGTCT
TTAGCGGCGTTTGTATAAAAACGCAACAAAAGTA
Found at i:1559789 original size:2 final size:2
Alignment explanation
Indices: 1559782--1559810 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1559772 CAATGGGATA
1559782 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 A
1559811 GATAGATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1559831 original size:24 final size:24
Alignment explanation
Indices: 1559802--1559850 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1559792 ATATATATAT
1559802 ATATATATAGATAGATAGATGGATGG
1 ATATAT-TA-ATAGATAGATGGATGG
* *
1559828 ATATATTAATGGATGGATGGATG
1 ATATATTAATAGATAGATGGATG
1559851 ATGCGAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 2 0.10
26 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.33
Consensus pattern (24 bp):
ATATATTAATAGATAGATGGATGG
Found at i:1561298 original size:22 final size:22
Alignment explanation
Indices: 1561272--1561317 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1561262 CTATAGTTGG
*
1561272 AAATTGATTT-TCTAATATGAAT
1 AAATT-ATTTATCTAATACGAAT
*
1561294 AAATTATTTATTTAATACGAAT
1 AAATTATTTATCTAATACGAAT
1561316 AA
1 AA
1561318 TTAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATTATTTATCTAATACGAAT
Found at i:1561326 original size:22 final size:22
Alignment explanation
Indices: 1561284--1561326 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1561274 ATTGATTTTC
* *
1561284 TAATATGAATAAATTATTTATT
1 TAATACGAATAAATTAATTATT
1561306 TAATACGAAT-AATTAAATTAT
1 TAATACGAATAAATT-AATTAT
1561327 ACAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
TAATACGAATAAATTAATTATT
Found at i:1564659 original size:31 final size:31
Alignment explanation
Indices: 1564621--1564683 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1564611 GGACCTATGT
*
1564621 AACTGTCCATATGTTTCGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
1564652 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
1564683 A
1 A
1564684 CCCTCGACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:1567023 original size:29 final size:29
Alignment explanation
Indices: 1566970--1567029 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
1566960 CTCATTTCTT
*
1566970 TTGTATTCTTCTTCTCCTTTAAAACTATA
1 TTGTATTCTTCTTCTCCATTAAAACTATA
* * * *
1566999 TTGTCTTCTTCTTCTTCATTCAAACTCTA
1 TTGTATTCTTCTTCTCCATTAAAACTATA
1567028 TT
1 TT
1567030 ATTTCCCTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.53
Consensus pattern (29 bp):
TTGTATTCTTCTTCTCCATTAAAACTATA
Found at i:1567766 original size:20 final size:20
Alignment explanation
Indices: 1567734--1567773 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1567724 ACTCATTCAA
1567734 TAAGTATCAATAC-TGTAGG
1 TAAGTATCAATACTTGTAGG
*
1567753 TAAGATATCGATACTTGTAGG
1 TAAG-TATCAATACTTGTAGG
1567774 ATGGTAACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAAGTATCAATACTTGTAGG
Found at i:1569602 original size:14 final size:14
Alignment explanation
Indices: 1569575--1569615 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1569565 GCTGGGCATC
1569575 CGACCGAGGCCATT
1 CGACCGAGGCCATT
* *
1569589 CGATCGAGGTCATT
1 CGACCGAGGCCATT
1569603 CGACCGAGGCCAT
1 CGACCGAGGCCAT
1569616 CCGAGAGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (14 bp):
CGACCGAGGCCATT
Found at i:1569619 original size:10 final size:10
Alignment explanation
Indices: 1569606--1569649 Score: 72
Period size: 10 Copynumber: 4.4 Consensus size: 10
1569596 GGTCATTCGA
1569606 CCGAGGCCAT
1 CCGAGGCCAT
1569616 CCGAGAG-CAT
1 CCGAG-GCCAT
1569626 CCGAGGCCAT
1 CCGAGGCCAT
1569636 CCGAGGCCAT
1 CCGAGGCCAT
1569646 CCGA
1 CCGA
1569650 ACGAGCTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 1 0.03
10 30 0.94
11 1 0.03
ACGTcount: A:0.23, C:0.39, G:0.30, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:1569675 original size:10 final size:10
Alignment explanation
Indices: 1569606--1569683 Score: 66
Period size: 10 Copynumber: 7.5 Consensus size: 10
1569596 GGTCATTCGA
*
1569606 CCGAGGCCAT
1 CCGAGGGCAT
*
1569616 CCGAGAGCAT
1 CCGAGGGCAT
*
1569626 CCGAGGCCAT
1 CCGAGGGCAT
*
1569636 CCGAGGCCAT
1 CCGAGGGCAT
*
1569646 CCGAACGAGCTAT
1 CCG-A-GGGC-AT
*
1569659 GCGAGGGCAT
1 CCGAGGGCAT
*
1569669 CCGAGGGCAA
1 CCGAGGGCAT
1569679 CCGAG
1 CCGAG
1569684 CGAGCTATGC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
10 44 0.80
11 4 0.07
12 3 0.05
13 4 0.07
ACGTcount: A:0.24, C:0.33, G:0.33, T:0.09
Consensus pattern (10 bp):
CCGAGGGCAT
Found at i:1569708 original size:33 final size:33
Alignment explanation
Indices: 1569634--1569720 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
1569624 ATCCGAGGCC
* * * * *
1569634 ATCCGAGGCCATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGAGA
1569667 ATCCGAGGGCAACCGAGCGAGCTATGCGAGAGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGAGA
1569700 ATCCGAGGG-AAGCCGAGCGAG
1 ATCCGAGGGCAA-CCGAGCGAG
1569721 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.28, C:0.26, G:0.37, T:0.09
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGAGA
Found at i:1569757 original size:29 final size:29
Alignment explanation
Indices: 1569724--1569808 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
1569714 GAGCGAGGGT
*
1569724 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
1569753 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
1569782 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
1569809 TGTGTTGGGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.20, C:0.31, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:1576165 original size:10 final size:10
Alignment explanation
Indices: 1576146--1576179 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1576136 TTCACCACAC
1576146 CAAATCCTCT
1 CAAATCCTCT
*
1576156 CAAATTCTCT
1 CAAATCCTCT
1576166 CAAATCCTCT
1 CAAATCCTCT
1576176 CAAA
1 CAAA
1576180 AACCAAACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:1576245 original size:28 final size:30
Alignment explanation
Indices: 1576214--1576281 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
1576204 TTATAATGTA
*
1576214 TATTTTATT-A-TATTTAATATTTTGTTAG
1 TATTTTATTAATTATTTAATATTTTATTAG
* *
1576242 TATTTTATTTAATTATTTAATTTTTTATTAT
1 TATTTTA-TTAATTATTTAATATTTTATTAG
1576273 TATTTTATT
1 TATTTTATT
1576282 TAAATATGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.21
29 2 0.06
30 3 0.09
31 22 0.65
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (30 bp):
TATTTTATTAATTATTTAATATTTTATTAG
Found at i:1576264 original size:18 final size:16
Alignment explanation
Indices: 1576242--1576284 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1576232 ATTTTGTTAG
1576242 TATTTTATTTAATTATT
1 TATTTTATTTAATTA-T
*
1576259 TAATTT-TTT-ATTAT
1 TATTTTATTTAATTAT
1576273 TATTTTATTTAA
1 TATTTTATTTAA
1576285 ATATGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 4 0.18
17 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTATTTAATTAT
Found at i:1576298 original size:31 final size:31
Alignment explanation
Indices: 1576223--1576288 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1576213 ATATTTTATT
* *
1576223 ATATTTAATATTTTGTTAGTATTTTATTTAA
1 ATATTTAATTTTTTATTAGTATTTTATTTAA
* *
1576254 TTATTTAATTTTTTATTATTATTTTATTTAA
1 ATATTTAATTTTTTATTAGTATTTTATTTAA
1576285 ATAT
1 ATAT
1576289 GTTTTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (31 bp):
ATATTTAATTTTTTATTAGTATTTTATTTAA
Found at i:1580429 original size:14 final size:15
Alignment explanation
Indices: 1580398--1580431 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1580388 TTTCTTGCTA
1580398 ATATTTTATCAAATT
