Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:274832 original size:13 final size:13
Alignment explanation
Indices: 274816--274852 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
274806 TTATATATTT
274816 ATATTAAATAATA
1 ATATTAAATAATA
*
274829 ATATTTAATAATA
1 ATATTAAATAATA
274842 ATAATTAAATA
1 AT-ATTAAATA
274853 TATTGCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTAAATAATA
Found at i:274893 original size:18 final size:17
Alignment explanation
Indices: 274872--274905 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
274862 TAAATATACA
274872 AAATTAAAATAATAAATT
1 AAATTAAAAT-ATAAATT
274890 AAATTAAAATATAAAT
1 AAATTAAAATATAAAT
274906 AACAGTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTAAAATATAAATT
Found at i:275829 original size:16 final size:17
Alignment explanation
Indices: 275808--275853 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
275798 TCTCTGTTTC
*
275808 TCGTCTCCCGTTCTGT-
1 TCGTCTCCCGTTCTCTG
275824 TCGTCTCCCGTTCTCTG
1 TCGTCTCCCGTTCTCTG
275841 T-GTCTCCCGTTCT
1 TCGTCTCCCGTTCT
275854 TTGTGTATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 27 0.96
17 1 0.04
ACGTcount: A:0.00, C:0.39, G:0.17, T:0.43
Consensus pattern (17 bp):
TCGTCTCCCGTTCTCTG
Found at i:275858 original size:16 final size:16
Alignment explanation
Indices: 275810--275859 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
275800 TCTGTTTCTC
*
275810 GTCTCCCGTTCTGTT-C
1 GTCTCCCGTTCT-TTGT
*
275826 GTCTCCCGTTCTCTGT
1 GTCTCCCGTTCTTTGT
275842 GTCTCCCGTTCTTTGT
1 GTCTCCCGTTCTTTGT
275858 GT
1 GT
275860 ATCTCTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 1 0.03
16 29 0.97
ACGTcount: A:0.00, C:0.34, G:0.20, T:0.46
Consensus pattern (16 bp):
GTCTCCCGTTCTTTGT
Found at i:276372 original size:3 final size:3
Alignment explanation
Indices: 276364--276449 Score: 73
Period size: 3 Copynumber: 27.7 Consensus size: 3
276354 TTTTATTTTA
* * * *
276364 AAT AAT AAT ATTT AAT AAT ATT ATT AAT AAT AAT ATAT ATAT AAT ATT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT
** * *
276412 AAT AAT AAT AAT AAT AAT TTT ACT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
276450 AACGAAATGA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 59 0.87
4 9 0.13
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:276407 original size:26 final size:25
Alignment explanation
Indices: 276364--276448 Score: 100
Period size: 26 Copynumber: 3.4 Consensus size: 25
276354 TTTTATTTTA
* *
276364 AATAATAATATTTAATAATATTATT
1 AATAATAATATATAATAATATTAAT
276389 AATAATAATATATATATAATATTAAT
1 AATAATAATATATA-ATAATATTAAT
** *
276415 AATAATAATA-ATAATTTTACTAAT
1 AATAATAATATATAATAATATTAAT
*
276439 AAAAATAATA
1 AATAATAATA
276449 AAACGAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
24 17 0.32
25 16 0.30
26 20 0.38
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAATAATATATAATAATATTAAT
Found at i:280419 original size:6 final size:6
Alignment explanation
Indices: 280408--280446 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
280398 ATGTACCAAC
* *
280408 GAGGTA GAGGTA GAGGTA GAGGTA GAGGCA GAGGGA GAG
1 GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAG
280447 AGAGAGTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.54, T:0.10
Consensus pattern (6 bp):
GAGGTA
Found at i:282999 original size:16 final size:16
Alignment explanation
Indices: 282974--283008 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
282964 ATTCATACAG
282974 AGCATCTGAATCATTC
1 AGCATCTGAATCATTC
*
282990 AGCATTTGAATCATTC
1 AGCATCTGAATCATTC
283006 AGC
1 AGC
283009 GCTTAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (16 bp):
AGCATCTGAATCATTC
Found at i:283018 original size:15 final size:16
Alignment explanation
Indices: 282980--283020 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
282970 ACAGAGCATC
*
282980 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
282996 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
283012 T-AATCATTC
1 TGAATCATTC
283021 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:283069 original size:19 final size:19
