Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003208.1 Hibiscus syriacus cultivar Beakdansim tig00006753_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: 1278004
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1155502 original size:20 final size:20
Alignment explanation
Indices: 1155479--1155519 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1155469 TCTGAAACTT
1155479 AAAATCGTAACACGAAAATG
1 AAAATCGTAACACGAAAATG
1155499 AAAATCGTAACACGAAAATG
1 AAAATCGTAACACGAAAATG
1155519 A
1 A
1155520 CTATCGCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATCGTAACACGAAAATG
Found at i:1155546 original size:20 final size:20
Alignment explanation
Indices: 1155511--1155573 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
1155501 AATCGTAACA
*
1155511 CGAAAATGACTATCGCAACG
1 CGAATATGACTATCGCAACG
*
1155531 CGAATTTGACTATCGCAACG
1 CGAATATGACTATCGCAACG
**
1155551 CG-ATATGAAAATCGCAACG
1 CGAATATGACTATCGCAACG
1155570 CGAA
1 CGAA
1155574 ACTAAAATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
CGAATATGACTATCGCAACG
Found at i:1155566 original size:19 final size:19
Alignment explanation
Indices: 1155522--1155572 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1155512 GAAAATGACT
* **
1155522 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCG-ATATGAAA
1155542 ATCGCAACGCGATATGAAA
1 ATCGCAACGCGATATGAAA
1155561 ATCGCAACGCGA
1 ATCGCAACGCGA
1155573 AACTAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGATATGAAA
Found at i:1155580 original size:19 final size:19
Alignment explanation
Indices: 1155479--1155584 Score: 79
Period size: 20 Copynumber: 5.4 Consensus size: 19
1155469 TCTGAAACTT
* *
1155479 AAAATCGTAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
* *
1155499 AAAATCGTAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
1155519 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
** *
1155539 ACTATCGCAACGCGATATG
1 AAAATCGCAACGCGAAATG
1155558 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
1155577 AAAATCGC
1 AAAATCGC
1155585 GTTGCGATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
19 26 0.35
20 48 0.65
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1156226 original size:20 final size:20
Alignment explanation
Indices: 1156201--1156386 Score: 155
Period size: 20 Copynumber: 9.2 Consensus size: 20
1156191 TTATCGCAAC
* *
1156201 GCGATAGTCAGAATCACGTT
1 GCGATAGTCAAAATCGCGTT
1156221 GCGATAGT-AAGAATCGCGTT
1 GCGATAGTCAA-AATCGCGTT
**
1156241 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAAAATCGCGTT
* * *
1156262 GTGATAGTCAGAATCTCGTT
1 GCGATAGTCAAAATCGCGTT
**
1156282 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAAAATCGCGTT
*
1156303 GCGATAGTCAAAATCGCATT
1 GCGATAGTCAAAATCGCGTT
1156323 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAAAATCGCGTT
* * * * *
1156343 GCGAT-TTACATATTCACATT
1 GCGATAGT-CAAAATCGCGTT
1156363 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAAAATCGCGTT
1156383 GCGA
1 GCGA
1156387 ATCTGGAAAC
Statistics
Matches: 131, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
19 6 0.05
20 92 0.70
21 28 0.21
22 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
GCGATAGTCAAAATCGCGTT
Found at i:1156259 original size:21 final size:21
Alignment explanation
Indices: 1156233--1156307 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
1156223 GATAGTAAGA
1156233 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* **
1156254 ATCGCGTTGTGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
*
1156274 ATCTCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
1156295 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
1156308 AGTCAAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 26 0.60
22 2 0.05
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:1156262 original size:41 final size:41
Alignment explanation
Indices: 1156217--1156327 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
1156207 GTCAGAATCA
1156217 CGTTGCGATAGTAAGAATCGCGTTGCGATTATGTATTATCG
1 CGTTGCGATAGTAAGAATCGCGTTGCGATTATGTATTATCG
* * *
1156258 CGTTGTGATAGTCAGAATCTCGTTGCGATTATGTATTATCG
1 CGTTGCGATAGTAAGAATCGCGTTGCGATTATGTATTATCG
*
1156299 CGTTGCGATAGTCAA-AATCGCATTGCGAT
1 CGTTGCGATAGT-AAGAATCGCGTTGCGAT
1156328 AGTCAAAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 61 0.98
42 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (41 bp):
CGTTGCGATAGTAAGAATCGCGTTGCGATTATGTATTATCG
Found at i:1156268 original size:61 final size:61
Alignment explanation
Indices: 1156171--1156347 Score: 189
Period size: 61 Copynumber: 2.9 Consensus size: 61
1156161 GCGCTTTGAA
* * **
1156171 AATCGCATTGCGATTTTGTATTATCGCAACGCGATAGTCAGAATCACGTTGCGATA-GTAAG
1 AATCGCGTTGCGATTATGTATTATCGCATTGCGATAGTCAGAATCACGTTGCGATATGT-AG
* * * *
1156232 AATCGCGTTGCGATTATGTATTATCGCGTTGTGATAGTCAGAATCTCGTTGCGATTATGTAT
1 AATCGCGTTGCGATTATGTATTATCGCATTGCGATAGTCAGAATCACGTTGCGA-TATGTAG
* ** * *
1156294 TATCGCGTTGCGA-TA-GTCAAAATCGCATTGCGATAGTCAAAATCGCGTTGCGAT
1 AATCGCGTTGCGATTATGT-ATTATCGCATTGCGATAGTCAGAATCACGTTGCGAT
1156348 TTACATATTC
Statistics
Matches: 98, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
60 3 0.03
61 78 0.80
62 15 0.15
63 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (61 bp):
AATCGCGTTGCGATTATGTATTATCGCATTGCGATAGTCAGAATCACGTTGCGATATGTAG
Found at i:1156348 original size:61 final size:60
Alignment explanation
Indices: 1156201--1156386 Score: 182
Period size: 61 Copynumber: 3.1 Consensus size: 60
1156191 TTATCGCAAC
* **
1156201 GCGATAGTCAGAATCACGTTGCGA-TA-GTAAGAATCGCGTTGCGATTATGT-ATTATCGCGTT
1 GCGATAGTCAGAATCACGTTGCGATTATGT-A-TATCGCGTTGCGA-TA-GTCAAAATCGCGTT
* * *
1156262 GTGATAGTCAGAATCTCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAAAATCGCATT
1 GCGATAGTCAGAATCACGTTGCGATTATGTA-TATCGCGTTGCGATAGTCAAAATCGCGTT
* * ** * *
1156323 GCGATAGTCAAAATCGCGTTGCGATT-TACATATTCACATTGCGATAGTCAAAATCGCGTT
1 GCGATAGTCAGAATCACGTTGCGATTATGTATA-TCGCGTTGCGATAGTCAAAATCGCGTT
1156383 GCGA
1 GCGA
1156387 ATCTGGAAAC
Statistics
Matches: 106, Mismatches: 15, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
59 2 0.02
60 32 0.30
61 55 0.52
62 15 0.14
63 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (60 bp):
GCGATAGTCAGAATCACGTTGCGATTATGTATATCGCGTTGCGATAGTCAAAATCGCGTT
Found at i:1156424 original size:20 final size:19
Alignment explanation
Indices: 1156401--1156446 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1156391 GGAAACTGAT
* *
1156401 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1156421 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1156440 TTGCGAT
1 TTGCGAT
1156447 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1156436 original size:19 final size:19
Alignment explanation
Indices: 1156412--1156448 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1156402 TGCGATACTG
*
1156412 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1156431 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1156449 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1160157 original size:27 final size:27
Alignment explanation
Indices: 1160125--1160180 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1160115 TATAACAATC
1160125 AGTACAAGCATCCTATCTTGTCCTTAA
1 AGTACAAGCATCCTATCTTGTCCTTAA
* *
1160152 AGTACATGCATCGTATCTTGTCCTTAA
1 AGTACAAGCATCCTATCTTGTCCTTAA
1160179 AG
1 AG
1160181 CACATATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (27 bp):
AGTACAAGCATCCTATCTTGTCCTTAA
Found at i:1160182 original size:48 final size:46
Alignment explanation
Indices: 1160072--1160167 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 46
1160062 ACAATTGATT
*
1160072 CAATCATTAAATGCATCCTATCTTGTCCTTAAAGTACATATCTTATAA
1 CAATCATTAAA-GCATCCTATCTTGTCCTTAAAGTACATATCGTAT-A
*
1160120 CAATCAGTACAAGCATCCTATCTTGTCCTTAAAGTACATGCATCGTAT
1 CAATCATTA-AAGCATCCTATCTTGTCCTTAAAGTACAT--ATCGTAT
1160168 CTTGTCCTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 35 0.81
49 2 0.05
50 6 0.14
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (46 bp):
CAATCATTAAAGCATCCTATCTTGTCCTTAAAGTACATATCGTATA
Found at i:1162098 original size:2 final size:2
Alignment explanation
Indices: 1162091--1162117 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1162081 TACCAAATAC
1162091 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1162118 CGTAATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1163575 original size:79 final size:80
Alignment explanation
Indices: 1163422--1163575 Score: 211
Period size: 80 Copynumber: 1.9 Consensus size: 80
1163412 GAATTACGAA
* * *
1163422 TGACTCCTTCGTCATGAAGTTGAGTCAATCTTGGATGACTTTGAGCATGATATCATTTGTCATGA
1 TGACCCCTTCGTCATGAAGTTGAGTCAATCTTGGATGACTTCGAACATGATATCATTTGTCATGA
*
1163487 AGTTGAAATCATGGT
66 AGTTAAAATCATGGT
* * * * **
1163502 TGACCCCTTTGTCGTGAAGTTGAGTTAATCTTGGATGA-TTCGAACATGATATCCTTTGTTGTGA
1 TGACCCCTTCGTCATGAAGTTGAGTCAATCTTGGATGACTTCGAACATGATATCATTTGTCATGA
1163566 AGTTAAAATC
66 AGTTAAAATC
1163576 TAGCTCGATG
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
79 30 0.47
80 34 0.53
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (80 bp):
TGACCCCTTCGTCATGAAGTTGAGTCAATCTTGGATGACTTCGAACATGATATCATTTGTCATGA
AGTTAAAATCATGGT
Found at i:1165757 original size:24 final size:24
Alignment explanation
Indices: 1165730--1165776 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1165720 AAACTGCCGC
*
1165730 GTAGAATTTGCACCGAAGTGCCAT
1 GTAGAATATGCACCGAAGTGCCAT
*
1165754 GTAGAATATGCACTGAAGTGCCA
1 GTAGAATATGCACCGAAGTGCCA
1165777 CATAGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (24 bp):