1 ATATTTTATCAAATT
*
1580413 ATATTTTAT-ATATT
1 ATATTTTATCAAATT
1580427 ATATT
1 ATATT
1580432 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTTATCAAATT
Found at i:1583067 original size:3 final size:3
Alignment explanation
Indices: 1583059--1583151 Score: 186
Period size: 3 Copynumber: 31.0 Consensus size: 3
1583049 TTAATTGTCC
1583059 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1583107 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1583152 GTAAAAGCAT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1583748 original size:8 final size:8
Alignment explanation
Indices: 1583735--1583785 Score: 81
Period size: 8 Copynumber: 6.8 Consensus size: 8
1583725 TGTTAGTATT
1583735 TTATTTAA
1 TTATTTAA
1583743 TTATTTAA
1 TTATTTAA
1583751 TTATTTAA
1 TTATTTAA
1583759 TTATTTAA
1 TTATTTAA
1583767 TTA-TT--
1 TTATTTAA
1583772 TTATTTAA
1 TTATTTAA
1583780 TTATTT
1 TTATTT
1583786 TGTTTTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 2 0.05
8 33 0.82
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATTTAA
Found at i:1583777 original size:13 final size:13
Alignment explanation
Indices: 1583731--1583786 Score: 71
Period size: 12 Copynumber: 4.5 Consensus size: 13
1583721 ATTTTGTTAG
1583731 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
1583744 TA-TTTAATTATT
1 TATTTTATTTAAT
*
1583756 TA-ATTATTTAAT
1 TATTTTATTTAAT
1583768 TATTTTATTTAAT
1 TATTTTATTTAAT
1583781 TATTTT
1 TATTTT
1583787 GTTTTTTTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
12 19 0.53
13 17 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:1583794 original size:21 final size:21
Alignment explanation
Indices: 1583743--1583786 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1583733 TTTTATTTAA
1583743 TTATTTAATTATTTAATTA-T
1 TTATTTAATTATTTAATTATT
* *
1583763 TTAATTATTTTATTTAATTATT
1 TTATTTA-ATTATTTAATTATT
1583785 TT
1 TT
1583787 GTTTTTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 11 0.55
22 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTAATTATTTAATTATT
Found at i:1584063 original size:8 final size:8
Alignment explanation
Indices: 1584061--1584095 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
1584051 AAAATAATTA
1584061 AATAAAAT
1 AATAAAAT
1584069 AATAAAAT
1 AATAAAAT
1584077 AATAAAAT
1 AATAAAAT
1584085 AATAAAAT
1 AATAAAAT
1584093 AAT
1 AAT
1584096 TAATACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AATAAAAT
Found at i:1584065 original size:13 final size:13
Alignment explanation
Indices: 1584047--1584098 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
1584037 AACTGTAAAA
1584047 AAATAAAATAATT
1 AAATAAAATAATT
*
1584060 AAATAAAATAATA
1 AAATAAAATAATT
1584073 AAATAATAA-AA-T
1 AAATAA-AATAATT
1584085 -AATAAAATAATT
1 AAATAAAATAATT
1584097 AA
1 AA
1584099 TACAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 7 0.21
12 1 0.03
13 21 0.64
14 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:1584066 original size:21 final size:21
Alignment explanation
Indices: 1584042--1584094 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1584032 TTTATAACTG
*
1584042 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAATAATAAAA
*
1584063 TAAAATAATAAAATAATAAAA
1 TAAAAAAATAAAATAATAAAA
*
1584084 TAATAAAATAA
1 TAAAAAAATAA
1584095 TTAATACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAAAATAAAATAATAAAA
Found at i:1588338 original size:21 final size:22
Alignment explanation
Indices: 1588314--1588354 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1588304 TGGTGTGGGG
1588314 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
*
1588335 ATGTTTTTGGTATTTTTATT
1 ATGTTTTTAGTATTTTTATT
1588355 TAATTTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:1589371 original size:55 final size:55
Alignment explanation
Indices: 1589301--1589411 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
1589291 CTCTAAAATG
1589301 AGATGAAAGTTATATTGTTATCTCCTTTTTACATTTATGTTTTAAAATTAAATTA
1 AGATGAAAGTTATATTGTTATCTCCTTTTTACATTTATGTTTTAAAATTAAATTA
*
1589356 AGATGAAAGTTATATTGTTATCTCCTTTTTACATTTATGTTTTAACATTAAATTA
1 AGATGAAAGTTATATTGTTATCTCCTTTTTACATTTATGTTTTAAAATTAAATTA
1589411 A
1 A
1589412 TTACATCTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (55 bp):
AGATGAAAGTTATATTGTTATCTCCTTTTTACATTTATGTTTTAAAATTAAATTA
Found at i:1594310 original size:36 final size:37
Alignment explanation
Indices: 1594263--1594350 Score: 133
Period size: 41 Copynumber: 2.3 Consensus size: 37
1594253 TTTTCCCAAT
1594263 TCGCAATGCGAATAAGTAAAT-CGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATACGCGAATTGGGAAAA
1594299 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAAT----ACGCGAATTGGGAAAA
1594340 TCGCAATGCGA
1 TCGCAATGCGA
1594351 TACTGACTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
36 21 0.45
41 26 0.55
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (37 bp):
TCGCAATGCGAATAAGTAAATACGCGAATTGGGAAAA
Found at i:1594311 original size:21 final size:21
Alignment explanation
Indices: 1594285--1594350 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
1594275 TAAGTAAATC
1594285 GCGAATTGGGAAAATCGCAAT
1 GCGAATTGGGAAAATCGCAAT
** * *
1594306 GCGAA-TAAGTAAATCGCAAC
1 GCGAATTGGGAAAATCGCAAT
1594326 GCGAATTGGGAAAATCGCAAT
1 GCGAATTGGGAAAATCGCAAT
1594347 GCGA
1 GCGA
1594351 TACTGACTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTGGGAAAATCGCAAT
Found at i:1594363 original size:41 final size:41
Alignment explanation
Indices: 1594284--1594411 Score: 118
Period size: 41 Copynumber: 3.1 Consensus size: 41
1594274 ATAAGTAAAT
* *
1594284 CGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-AATCGCAA
1 CGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACTATCGCAA
1594325 CGCGAATTGGGAAAATCGCAATGCGATACTGACTATCGCAA
1 CGCGAATTGGGAAAATCGCAATGCGATACTGACTATCGCAA
* * ** * * * *
1594366 TGCGATAAT-AAAAAATCGCAACGAGATACTTACTTTCGCAA
1 CGCGA-ATTGGGAAAATCGCAATGCGATACTGACTATCGCAA
1594407 CGCGA
1 CGCGA
1594412 TACTGACTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.05
41 67 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (41 bp):
CGCGAATTGGGAAAATCGCAATGCGATACTGACTATCGCAA
Found at i:1594364 original size:20 final size:20
Alignment explanation
Indices: 1594339--1594433 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1594329 AATTGGGAAA
*
1594339 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1594359 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1594380 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1594400 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1594420 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1594434 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1594649 original size:22 final size:22
Alignment explanation
Indices: 1594621--1594664 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1594611 CACTCTCTCA
1594621 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1594643 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1594665 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1594953 original size:20 final size:20
Alignment explanation
Indices: 1594928--1594965 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1594918 TGATTCTCTC
1594928 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1594948 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1594966 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1596306 original size:18 final size:18
Alignment explanation
Indices: 1596285--1596329 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1596275 TCCACTTCAG