Alignment explanation
Indices: 283045--283082 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
283035 AACCCCTAAT
283045 TTAATTTTAAGGGCTTAAA
1 TTAATTTTAAGGGCTTAAA
*
283064 TTAATTTTAAGTGCTTAAA
1 TTAATTTTAAGGGCTTAAA
283083 GAATTTGTAG
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:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (19 bp):
TTAATTTTAAGGGCTTAAA
Found at i:284301 original size:20 final size:19
Alignment explanation
Indices: 284268--284306 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
284258 ATCTAGACTA
284268 AATTGAGTAATAAAATAAT
1 AATTGAGTAATAAAATAAT
*
284287 AATTGAAGTAGTAAAATAAT
1 AATTG-AGTAATAAAATAAT
284307 TATTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (19 bp):
AATTGAGTAATAAAATAAT
Found at i:286183 original size:21 final size:23
Alignment explanation
Indices: 286157--286198 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
286147 ATGGATTCTC
286157 TTTCCTT-TT-TTTTTTCAAAAT
1 TTTCCTTATTATTTTTTCAAAAT
286178 TTTCCTTATTATTTTTTCAAA
1 TTTCCTTATTATTTTTTCAAA
286199 TGTTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTCCTTATTATTTTTTCAAAAT
Found at i:286626 original size:32 final size:32
Alignment explanation
Indices: 286590--286653 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
286580 AAAAGAGAAG
286590 AGGTGAATCATACCTAGAGCATTAGGGAGAGT
1 AGGTGAATCATACCTAGAGCATTAGGGAGAGT
*
286622 AGGTGAATCATACCTATAGCATTAGGGAGAGT
1 AGGTGAATCATACCTAGAGCATTAGGGAGAGT
286654 CTAAGGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.23
Consensus pattern (32 bp):
AGGTGAATCATACCTAGAGCATTAGGGAGAGT
Found at i:289076 original size:21 final size:21
Alignment explanation
Indices: 289050--289089 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
289040 AATATTGTGT
*
289050 ATCGATGCACTGCTATAGTGC
1 ATCGATGCACAGCTATAGTGC
289071 ATCGATGCACAGCTATAGT
1 ATCGATGCACAGCTATAGT
289090 ACCGCTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
ATCGATGCACAGCTATAGTGC
Found at i:289755 original size:61 final size:61
Alignment explanation
Indices: 289643--289757 Score: 176
Period size: 61 Copynumber: 1.9 Consensus size: 61
289633 GTAGTGCTAA
* *
289643 ACCTGCACTAAGCTTACGCCATAGTGCTAATCCGGATATGACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGTGCCCACC
* * * *
289704 ACCTACACTAAGCTTACGCTATAGTGTTAATCCGGACATGATACATTAGGTCGT
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGT
289758 ATCCACCTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGTGCCCACC
Found at i:293067 original size:60 final size:60
Alignment explanation
Indices: 292999--293111 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
292989 ATTCTCCCCT
* ** * *
292999 GACTATAGGGTGATGTTTCGTTGAGTCTTTCGACTATTAAAAGTTATAAAATGATTTTTC
1 GACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTTTTC
* *
293059 GACTATAGGGTGTTGTTTTGTTCAGTCCCTCGACTATCAAAAGTTACAAAATG
1 GACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATG
293112 GTTATCCAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (60 bp):
GACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTTTTC
Found at i:293124 original size:60 final size:60
Alignment explanation
Indices: 293000--293124 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
292990 TTCTCCCCTG
* ** * * * * *
293000 ACTATAGGGTGATGTTTCGTTGAGTCTTTCGACTATTAAAAGTTATAAAATGATTTTTCG
1 ACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTATCCA
* * *
293060 ACTATAGGGTGTTGTTTTGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGGTTATCCA
1 ACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTATCCA
293120 ACTAT
1 ACTAT
293125 TTAGTATGTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (60 bp):
ACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTATCCA
Found at i:298254 original size:3 final size:3
Alignment explanation
Indices: 298246--298291 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
298236 AACAAGTTGC
298246 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
298292 GTGGACAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:298394 original size:3 final size:3