GTAGAATATGCACCGAAGTGCCAT
Found at i:1165782 original size:24 final size:24
Alignment explanation
Indices: 1165731--1165782 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1165721 AACTGCCGCG
* **
1165731 TAGAATTTGCACCGAAGTGCCATG
1 TAGAATATGCACCGAAGTGCCACA
*
1165755 TAGAATATGCACTGAAGTGCCACA
1 TAGAATATGCACCGAAGTGCCACA
1165779 TAGA
1 TAGA
1165783 TTTTTCCCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (24 bp):
TAGAATATGCACCGAAGTGCCACA
Found at i:1165803 original size:23 final size:23
Alignment explanation
Indices: 1165777--1165875 Score: 81
Period size: 23 Copynumber: 4.3 Consensus size: 23
1165767 TGAAGTGCCA
* *
1165777 CATAGATTTTTCCCGAAGGACCG
1 CATAGAATTGTCCCGAAGGACCG
* *
1165800 CATAGAATTGTCCCGAATGACCT
1 CATAGAATTGTCCCGAAGGACCG
* * * **
1165823 CGTAGAATTGTCTCGAATGACAA
1 CATAGAATTGTCCCGAAGGACCG
* **
1165846 CATGGAATTGTCTTGAAGGACCG
1 CATAGAATTGTCCCGAAGGACCG
*
1165869 CGTAGAA
1 CATAGAA
1165876 CCCTCGACTC
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
CATAGAATTGTCCCGAAGGACCG
Found at i:1166043 original size:57 final size:57
Alignment explanation
Indices: 1165981--1166153 Score: 201
Period size: 57 Copynumber: 3.0 Consensus size: 57
1165971 TGTCATTTGC
*
1165981 TCACATAAAACATATA-TTCATAGTACTTCATATAGCATTACTCAATTTATCATTTAT
1 TCACATAAAACATATACTT-ATAGTATTTCATATAGCATTACTCAATTTATCATTTAT
* * * *
1166038 TCACATAAAACA-ATTACTTAT-CTCATTTTACATAGCATTACTCAATTTATAATTTAT
1 TCACATAAAACATA-TACTTATAGT-ATTTCATATAGCATTACTCAATTTATCATTTAT
* * * *
1166095 TCACATAGATCATATACTTATAGTTTTTCATATAGCATTATTCGAA-TTATCATTTAT
1 TCACATAAAACATATACTTATAGTATTTCATATAGCATTACTC-AATTTATCATTTAT
1166152 TC
1 TC
1166154 TATAGAACAT
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
56 2 0.02
57 89 0.92
58 6 0.06
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (57 bp):
TCACATAAAACATATACTTATAGTATTTCATATAGCATTACTCAATTTATCATTTAT
Found at i:1166209 original size:2 final size:2
Alignment explanation
Indices: 1166204--1166243 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1166194 TTAACATAGG
1166204 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
1166244 GAAATAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1168948 original size:24 final size:23
Alignment explanation
Indices: 1168916--1169006 Score: 105
Period size: 24 Copynumber: 3.9 Consensus size: 23
1168906 GTCGAGGGTT
*
1168916 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
1168939 CCTATGTGGTCATTCGGGA-ATAAA
1 -CTATGTGGTCATTCGGGACA-AAA
* *
1168963 TCTATGTGGTCCTTTGGGAC-AAA
1 -CTATGTGGTCATTCGGGACAAAA
*
1168986 TTATGTGGTCATTCGGGACAA
1 CTATGTGGTCATTCGGGACAA
1169007 TTATGTGGCA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
22 16 0.28
23 5 0.09
24 36 0.63
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:1175759 original size:24 final size:24
Alignment explanation
Indices: 1175732--1175797 Score: 98
Period size: 23 Copynumber: 2.8 Consensus size: 24
1175722 CGAGGGTTTA
*
1175732 ATGTGGTCATTCGGGATAAAACCT
1 ATGTGGTCATTCGGGACAAAACCT
* *
1175756 ATGT-GTCGTTCAGGACAAAACCT
1 ATGTGGTCATTCGGGACAAAACCT
1175779 ATGTGGTCATTCGGGACAA
1 ATGTGGTCATTCGGGACAA
1175798 TTACGTGGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 20 0.56
24 16 0.44
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (24 bp):
ATGTGGTCATTCGGGACAAAACCT
Found at i:1180650 original size:24 final size:24
Alignment explanation
Indices: 1180623--1180688 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
1180613 GAAAATGTCG
1180623 CATAGAATTTGCACCGAAGTGCCA
1 CATAGAATTTGCACCGAAGTGCCA
*
1180647 CATAGAATATGCACCGAAGTGCCA
1 CATAGAATTTGCACCGAAGTGCCA
*
1180671 CATAG-ATTTGCCCCGAAG
1 CATAGAATTTGCACCGAAG
1180689 GACCGTGTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 11 0.28
24 28 0.72
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (24 bp):
CATAGAATTTGCACCGAAGTGCCA
Found at i:1180722 original size:23 final size:23
Alignment explanation
Indices: 1180623--1180769 Score: 122
Period size: 23 Copynumber: 6.3 Consensus size: 23
1180613 GAAAATGTCG
1180623 CATAGAATT-TGCACCGAAGTG-CCA
1 CATAGAATTGT-C-CCGAAG-GACCA
1180647 CATAGAATATG-CACCGAAGTG-CCA
1 CATAGAAT-TGTC-CCGAAG-GACCA
* * *
1180671 CATAGATTTGCCCCGAAGGACCG
1 CATAGAATTGTCCCGAAGGACCA
** *
1180694 TGTAGAATTGTCCCGAATGACCA
1 CATAGAATTGTCCCGAAGGACCA
*
1180717 CATAGAATTGTCCTGAAGGACCA
1 CATAGAATTGTCCCGAAGGACCA
* *
1180740 CATAGAATTGTTCTGAAGGACCA
1 CATAGAATTGTCCCGAAGGACCA
*
1180763 CGTAGAA
1 CATAGAA
1180770 CTCTCGACTG
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.01
23 74 0.70
24 29 0.28
25 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.21
Consensus pattern (23 bp):
CATAGAATTGTCCCGAAGGACCA
Found at i:1180928 original size:57 final size:57
Alignment explanation
Indices: 1180841--1181028 Score: 184
Period size: 57 Copynumber: 3.3 Consensus size: 57
1180831 ACCATATAAT
* * * **
1180841 TATTTCACATCGTATTAATCAAATTT-TCATTTGCTCACATAAAACATATATTTATAG
1 TATTTCACATAGCATTACTC-AATTTATCATTTATTCACATAAAACATATATTTATAG
* * *
1180898 TACTTCACATAGCATTACTCAATTTATCATTTATTCAAATAAAACA-ATTATTTAT-C
1 TATTTCACATAGCATTACTCAATTTATCATTTATTCACATAAAACATA-TATTTATAG
* * * * * *
1180954 TAATTTCACATAGCATTACTTAACTTATCATTTATTCACATAGATCATATACTCATAG
1 T-ATTTCACATAGCATTACTCAATTTATCATTTATTCACATAAAACATATATTTATAG
* *
1181012 TGTTTCAAATAGCATTA
1 TATTTCACATAGCATTA
1181029 TTTGAATTAT
Statistics
Matches: 107, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
56 7 0.07
57 98 0.92
58 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (57 bp):
TATTTCACATAGCATTACTCAATTTATCATTTATTCACATAAAACATATATTTATAG
Found at i:1181068 original size:57 final size:57
Alignment explanation
Indices: 1180957--1181068 Score: 138
Period size: 57 Copynumber: 2.0 Consensus size: 57
1180947 ATTTATCTAA
* * * *
1180957 TTTCACATAGCATTACTTAACTTATCATTTATTCACATAGATCATATACTCATAGTG
1 TTTCAAATAGCATTACTTAACTTATAATTTATTCACATAGAACATATACACATAGTG
* *
1181014 TTTCAAATAGCATTATTTGAA-TTATAATTTATTC-CTATAGAACATATTCACATAG
1 TTTCAAATAGCATTACTT-AACTTATAATTTATTCAC-ATAGAACATATACACATAG
1181069 ATCATATACT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 1 0.02
57 44 0.94
58 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (57 bp):
TTTCAAATAGCATTACTTAACTTATAATTTATTCACATAGAACATATACACATAGTG
Found at i:1181253 original size:4 final size:4
Alignment explanation
Indices: 1181244--1181272 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1181234 ATCGTATATA
1181244 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1181273 GTACTCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1193383 original size:9 final size:10
Alignment explanation
Indices: 1193348--1193547 Score: 107
Period size: 9 Copynumber: 19.5 Consensus size: 10
1193338 AAAACAATAT
*
1193348 TAATAAATAA
1 TAATATATAA
1193358 TAATATATAACA
1 TAATATAT-A-A
*
1193370 TAATA-ATTA
1 TAATATATAA
1193379 TAATATAT-A
1 TAATATATAA
1193388 TAATATTATAA
1 TAATA-TATAA
1193399 TATATATATAA
1 TA-ATATATAA
1193410 T-ATATACTATA
1 TAATATA-TA-A
1193421 TAATATATAATA
1 TAATATAT-A-A
1193433 TAAATACTATAA
1 T-AATA-TATAA
*
1193445 TAATATATAC
1 TAATATATAA
1193455 T-AT-T-TAA
1 TAATATATAA
1193462 T-ATACTATATA
1 TAATA-TATA-A
*
1193473 TACTATATAA
1 TAATATATAA
1193483 T-ATACTATAA
1 TAATA-TATAA
1193493 T-ATATATACCA
1 TAATATATA--A
*
1193504 TACTATATATA
1 TAATATATA-A
* *
1193515 TAATATAGAC
1 TAATATATAA
*
1193525 T-ATATAAAA
1 TAATATATAA
1193534 TAATATAT-A
1 TAATATATAA
1193543 TAATA
1 TAATA
1193548 GTAAATAAAA
Statistics
Matches: 154, Mismatches: 14, Indels: 45
0.72 0.07 0.21
Matches are distributed among these distances:
7 5 0.03
8 1 0.01
9 39 0.25
10 38 0.25
11 35 0.23
12 28 0.18
13 5 0.03
14 3 0.02
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.41
Consensus pattern (10 bp):
TAATATATAA
Found at i:1193383 original size:21 final size:21
Alignment explanation
Indices: 1193343--1193486 Score: 89
Period size: 19 Copynumber: 7.3 Consensus size: 21
1193333 AAATAAAAAC
*
1193343 AATATTAATAAATAATAATATAT
1 AATA-TAAT-AATTATAATATAT
*
1193366 AACATAATAATTAT-A-ATAT
1 AATATAATAATTATAATATAT
1193385 -ATATAAT-ATTATAATATAT
1 AATATAATAATTATAATATAT
*
1193404 -ATATAAT-A-TATACTATAT
1 AATATAATAATTATAATATAT
1193422 AATAT-ATAA-TAT-A-A-AT
1 AATATAATAATTATAATATAT
* * *
1193438 ACTATAATAATATATACTATTT
1 AATATAATAAT-TATAATATAT
* *
1193460 AATATACT-ATATATACTATAT
1 AATATAATAAT-TATAATATAT
1193481 AATATA
1 AATATA
1193487 CTATAATATA
Statistics
Matches: 100, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
16 6 0.06
17 10 0.10
18 18 0.18
19 27 0.27
20 1 0.01
21 24 0.24
22 11 0.11
23 3 0.03
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATAATAATTATAATATAT
Found at i:1193388 original size:2 final size:2
Alignment explanation
Indices: 1193377--1193544 Score: 105
Period size: 2 Copynumber: 87.0 Consensus size: 2
1193367 ACATAATAAT
1193377 TA TA -A TA TA TA TA -A TA T- TA TA -A TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1193414 TA CTA TA TA -A TA TA TA -A TA TA AA TA CTA TA -A TA -A TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
1193454 CTA TT TA -A TA TA CTA TA TA TA CTA TA TA -A TA TA CTA TA -A TA
1 -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
* * *
1193495 TA TA TA CCA TA CTA TA TA TA TA -A TA TA GA CTA TA TA -A AA TA
1 TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
1193536 -A TA TA TA TA
1 TA TA TA TA TA
1193545 ATAGTAAATA
Statistics
Matches: 133, Mismatches: 9, Indels: 48
0.70 0.05 0.25
Matches are distributed among these distances:
1 15 0.11
2 102 0.77