*
1596285 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1596303 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1596321 GAGCCATCA
1 GAGCCATCA
1596330 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1596850 original size:19 final size:20
Alignment explanation
Indices: 1596796--1596862 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1596786 TAATTTACTT
* *
1596796 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1596816 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1596836 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1596855 TCGCAACG
1 TCGCAACG
1596863 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1596889 original size:18 final size:18
Alignment explanation
Indices: 1596835--1596929 Score: 107
Period size: 18 Copynumber: 5.7 Consensus size: 18
1596825 GGAAATGGCT
1596835 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
1596854 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
1596868 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
1596886 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
1596904 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
1596918 ATCGCAATGCGA
1 ATCGCAATGCGA
1596930 TTTGTGTTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
14 18 0.27
16 11 0.16
17 4 0.06
18 27 0.40
19 7 0.10
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:1596960 original size:14 final size:14
Alignment explanation
Indices: 1596941--1596998 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1596931 TTGTGTTTCG
1596941 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1596955 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1596971 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1596987 CGTTGCGATTTT
1 CGTTGCGATTTT
1596999 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1596975 original size:32 final size:33
Alignment explanation
Indices: 1596936--1597014 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1596926 GCGATTTGTG
1596936 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1596968 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1597001 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1597015 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1597013 original size:19 final size:19
Alignment explanation
Indices: 1596955--1597072 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
1596945 GCGATTTTGT
1596955 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1596973 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1596987 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1597006 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1597026 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1597045 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1597065 TGTTGCGA
1 CGTTGCGA
1597073 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1598923 original size:42 final size:41
Alignment explanation
Indices: 1598838--1598960 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 41
1598828 GTGAATCGGG
* * * * *
1598838 CTCTTGAATGGTGGGAGG-GACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGTGA-CTC-TCGAGGATGATAGGGGC
1598880 CTCTTGAACGGTGGGAGGTGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGTGACTCTCGAGG-ATGATAGGGGC
* * * *
1598922 CTCTTCAACGATAGGA-GTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGT-GACTCTCGA-GGATGATAGG
1598961 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 6 0.09
42 58 0.85
43 4 0.06
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGTGACTCTCGAGGATGATAGGGGC
Found at i:1600951 original size:33 final size:33
Alignment explanation
Indices: 1600894--1600980 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
1600884 ACGAGATAAT
*
1600894 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1600928 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
1600961 GACAATCGCAACCGCGAAAT
1 GAGAATCGCAA-CGCGAAAT
1600981 AAAAATCGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
33 27 0.55
34 22 0.45
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1600997 original size:19 final size:19
Alignment explanation
Indices: 1600869--1601034 Score: 136
Period size: 19 Copynumber: 9.1 Consensus size: 19
1600859 TCTTTTGGTT
*
1600869 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1600888 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1600908 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1600926 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1600942 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1600960 ---A-GACAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1600976 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1600995 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1601014 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1601033 GA
1 GA
1601035 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 18 0.15
15 3 0.03
16 3 0.03
17 1 0.01
18 3 0.03
19 53 0.45
20 36 0.30
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1601063 original size:19 final size:19
Alignment explanation
Indices: 1601030--1601096 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1601020 AAAATCGCAA
**
1601030 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1601049 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1601068 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1601088 TGCGATTTT
1 TGCGATTTT
1601097 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1601683 original size:21 final size:21
Alignment explanation
Indices: 1601650--1601750 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
1601640 TGCGAAAGTA
* * *
1601650 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
1601671 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
1601691 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
1601713 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
1601734 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
1601751 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:1601706 original size:20 final size:20
Alignment explanation
Indices: 1601613--1601706 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1601603 CGCTATGTAA
*
1601613 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
1601633 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1601653 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1601674 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1601694 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1601707 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1601725 original size:41 final size:41
Alignment explanation
Indices: 1601634--1601768 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1601624 AAAGTCAGTA
* * * ** *
1601634 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1601674 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1601716 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1601757 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1601769 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1601739 original size:20 final size:20
Alignment explanation
Indices: 1601714--1601780 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1601704 GATTTTCCCA
1601714 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
1601734 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
1601755 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
1601775 ATTCGC
1 ATTCGC
1601781 ATTGTGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:1601760 original size:21 final size:21