Alignment explanation
Indices: 298386--298428 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
298376 AACAAGTTGC
298386 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
298429 GTGGACAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:298498 original size:140 final size:138
Alignment explanation
Indices: 298218--298495 Score: 522
Period size: 137 Copynumber: 2.0 Consensus size: 138
298208 ATTGTTAACA
298218 AAAATTTATCTTTTTAAGAACAAGTTGCATTATTATTATTATTATTATTATTATTATTATTATTA
1 AAAATTTATCTTTTTAAGAACAAGTTGC--TATTATTATTATTATTATTATTATTATTATTATTA
298283 TTATTATTAGTGGACAATTCTATTTATTTAATGACACATAAACATTTATTAAAAAATTGAAACAA
64 TTATTATTAGTGGACAATTCTATTTATTTAATGACACATAAACATTTATTAAAAAATTGAAACAA
298348 ACATCATATT
129 ACATCATATT
298358 AAAATTTATCTTTTTAAGAACAAGTTGC-ATTATTATTATTATTATTATTATTATTATTATTATT
1 AAAATTTATCTTTTTAAGAACAAGTTGCTATTATTATTATTATTATTATTATTATTATTATTATT
*
298422 ATTATTAGTGGACAGTTCTATTTATTTAATGACACATAAACATTTATTAAAAAATTGAAACAAAC
66 ATTATTAGTGGACAATTCTATTTATTTAATGACACATAAACATTTATTAAAAAATTGAAACAAAC
298487 ATCATATT
131 ATCATATT
298495 A
1 A
298496 TTATCATAAA
Statistics
Matches: 137, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
137 109 0.80
140 28 0.20
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AAAATTTATCTTTTTAAGAACAAGTTGCTATTATTATTATTATTATTATTATTATTATTATTATT
ATTATTAGTGGACAATTCTATTTATTTAATGACACATAAACATTTATTAAAAAATTGAAACAAAC
ATCATATT
Found at i:298513 original size:18 final size:16
Alignment explanation
Indices: 298490--298522 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
298480 AACAAACATC
298490 ATAT-TATTATCATAA
1 ATATATATTATCATAA
298505 ATA-ATATTATCATAA
1 ATATATATTATCATAA
298520 ATA
1 ATA
298523 ATAATATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATTATCATAA
Found at i:298514 original size:15 final size:15
Alignment explanation
Indices: 298494--298525 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
298484 AACATCATAT
298494 TATTATCATAAATAA
1 TATTATCATAAATAA
298509 TATTATCATAAATAA
1 TATTATCATAAATAA
298524 TA
1 TA
298526 ATATTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTATCATAAATAA
Found at i:299913 original size:13 final size:14
Alignment explanation
Indices: 299895--299937 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
299885 GCAAACGAAT
299895 ATAAACGAACAC-A
1 ATAAACGAACACAA
*
299908 ATAAACAAACACAA
1 ATAAACGAACACAA
* *
299922 ATGAACGAACATAA
1 ATAAACGAACACAA
299936 AT
1 AT
299938 GAAAATAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.63, C:0.19, G:0.07, T:0.12
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:300143 original size:14 final size:14
Alignment explanation
Indices: 300136--300204 Score: 92
Period size: 14 Copynumber: 5.2 Consensus size: 14
300126 AACAAACATA
300136 AACGAACATAAATG
1 AACGAACATAAATG
300150 AACGAACATAAATG
1 AACGAACATAAATG
300164 AACGAACAT--A--
1 AACGAACATAAATG
300174 AACGAACATAAATG
1 AACGAACATAAATG
* *
300188 TATGAACATAAATG
1 AACGAACATAAATG
300202 AAC
1 AAC
300205 ATACTACCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
10 9 0.19
12 2 0.04
14 36 0.77
ACGTcount: A:0.57, C:0.14, G:0.13, T:0.16
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:300204 original size:24 final size:24
Alignment explanation
Indices: 300106--300207 Score: 116
Period size: 24 Copynumber: 4.2 Consensus size: 24
300096 GATTAGGCTA
* *
300106 AACATAAATGAACGCACATAAACA
1 AACATAAATGAACGAACATAAACG
* * *
300130 AACATAAACGAAC-ATAAATGAACG
1 AACATAAATGAACGA-ACATAAACG
300154 AACATAAATGAACGAACATAAACG
1 AACATAAATGAACGAACATAAACG
* * *
300178 AACATAAATGTATGAACATAAATG
1 AACATAAATGAACGAACATAAACG
300202 AACATA
1 AACATA
300208 CTACCGAACG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
24 64 0.98
25 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:305737 original size:2 final size:2
Alignment explanation
Indices: 305730--305827 Score: 162
Period size: 2 Copynumber: 49.5 Consensus size: 2
305720 TGAGAAACCA
* *
305730 TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC TC TC TC GC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