3 16 0.12
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1193390 original size:23 final size:24
Alignment explanation
Indices: 1193348--1193545 Score: 113
Period size: 24 Copynumber: 7.8 Consensus size: 24
1193338 AAAACAATAT
*
1193348 TAATAAATAATAATATATAACATAA
1 TAATATATAAT-ATATATAACATAA
* *
1193373 TAAT-TATAATATATATAATATTA
1 TAATATATAATATATATAACATAA
1193396 TAATATAT-ATATAATATATAC-TATA
1 TAATATATAATAT-ATATA-ACATA-A
*
1193421 TAATATATAATATAAAT-ACTATAA
1 TAATATATAATATATATAAC-ATAA
* *
1193445 TAATATATACTATTTAATATACTATATA
1 TAATATATAATATAT-ATA-AC-ATA-A
* *
1193473 TACTATATAATATACTATAATATATA
1 TAATATATAATATA-TATAACATA-A
1193499 TACCATACTATATATATAATATAGAC-TATA
1 TA--ATA-TATA-ATAT-ATATA-ACATA-A
1193529 TAA-A-ATAATATATATAA
1 TAATATATAATATATATAA
1193546 TAGTAAATAA
Statistics
Matches: 140, Mismatches: 15, Indels: 39
0.72 0.08 0.20
Matches are distributed among these distances:
22 1 0.01
23 26 0.19
24 31 0.22
25 24 0.17
26 11 0.08
27 8 0.06
28 18 0.13
29 5 0.04
30 14 0.10
31 2 0.01
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.40
Consensus pattern (24 bp):
TAATATATAATATATATAACATAA
Found at i:1193404 original size:38 final size:36
Alignment explanation
Indices: 1193353--1193542 Score: 133
Period size: 38 Copynumber: 5.4 Consensus size: 36
1193343 AATATTAATA
1193353 AATA-ATAATATATAACATAATAATTATAATA-TATAT
1 AATATATAATATATAACATAATAA-TAT-ATACTATAT
1193389 AATATTATAATATAT---AT-ATAATATATACTATAT
1 AATA-TATAATATATAACATAATAATATATACTATAT
* *
1193422 AATATATAATATAAATACTATAATAATATATACTATTT
1 AATATATAATATATA-AC-ATAATAATATATACTATAT
1193460 AATATACT-ATATAT-AC-T-AT-ATAATATACTATA-
1 AATATA-TAATATATAACATAATAAT-ATATACTATAT
* *
1193492 ATATATATACCATACTAT-ATAT-ATAATATAGACTATAT
1 A-ATATATA--ATA-TATAACATAATAATATATACTATAT
1193530 AA-A-ATAATATATA
1 AATATATAATATATA
1193543 TAATAGTAAA
Statistics
Matches: 128, Mismatches: 6, Indels: 43
0.72 0.03 0.24
Matches are distributed among these distances:
32 19 0.15
33 31 0.24
34 5 0.04
35 8 0.06
36 11 0.09
37 15 0.12
38 38 0.30
39 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.41
Consensus pattern (36 bp):
AATATATAATATATAACATAATAATATATACTATAT
Found at i:1193420 original size:14 final size:13
Alignment explanation
Indices: 1193377--1193547 Score: 152
Period size: 14 Copynumber: 12.5 Consensus size: 13
1193367 ACATAATAAT
1193377 TATAATATATATAA
1 TATAATATATAT-A
*
1193391 TATTATAATATATA
1 TATAAT-ATATATA
1193405 TATAATATATACTA
1 TATAATATATA-TA
1193419 TATAATATATA-A
1 TATAATATATATA
1193431 TATAA-ATACTATA
1 TATAATATA-TATA
1193444 -ATAATATATACTA
1 TATAATATATA-TA
*
1193457 TTTAATATACTATA
1 TATAATATA-TATA
*
1193471 TATACTATATA-A
1 TATAATATATATA
*
1193483 TATACTATAATATA
1 TATAATAT-ATATA
1193497 TATACCATACTATATA
1 TATA--ATA-TATATA
*
1193513 TATAATATAGACTA
1 TATAATATATA-TA
*
1193527 TATAAAATAATATA
1 TATAATAT-ATATA
1193541 TATAATA
1 TATAATA
1193548 GTAAATAAAA
Statistics
Matches: 132, Mismatches: 10, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
11 3 0.02
12 23 0.17
13 19 0.14
14 65 0.49
15 10 0.08
16 11 0.08
17 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.42
Consensus pattern (13 bp):
TATAATATATATA
Found at i:1193433 original size:7 final size:7
Alignment explanation
Indices: 1193353--1193542 Score: 125
Period size: 7 Copynumber: 27.1 Consensus size: 7
1193343 AATATTAATA
1193353 AATA-AT
1 AATATAT
1193359 AATATAT
1 AATATAT
*
1193366 AACATAAT
1 AATAT-AT
1193374 AAT-TAT
1 AATATAT
1193380 AATATAT
1 AATATAT
1193387 -ATA-AT
1 AATATAT
*
1193392 ATTATAAT
1 AATAT-AT
1193400 ATATATAT
1 A-ATATAT
1193408 AATATAT
1 AATATAT
*
1193415 ACTATAT
1 AATATAT
1193422 AATATAT
1 AATATAT
1193429 AATATA-
1 AATATAT
1193435 AATACTAT
1 AATA-TAT
1193443 AATAATAT
1 AAT-ATAT
*
1193451 ATACTATTT
1 A-A-TATAT
1193460 AATATACT
1 AATATA-T
1193468 -ATATAT
1 AATATAT
*
1193474 ACTATAT
1 AATATAT
1193481 AATATACT
1 AATATA-T
1193489 -ATA-AT
1 AATATAT
1193494 -ATATAT
1 AATATAT
1193500 ACCATACTAT
1 A--ATA-TAT
1193510 -ATATAT
1 AATATAT
*
1193516 AATATAG
1 AATATAT
*
1193523 ACTATAT
1 AATATAT
1193530 AA-A-AT
1 AATATAT
1193535 AATATAT
1 AATATAT
1193542 A
1 A
1193543 TAATAGTAAA
Statistics
Matches: 147, Mismatches: 14, Indels: 45
0.71 0.07 0.22
Matches are distributed among these distances:
5 10 0.07
6 27 0.18
7 74 0.50
8 20 0.14
9 12 0.08
10 4 0.03
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.41
Consensus pattern (7 bp):
AATATAT
Found at i:1193561 original size:28 final size:28
Alignment explanation
Indices: 1193508--1193562 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1193498 ATACCATACT
* * *
1193508 ATATATATAATATAGACTATATAAAATA
1 ATATATATAATATAGAATAAAAAAAATA
1193536 ATATATATAATAGTA-AATAAAAAAAAT
1 ATATATATAATA-TAGAATAAAAAAAAT
1193563 CTCGAACGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (28 bp):
ATATATATAATATAGAATAAAAAAAATA
Found at i:1197329 original size:14 final size:14
Alignment explanation
Indices: 1197310--1197355 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1197300 ATATATTGAA
1197310 AATTAATCATGTTC
1 AATTAATCATGTTC
1197324 AATTAATCA-----
1 AATTAATCATGTTC
1197333 AATTAATCATGTTC
1 AATTAATCATGTTC
1197347 AATTAATCA
1 AATTAATCA
1197356 AATTAATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
9 9 0.33
14 18 0.67
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (14 bp):
AATTAATCATGTTC
Found at i:1197339 original size:23 final size:23
Alignment explanation
Indices: 1197309--1197363 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
1197299 CATATATTGA
1197309 AAATTAATCATGTTCAATTAATC
1 AAATTAATCATGTTCAATTAATC
1197332 AAATTAATCATGTTCAATTAATC
1 AAATTAATCATGTTCAATTAATC
1197355 AAATTAATC
1 AAATTAATC
1197364 TTTAAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATTAATCATGTTCAATTAATC
Found at i:1207158 original size:61 final size:61
Alignment explanation
Indices: 1207092--1207215 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
1207082 ATAGTCATTG
*
1207092 GAAAGGAAAAACTACTAATCAGGTATAAAAGAAATTTAGAAAAACATAAAACCTTTTAATT
1 GAAAGGAAAAACTACTAATCAGGTATAAAAGAAATTTAGAAAAACAGAAAACCTTTTAATT
*
1207153 GAAAGGAAAAACTACTAATCAGGTATAAAAGAAATTTAGAAAAGCAGAAAACCTTTTAATT
1 GAAAGGAAAAACTACTAATCAGGTATAAAAGAAATTTAGAAAAACAGAAAACCTTTTAATT
1207214 GA
1 GA
1207216 GTGAAGAAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.23
Consensus pattern (61 bp):
GAAAGGAAAAACTACTAATCAGGTATAAAAGAAATTTAGAAAAACAGAAAACCTTTTAATT
Found at i:1207479 original size:82 final size:82
Alignment explanation
Indices: 1207342--1207507 Score: 287
Period size: 82 Copynumber: 2.0 Consensus size: 82
1207332 TCCCCTGAGT
* * *
1207342 TAATATTAATAATTGACAACTGAGTATGGATATAACCTTTCTAAAACTCTTCAAATACATTAAAT
1 TAATATTAATAACTGACAACTGAGTAGGGATATAACCATTCTAAAACTCTTCAAATACATTAAAT
1207407 AAAAATCTTAAAAATTA
66 AAAAATCTTAAAAATTA
* *
1207424 TAATATTTATAACTGACAACTGAGTAGGGATATAATCATTCTAAAACTCTTCAAATACATTAAAT
1 TAATATTAATAACTGACAACTGAGTAGGGATATAACCATTCTAAAACTCTTCAAATACATTAAAT
1207489 AAAAATCTTAAAAATTA
66 AAAAATCTTAAAAATTA
1207506 TA
1 TA
1207508 TACCTGTATC
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.34
Consensus pattern (82 bp):
TAATATTAATAACTGACAACTGAGTAGGGATATAACCATTCTAAAACTCTTCAAATACATTAAAT
AAAAATCTTAAAAATTA
Found at i:1211321 original size:13 final size:13
Alignment explanation
Indices: 1211305--1211340 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1211295 ACCCAACCCG
1211305 TTGACCCGACTCA
1 TTGACCCGACTCA
* *
1211318 TTGACCTGACTCG
1 TTGACCCGACTCA
1211331 TTGACCCGAC
1 TTGACCCGAC
1211341 CTGTTAATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (13 bp):
TTGACCCGACTCA
Found at i:1212285 original size:38 final size:38
Alignment explanation
Indices: 1212211--1212506 Score: 323
Period size: 38 Copynumber: 8.1 Consensus size: 38
1212201 TTAAAAAAAC
* *
1212211 ATATATTATATAGTTTTGAGAACA-TTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
* *
1212248 ATATAATGTATAGTTTTGAAAACAATTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
*
1212286 ATATAATATATAGTTTTGAAAATA-TTTTTG-AAA-AT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
*
1212321 ATATAATATATAGTTTT-AAAAC--GTTTTG-AAA-AT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
* ***** *
1212354 ATAT-A-ATATAG-CTTGATTTTTTTTTTCTGAAAACAT
1 ATATAATATATAGTTTTGAAAACATTTTT-TGAAAATAT
*
1212390 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATGT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
* *
1212428 ATATAATATATAG-TTTGAAAACTTTTTTTG-AAATGT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
* *
1212464 ATATAATATATAGTTTTGAAAACATTTTTTCAAAACAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
1212502 ATATA
1 ATATA
1212507 GTTTGAATTT
Statistics
Matches: 221, Mismatches: 26, Indels: 23
0.82 0.10 0.09
Matches are distributed among these distances:
30 2 0.01
31 7 0.03
32 1 0.00
33 17 0.08
34 6 0.03
35 22 0.10
36 28 0.13
37 59 0.27
38 70 0.32
39 9 0.04
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (38 bp):
ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
Found at i:1212316 original size:12 final size:12
Alignment explanation
Indices: 1212261--1212322 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
1212251 TAATGTATAG
*
1212261 TTTTGAAAACAAT
1 TTTTGAAAA-TAT
1212274 TTTTGAAAATAT
1 TTTTGAAAATAT
* * *
1212286 ATAT-AATATATAG
1 TTTTGAA-A-ATAT
1212299 TTTTGAAAATAT
1 TTTTGAAAATAT
1212311 TTTTGAAAATAT
1 TTTTGAAAATAT
1212323 ATAATATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
11 2 0.05
12 20 0.51
13 15 0.38