Alignment explanation
Indices: 1601695--1601770 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1601685 ATAGTCAGTA
1601695 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1601716 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1601736 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
1601757 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
1601771 ACTTATTCGC
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:1601769 original size:41 final size:41
Alignment explanation
Indices: 1601695--1601784 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
1601685 ATAGTCAGTA
1601695 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1601736 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1601777 TCGCATTG
1 TCGCATTG
1601785 TGAATTGGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1602981 original size:15 final size:15
Alignment explanation
Indices: 1602920--1603000 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
1602910 TTATTTTATG
1602920 TATATATATATAATAT
1 TATATATATATAAT-T
* *
1602936 TA-ATAAATTTAATT
1 TATATATATATAATT
* * *
1602950 TAAAT-TA-AAAATA
1 TATATATATATAATT
1602963 TATATATA-AT-ATT
1 TATATATATATAATT
1602976 TATATAT-T-TAATT
1 TATATATATATAATT
*
1602989 TAAATATATATA
1 TATATATATATA
1603001 CCCGGCCCGA
Statistics
Matches: 49, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
12 1 0.02
13 25 0.51
14 8 0.16
15 13 0.27
16 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:1607446 original size:2 final size:2
Alignment explanation
Indices: 1607439--1607472 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1607429 ACTTTGCCAT
* *
1607439 TC TC TC TC TC TT TC TC TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1607473 CATTCAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:1607455 original size:12 final size:12
Alignment explanation
Indices: 1607438--1607472 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1607428 CACTTTGCCA
1607438 TTCTCTCTCTCT
1 TTCTCTCTCTCT
1607450 TTCTCTCTCTCT
1 TTCTCTCTCTCT
1607462 TTCTCTCTCTC
1 TTCTCTCTCTC
1607473 CATTCAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (12 bp):
TTCTCTCTCTCT
Found at i:1608979 original size:42 final size:42
Alignment explanation
Indices: 1608912--1608994 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1608902 ATTCATCAAC
*
1608912 ATTGCATCAGTGACTCGTTACGTTTGGAAACAAAAGGTTGTA
1 ATTGCATCAGTGACTCGTTAAGTTTGGAAACAAAAGGTTGTA
1608954 ATTGCATCAGTGAC-CTGTTAAGTTTGGAAACAAAAGGTTGT
1 ATTGCATCAGTGACTC-GTTAAGTTTGGAAACAAAAGGTTGT
1608995 TACAGTTACT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (42 bp):
ATTGCATCAGTGACTCGTTAAGTTTGGAAACAAAAGGTTGTA
Found at i:1615192 original size:27 final size:26
Alignment explanation
Indices: 1615145--1615198 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
1615135 AATTTCGGGT
*
1615145 TCGGGTTGAGTCGATTTTTTTAAGTG
1 TCGGGTTGAGTCGAGTTTTTTAAGTG
*
1615171 TCGGGTTCGGGTCGAGTTTTTTAAGTG
1 TCGGGTT-GAGTCGAGTTTTTTAAGTG
1615198 T
1 T
1615199 GATAATCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.13, C:0.09, G:0.33, T:0.44
Consensus pattern (26 bp):
TCGGGTTGAGTCGAGTTTTTTAAGTG
Found at i:1615821 original size:18 final size:17
Alignment explanation
Indices: 1615772--1615824 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
1615762 TCAGATTCAG
1615772 ATTCCAATTCCT-ACAA
1 ATTCCAATTCCTCACAA
* *
1615788 ATTCAAATTCCTTCACAT
1 ATTCCAATTCC-TCACAA
1615806 ATTCCAATTCGCTCACAA
1 ATTCCAATTC-CTCACAA
1615824 A
1 A
1615825 CATTCCAGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 10 0.33
17 1 0.03
18 18 0.60
19 1 0.03
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (17 bp):
ATTCCAATTCCTCACAA
Found at i:1619056 original size:20 final size:21
Alignment explanation
Indices: 1619033--1619086 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
1619023 TCTACAATAT
1619033 AATAGAAAGTTCTAAAACA-C
1 AATAGAAAGTTCTAAAACATC
* *
1619053 AATA-AAAATGTCTAGAACATC
1 AATAGAAAGT-TCTAAAACATC
*
1619074 -ATGGAAAGTTCTA
1 AATAGAAAGTTCTA
1619087 GAATATTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.15
20 18 0.67
21 5 0.19
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (21 bp):
AATAGAAAGTTCTAAAACATC
Found at i:1619143 original size:20 final size:20
Alignment explanation
Indices: 1619118--1619155 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1619108 ATTACTCTAA
*
1619118 AATGTTCTAGAACTTCATGG
1 AATGTTCTAAAACTTCATGG
1619138 AATGTTCTAAAACTTCAT
1 AATGTTCTAAAACTTCAT
1619156 AAAAGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
AATGTTCTAAAACTTCATGG
Found at i:1623191 original size:16 final size:17
Alignment explanation
Indices: 1623157--1623196 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1623147 TTATATGAAA
*
1623157 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
1623174 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
1623190 TGATATG
1 TGATATG
1623197 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:1623792 original size:23 final size:23
Alignment explanation
Indices: 1623758--1623844 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
1623748 ACATATTATA
1623758 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1623781 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
1623804 CGGTC-CTTCGG-GACAAAATTCTAGG
1 TGG-CACTACGGTG-C--AATTCTACG
1623829 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
1623845 AATTTATATG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.63
24 2 0.04
25 15 0.29
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1629208 original size:16 final size:17
Alignment explanation
Indices: 1629174--1629213 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1629164 TTATATGAAA
*
1629174 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
1629191 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
1629207 TGATATG
1 TGATATG
1629214 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:1629813 original size:23 final size:23
Alignment explanation
Indices: 1629779--1629865 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
1629769 ACATATTATA
1629779 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1629802 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
1629825 CGGTC-CTTCGG-GACAAAATTCTAGG
1 TGG-CACTACGGTG-C--AATTCTACG
1629850 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
1629866 AATTTATATG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.63
24 2 0.04
25 15 0.29
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1634241 original size:14 final size:16
Alignment explanation
Indices: 1634222--1634260 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1634212 CGTTCATTTA
1634222 ATAAAT-AA-ACAAAC
1 ATAAATGAACACAAAC
*
1634236 ATAAATGAACACGAAC
1 ATAAATGAACACAAAC
1634252 ATAAATGAA
1 ATAAATGAA
1634261 TAAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 2 0.09
16 14 0.64
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (16 bp):
ATAAATGAACACAAAC
Found at i:1634352 original size:16 final size:16
Alignment explanation
Indices: 1634329--1634389 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
1634319 TAATAAATAA
1634329 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1634345 AAGAACATAAACGAAC
1 ACGAACATAAACGAAC
**
1634361 ACGAACATAAATAAAC
1 ACGAACATAAACGAAC
1634377 ACGAACATAAACG
1 ACGAACATAAACG
1634390 TTAGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1634757 original size:14 final size:14
Alignment explanation
Indices: 1634749--1634809 Score: 122
Period size: 14 Copynumber: 4.4 Consensus size: 14