305771 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
305813 TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC T
305828 TCTAATTTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
1 1 0.01
2 88 0.99
ACGTcount: A:0.00, C:0.49, G:0.01, T:0.50
Consensus pattern (2 bp):
TC
Found at i:309004 original size:27 final size:27
Alignment explanation
Indices: 308962--309056 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
308952 TTGTAGGAAT
308962 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
308987 TATAGAGATATGATTTGTTTCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
309014 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
309041 TATAGAGATATGATTT
1 TATAGAGATATGATTT
309057 TGTAAATAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 7 0.11
27 59 0.89
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:312815 original size:27 final size:27
Alignment explanation
Indices: 312773--312867 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
312763 GTGTAGGAAT
312773 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
312798 TATAGAGATATGATTTGTTTCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
312825 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
312852 TATAGAGATATGATTT
1 TATAGAGATATGATTT
312868 TGTAAATAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 7 0.11
27 59 0.89
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:313914 original size:449 final size:450
Alignment explanation
Indices: 313055--314003 Score: 1647
Period size: 449 Copynumber: 2.1 Consensus size: 450
313045 GATTTCTACA
313055 AGTATGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCATTTATTTTATATCTTCTTAGG
1 AGTATGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCATTTATTTTATATCTTCTTAGG
*
313120 CTAATGTTTTTTAAATTCATCTTTTAGTTCAACTAATAACTGTTAAGTGGTCTCATCTCACATTA
66 CTAATGTTTTTTAAATTCATCTTTTAGTTCAACTAATAAATGTTAAGTGGTCTCATCTCACATTA
*
313185 CCTTCATTTACAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGCCTCTGCACCTATTGCTATTAA
131 CCTTCATTTACAGTTTGTTTTGTCTTTGCATTCAATTTTAGGGCCTCTGCACCTATTGCTATTAA
*
313250 TTTTAGGTTGGATGATCAACAGAACTACCTTCTATTTGTTTAAGCCTTTTGGACTTTACCTTTCA
196 TTCTAGGTTGGATGATCAACAGAACTACCTTCTATTTGTTTAAGCCTTTTGGACTTTACCTTTCA
* *
313315 ACCATGGTAATGTACTTATGCATCCTTCTTACCTGCAGCCAAATCAAATTTTTACTCACCATGGG
261 ACCATGGTAATGTACTTATGCATCCTTCTTACCTGCAACCAAATCAAATTTTCACTCACCATGGG
* * *
313380 TTCGCTGGACCTGGATTCGTTGATGTCCTCCACTTTTGGACTGACTGAATCTAATGGAAAAAAAA
326 TTCGCTGGACCTAGATCCGTTGATGTCCTCCACTTTTGGAATGACTGAATCTAATGGAAAAAAAA
*
313445 TACATATTCTGCATAATGAA-G-GTGCTACAACATGGAATGATAGCATTTATGTCAGCCT
391 TACATATTCTGCACAATGAAGGTGTGCTACAACATGGAATGATAGCATTTATGTCAGCCT
*
313503 AGTATGCTACTTTCAGGCTTTTTTTCCAGTGACTTACAAAGCTCATTTATTTTATATCTTCTTAG
1 AGTATGCTACCTTCAGGC-TTTTTTCCAGTGACTTACAAAGCTCATTTATTTTATATCTTCTTAG
313568 GCTAATGTTTTTTAAATTCATCTTTTAGTTCAACTAATAAATGTTAAGTGGTCTCATCTCACATT
65 GCTAATGTTTTTTAAATTCATCTTTTAGTTCAACTAATAAATGTTAAGTGGTCTCATCTCACATT
*
313633 AGCTTCATTTACAGTTTGTTTTGTCTTTGCATTCAATTTTAGGGCCTCTGCACCTATTGCTATTA
130 ACCTTCATTTACAGTTTGTTTTGTCTTTGCATTCAATTTTAGGGCCTCTGCACCTATTGCTATTA
* *
313698 GTTCTAGGTTCGG-TGATCAACAGAACTACCTTCTATTTGTTTAAGCATTTTTGGACTTTACCTT
195 ATTCTAGGTT-GGATGATCAACAGAACTACCTTCTATTTGTTTAAGC-CTTTTGGACTTTACCTT
*
313762 TCAACCATGGTAATGTACTTATGCATCCTTCTTACCTGCAACCAAATCAAATTTTCACTCACCCT
258 TCAACCATGGTAATGTACTTATGCATCCTTCTTACCTGCAACCAAATCAAATTTTCACTCACCAT
313827 GGGTTCGCTGGACCTAGATCCGTTGATGTCCTCCACTTTTGGAATGACTGAATCTAATGG-AAAA
323 GGGTTCGCTGGACCTAGATCCGTTGATGTCCTCCACTTTTGGAATGACTGAATCTAATGGAAAAA
*
313891 AAATACATATTCTGCACAATGAAGGTGGTTGTGCTACAACATGGAATGGTAGCATTTATGTCAGC
388 AAATACATATTCTGCACAATGAA---GG-TGTGCTACAACATGGAATGATAGCATTTATGTCAGC
313956 CT
449 CT
* *
313958 AGTGTGCTACCTTCAGGC-TTTTTCCAGTGAATTACAAAGCTCATTT
1 AGTATGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCATTT
314004 GCTTGAGCAA
Statistics
Matches: 474, Mismatches: 18, Indels: 13
0.94 0.04 0.03
Matches are distributed among these distances:
448 17 0.04
449 240 0.51
450 137 0.29