14 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:1212504 original size:36 final size:36
Alignment explanation
Indices: 1212206--1212586 Score: 298
Period size: 37 Copynumber: 10.8 Consensus size: 36
1212196 CGCTTTTAAA
* * *
1212206 AAAACATATATTATATAGTTTTGAGAACA-TTTTTG
1 AAAATATATAATATATAGTTTTGAAAACATTTTTTG
* *
1212241 AAAATATATATAATGTATAGTTTTGAAAACAATTTTTG
1 -AAA-ATATATAATATATAGTTTTGAAAACATTTTTTG
*
1212279 AAAATATATATAATATATAGTTTTGAAAATA-TTTTTG
1 -AAA-ATATATAATATATAGTTTTGAAAACATTTTTTG
*
1212316 AAAATATATAATATATAGTTTT-AAAAC--GTTTTG
1 AAAATATATAATATATAGTTTTGAAAACATTTTTTG
* *****
1212349 AAAATATAT-A-ATATAG-CTTGATTTTTTTTTTCTG
1 AAAATATATAATATATAGTTTTGAAAACATTTTT-TG
1212383 AAAACATATATAATATATAGTTTTGAAAACATTTTTTG
1 -AAA-ATATATAATATATAGTTTTGAAAACATTTTTTG
*
1212421 AAAATGTATATAATATATAG-TTTGAAAACTTTTTTTG
1 AAAA--TATATAATATATAGTTTTGAAAACATTTTTTG
*
1212458 AAATGTATATAATATATAGTTTTGAAAACATTTTTT-
1 AAA-ATATATAATATATAGTTTTGAAAACATTTTTTG
* * *
1212494 -CAA-A-A-CATATATAG-TTTG--AA-TTTTTTTG
1 AAAATATATAATATATAGTTTTGAAAACATTTTTTG
* **
1212522 AAAACATACATAATATATAGTTTTTTAAA-ATATTTTTG
1 -AAA-ATATATAATATATAGTTTTGAAAACAT-TTTTTG
*
1212560 AAAACT-TATAATATATAGTTTTTAAAA
1 AAAA-TATATAATATATAGTTTTGAAAA
1212587 TGAATTTGAA
Statistics
Matches: 285, Mismatches: 33, Indels: 54
0.77 0.09 0.15
Matches are distributed among these distances:
27 6 0.02
28 2 0.01
30 7 0.02
31 16 0.06
32 3 0.01
33 19 0.07
34 14 0.05
35 26 0.09
36 47 0.16
37 73 0.26
38 63 0.22
39 9 0.03
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (36 bp):
AAAATATATAATATATAGTTTTGAAAACATTTTTTG
Found at i:1212610 original size:73 final size:72
Alignment explanation
Indices: 1212518--1212654 Score: 170
Period size: 73 Copynumber: 1.9 Consensus size: 72
1212508 TTTGAATTTT
* * * * * * *
1212518 TTTGAAAACATACATAATATATA-GTTTTTTAAAATATTTTTGAAAACTTATA-ATATATAGTTT
1 TTTGAAAACATAAAAAATATA-AGGGTTTTGAAAACA-TTTAGAAAACATATATA-ATATAGTTT
1212581 TTAAAATGAA
63 TTAAAATGAA
1212591 TTTGAAAACATAAAAAATATAAGGGTTTTGAAAACATTTAGAAAACATATATAATATAGTTTTT
1 TTTGAAAACATAAAAAATATAAGGGTTTTGAAAACATTTAGAAAACATATATAATATAGTTTTT
1212655 CATTATTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
72 25 0.45
73 30 0.55
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (72 bp):
TTTGAAAACATAAAAAATATAAGGGTTTTGAAAACATTTAGAAAACATATATAATATAGTTTTTA
AAATGAA
Found at i:1212619 original size:139 final size:140
Alignment explanation
Indices: 1212235--1212629 Score: 364
Period size: 142 Copynumber: 2.8 Consensus size: 140
1212225 TTTGAGAACA
* * * * *
1212235 TTTT-TGAAAATATATATAATGTATAGTTTTGAAAACAATTTTTGAAAATATATATAATATATAG
1 TTTTCTGAAAACATACATAATATATAGTTTTGAAAACATTTTTTGAAAATCTATATAATATATAG
* * * * ** *
1212299 TTTTGAAAA-T-ATTTTTGAAA-ATATATAATATATAGTTTT-AAAAC-GTTTTGAAAATATATA
66 -TTTGAAAACTGA-ATTTGAAACATAAAAAATATATAGTTTTGAAAACATTTTTTCAAA-ACAT-
* *
1212359 ATATAGCTTGATTTTTT
127 ATATAGTTTGA---ATT
* *
1212376 TTTTCTGAAAACATATATAATATATAGTTTTGAAAACATTTTTTGAAAATGTATATAATATATAG
1 TTTTCTGAAAACATACATAATATATAGTTTTGAAAACATTTTTTGAAAATCTATATAATATATAG
*** ** * *
1212441 TTTGAAAACTTTTTTTGAAATGTATATAATATATAGTTTTGAAAACATTTTTTCAAAACATATAT
66 TTTGAAAACTGAATTTGAAACATAAAAAATATATAGTTTTGAAAACATTTTTTCAAAACATATAT
1212506 AGTTTGAATT
131 AGTTTGAATT
**
1212516 TTTT-TGAAAACATACATAATATATAGTTTTTTAAA-ATATTTTTGAAAA-CT-TATAATATATA
1 TTTTCTGAAAACATACATAATATATAGTTTTGAAAACAT-TTTTTGAAAATCTATATAATATATA
*
1212577 GTTTTTAAAA-TGAATTTGAAAACATAAAAAATATA-AGGGTTTTGAAAACATTT
65 G-TTTGAAAACTGAATTTG-AAACATAAAAAATATATA--GTTTTGAAAACATTT
1212630 AGAAAACATA
Statistics
Matches: 219, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
137 18 0.08
138 22 0.10
139 53 0.24
140 6 0.03
141 12 0.05
142 65 0.30
143 28 0.13
144 8 0.04
145 7 0.03
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (140 bp):
TTTTCTGAAAACATACATAATATATAGTTTTGAAAACATTTTTTGAAAATCTATATAATATATAG
TTTGAAAACTGAATTTGAAACATAAAAAATATATAGTTTTGAAAACATTTTTTCAAAACATATAT
AGTTTGAATT
Found at i:1212673 original size:21 final size:21
Alignment explanation
Indices: 1212644--1212707 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1212634 AACATATATA
*
1212644 ATATAGTTTTTCATTA-TTATT
1 ATATAGTTTAT-ATTATTTATT
*
1212665 ATATTGTTTATATTATTTATT
1 ATATAGTTTATATTATTTATT
* * *
1212686 ATTTATTTTCT-TTATTTATT
1 ATATAGTTTATATTATTTATT
1212706 AT
1 AT
1212708 TTATTTTTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
ATATAGTTTATATTATTTATT
Found at i:1212684 original size:24 final size:21
Alignment explanation
Indices: 1212657--1212715 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 21
1212647 TAGTTTTTCA
1212657 TTATTATTATATTGTTTATATTAT
1 TTATTATT-TATT-TTTAT-TTAT
*
1212681 TTATTATTTA-TTTTCTTTAT
1 TTATTATTTATTTTTATTTAT
1212701 TTATTATTTATTTTT
1 TTATTATTTATTTTT
1212716 TCTTTTTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 14 0.42
21 8 0.24
22 1 0.03
23 2 0.06
24 8 0.24
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTATTATTTATTTTTATTTAT
Found at i:1212687 original size:7 final size:7
Alignment explanation
Indices: 1212675--1212712 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
1212665 ATATTGTTTA
1212675 TATTATT
1 TATTATT
1212682 TATTATT
1 TATTATT
1212689 TATT-TT
1 TATTATT
1212695 CT-TTATT
1 -TATTATT
1212702 TATTATT
1 TATTATT
1212709 TATT
1 TATT
1212713 TTTTCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTATT
Found at i:1212690 original size:16 final size:15
Alignment explanation
Indices: 1212658--1212713 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
1212648 AGTTTTTCAT
1212658 TATTATTATATTGTTTA
1 TATTATT-TATT-TTTA
1212675 TATTATTTATTATTTA
1 TATTATTTATT-TTTA
* *
1212691 TTTTCTTTATTTATTA
1 TATTATTTATTT-TTA
1212707 T-TTATTT
1 TATTATTT
1212714 TTTCTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 21 0.62
17 7 0.21
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TATTATTTATTTTTA
Found at i:1212700 original size:20 final size:20
Alignment explanation
Indices: 1212677--1212714 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1212667 ATTGTTTATA
1212677 TTATTTATTATTTATTTTCT
1 TTATTTATTATTTATTTTCT
1212697 TTATTTATTATTTATTTT
1 TTATTTATTATTTATTTT
1212715 TTCTTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (20 bp):
TTATTTATTATTTATTTTCT
Found at i:1212723 original size:20 final size:19
Alignment explanation
Indices: 1212657--1212723 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 19
1212647 TAGTTTTTCA
1212657 TTATTATTATATTGTTTATATTAT
1 TTATTATT-TATT-TTT-T-TT-T
*
1212681 TTATTATTTATTTTCTTTAT
1 TTATTATTTATTTT-TTTTT
1212701 TTATTATTTATTTTTTCTTT
1 TTATTATTTATTTTTT-TTT
1212721 TTA
1 TTA
1212724 GGGGTCCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 2 0.05
20 20 0.51
21 1 0.03
22 3 0.08
23 5 0.13
24 8 0.21
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.73
Consensus pattern (19 bp):
TTATTATTTATTTTTTTTT
Found at i:1213834 original size:10 final size:10
Alignment explanation
Indices: 1213810--1213860 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
1213800 TTTGAATGTT
*
1213810 ATTTTATTTC
1 ATTTTATTTA
*
1213820 TTTTTATTTA
1 ATTTTATTTA
1213830 ATTTTAATTTA
1 ATTTT-ATTTA
*
1213841 ATTTAATTTA
1 ATTTTATTTA
1213851 ATTTTTATTT
1 A-TTTTATTT
1213861 GTTTTAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 18 0.53
11 16 0.47
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTATTTA
Found at i:1213839 original size:11 final size:11
Alignment explanation
Indices: 1213820--1213860 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1213810 ATTTTATTTC
*
1213820 TTTTTATTTAA
1 TTTTAATTTAA
1213831 TTTTAATTTAA
1 TTTTAATTTAA
1213842 -TTTAATTTAA
1 TTTTAATTTAA
*
1213852 TTTTTATTT
1 TTTTAATTT
1213861 GTTTTAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:1213840 original size:15 final size:15
Alignment explanation
Indices: 1213825--1213854 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1213815 ATTTCTTTTT
1213825 ATTTAATTTTAATTTA
1 ATTTAA-TTTAATTTA
1213841 ATTTAATTTAATTT
1 ATTTAATTTAATTT
1213855 TTATTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTAATTTAATTTA
Found at i:1213866 original size:21 final size:21
Alignment explanation
Indices: 1213811--1213868 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
1213801 TTGAATGTTA
* *
1213811 TTTTATTTCTTTTTATTTAAT
1 TTTTATTTATTTTAATTTAAT
* *
1213832 TTTAATTTAATTTAATTTAAT
1 TTTTATTTATTTTAATTTAAT
*
1213853 TTTTATTTGTTTTAAT
1 TTTTATTTATTTTAAT
1213869 AGAGGCAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTATTTATTTTAATTTAAT
Found at i:1214907 original size:17 final size:18
Alignment explanation
Indices: 1214885--1214918 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1214875 TTTTACTAAC
1214885 TTGTTTT-TTTCATCTTT
1 TTGTTTTCTTTCATCTTT
*
1214902 TTGTTTTCTTTTATCTT
1 TTGTTTTCTTTCATCTT
1214919 ATCATTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (18 bp):
TTGTTTTCTTTCATCTTT
Found at i:1223306 original size:12 final size:12
Alignment explanation
Indices: 1223289--1223313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1223279 AGATGAATGG
1223289 AGCAGTAGAAGC
1 AGCAGTAGAAGC
1223301 AGCAGTAGAAGC
1 AGCAGTAGAAGC
1223313 A
1 A
1223314 ACAAACAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.32, T:0.08
Consensus pattern (12 bp):
AGCAGTAGAAGC
Found at i:1225385 original size:21 final size:21
Alignment explanation
Indices: 1225356--1225408 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1225346 ATTCTGACTA
1225356 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1225377 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1225398 TCGCAATGCGA