1634739 AAACATAAAT
1634749 GAACGAACATAACC
1 GAACGAACATAACC
1634763 GAACGAACATAACC
1 GAACGAACATAACC
1634777 GAACGAACATAACC
1 GAACGAACATAACC
1634791 GAACGAACATAACC
1 GAACGAACATAACC
1634805 GAACG
1 GAACG
1634810 TTCACGAACG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 47 1.00
ACGTcount: A:0.49, C:0.28, G:0.16, T:0.07
Consensus pattern (14 bp):
GAACGAACATAACC
Found at i:1634780 original size:28 final size:28
Alignment explanation
Indices: 1634740--1634809 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
1634730 GATTGAGTTA
**
1634740 AACATAAATGAACGAACATAACCGAACG
1 AACATAACCGAACGAACATAACCGAACG
1634768 AACATAACCGAACGAACATAACCGAACG
1 AACATAACCGAACGAACATAACCGAACG
1634796 AACATAACCGAACG
1 AACATAACCGAACG
1634810 TTCACGAACG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.51, C:0.26, G:0.14, T:0.09
Consensus pattern (28 bp):
AACATAACCGAACGAACATAACCGAACG
Found at i:1640237 original size:15 final size:16
Alignment explanation
Indices: 1640209--1640240 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1640199 AAAATCTTTC
1640209 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
1640225 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
1640240 T
1 T
1640241 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:1641015 original size:16 final size:16
Alignment explanation
Indices: 1640991--1641024 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1640981 TATCGCCGAC
*
1640991 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1641007 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1641023 CG
1 CG
1641025 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1648947 original size:39 final size:39
Alignment explanation
Indices: 1648903--1649019 Score: 180
Period size: 39 Copynumber: 3.0 Consensus size: 39
1648893 AAAATAAAAG
1648903 GATAGAGTTATAGTTAATCTAAACTACTAAATCAAATAA
1 GATAGAGTTATAGTTAATCTAAACTACTAAATCAAATAA
* * * *
1648942 GATAGAGTTACAGTTAACCTAAAATACTAAATCAAATAG
1 GATAGAGTTATAGTTAATCTAAACTACTAAATCAAATAA
* *
1648981 GATAGAATTCTAGTTAATCTAAACTACTAAATCAAATAA
1 GATAGAGTTATAGTTAATCTAAACTACTAAATCAAATAA
1649020 TTTAATGCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (39 bp):
GATAGAGTTATAGTTAATCTAAACTACTAAATCAAATAA
Found at i:1652795 original size:2 final size:2
Alignment explanation
Indices: 1652788--1652818 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1652778 AAATATAAAT
1652788 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 T
1652819 GAAAAGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1655260 original size:29 final size:29
Alignment explanation
Indices: 1655227--1655287 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
1655217 TTTCCCTTGA
* **
1655227 ATCTAA-CCTGTCCCGTTTTCAAACCATAT
1 ATCTAATCCTGACCCGTTTGAAAACCA-AT
1655256 ATCTAATCCTGACCCGTTTGAAAACCAAT
1 ATCTAATCCTGACCCGTTTGAAAACCAAT
1655285 ATC
1 ATC
1655288 GTTTCCGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (29 bp):
ATCTAATCCTGACCCGTTTGAAAACCAAT
Found at i:1663108 original size:87 final size:87
Alignment explanation
Indices: 1662960--1663122 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
1662950 TATGTTATAT
* * *
1662960 TATTTAACTGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
1 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATATAATAGAT
1663025 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
1663047 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
1 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATATAATAGAT
1663112 AGCGCTTATAT
66 AGCGCTTATAT
1663123 TGACCTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATATAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:1663121 original size:21 final size:23
Alignment explanation
Indices: 1663075--1663122 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1663065 ATCAAGTACA
*
1663075 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
1663098 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1663121 AT
1 AT
1663123 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1663570 original size:182 final size:182
Alignment explanation
Indices: 1663258--1664100 Score: 1427
Period size: 182 Copynumber: 4.6 Consensus size: 182
1663248 TGCATTCACC
** * * *
1663258 TTTTGTCATTTATAGACCGATTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1663323 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
* *
1663387 ATACTTATAATAAATTATCGACACTTTCAACATATCTGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
1663440 TTTTGTCATTTCAAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTTTGGATCGATACATT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
* * * *
1663505 ATTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTTTTTTAAATTCTAAAATTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* *
1663570 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCAG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * *
1663622 TTTTGTCATTTCGAGACTGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
* *
1663687 TTTATAAAGTTTCGACACTTTATTGGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
1663752 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
1663804 TTTTGTCATTTCGAGACCGCTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACGTT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
*
1663869 TTTATAAAATATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
1663934 TACTTATAATAAATTATCGACACTTTCAACATAACCAGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
1663986 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
*
1664051 TTTATAAAGTATCGACATTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
1664101 AAAGGTAAAA
Statistics
Matches: 619, Mismatches: 41, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
181 2 0.00
182 617 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:1665750 original size:194 final size:191
Alignment explanation
Indices: 1665421--1665787 Score: 587
Period size: 194 Copynumber: 1.9 Consensus size: 191
1665411 ATACTTATGG
* *
1665421 GACACAAAATTAAAAAGTGTCGATACATATATTACACTTATTCTATATAAATCTGATACTTATAC
1 GACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTATATAAATCGGATACTTATAC
*
1665486 CGGTTAGATTGAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGATCGACACCTT
66 CGGTTAGATTGAAAATTACC--TTACA-TATACATATGGGTTTCGATGTTTCTGATCGACACCTT
1665551 TTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAATAGTATC
128 TTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAATAGTATC
*
1665615 GACACAAAATTTAAAAGTGTCGATACATATATTACACCTATTCT-TCATAAATCCGGTATACTTA
1 GACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTAT-ATAAAT-CGG-ATACTTA
*
1665679 TACTGGTTAGATTGAAAAATTACC-TAC-TATACATATGGGTTTCGATGTTTCTGGGATCGACAC
63 TACCGGTTAGATTG-AAAATTACCTTACATATACATATGGGTTTCGATGTTTCT--GATCGACAC
1665742 CTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
125 CTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
1665788 ATTGTACTAC
Statistics
Matches: 162, Mismatches: 5, Indels: 12
0.91 0.03 0.07
Matches are distributed among these distances:
192 24 0.15
193 1 0.01
194 106 0.65
195 2 0.01
196 20 0.12
197 9 0.06
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (191 bp):
GACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTATATAAATCGGATACTTATAC
CGGTTAGATTGAAAATTACCTTACATATACATATGGGTTTCGATGTTTCTGATCGACACCTTTTA
TATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAATAGTATC
Found at i:1665977 original size:19 final size:19
Alignment explanation
Indices: 1665953--1666001 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1665943 TTACATTCAC