453 28 0.06
455 52 0.11
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (450 bp):
AGTATGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCATTTATTTTATATCTTCTTAGG
CTAATGTTTTTTAAATTCATCTTTTAGTTCAACTAATAAATGTTAAGTGGTCTCATCTCACATTA
CCTTCATTTACAGTTTGTTTTGTCTTTGCATTCAATTTTAGGGCCTCTGCACCTATTGCTATTAA
TTCTAGGTTGGATGATCAACAGAACTACCTTCTATTTGTTTAAGCCTTTTGGACTTTACCTTTCA
ACCATGGTAATGTACTTATGCATCCTTCTTACCTGCAACCAAATCAAATTTTCACTCACCATGGG
TTCGCTGGACCTAGATCCGTTGATGTCCTCCACTTTTGGAATGACTGAATCTAATGGAAAAAAAA
TACATATTCTGCACAATGAAGGTGTGCTACAACATGGAATGATAGCATTTATGTCAGCCT
Found at i:314987 original size:17 final size:17
Alignment explanation
Indices: 314944--314979 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
314934 TAAAGGTGTG
314944 TTTATTTTTCTATCTTC
1 TTTATTTTTCTATCTTC
314961 TTTATTTTTCTATCTTC
1 TTTATTTTTCTATCTTC
314978 TT
1 TT
314980 CTTTTTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTTCTATCTTC
Found at i:318974 original size:121 final size:122
Alignment explanation
Indices: 318759--318997 Score: 417
Period size: 121 Copynumber: 2.0 Consensus size: 122
318749 GCCCTAATGG
** *
318759 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGGCCGTAGCCCTCCGGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
318824 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGACCA
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGACCA
* * *
318881 TACATATGTAGATTATGGTACGAAACTACCATTGG-CATACAATGAACGTAGCCCTCCAGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
318945 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTG
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTG
318998 GACTCTTTAA
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 79 0.71
122 32 0.29
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGACCA
Found at i:328923 original size:17 final size:17
Alignment explanation
Indices: 328901--328943 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
328891 TAACTTTATT
*
328901 TAAATTATTATTATAAA
1 TAAATTATTAATATAAA
*
328918 TAAATTTTTAATATAAA
1 TAAATTATTAATATAAA
328935 TATAATTAT
1 TA-AATTAT
328944 AAATGAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATTATTAATATAAA
Found at i:330034 original size:21 final size:21
Alignment explanation
Indices: 330010--330050 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
330000 AAATGTTAAA
*
330010 AAACATTAATGTTTTAGGTAG
1 AAACAATAATGTTTTAGGTAG
330031 AAACAATAATGTTTTAGGTA
1 AAACAATAATGTTTTAGGTA
330051 ATTGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (21 bp):
AAACAATAATGTTTTAGGTAG
Found at i:330438 original size:39 final size:39
Alignment explanation
Indices: 330366--330441 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
330356 GCGTTTATTT
**
330366 ATTAAATGAACGAACATGAACAAGATTTACGTTCGTTTA
1 ATTAAATGAACGAACATGAACAAGAGCTACGTTCGTTTA
*
330405 ATTAAATGAACGAACATGAACAAAGGGCT-CGTTCGTT
1 ATTAAATGAACGAACATGAAC-AAGAGCTACGTTCGTT
330442 CATTTACGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 29 0.88
40 4 0.12
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (39 bp):
ATTAAATGAACGAACATGAACAAGAGCTACGTTCGTTTA
Found at i:330493 original size:14 final size:14
Alignment explanation
Indices: 330471--330508 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
330461 TCGATTATAT
*
330471 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
330485 GTTCATTTATGTTC
1 GTTCATTTATGTTC
330499 GTTCATTTAT
1 GTTCATTTAT
330509 TAAATGAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:335363 original size:36 final size:36
Alignment explanation
Indices: 335316--335390 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
335306 TCTTTAGAAG
*
335316 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
1 CATGAGACTCAACAAAATAGTGTTATAGTCGAAAAT
335352 CATGAGACTCAACAAAATAGTGTTATAGTCGAAAAT
1 CATGAGACTCAACAAAATAGTGTTATAGTCGAAAAT
335388 CAT
1 CAT
335391 TTATATACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
CATGAGACTCAACAAAATAGTGTTATAGTCGAAAAT
Found at i:335771 original size:20 final size:20
Alignment explanation
Indices: 335679--335896 Score: 96