1 TCGCATTGCGA
1225409 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1225444 original size:41 final size:40
Alignment explanation
Indices: 1225398--1225514 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 40
1225388 TTTTCCTAAT
* **
1225398 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAA-TACGAAAA
* *
1225439 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATACGAAAA
*
1225479 TCGCAATGCGATTACGTAAATCGCAATGCGGAATAC
1 TCGCAATGCGATTACGTAAATCGCAACGC-GAATAC
1225515 ATATTCGCAA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 34 0.49
41 36 0.51
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGATTACGTAAATCGCAACGCGAATACGAAAA
Found at i:1225524 original size:20 final size:20
Alignment explanation
Indices: 1225398--1225514 Score: 162
Period size: 20 Copynumber: 5.8 Consensus size: 20
1225388 TTTTCCTAAT
1225398 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1225418 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1225439 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1225459 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1225479 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1225499 TCGCAATGCGGAATAC
1 TCGCAATGC-GAATAC
1225515 ATATTCGCAA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
20 63 0.76
21 20 0.24
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1226413 original size:24 final size:24
Alignment explanation
Indices: 1226386--1226439 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1226376 GTATTCGAAA
1226386 TTTGATCTTGGTCAATACACGGAC
1 TTTGATCTTGGTCAATACACGGAC
* * *
1226410 TTTGACCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACACGGAC
1226434 TTTGAT
1 TTTGAT
1226440 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACACGGAC
Found at i:1228991 original size:19 final size:20
Alignment explanation
Indices: 1228949--1229003 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1228939 CAATCATCTT
*
1228949 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
*
1228969 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
**
1228988 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
1229004 AGAGAATCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:1229023 original size:33 final size:33
Alignment explanation
Indices: 1228976--1229097 Score: 217
Period size: 33 Copynumber: 3.7 Consensus size: 33
1228966 GGAAATGACT
1228976 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1229009 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1229042 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1229075 ATCGCAAAGCGAAATGAAAATCG
1 ATCGCAATGCGAAATGAAAATCG
1229098 TTTTGTCATT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1229046 original size:14 final size:14
Alignment explanation
Indices: 1228994--1229081 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1228984 GCGAAATGAA
1228994 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1229008 AATCGTAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1229027 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1229041 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1229060 AATCGCAACGAGGG
1 AATCGCAACGAGAG
1229074 AATCGCAA
1 AATCGCAA
1229082 AGCGAAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 26 0.46
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 19 0.33
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1229065 original size:19 final size:19
Alignment explanation
Indices: 1228956--1229067 Score: 91
Period size: 19 Copynumber: 6.4 Consensus size: 19
1228946 CTTAATGTCT
* **
1228956 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
1228976 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1228995 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1229009 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1229028 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1229042 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1229061 ATCGCAA
1 ATCGCAA
1229068 CGAGGGAATC
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.26
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 33 0.45
20 9 0.12
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1229172 original size:19 final size:19
Alignment explanation
Indices: 1229104--1229164 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
1229094 ATCGTTTTGT
1229104 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
1229123 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
1229139 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1229156 CATTGCGAT
1 CATTGCGAT
1229165 AGTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 6 0.17
16 7 0.20
17 7 0.20
19 15 0.43
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:1229290 original size:14 final size:14
Alignment explanation
Indices: 1229271--1229307 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1229261 CATCAATTAA
1229271 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1229285 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1229299 ACAAATCAA
1 ACAAATCAA
1229308 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1230724 original size:21 final size:21
Alignment explanation
Indices: 1230658--1230724 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1230648 GTGAATCGGG
*
1230658 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1230678 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1230700 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1230721 CTCT
1 CTCT
1230725 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1231217 original size:19 final size:20
Alignment explanation
Indices: 1231177--1231228 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1231167 TCTGGAACTT
1231177 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGTG-AAAATG
**
1231198 ACTATCGCAACGTG-AAATG
1 AAAATCGCAACGTGAAAATG
1231217 AAAATCGCAACG
1 AAAATCGCAACG
1231229 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGTGAAAATG
Found at i:1231257 original size:19 final size:19
Alignment explanation
Indices: 1231177--1231264 Score: 69
Period size: 19 Copynumber: 4.8 Consensus size: 19
1231167 TCTGGAACTT
*
1231177 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
1231198 ACTATCGCAACGTGAAATG
1 AAAATCGCAACGCGAAATG
1231217 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
1231231 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
1231250 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1231265 TTATAGTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 1 0.02
18 1 0.02
19 27 0.50
21 12 0.22
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1231283 original size:19 final size:19
Alignment explanation
Indices: 1231261--1231304 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1231251 AAATCGCAAC
1231261 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
1231280 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
*
1231299 CCGATT
1 GCGATT
1231305 TTGTCGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.27, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:1231305 original size:19 final size:19
Alignment explanation
Indices: 1231270--1231307 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1231260 CGCGATTATA
*
1231270 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTCCGATTTTG
1231289 GTTTCGCGTTCCGATTTTG
1 GTTTCGCGTTCCGATTTTG
1231308 TCGTTGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.18, G:0.29, T:0.47
Consensus pattern (19 bp):
GTTTCGCGTTCCGATTTTG
Found at i:1231361 original size:19 final size:19
Alignment explanation
Indices: 1231320--1231376 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1231310 GTTGTGATTT
* * *
1231320 TCATTTCGCGTTGCGAAAT
1 TCATTTCACGTTGCGATAG
1231339 TCATTTCACGTTGCGATAG
1 TCATTTCACGTTGCGATAG
1231358 TCATTTTTCACGTTGCGAT
1 TCA--TTTCACGTTGCGAT
1231377 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (19 bp):
TCATTTCACGTTGCGATAG
Found at i:1231592 original size:94 final size:94
Alignment explanation
Indices: 1231446--1231825 Score: 595
Period size: 94 Copynumber: 4.1 Consensus size: 94
1231436 ATGGATTGCA
* * *
1231446 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCAGAGTATTAAAGAATATACAGT
1 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
*
1231510 TTAGCAGAATTGGAAGCAACCGAACAAAT
66 TTAGCAGAATTGGAAGCAACCGAATAAAT
*
1231539 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
1 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
*
1231603 TTTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGAAGCAACCGAATAAAT
* *
1231633 TTACTTCAACCAAAAGATAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAAT
1 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
* *
1231698 TTAGTAGTATT-GACAGCAACCGAATAAAT
66 TTAGCAGAATTGGA-AGCAACCGAATAAAT
* *
1231727 TTACTTCAACCAAAAGACAAAACAAAAGACCAATACTAACTTCACAATGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
* *
1231792 TTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGAAGCAACCGAATAAAT
1231821 TTACT
1 TTACT
1231826 AAGCAATCTA
Statistics
Matches: 266, Mismatches: 17, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
93 23 0.09
94 242 0.91
95 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
TTAGCAGAATTGGAAGCAACCGAATAAAT
Found at i:1232429 original size:33 final size:33
Alignment explanation
Indices: 1232387--1232451 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1232377 TGTTGGCCTC
**
1232387 CGTTGCGATTATCTCGTTGTGATTTTCATTTCG
1 CGTTGCGATTATCTCGTTGCAATTTTCATTTCG
*