1665953 ATACAAAATTATAAATCGT-
1 ATACAAAATTATAAATC-TA
1665972 ATACAAAATTATAAATCTA
1 ATACAAAATTATAAATCTA
1665991 ATACAAAATTA
1 ATACAAAATTA
1666002 ACCCTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCTA
Found at i:1668109 original size:15 final size:15
Alignment explanation
Indices: 1668089--1668121 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1668079 ACTCTGTTTT
*
1668089 CCCTCACCGTCGTCC
1 CCCTCACCGTCATCC
1668104 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
1668119 CCC
1 CCC
1668122 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.64, G:0.09, T:0.18
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:1670603 original size:181 final size:180
Alignment explanation
Indices: 1670242--1670715 Score: 628
Period size: 182 Copynumber: 2.6 Consensus size: 180
1670232 CGTACTTACG
* * * * *
1670242 AAAGTATCGACACTTTTAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATGTCCGTTT
1 AAAGTATCGACACTTTAAATATATCAGGTACCGTTTTACCGGTTTTATCA-TTTGAT-ACCGTTT
* *
1670307 TATTATATTTTTACCTGTTATATCGTTGTTTGATCGATACATTTTTTTAAAGTATCGACACTTTA
64 TATCATATTTTTACCTGTTATATCGTTG-TTGATCGATACATTTTTTGAAAGTATCGACACTTTA
* * * *
1670372 TAGACGTTAAAACTGCTTCTCTTTTAAATTCACAATGTGTCGATCCTTATA-T
128 TAGACGCTAAAAATGCTTCTCTTTTAAATTAACAATGTGTCAATCCTTATATT
* * * *
1670424 AAAGTTTCGACACTTTCAATATATCAGGTAGCGTTTTACCGGTTTCATCACTTTGATACCAGTTT
1 AAAGTATCGACACTTTAAATATATCAGGTACCGTTTTACCGGTTTTATCA-TTTGATACC-GTTT
*
1670489 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCGACACTTTAT
64 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTAT
*
1670554 AGGCGCTAAAAATGCTTCTCTTTTAAATTAACGAA-GTGTCAATCCTTATATT
129 AGACGCTAAAAATGCTTCTCTTTTAAATTAAC-AATGTGTCAATCCTTATATT
* ** * * *
1670606 AAAGTACCGACACTTTAAATATATTTGGTACCGCTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCAGGTACCGTTTTACCGGTTTTATCATTT-GATAC-CGTTT
* * *
1670671 TGTCATAGTTTTACATGTTATATCGTTGTTGATCGATACATTTTT
64 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTT
1670716 AAATTGGATC
Statistics
Matches: 257, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
181 82 0.32
182 175 0.68
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCAGGTACCGTTTTACCGGTTTTATCATTTGATACCGTTTTA
TCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTATAG
ACGCTAAAAATGCTTCTCTTTTAAATTAACAATGTGTCAATCCTTATATT
Found at i:1671533 original size:15 final size:15
Alignment explanation
Indices: 1671513--1671542 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1671503 TGAACTATTC
1671513 TTTCACTTCAATCAA
1 TTTCACTTCAATCAA
1671528 TTTCACTTCAATCAA
1 TTTCACTTCAATCAA
1671543 GCTCGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTCACTTCAATCAA
Found at i:1673403 original size:18 final size:19
Alignment explanation
Indices: 1673382--1673420 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1673372 AAATTTTAAA
*
1673382 TTATCATATATTTTT-TAT
1 TTATAATATATTTTTATAT
*
1673400 TTATAATTTATTTTTATAT
1 TTATAATATATTTTTATAT
1673419 TT
1 TT
1673421 TTATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATAATATATTTTTATAT
Found at i:1679299 original size:24 final size:25
Alignment explanation
Indices: 1679262--1679308 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1679252 TATTATTTTA
1679262 AAAAATGATTATGA-CTTTAATTTG
1 AAAAATGATTATGATCTTTAATTTG
*
1679286 AAAAAT-ATTGATGATTTTTAATT
1 AAAAATGATT-ATGATCTTTAATT
1679309 GATTTGGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 10 0.50
25 7 0.35
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (25 bp):
AAAAATGATTATGATCTTTAATTTG
Found at i:1680194 original size:30 final size:30
Alignment explanation
Indices: 1680160--1680289 Score: 147
Period size: 30 Copynumber: 4.3 Consensus size: 30
1680150 ATACATAAAG
* *
1680160 TTAAAGGA-TCAAAATAACAAATATAGAAAC
1 TTAAAGGACT-AAAATAACAAAAACAGAAAC
* * *
1680190 TTAAAGGACTAAAATAGCTAAAACAGAAAA
1 TTAAAGGACTAAAATAACAAAAACAGAAAC
*
1680220 TTAAAGGACTAAAATAACAAAAATAGAAAC
1 TTAAAGGACTAAAATAACAAAAACAGAAAC
* *
1680250 TTGAAGGACCAAAATAGA-AAAAACAGAAAC
1 TTAAAGGACTAAAATA-ACAAAAACAGAAAC
*
1680280 TGAAAGGACT
1 TTAAAGGACT
1680290 GAACTATAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
30 81 0.98
31 2 0.02
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (30 bp):
TTAAAGGACTAAAATAACAAAAACAGAAAC
Found at i:1680234 original size:60 final size:61
Alignment explanation
Indices: 1680160--1680289 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 61
1680150 ATACATAAAG
* * **
1680160 TTAAAGGA-TCAAAATAACAAATATAGAAACTTAAAGGACTAAAATAGCTAAAACAGAAAA
1 TTAAAGGACTCAAAATAACAAAAATAGAAACTTAAAGGACCAAAATAGAAAAAACAGAAAA
* *
1680220 TTAAAGGACT-AAAATAACAAAAATAGAAACTTGAAGGACCAAAATAGAAAAAACAGAAAC
1 TTAAAGGACTCAAAATAACAAAAATAGAAACTTAAAGGACCAAAATAGAAAAAACAGAAAA
*
1680280 TGAAAGGACT
1 TTAAAGGACT
1680290 GAACTATAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 61 0.98
61 1 0.02
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (61 bp):
TTAAAGGACTCAAAATAACAAAAATAGAAACTTAAAGGACCAAAATAGAAAAAACAGAAAA
Found at i:1684360 original size:42 final size:42
Alignment explanation
Indices: 1684313--1684393 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 42
1684303 AACCTCACCG
*
1684313 ACATTAATA-TCCTCTTTATCAG-CATGTACATTTGGACCATCA
1 ACATTAATACT-CTCTTTACCAGTC-TGTACATTTGGACCATCA
1684355 ACATTAATACTCTCTTTACCAGTCTGTACATTTGGACCA
1 ACATTAATACTCTCTTTACCAGTCTGTACATTTGGACCA
1684394 CCAAATCATC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.36
Consensus pattern (42 bp):
ACATTAATACTCTCTTTACCAGTCTGTACATTTGGACCATCA
Found at i:1684454 original size:24 final size:24
Alignment explanation
Indices: 1684412--1684461 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1684402 TCAGTTAGCC
* *
1684412 CACCATCAATTGACTCATTAACAT
1 CACCATCAACTGACCCATTAACAT
* *
1684436 CACCATCAACTGGCCCATTATCAT
1 CACCATCAACTGACCCATTAACAT
1684460 CA
1 CA
1684462 TCAAGATCGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (24 bp):
CACCATCAACTGACCCATTAACAT
Found at i:1686503 original size:22 final size:20
Alignment explanation
Indices: 1686457--1686507 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
1686447 TTTTAAATAG
1686457 TTTTTAAAAGTTATTTTATA
1 TTTTTAAAAGTTATTTTATA
* *
1686477 ATTTTAATAGTTTATATTTATA
1 TTTTTAAAAG-TTAT-TTTATA
1686499 TTTTTAAAA
1 TTTTTAAAA
1686508 AATATCAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 4 0.16
22 13 0.52
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTTAAAAGTTATTTTATA
Found at i:1694818 original size:20 final size:20
Alignment explanation
Indices: 1694795--1694833 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1694785 TTAATATATT
1694795 TATGAGT-AATTTATTAAGTA
1 TATGAGTCAATTT-TTAAGTA
*
1694815 TATGATTCAATTTTTAAGT
1 TATGAGTCAATTTTTAAGT
1694834 GAAGGTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (20 bp):
TATGAGTCAATTTTTAAGTA
Found at i:1697323 original size:30 final size:28
Alignment explanation
Indices: 1697273--1697382 Score: 80
Period size: 29 Copynumber: 3.7 Consensus size: 28
1697263 TCCTTTAATT
1697273 TAAGGACTAAGGTGGTAAAAATATAACATCA
1 TAAGGACTAA-GT-GTAAAAATATAACAT-A
* * *
1697304 TAAGGACCTAAGTGTAAAAAATCTAACGTT
1 TAAGGA-CTAAGTGT-AAAAATATAACATA
*
1697334 TAGGGACCTAAGTGTAAAAA-ACTAA-ATTA
1 TAAGGA-CTAAGTGTAAAAATA-TAACA-TA
*
1697363 TAGGGACTAAAGTGTAAAAA
1 TAAGGACT-AAGTGTAAAAA
1697383 CCTAAAGTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.03
29 26 0.39
30 16 0.24
31 19 0.28
32 4 0.06
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (28 bp):
TAAGGACTAAGTGTAAAAATATAACATA
Found at i:1697324 original size:31 final size:30