1232420 CGTTGCGATTCTCTCGTTGCAATTTTCATTTC
1 CGTTGCGATTATCTCGTTGCAATTTTCATTTC
1232452 TCTCGTTGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTATCTCGTTGCAATTTTCATTTCG
Found at i:1232454 original size:21 final size:21
Alignment explanation
Indices: 1232428--1232506 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
1232418 CGCGTTGCGA
*
1232428 TTCTCTCGTTGCAATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
1232449 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
1232470 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
1232490 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
1232507 AAGTTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1233081 original size:20 final size:20
Alignment explanation
Indices: 1233058--1233175 Score: 155
Period size: 20 Copynumber: 5.8 Consensus size: 20
1233048 CGATAGTCAG
1233058 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1233078 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
1233098 AATTCGCATTGTGATTTACGT
1 -ATTCGCATTGCGATTTACGT
*
1233119 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
1233139 AATCGCGTTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1233159 ATTCGTATTGCGATTTA
1 ATTCGCATTGCGATTTA
1233176 GGAAAATCAC
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 67 0.80
21 17 0.20
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1233114 original size:41 final size:41
Alignment explanation
Indices: 1233058--1233175 Score: 166
Period size: 41 Copynumber: 2.9 Consensus size: 41
1233048 CGATAGTCAG
*
1233058 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACCTA
* * *
1233099 ATTCGCATTGTGATTTACGTATTCGCGTTGCGATTTACGTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACCTA
* * *
1233140 A-TCGCGTTACGATTTACGTATTCGTATTGCGATTTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTA
1233176 GGAAAATCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 30 0.44
41 38 0.56
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACCTA
Found at i:1233213 original size:21 final size:22
Alignment explanation
Indices: 1233161--1233213 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1233151 ATTTACGTAT
*
1233161 TCGTATTGCG-ATTTAGGAAAA
1 TCGTAATGCGAATTTAGGAAAA
** *
1233182 TCACAACGCGAATTTAGG-AAA
1 TCGTAATGCGAATTTAGGAAAA
1233203 TCGTAATGCGA
1 TCGTAATGCGA
1233214 TAGTCAGAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (22 bp):
TCGTAATGCGAATTTAGGAAAA
Found at i:1233509 original size:38 final size:37
Alignment explanation
Indices: 1233423--1233840 Score: 415
Period size: 38 Copynumber: 11.5 Consensus size: 37
1233413 GATTTTAAAA
*
1233423 AAAACATATAT--TATATAGTTTTGAGAACATTTTTG
1 AAAACATATATAATATATAGTTTTGAAAACATTTTTG
* * *
1233458 AAAATATATATAATGTATAGTTTTGAAAACATTTTTCA
1 AAAACATATATAATATATAGTTTTGAAAACATTTTT-G
* * *
1233496 AAAATATATATAATATATAGTTTAGAAAATATTTTTG
1 AAAACATATATAATATATAGTTTTGAAAACATTTTTG
*
1233533 -AAA-ATATATAATATATAGTTTT-AAAAC-GTTTTG
1 AAAACATATATAATATATAGTTTTGAAAACATTTTTG
*
1233566 -AAA-ATATAT-A-ATATAG-TTTGAAAAAAATATTTTTTG
1 AAAACATATATAATATATAGTTTTG---AAAACA-TTTTTG
1233602 AAAACATATATAATATATAGTTTTGAAAACATTTTTTG
1 AAAACATATATAATATATAGTTTTGAAAACA-TTTTTG
* *
1233640 AAAACGTATATGATATATAG-TTTGAAAACAGTTTTTG
1 AAAACATATATAATATATAGTTTTGAAAACA-TTTTTG
* *
1233677 -AAACGTATATAATATATAGTTTTGAAATCATTTTTTG
1 AAAACATATATAATATATAGTTTTGAAAACA-TTTTTG
* * *
1233714 AAAACGTATATAATATATAGTTTTTTAAAATATTTTTG
1 AAAACATATATAATATATAG-TTTTGAAAACATTTTTG
*
1233752 AAAAC-T-TATAATATATAGGTTTT-AAAATGA-TTTTG
1 AAAACATATATAATATATA-GTTTTGAAAA-CATTTTTG
* *
1233787 AAAACATATAAAATATA-AGGGTTTTGAAAACA-TTTAG
1 AAAACATATATAATATATA--GTTTTGAAAACATTTTTG
1233824 AAAACATATATAATATA
1 AAAACATATATAATATA
1233841 GTTTTTCATT
Statistics
Matches: 332, Mismatches: 28, Indels: 44
0.82 0.07 0.11
Matches are distributed among these distances:
30 3 0.01
31 6 0.02
32 1 0.00
33 14 0.04
34 8 0.02
35 42 0.13
36 44 0.13
37 92 0.28
38 103 0.31
39 9 0.03
40 6 0.02
41 4 0.01
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (37 bp):
AAAACATATATAATATATAGTTTTGAAAACATTTTTG
Found at i:1233580 original size:31 final size:33
Alignment explanation
Indices: 1233423--1233844 Score: 195
Period size: 37 Copynumber: 11.6 Consensus size: 33
1233413 GATTTTAAAA
* * * *
1233423 AAAACATATATTATATAGTTTTGAGAACATTTTTG
1 AAAATATATAATATATAG-TTTGAAAAC-GTTTTG
* * *
1233458 AAAATATATATAATGTATAGTTTTGAAAACATTTTTCAA
1 -AAA-ATATATAATATATAG-TTTGAAAAC-GTTTT--G
**
1233497 AAATATATATAATATATAGTTTAGAAAATATTTTTG
1 AAA-ATATATAATATATAGTTT-GAAAA-CGTTTTG
*
1233533 AAAATATATAATATATAGTTTTAAAACGTTTTG
1 AAAATATATAATATATAGTTTGAAAACGTTTTG
**
1233566 AAAATATAT-A-ATATAGTTTGAAAAAAATATTTTTTG
1 AAAATATATAATATATAGTTTG----AAA-ACGTTTTG
*
1233602 AAAACATATATAATATATAGTTTTGAAAACATTTTTTG
1 -AAA-ATATATAATATATAG-TTTGAAAAC--GTTTTG
*
1233640 AAAACGTATATGATATATAGTTTGAAAACAGTTTTTG
1 AAAA--TATATAATATATAGTTTGAAAAC-G-TTTTG
* **
1233677 AAACGTATATAATATATAGTTTTGAAATCATTTTTTG
1 AAA-ATATATAATATATAG-TTTGAAA--ACGTTTTG
* **
1233714 AAAACGTATATAATATATAGTTTTTTAAAATATTTTTG
1 AAAA--TATATAATATATAG--TTTGAAAA-CGTTTTG
* *
1233752 AAAACT-TATAATATATAGGTTTTAAAATGATTTTG
1 AAAA-TATATAATATATA-GTTTGAAAACG-TTTTG
* * * *
1233787 AAAACATATAAAATATAAGGGTTTTGAAAACATTTAG
1 AAAATATATAATATAT-A--G-TTTGAAAACGTTTTG
*
1233824 AAAACATAT-ATAATATAGTTT
1 AAAATATATAAT-ATATAGTTT
1233845 TTCATTATTA
Statistics
Matches: 316, Mismatches: 35, Indels: 73
0.75 0.08 0.17
Matches are distributed among these distances:
31 9 0.03
32 1 0.00
33 17 0.05
34 5 0.02
35 47 0.15
36 41 0.13
37 93 0.29
38 84 0.27
39 9 0.03
40 6 0.02
41 4 0.01
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (33 bp):
AAAATATATAATATATAGTTTGAAAACGTTTTG
Found at i:1233836 original size:74 final size:73
Alignment explanation
Indices: 1233428--1233840 Score: 347
Period size: 74 Copynumber: 5.7 Consensus size: 73
1233418 TAAAAAAAAC
* * * * *
1233428 ATATATTATATA-GTTTTGAGAACATTTTTGAAAATATATATAATGTATAGTTTTGAAAACATTT
1 ATATAATATATAGGTTTTGAAAACATTTTTGAAAACATATATAATATATAGTTTT-AAAATA-TT
* **
1233492 TTCAAAAATAT
64 TT-GAAAACGT
* * **
1233503 ATATAATATATA-GTTTAGAAAATATTTTTG-AAA-ATATATAATATATAGTTTTAAAACGTTTT
1 ATATAATATATAGGTTTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTAAAATATTTT
1233565 GAAAA--T
66 GAAAACGT
*
1233571 ATAT-A-ATATA-G-TTTGAAAAAAATATTTTTTGAAAACATATATAATATATAGTTTTGAAAAC
1 ATATAATATATAGGTTTTG---AAAACA-TTTTTGAAAACATATATAATATATAGTTTT--AAA-
*
1233632 ATTTTTTGAAAACGT
59 ATATTTTGAAAACGT
* * *
1233647 ATATGATATATA-G-TTTGAAAACAGTTTTTG-AAACGTATATAATATATAGTTTTGAAATCATT
1 ATATAATATATAGGTTTTGAAAACA-TTTTTGAAAACATATATAATATATAGTTTT-AAA--ATA
1233709 TTTTGAAAACGT
62 TTTTGAAAACGT
* * *
1233721 ATATAATATATAGTTTTTTAAAATATTTTTGAAAAC-T-TATAATATATAGGTTTTAAAATGATT
1 ATATAATATATAGGTTTTGAAAACATTTTTGAAAACATATATAATATATA-GTTTTAAAAT-ATT
*
1233784 TTGAAAACAT
64 TTGAAAACGT
* *
1233794 ATAAAATATA-AGGGTTTTGAAAACA-TTTAGAAAACATATATAATATA
1 ATATAATATATA-GGTTTTGAAAACATTTTTGAAAACATATATAATATA
1233841 GTTTTTCATT
Statistics
Matches: 291, Mismatches: 25, Indels: 45
0.81 0.07 0.12
Matches are distributed among these distances:
65 3 0.01
66 6 0.02
67 1 0.00
68 11 0.04
69 6 0.02
70 7 0.02
71 23 0.08
72 17 0.06
73 55 0.19
74 85 0.29
75 49 0.17
76 17 0.06
77 1 0.00
78 10 0.03
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (73 bp):
ATATAATATATAGGTTTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTAAAATATTTT
GAAAACGT
Found at i:1235050 original size:10 final size:10
Alignment explanation
Indices: 1235044--1235077 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1235034 ATTTATTTCT
1235044 TTTTATTTAA
1 TTTTATTTAA
1235054 TTTTATTTAA
1 TTTTATTTAA
*
1235064 TTTAATTT-A
1 TTTTATTTAA
1235073 TTTTA
1 TTTTA
1235078 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:1235066 original size:15 final size:15
Alignment explanation
Indices: 1235034--1235081 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1235024 TTTGAATGTT
* *
1235034 ATTT-ATTTCTTTTT
1 ATTTAATTTATTTTA
1235048 ATTTAATTT-TATTTA
1 ATTTAATTTAT-TTTA
1235063 ATTTAATTTATTTTA
1 ATTTAATTTATTTTA
1235078 ATTT
1 ATTT
1235082 TTATTTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 5 0.17
15 24 0.80
16 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTAATTTATTTTA
Found at i:1235211 original size:12 final size:12
Alignment explanation
Indices: 1235194--1235220 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1235184 GAATCGAATC
1235194 TTTAAATTTTCA
1 TTTAAATTTTCA
1235206 TTTAAATTTTCA
1 TTTAAATTTTCA
1235218 TTT
1 TTT
1235221 TTGTAATTAA
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:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAAATTTTCA
Found at i:1236225 original size:30 final size:31
Alignment explanation
Indices: 1236147--1236227 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
1236137 TATCTGATCT
1236147 ATTTAGTATAATAATGGTCCATAACGTTACCA
1 ATTTAGTATAA-AATGGTCCATAACGTTACCA
* *
1236179 ATTTAATATAAAATGGTCCATAACGTTACCG
1 ATTTAGTATAAAATGGTCCATAACGTTACCA
1236210 ATTTAGTAT-AAATGGTCC
1 ATTTAGTATAAAATGGTCC
1236228 CTCAGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 9 0.20
31 27 0.59
32 10 0.22
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (31 bp):
ATTTAGTATAAAATGGTCCATAACGTTACCA
Found at i:1238124 original size:15 final size:16
Alignment explanation
Indices: 1238098--1238127 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1238088 AACAAGTTCA
1238098 ATGAATGAAGAACAAT
1 ATGAATGAAGAACAAT
1238114 ATGAA-GAAGAACAA
1 ATGAATGAAGAACAA
1238128 GTTGCTGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.13
Consensus pattern (16 bp):
ATGAATGAAGAACAAT
Found at i:1249750 original size:24 final size:24
Alignment explanation
Indices: 1249723--1249770 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1249713 GAACTTGACT
1249723 TAGTTTGGCCAAAATCTTTTGTGA
1 TAGTTTGGCCAAAATCTTTTGTGA
** *
1249747 TAGTTTGGGGAAACTCTTTTGTGA
1 TAGTTTGGCCAAAATCTTTTGTGA
1249771 ATTTATCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (24 bp):
TAGTTTGGCCAAAATCTTTTGTGA
Found at i:1250017 original size:22 final size:22
Alignment explanation
Indices: 1249989--1250037 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1249979 TCATGCACAA
1249989 CAATTTAAGCTTAAACAAAAAT
1 CAATTTAAGCTTAAACAAAAAT
* *
1250011 CAATTTAAGCTTCAACATAAAT
1 CAATTTAAGCTTAAACAAAAAT
1250033 -AATTT
1 CAATTT
1250038 CATTACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (22 bp):
CAATTTAAGCTTAAACAAAAAT
Found at i:1250500 original size:13 final size:13
Alignment explanation
Indices: 1250482--1250524 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1250472 TCCATTCTTT
*
1250482 TTTTTTCCGTCTC
1 TTTTTTCTGTCTC
*
1250495 TTTTTTTTGTCTC
1 TTTTTTCTGTCTC
1250508 TTCTTCTTCTGTCTC
1 TT-TT-TTCTGTCTC
1250523 TT
1 TT
1250525 CTCCCTCGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.52
14 2 0.08
15 10 0.40
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (13 bp):
TTTTTTCTGTCTC
Found at i:1250525 original size:15 final size:14
Alignment explanation
Indices: 1250484--1250526 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
1250474 CATTCTTTTT
*
1250484 TTTTCCGTCTCTT-
1 TTTTCTGTCTCTTC
*
1250497 TTTTTTGTCTCTTC
1 TTTTCTGTCTCTTC
1250511 TTCTTCTGTCTCTTC
1 TT-TTCTGTCTCTTC
1250526 T
1 T
1250527 CCCTCGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.44
14 2 0.08
15 12 0.48
ACGTcount: A:0.00, C:0.28, G:0.07, T:0.65
Consensus pattern (14 bp):
TTTTCTGTCTCTTC
Found at i:1250830 original size:20 final size:21
Alignment explanation
Indices: 1250805--1250856 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1250795 TTTTCCCAAT
*
1250805 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1250825 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1250846 TCGCAATGCGA
1 TCGCAATGCGA
1250857 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1250870 original size:20 final size:19
Alignment explanation
Indices: 1250845--1250957 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 19
1250835 AATTGGGAAA
1250845 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
*
1250865 ATCGCAATGTGATACTTACT
1 ATCGCAATGCGATAC-TACT
*
1250885 ATCGCAATGCGATA-TACAAA
1 ATCGCAATGCGATACTAC--T
* *
1250905 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACT-ACT
* *
1250925 -TCGCAATGTGATAATACAT
1 ATCGCAATGCGATACTAC-T
1250944 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1250958 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
18 5 0.07
19 13 0.17
20 42 0.56
21 13 0.17
22 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:1250909 original size:40 final size:40
Alignment explanation
Indices: 1250865--1250953 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
1250855 GATACTGACT
* *
1250865 ATCGCAATGTGATACTTACTATCGCAATGCGAT-ATACAAA
1 ATCGCAATGAGATACTGACT-TCGCAATGCGATAATACAAA
* * *
1250905 ATCGCAACGAGATACTGACTTCGCAATGTGATAATACATA
1 ATCGCAATGAGATACTGACTTCGCAATGCGATAATACAAA
1250945 ATCGCAATG
1 ATCGCAATG
1250954 CGATTTTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 11 0.26
40 31 0.74
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (40 bp):
ATCGCAATGAGATACTGACTTCGCAATGCGATAATACAAA
Found at i:1250919 original size:60 final size:60
Alignment explanation
Indices: 1250842--1250957 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
1250832 GCGAATTGGG
* * *
1250842 AAAATCGCAATGCGATACTGACTATCGCAATGTGATACTTAC-T-ATCGCAATGCGATATAC
1 AAAATCGCAACGAGATACTGACT-TCGCAATGTGATA-ATACATAATCGCAATGCGATATAC
1250902 AAAATCGCAACGAGATACTGACTTCGCAATGTGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTGACTTCGCAATGTGATAATACATAATCGCAATGCGAT
1250958 TTTCAAAGCG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 3 0.06
59 14 0.27
60 34 0.67
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (60 bp):
AAAATCGCAACGAGATACTGACTTCGCAATGTGATAATACATAATCGCAATGCGATATAC
Found at i:1251443 original size:19 final size:20
Alignment explanation
Indices: 1251400--1251447 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
1251390 GCGATTCTCT
1251400 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1251420 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
1251439 TGTTGCGAT
1 CGTTGCGAT
1251448 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1252794 original size:17 final size:18
Alignment explanation
Indices: 1252769--1252812 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1252759 TCCACTTCGG
*
1252769 GAGCCATCACCT-GCCCA
1 GAGCCATCACCTCACCCA
*
1252786 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1252804 GAGCCATCA
1 GAGCCATCA
1252813 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.27, C:0.43, G:0.16, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1253340 original size:19 final size:20
Alignment explanation
Indices: 1253286--1253352 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1253276 TAGTTTACTT
* *
1253286 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1253306 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1253326 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1253345 TCGCAACG
1 TCGCAACG
1253353 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:1253348 original size:39 final size:34
Alignment explanation
Indices: 1253305--1253406 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 34
1253295 GAAAATGACT
*
1253305 ATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAA
1 ATCGCAACGC-GAAAT-G--ATCGCAATGCGAAA-CAAA
1253344 ATCGCAACGAC-AAA--ATCGCAATGCGAAACAAA
1 ATCGCAACG-CGAAATGATCGCAATGCGAAACAAA
1253376 ATCGCAACGCGAAATGAAAATCGCAATGCGA
1 ATCGCAACGCGAAATG---ATCGCAATGCGA
1253407 TTTTGTCGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 16
0.76 0.01 0.22
Matches are distributed among these distances:
31 1 0.02
32 15 0.27
33 14 0.25
37 12 0.22
38 3 0.05
39 9 0.16
40 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGCGAAATGATCGCAATGCGAAACAAA
Found at i:1253360 original size:14 final size:15
Alignment explanation
Indices: 1253341--1253384 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
1253331 ATGCGAAATG
1253341 AAAATCGCAACG-AC
1 AAAATCGCAACGAAC
1253355 AAAATCGCAATGCGAAAC
1 AAAATCGCAA--CG-AAC
1253373 AAAATCGCAACG
1 AAAATCGCAACG
1253385 CGAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.38
16 4 0.15
18 12 0.46
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (15 bp):
AAAATCGCAACGAAC
Found at i:1253397 original size:19 final size:19
Alignment explanation
Indices: 1253286--1253406 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
1253276 TAGTTTACTT
* **
1253286 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1253306 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1253326 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1253345 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
* *
1253359 TCGCAATGCGAAA-CAAAA
1 TCGCAACGCGAAATGAAAA
1253377 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1253396 TCGCAATGCGA
1 TCGCAACGCGA
1253407 TTTTGTCGTT
Statistics
Matches: 85, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.21
19 27 0.32
20 24 0.28
21 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1253438 original size:32 final size:32
Alignment explanation
Indices: 1253396--1253471 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
1253386 GAAATGAAAA
*
1253396 TCGCAATGCGATTTTGTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTT-TCGTTGCGATTTTCATT
1253428 TCGCATTGCGATTTTTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTTCGTTGCGATTTTCATT
1253460 TCGCATTGCGAT
1 TCGCATTGCGAT
1253472 AGCCATTTCC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 9 0.21
32 33 0.79
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (32 bp):
TCGCATTGCGATTTTTCGTTGCGATTTTCATT
Found at i:1253449 original size:13 final size:13
Alignment explanation
Indices: 1253402--1253455 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 13
1253392 AAAATCGCAA
1253402 TGCGATTTTGTCGT
1 TGCGATTTT-TCGT
1253416 TGCGATTTCATTTCGCAT
1 TGCGA-TT--TTTCG--T
1253434 TGCGATTTTTCGT
1 TGCGATTTTTCGT
1253447 TGCGATTTT
1 TGCGATTTT
1253456 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.29
14 5 0.14
15 7 0.20
16 3 0.09
17 4 0.11
18 6 0.17
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (13 bp):
TGCGATTTTTCGT
Found at i:1253468 original size:19 final size:18
Alignment explanation
Indices: 1253415--1253471 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 18
1253405 GATTTTGTCG
1253415 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
1253433 TTGCGA-TT--TTTCG--
1 TTGCGATTTCATTTCGCA
1253446 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
1253465 TTGCGAT
1 TTGCGAT
1253472 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 6 0.18
15 7 0.21
17 7 0.21
18 7 0.21
19 6 0.18
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:1253508 original size:20 final size:20
Alignment explanation
Indices: 1253456--1253499 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1253446 TTGCGATTTT
* *
1253456 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCAATAGC
*
1253475 CATTTCCGCGTTGCAATAGT