Alignment explanation
Indices: 1697273--1697354 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
1697263 TCCTTTAATT
1697273 TAAGGA-CTAAGGTGGT-AAAAATATAACATCA
1 TAAGGACCTAA-GT-GTAAAAAATATAACAT-A
* * *
1697304 TAAGGACCTAAGTGTAAAAAATCTAACGTT
1 TAAGGACCTAAGTGTAAAAAATATAACATA
*
1697334 TAGGGACCTAAGTGTAAAAAA
1 TAAGGACCTAAGTGTAAAAAA
1697355 CTAAATTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
30 22 0.49
31 19 0.42
32 4 0.09
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (30 bp):
TAAGGACCTAAGTGTAAAAAATATAACATA
Found at i:1697458 original size:29 final size:28
Alignment explanation
Indices: 1697311--1697458 Score: 118
Period size: 29 Copynumber: 5.1 Consensus size: 28
1697301 TCATAAGGAC
*
1697311 CTAAGTGTAAAAAATCTAACGTTTAGGGA
1 CTAAGTGT-AAAAATCTAAAGTTTAGGGA
*
1697340 CCTAAGTGTAAAAAACTAAA-TTATAGGGA
1 -CTAAGTGTAAAAATCTAAAGTT-TAGGGA
* * *
1697369 CTAAAGTGTAAAAACCTAAAGTATAGAGA
1 CT-AAGTGTAAAAATCTAAAGTTTAGGGA
* * * ** *
1697398 CTACGACGTAATAATTCTAAAGGCTATGGA
1 CTAAG-TGTAA-AAATCTAAAGTTTAGGGA
*
1697428 CTAAGGTGTAAAAATCTAAAGTTTAGTGA
1 CTAA-GTGTAAAAATCTAAAGTTTAGGGA
1697457 CT
1 CT
1697459 TAGATAAAAA
Statistics
Matches: 92, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
28 6 0.07
29 57 0.62
30 28 0.30
31 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.26
Consensus pattern (28 bp):
CTAAGTGTAAAAATCTAAAGTTTAGGGA
Found at i:1699383 original size:28 final size:29
Alignment explanation
Indices: 1699347--1699514 Score: 123
Period size: 29 Copynumber: 5.7 Consensus size: 29
1699337 CATTTTCATT
1699347 TAAGTACCTAAAGT-TTTTTTTGTCAAAA
1 TAAGTACCTAAAGTATTTTTTTGTCAAAA
* *
1699375 TAAGCACCTAAAATTATCTTCTTTTTTGTCAAAA
1 TAAGTACCT-AAAGTA---T-TTTTTTGTCAAAA
* * *
1699409 TAGGTATCTAAAGTATTTTTTGGTCAAAA
1 TAAGTACCTAAAGTATTTTTTTGTCAAAA
* * *
1699438 TAGGTACTTAAAGTGTTTTTTTGGTCAAAA
1 TAAGTACCTAAAGTATTTTTTT-GTCAAAA
** *
1699468 TTGGTACCT-AAGTATTCATTTTTTTC----
1 TAAGTACCTAAAGTATT--TTTTTGTCAAAA
1699494 TAAGTACCTAAAGTATTTTTT
1 TAAGTACCTAAAGTATTTTTT
1699515 AATTAATGTC
Statistics
Matches: 113, Mismatches: 17, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
25 4 0.04
26 7 0.06
27 7 0.06
28 8 0.07
29 40 0.35
30 17 0.15
31 5 0.04
33 6 0.05
34 19 0.17
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (29 bp):
TAAGTACCTAAAGTATTTTTTTGTCAAAA
Found at i:1700803 original size:182 final size:182
Alignment explanation
Indices: 1700510--1700854 Score: 548
Period size: 182 Copynumber: 1.9 Consensus size: 182
1700500 CGATACAAAT
* * * * * *
1700510 TAAAAATGTATCGATCCATAGTAATATAACATGTAAAAATATGATAAAACCGGTGTCATTATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCATAATGAT
* ** *
1700575 AAAACTGGTAAAGCGCTACCGGATATATTGAAAGTGTAGATAAATTAATATAAGTGTCGACACTT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTAGATAAATTAATATAAGTATCGACACTT
1700640 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCGATACTTTA
131 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCGATACTTTA
* *
1700692 TAAAAATGTGTCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-AATGA
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTC-ATAATGA
* *
1700756 TAAAACCGGTAAAAAGTTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
65 TAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTAGATAAATTAATATAAGTATCGACACT
1700821 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT
130 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT
1700855 GTGTCGATAC
Statistics
Matches: 148, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
182 147 0.99
183 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (182 bp):
TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCATAATGAT
AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTAGATAAATTAATATAAGTATCGACACTT
TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCGATACTTTA
Found at i:1701440 original size:15 final size:16
Alignment explanation
Indices: 1701409--1701443 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1701399 ATATGGAAAG
1701409 TGATCTTCTAGGTAGA
1 TGATCTTCTAGGTAGA
1701425 TGATCTTCTA-GTAGA
1 TGATCTTCTAGGTAGA
1701440 TGAT
1 TGAT
1701444 AAATATCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (16 bp):
TGATCTTCTAGGTAGA
Found at i:1702908 original size:200 final size:198
Alignment explanation
Indices: 1702507--1703486 Score: 1106
Period size: 200 Copynumber: 4.9 Consensus size: 198
1702497 GTTTTCCAAA
* * **
1702507 CAAAACAAGTTCAC-AAATAAGTGTCGACACATTTATATCAAGTGTCGATCCCAAAAACATCGAA
1 CAAACCAAGTTCACGAAA-AAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAA
*
1702571 ACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACC-GTTTTATGA
65 ACCCGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGA
* * * *
1702635 GAAAATAGGTCTACAATATGTGTCGACACTTTATTCATTTGTGTCGATACATGTTGTCCAGAATG
130 GAAAATAGGTCTACAA-ATGTATCGACACTTTATACATTTGTGTCGATAC-TTTTGTCCATAATG
*
1702700 TATTTC
193 TTTTTC
* * *
1702706 CAAACCAAGTGCACGAACAAAGTGTCGATACTTTTATAAAAAGTATCGATCCCAAAAACATCGAA
1 CAAACCAAGTTCACGAA-AAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAA
* * * ** * * *
1702771 ATCCGTAATTATAATCTAATAGGTAAAATAACAATGTAACCGGTCTAAATATACCGGTTTTATGA
65 ACCCGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGA
* * * * **
1702836 G-AAATA-GTATTCATAAAGTATCGACACTTTATAAATTTGTACCGATACTTTATGTCCATAATG
130 GAAAATAGGTCTACA-AATGTATCGACACTTTATACATTTGTGTCGATACTTT-TGTCCATAATG
1702899 TGTTTTC
193 T-TTTTC
* * **
1702906 CAACAAACAAGTTCAC-AAATAAGTGTCGACAC-TTTATATCAAGTGTCGATCCC-AAAACATCG
1 C-A-AACCAAGTTCACGAAA-AAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCG
*
1702968 AAACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTAT
63 AAACCCGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTAT
* * * * ** *
1703033 GAGAAAACAGGTCTACAATATGTGTCGACACTTTATTCATTTGTTTCGATACAAGTTGTCCAGAA
128 GAGAAAATAGGTCTACAA-ATGTATCGACACTTTATACATTTGTGTCGATAC-TTTTGTCCATAA
*
1703098 TGTATTTC
191 TGTTTTTC
* * *
1703106 CAAACCAAGTGCACGAACAAAGTGTCGATACATTTATAAAAAGTGTCGATCCTACAAACATCGAA
1 CAAACCAAGTTCACGAA-AAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAA
* * * * * * * **
1703171 ACACATAATTATAATGTAAT-CGTAACATAACAAATGTAACCGGTCTAAA--TACTTGTTATT-T
65 ACCCGTAATTATAATGTAATAGGTCACTTTAC-AATGTAACCGGTTTAAATTTACCGGTT-TTAT
* * * *
1703232 -A-AAAAAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAA
128 GAGAAAATAGGTCTACA-AATGTATCGACACTTTATACATTTGTGTCGATACTTT-TGTCCATAA
**
1703295 TAAATTTTC
191 T-GTTTTTC
* *
1703304 CAAA-CAAGTTCACGAAAAAGTGTCGATACATTTAGAAAAAGTGTCGATCCTAAAAACATCGAAA
1 CAAACCAAGTTCACGAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAA
* *
1703368 CCCGTAATTATAATGTAATAGGTCACTTTATAATGTAACCGGTTTAAATTTACCGATTTTATGAG
66 CCCGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAG
* * *
1703433 AAAATAGGTCTACAGAATGTATCGACACTTTTTAAATTAGTGTCGATACTTTTG
131 AAAATAGGTCTACA-AATGTATCGACACTTTATACATTTGTGTCGATACTTTTG
1703487 AAAATTATGC
Statistics
Matches: 646, Mismatches: 107, Indels: 56
0.80 0.13 0.07
Matches are distributed among these distances:
196 80 0.12
197 68 0.11
198 28 0.04
199 147 0.23
200 201 0.31
201 111 0.17
202 11 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (198 bp):
CAAACCAAGTTCACGAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAA
CCCGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAG
AAAATAGGTCTACAAATGTATCGACACTTTATACATTTGTGTCGATACTTTTGTCCATAATGTTT
TTC
Found at i:1703266 original size:22 final size:21
Alignment explanation
Indices: 1703241--1703286 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1703231 TAAAAAAAGG