1 CATTTCCGCGTTGCAATAGC
1253495 CATTT
1 CATTT
1253500 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCAATAGC
Found at i:1255379 original size:14 final size:14
Alignment explanation
Indices: 1255360--1255395 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1255350 ATTGTTTAAT
1255360 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1255374 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1255388 TGATTTGT
1 TGATTTGT
1255396 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1255543 original size:19 final size:17
Alignment explanation
Indices: 1255519--1255564 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
1255509 TCGCAACGAG
1255519 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
1255538 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
1255552 AATCGCAATGCGA
1 AATCGCAATGCGA
1255565 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:1256832 original size:12 final size:12
Alignment explanation
Indices: 1256815--1256839 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1256805 TCATAATCCT
1256815 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1256827 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1256839 G
1 G
1256840 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1259168 original size:33 final size:33
Alignment explanation
Indices: 1259122--1259248 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1259112 GGAAATTACT
1259122 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
1259155 ATCGCAATACGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1259187 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1259221 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1259249 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1259234 original size:66 final size:66
Alignment explanation
Indices: 1259123--1259255 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1259113 GAAATTACTA
*
1259123 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGCGAAT
1259188 T
66 T
* *
1259189 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGCGAAT
1259254 T
66 T
1259255 T
1 T
1259256 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGCGAAT
T
Found at i:1259290 original size:19 final size:18
Alignment explanation
Indices: 1259252--1259322 Score: 78
Period size: 19 Copynumber: 4.1 Consensus size: 18
1259242 CGCAACGCGA
*
1259252 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
1259270 ATTTTCATTTCGCGTTGCG
1 A-TTTCATTTCGCGTTGCG
*
1259289 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
1259303 ATTTCATTTCGCATTGCG
1 ATTTCATTTCGCGTTGCG
1259321 AT
1 AT
1259323 AGTACTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 10 0.23
15 3 0.07
17 3 0.07
18 11 0.25
19 17 0.39
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:1259447 original size:14 final size:14
Alignment explanation
Indices: 1259428--1259464 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1259418 CATCAATTAA
1259428 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1259442 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1259456 ACAAATCAA
1 ACAAATCAA
1259465 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1260883 original size:21 final size:21
Alignment explanation
Indices: 1260817--1260883 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1260807 GTGAATCGGG
*
1260817 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1260837 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1260859 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1260880 CTCT
1 CTCT
1260884 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1261023 original size:83 final size:84
Alignment explanation
Indices: 1260847--1261023 Score: 320
Period size: 83 Copynumber: 2.1 Consensus size: 84
1260837 CCTCTTCAAC
*
1260847 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGGCCTCTTCAATG
1 GATGACAG-GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGGCCTCTTCAACG
1260912 ATAGGAGTGGACTCTTGAGG
65 ATAGGAGTGGACTCTTGAGG
*
1260932 GATGACAGGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATA-GGGGCCTCTTCAACGA
1 GATGACAGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGGCCTCTTCAACGA
1260996 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1261015 GATGACAGG
1 GATGACAGG
1261024 CGAGTCGGGC
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
83 43 0.48
84 39 0.43
85 8 0.09
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.21
Consensus pattern (84 bp):
GATGACAGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1261357 original size:92 final size:90
Alignment explanation
Indices: 1261243--1261427 Score: 284
Period size: 89 Copynumber: 2.0 Consensus size: 90
1261233 ATATTTCAAA
* *
1261243 ACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTT
1 ACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAATGTT----AATAAACAGTTT
1261307 AGCAGAATTGGCAGCAA-CGAATAAATTT
62 AGCAGAATTGGCAGCAACCGAATAAATTT
*
1261335 ACTTCAACCAAAAGATAAAACAAAAGACAAATACTAACTTCACAATGTTAATAAACAGTTTAGCA
1 ACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAATGTTAATAAACAGTTTAGCA
*
1261400 GTATTGGCAGCAACCGAATAAATTT
66 GAATTGGCAGCAACCGAATAAATTT
1261425 ACT
1 ACT
1261428 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
89 27 0.31
90 14 0.16
92 20 0.23
93 26 0.30
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAATGTTAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:1263149 original size:19 final size:19
Alignment explanation
Indices: 1263096--1263278 Score: 179
Period size: 19 Copynumber: 10.1 Consensus size: 19
1263086 GTCTTTGGTT
*
1263096 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
1263115 GATAAAGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1263135 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
* * *
1263152 G--A-GAGAATCACAACAC
1 GAAATGAAAATCGCAACGC
*
1263168 GAAATGAAAATTGCAACGC
1 GAAATGAAAATCGCAACGC
1263187 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1263206 GAAATGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGC
1263225 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1263242 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1263258 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1263277 GA
1 GA
1263279 TTTTGGTTTC
Statistics
Matches: 134, Mismatches: 19, Indels: 22
0.77 0.11 0.13
Matches are distributed among these distances:
14 18 0.13
15 2 0.01
16 4 0.03
17 3 0.02
18 2 0.01
19 89 0.66
20 16 0.12
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1263211 original size:71 final size:69
Alignment explanation
Indices: 1263096--1263278 Score: 206
Period size: 71 Copynumber: 2.6 Consensus size: 69
1263086 GTCTTTGGTT
* * * **
1263096 GAAATGAAAATCGCAACGAGATAAAGAGAATCGCAACGCGAAATGACTATCGCAACGAGAGAATC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGA-AATC
1263161 ACAACA-C
64 A-AA-ATC
* * *
1263168 GAAATGAAAATTGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGTGAAATGAA
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAAATCAA
1263233 AATC
66 AATC
* * *
1263237 GCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAAATGA-A-AATCGCAACGCGAAATGAAAATCGCAACGCGA
1263279 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
68 1 0.01
69 8 0.08
70 5 0.05
71 63 0.66
72 19 0.20
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (69 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAAATCAA
AATC
Found at i:1263251 original size:33 final size:36
Alignment explanation
Indices: 1263098--1263273 Score: 143
Period size: 33 Copynumber: 4.9 Consensus size: 36
1263088 CTTTGGTTGA
* * *
1263098 AATGAAAATCGCAACGAGATAAAGAGAATCGCAACGCG
1 AATGAAAATCGCAACGCGA-AATGAAAATCGCAAC-CG
** * *
1263136 AAATGACTATCGCAA--CG--A-GAGAATCACAACACG
1 -AATGAAAATCGCAACGCGAAATGAAAATCGCAAC-CG
*
1263169 AAATGAAAATTGCAACGCGAAATGAAAATCGCAACGCG
1 -AATGAAAATCGCAACGCGAAATGAAAATCGCAAC-CG
*
1263207 AAATGAAAATCGCAACGTGAAATGAAAATCGCAA-CG
1 -AATGAAAATCGCAACGCGAAATGAAAATCGCAACCG
*
1263243 -A-GAGAATCGCAACGCGAAATGAAAATCGCAA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAA
1263274 TGCGATTTTG
Statistics
Matches: 117, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
33 53 0.45
34 2 0.02
35 2 0.02
36 2 0.02
37 2 0.02
38 44 0.38
39 12 0.10
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (36 bp):
AATGAAAATCGCAACGCGAAATGAAAATCGCAACCG
Found at i:1263296 original size:19 final size:19
Alignment explanation
Indices: 1263274--1263321 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1263264 AAAATCGCAA
*
1263274 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
1263293 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
1263313 TGCGATTTT
1 TGCGATTTT
1263322 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:1263860 original size:20 final size:20
Alignment explanation
Indices: 1263836--1263969 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
1263826 CGCTATGTAA
* * *
1263836 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1263856 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * * *
1263876 AACTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
1263897 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1263917 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1263937 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1263957 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1263970 TTTCCCAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
19 3 0.03
20 84 0.84
21 11 0.11
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Done.