*
1703241 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
1703263 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
1703284 TAT
1 TAT
1703287 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:1728336 original size:17 final size:17
Alignment explanation
Indices: 1728291--1728337 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1728281 TTTATTGTTC
* * *
1728291 TGTATGTTTTAATGTAC
1 TGTATCTTTTACTGTAA
*
1728308 TATATCTTTTACTGTAA
1 TGTATCTTTTACTGTAA
1728325 TGTATCTTTTACT
1 TGTATCTTTTACT
1728338 ATATTATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (17 bp):
TGTATCTTTTACTGTAA
Found at i:1728632 original size:47 final size:47
Alignment explanation
Indices: 1728578--1728705 Score: 141
Period size: 47 Copynumber: 2.7 Consensus size: 47
1728568 CTCATACGAA
* *
1728578 AGTGCACAA-AGCACTAATAGAGGAGTGCGTATTCACACTAATACAAG
1 AGTGCACAATAGCACT-ATACAGGAGTGCATATTCACACTAATACAAG
* * * * * *
1728625 AGTGCACAATTGCACTATACATGAGTGCATATTCGCATTAATATAGG
1 AGTGCACAATAGCACTATACAGGAGTGCATATTCACACTAATACAAG
* * *
1728672 AGTGCACAATTGCACTATACAAGAGTACATATTC
1 AGTGCACAATAGCACTATACAGGAGTGCATATTC
1728706 GTACTAATTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
47 65 0.93
48 5 0.07
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (47 bp):
AGTGCACAATAGCACTATACAGGAGTGCATATTCACACTAATACAAG
Found at i:1728650 original size:23 final size:24
Alignment explanation
Indices: 1728613--1728697 Score: 95
Period size: 23 Copynumber: 3.6 Consensus size: 24
1728603 TGCGTATTCA
1728613 CACTAATACAAGAGTGCACAATTG
1 CACTAATACAAGAGTGCACAATTG
* *
1728637 CACT-ATACATGAGTGCA-TATTCG
1 CACTAATACAAGAGTGCACAATT-G
* * *
1728660 CATTAATATAGGAGTGCACAATTG
1 CACTAATACAAGAGTGCACAATTG
1728684 CACT-ATACAAGAGT
1 CACTAATACAAGAGT
1728698 ACATATTCGT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
22 3 0.06
23 24 0.49
24 19 0.39
25 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
CACTAATACAAGAGTGCACAATTG
Found at i:1729675 original size:149 final size:151
Alignment explanation
Indices: 1729505--1729799 Score: 576
Period size: 149 Copynumber: 2.0 Consensus size: 151
1729495 TAATTAAAAT
1729505 TTTATATGAAGTTCAGGGGTTAAATTTTTTTTACCTTTTCATTAAACCTTTTTTATATTTTTAAT
1 TTTATATGAAGTTCAGGGGTTAAATTTTTTTTACCTTTTCATTAAACCTTTTTTATATTTTTAAT
1729570 TTTGTAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATATAAAT-TTTTA
66 TTTGTAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATATAAATATTTTA
1729634 CAATTTGTAATATTATCAATA
131 CAATTTGTAATATTATCAATA
1729655 TTTATATGAAGTTCA-GGGTTAAATTTTTTTTACCTTTTCATTAAACCTTTTTTATATTTTTAAT
1 TTTATATGAAGTTCAGGGGTTAAATTTTTTTTACCTTTTCATTAAACCTTTTTTATATTTTTAAT
1729719 TTTGTAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATATAAATATTTTA
66 TTTGTAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATATAAATATTTTA
1729784 CAATTTGTAATATTAT
131 CAATTTGTAATATTAT
1729800 ACAAATATAT
Statistics
Matches: 144, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
149 108 0.75
150 36 0.25
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (151 bp):
TTTATATGAAGTTCAGGGGTTAAATTTTTTTTACCTTTTCATTAAACCTTTTTTATATTTTTAAT
TTTGTAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATATAAATATTTTA
CAATTTGTAATATTATCAATA
Found at i:1729789 original size:37 final size:37
Alignment explanation
Indices: 1729713--1729789 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1729703 TTTTTATATT
*
1729713 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
1729750 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
1729787 TTT
1 TTT
1729790 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:1730909 original size:41 final size:41
Alignment explanation
Indices: 1730853--1731383 Score: 464
Period size: 41 Copynumber: 13.0 Consensus size: 41
1730843 TGTTTTTTGA
* * *
1730853 ACAAACGCCGGTAAATACTTGTTCTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAT
* * * * *
1730894 ATAAATGCCGCTAAATACT-ATACTTTAGTGGCGTTTTAAGC
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTA-T
* * * *
1730935 ACAAACGCCGCTAAA-AGCTAGTACTTTTGTGGCGTGTTTGT
1 ACAAACGCCGCTAAATA-CTCGTACTTTAGTGGCGTTTTTAT
* * * * *
1730976 ATAAACACCGCTAAATAAT-GTACTTTAGTGGCGTTTTAAGC
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTA-T
* * * *
1731017 ACAAATGCCGCTAAATGCTCATACTTTAGTGGCGTTTTTGT
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAT
* * * *
1731058 ATAAACGCCGCTAAATACT-TTACTTTAGTGGCGTTTTAAGC
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTA-T
* * * * * * * *
1731099 ACAAATGCCGCCAAAGAGTCATACTTTAGTGGTGTTTCTAA
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAT
* * *
1731140 ACAATA--CCGCTAAATACTCGTACTGTAGTGGCGTTTTAAGC
1 ACAA-ACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTA-T
* * *
1731181 ACAAACGCCGCTAAATACCCATACTTTAGTGGCGTTTTAAT
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAT
* * *
1731222 ACAAACGCCGCCAAAGACCCGTACTTTTA-TGGCGTTTTTAT
1 ACAAACGCCGCTAAATACTCGTAC-TTTAGTGGCGTTTTTAT
* * * *
1731263 ACAAACGCCGCCAAAGACCCGTACTTTCGTGGCGTTTTTAT
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAT
* * * *
1731304 ACAAACGCCGCCAAAGACCCGTACTTTTGTGGCGTTTTTAT
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAT
* * * *
1731345 ACAAACGCCGCCAAAGACCCGTACTTTAGTGGCTTTTTT
1 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTT
1731384 TTGAATAAAC
Statistics
Matches: 406, Mismatches: 70, Indels: 28
0.81 0.14 0.06
Matches are distributed among these distances:
40 80 0.20
41 242 0.60
42 84 0.21
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (41 bp):
ACAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAT
Found at i:1731171 original size:164 final size:164
Alignment explanation
Indices: 1730853--1731383 Score: 520
Period size: 164 Copynumber: 3.2 Consensus size: 164
1730843 TGTTTTTTGA
* *** * *
1730853 ACAAACGCCGGTAAATACTTGTTCTTTAGTGGCGTTTTTATATAAATGCCGCTAAATACTATACT
1 ACAAACGCCGCTAAATACCCATACTTTAGTGGCGTTTTTATATAAACGCCGCTAAATACTATACT
* * * *
1730918 TTAGTGGCGTTTTAAGCACAAACGCCGCTAAAAGCTAGTACTTTTGTGGCGTGTTTGTATAAACA
66 TTAGTGGCGTTTTAAGCACAAACGCCGCCAAAAGCTAGTACTTTAGTGGCGTGTTTCTAAAAACA
*
1730983 CCGCTAAATAATGTACTTTAGTGGCGTTTTAAGC
131 CCGCTAAATAATGTACTGTAGTGGCGTTTTAAGC
* * * * *
1731017 ACAAATGCCGCTAAATGCTCATACTTTAGTGGCGTTTTTGTATAAACGCCGCTAAATACTTTACT
1 ACAAACGCCGCTAAATACCCATACTTTAGTGGCGTTTTTATATAAACGCCGCTAAATACTATACT
*
1731082 TTAGTGGCGTTTTAAGCACAAATGCCGCCAAAGAG-TCA-TACTTTAGT-G-GTGTTTCTAAACA
66 TTAGTGGCGTTTTAAGCACAAACGCCGCCAAA-AGCT-AGTACTTTAGTGGCGTGTTTCTAAA-A
* *
1731143 ATACCGCTAAATACTCGTACTGTAGTGGCGTTTTAAGC
128 ACACCGCTAAATAAT-GTACTGTAGTGGCGTTTTAAGC
* * * * **
1731181 ACAAACGCCGCTAAATACCCATACTTTAGTGGCGTTTTAATACAAACGCCGCCAAAGACCCGTAC
1 ACAAACGCCGCTAAATACCCATACTTTAGTGGCGTTTTTATATAAACGCCGCTAAATA-CTATAC
* * ** * * * *
1731246 TTTTA-TGGCGTTTTTA-TACAAACGCCGCC-AAAGACCCGTACTTTCGTGGCGTTTTTATACAA
65 -TTTAGTGGCGTTTTAAGCACAAACGCCGCCAAAAG-CTAGTACTTTAGTGGCGTGTTTCTAAAA
* * * ** * * * *
1731308 ACGCCGCCAAAGACCCGTACTTTTGTGGCGTTTTTA-T
128 ACACCGCTAAATA-ATGTACTGTAGTGGCGTTTTAAGC
* * * *
1731345 ACAAACGCCGCCAAAGACCCGTACTTTAGTGGCTTTTTT
1 ACAAACGCCGCTAAATACCCATACTTTAGTGGCGTTTTT
1731384 TTGAATAAAC
Statistics
Matches: 305, Mismatches: 50, Indels: 24
0.80 0.13 0.06
Matches are distributed among these distances:
162 11 0.04
163 17 0.06
164 219 0.72
165 45 0.15
166 13 0.04
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (164 bp):
ACAAACGCCGCTAAATACCCATACTTTAGTGGCGTTTTTATATAAACGCCGCTAAATACTATACT
TTAGTGGCGTTTTAAGCACAAACGCCGCCAAAAGCTAGTACTTTAGTGGCGTGTTTCTAAAAACA
CCGCTAAATAATGTACTGTAGTGGCGTTTTAAGC
Done.