Period size: 20 Copynumber: 10.7 Consensus size: 20
335669 ATGGCCCCAT
*
335679 TTCGCGTTGCGATTTTCCAGA
1 TTCGCATTGCGATTTT-CAGA
* * * *
335700 TTCGTATTGCGATAGTCCAAA
1 TTCGCATTGCGAT-TTTCAGA
* ** * *
335721 ATCGCAACGCGGTTTTAAGA
1 TTCGCATTGCGATTTTCAGA
*
335741 TTCGCAGTGCGATTTTCAGA
1 TTCGCATTGCGATTTTCAGA
* ** *
335761 TTCGTATTGCGATAGTCGAAA
1 TTCGCATTGCGATTTTC-AGA
* * ** * *
335782 ATCACAACGCGGTTTTAAGA
1 TTCGCATTGCGATTTTCAGA
* *
335802 TTCGCATTGCGATAGTAT-AAA
1 TTCGCATTGCGAT--TTTCAGA
* **
335823 ATCGCAACGCGATTTTCAGA
1 TTCGCATTGCGATTTTCAGA
* * *
335843 TTCGCATTGCGATAGTCCAAA
1 TTCGCATTGCGAT-TTTCAGA
* *
335864 ATCGCAATGCGATTTTCAGA
1 TTCGCATTGCGATTTTCAGA
335884 TTCGCATTGCGAT
1 TTCGCATTGCGAT
335897 AGTTGAAAAT
Statistics
Matches: 132, Mismatches: 59, Indels: 13
0.65 0.29 0.06
Matches are distributed among these distances:
19 2 0.02
20 68 0.52
21 59 0.45
22 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCAGA
Found at i:335775 original size:61 final size:62
Alignment explanation
Indices: 335686--335814 Score: 224
Period size: 61 Copynumber: 2.1 Consensus size: 62
335676 CATTTCGCGT
*
335686 TGCGATTTTCCAGATTCGTATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCAG
1 TGCGATTTTCCAGATTCGTATTGCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAG
* *
335748 TGCGATTTT-CAGATTCGTATTGCGATAGTCGAAAATCACAACGCGGTTTTAAGATTCGCAT
1 TGCGATTTTCCAGATTCGTATTGCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAG
335809 TGCGAT
1 TGCGAT
335815 AGTATAAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
61 55 0.86
62 9 0.14
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (62 bp):
TGCGATTTTCCAGATTCGTATTGCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAG
Found at i:335815 original size:41 final size:41
Alignment explanation
Indices: 335749--335916 Score: 246
Period size: 41 Copynumber: 4.1 Consensus size: 41
335739 GATTCGCAGT
* *
335749 GCGATTTTCAGATTCGTATTGCGATAGTCGAAAATCACAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
* * **
335790 GCGGTTTTAAGATTCGCATTGCGATAGTATAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
* *
335831 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAT
1 GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
* *
335872 GCGATTTTCAGATTCGCATTGCGATAGTTGAAAATCGCAAT
1 GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
335913 GCGA
1 GCGA
335917 CTGGTGGTAT
Statistics
Matches: 114, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 114 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
Found at i:335874 original size:21 final size:21
Alignment explanation
Indices: 335803--335916 Score: 90
Period size: 21 Copynumber: 5.5 Consensus size: 21
335793 GTTTTAAGAT
*
335803 TCGCATTGCGATAGTAT-AAAA
1 TCGCAATGCGATAGT-TCAAAA
* * * *
335824 TCGCAACGCGAT-TTTCAGAT
1 TCGCAATGCGATAGTTCAAAA
* *
335844 TCGCATTGCGATAGTCCAAAA
1 TCGCAATGCGATAGTTCAAAA
* * *
335865 TCGCAATGCGAT-TTTCAGAT
1 TCGCAATGCGATAGTTCAAAA
* *
335885 TCGCATTGCGATAGTTGAAAA
1 TCGCAATGCGATAGTTCAAAA
335906 TCGCAATGCGA
1 TCGCAATGCGA
335917 CTGGTGGTAT
Statistics
Matches: 68, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
19 1 0.01
20 28 0.41
21 39 0.57
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (21 bp):
TCGCAATGCGATAGTTCAAAA
Found at i:340228 original size:36 final size:37
Alignment explanation
Indices: 340172--340243 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
340162 TTTTGTTCGG
*
340172 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
340209 GTCGGATC-GGTTTTTTAAGTGTGATATTCGGGTCG
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCG
340244 GGCCGGGTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 27 0.79
37 7 0.21
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.39
Consensus pattern (37 bp):
GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:340492 original size:299 final size:295
Alignment explanation
Indices: 339921--340512 Score: 1053
Period size: 298 Copynumber: 2.0 Consensus size: 295
339911 CGGGTCGGGT
* *
339921 TTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGAC
1 TTTTTTAAGTGTGATATTCGGGTCAGGCCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGGAC
339986 CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTAT
66 CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC---
*
340051 ATATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGGG
128 ATATTTTTTTCAATTAAGTCACTATTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGGG
340116 TCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTCG
193 TCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTCG
340181 GGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGATCGG
258 GGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGATCGG
*
340219 TTTTTTAAGTGTGATATTCGGGTCGGGCCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGGAC
1 TTTTTTAAGTGTGATATTCGGGTCAGGCCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGGAC
340284 CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC-T-
66 CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCATA
340347 TTTTTTTCAATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC
131 TTTTTTTCAATTAAGTCACTATTTTTATTAAATAAAAAT-ATTTTTTATTA-TT----TCGGGTC
340412 GGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGG
190 GGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGG
340477 TCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGG
255 TCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGG
340513 GAAACAAAAA
Statistics
Matches: 284, Mismatches: 4, Indels: 11
0.95 0.01 0.04
Matches are distributed among these distances:
293 38 0.13
294 12 0.04
295 2 0.01
298 124 0.44
299 108 0.38
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (295 bp):
TTTTTTAAGTGTGATATTCGGGTCAGGCCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGGAC
CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCATA
TTTTTTTCAATTAAGTCACTATTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGGGTCG
GATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTCGGGT
TTTTTAAGTGTGATATTCGGGTCGAGTCGGATCGG
Found at i:343424 original size:12 final size:12
Alignment explanation
Indices: 343407--343431 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
343397 CCCACCTTCC
343407 TCAAATTTGTAA
1 TCAAATTTGTAA
343419 TCAAATTTGTAA
1 TCAAATTTGTAA
343431 T
1 T
343432 TCAGATATCA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TCAAATTTGTAA
Found at i:346258 original size:36 final size:36
Alignment explanation
Indices: 346211--346285 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
346201 TCTTTAGAAG
*
346211 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
1 CATGAGACTCAACAAAATAGTGTTATAGTCGAAAAT
346247 CATGAGACTCAACAAAATAGTGTTATAGTCGAAAAT
1 CATGAGACTCAACAAAATAGTGTTATAGTCGAAAAT
346283 CAT
1 CAT
346286 TTATATACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
CATGAGACTCAACAAAATAGTGTTATAGTCGAAAAT
Found at i:346667 original size:20 final size:20
Alignment explanation
Indices: 346575--346791 Score: 96
Period size: 20 Copynumber: 10.7 Consensus size: 20
346565 ATGGCCCCAT
*
346575 TTCGCGTTGCGATTTTCCAGA
1 TTCGCATTGCGATTTT-CAGA
* * * *
346596 TTCGTATTGCGATAGTCCAAA
1 TTCGCATTGCGAT-TTTCAGA
* ** * *
346617 ATCGCAACGCGGTTTTAAGA
1 TTCGCATTGCGATTTTCAGA
*
346637 TTCGCAGTGCGATTTTCAGA
1 TTCGCATTGCGATTTTCAGA
* ** *
346657 TTCGTATTGCGATAGTCGAAA
1 TTCGCATTGCGATTTTC-AGA
* * ** * *
346678 ATCACAACGCGGTTTTAAGA
1 TTCGCATTGCGATTTTCAGA
*
346698 TTCGCATTGCGATAGTAT-A-A
1 TTCGCATTGCGAT--TTTCAGA
* **
346718 ATCGCAACGCGATTTTCAGA
1 TTCGCATTGCGATTTTCAGA
* * *
346738 TTCGCATTGCGATAGTCCAAA
1 TTCGCATTGCGAT-TTTCAGA
* *
346759 ATCGCAATGCGATTTTCAGA
1 TTCGCATTGCGATTTTCAGA
346779 TTCGCATTGCGAT
1 TTCGCATTGCGAT
346792 AGTTGAAAAT
Statistics
Matches: 132, Mismatches: 57, Indels: 15
0.65 0.28 0.07
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 78 0.59
21 48 0.36
22 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCAGA
Found at i:346671 original size:61 final size:62
Alignment explanation
Indices: 346582--346710 Score: 224
Period size: 61 Copynumber: 2.1 Consensus size: 62
346572 CATTTCGCGT
*
346582 TGCGATTTTCCAGATTCGTATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCAG
1 TGCGATTTTCCAGATTCGTATTGCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAG
* *
346644 TGCGATTTT-CAGATTCGTATTGCGATAGTCGAAAATCACAACGCGGTTTTAAGATTCGCAT
1 TGCGATTTTCCAGATTCGTATTGCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAG
346705 TGCGAT
1 TGCGAT
346711 AGTATAAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
61 55 0.86
62 9 0.14
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (62 bp):
TGCGATTTTCCAGATTCGTATTGCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAG
Found at i:346711 original size:41 final size:41
Alignment explanation
Indices: 346645--346811 Score: 239
Period size: 41 Copynumber: 4.1 Consensus size: 41
346635 GATTCGCAGT
* *
346645 GCGATTTTCAGATTCGTATTGCGATAGTCGAAAATCACAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
* *
346686 GCGGTTTTAAGATTCGCATTGCGATAGT--ATAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCGA-AAATCGCAAC
* *
346726 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAT
1 GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
* *
346767 GCGATTTTCAGATTCGCATTGCGATAGTTGAAAATCGCAAT
1 GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
346808 GCGA
1 GCGA
346812 CTGGTGGTAT
Statistics
Matches: 114, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 35 0.31
41 77 0.68
42 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCGAAAATCGCAAC
Found at i:346730 original size:61 final size:61
Alignment explanation
Indices: 346604--346730 Score: 150
Period size: 61 Copynumber: 2.1 Consensus size: 61
346594 GATTCGTATT
* * * * **
346604 GCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCAGTGCGATTTTCAGATTCGTATT
1 GCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAGTGCGATTATCAGAATCGCAAC
* *
346665 GCGATAGTCGAAAATCACAACGCGGTTTTAAGATTCGCATTGCGATAGTAT-A-AATCGCAAC
1 GCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAGTGCGAT--TATCAGAATCGCAAC
346726 GCGAT
1 GCGAT
346731 TTTCAGATTC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 53 0.95
62 1 0.02
63 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (61 bp):
GCGATAGTCCAAAATCACAACGCGGTTTTAAGATTCGCAGTGCGATTATCAGAATCGCAAC
Found at i:346737 original size:81 final size:81
Alignment explanation
Indices: 346645--346811 Score: 246
Period size: 81 Copynumber: 2.0 Consensus size: 81
346635 GATTCGCAGT
* * *
346645 GCGATTTTCAGATTCGTATTGCGATAGTCGAAAATCACAACGCGGTTTTAAGATTCGCATTGCGA
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCACAACGCGATTTTAAGATTCGCATTGCGA
346710 TAG-TATAAATCGCAAC
66 TAGTTA-AAATCGCAAC
* * *
346726 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAATGCGATTTTCAGATTCGCATTGCGA
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCACAACGCGATTTTAAGATTCGCATTGCGA
*
346791 TAGTTGAAAATCGCAAT
66 TAGTT-AAAATCGCAAC
346808 GCGA
1 GCGA
346812 CTGGTGGTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
81 62 0.81
82 14 0.18
83 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (81 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCACAACGCGATTTTAAGATTCGCATTGCGA
TAGTTAAAATCGCAAC
Found at i:346764 original size:21 final size:21
Alignment explanation
Indices: 346699--346811 Score: 81
Period size: 20 Copynumber: 5.5 Consensus size: 21
346689 GTTTTAAGAT
*
346699 TCGCATTGCGATAG-T-ATAAA
1 TCGCAATGCGATAGTTCA-AAA
* * * *
346719 TCGCAACGCGAT-TTTCAGAT
1 TCGCAATGCGATAGTTCAAAA
* *
346739 TCGCATTGCGATAGTCCAAAA
1 TCGCAATGCGATAGTTCAAAA
* * *
346760 TCGCAATGCGAT-TTTCAGAT
1 TCGCAATGCGATAGTTCAAAA
* *
346780 TCGCATTGCGATAGTTGAAAA
1 TCGCAATGCGATAGTTCAAAA
346801 TCGCAATGCGA
1 TCGCAATGCGA
346812 CTGGTGGTAT
Statistics
Matches: 67, Mismatches: 22, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
20 37 0.55
21 30 0.45
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (21 bp):
TCGCAATGCGATAGTTCAAAA
Found at i:351126 original size:36 final size:37
Alignment explanation
Indices: 351070--351141 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
351060 TTTTGTTCGG
*
351070 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
351107 GTCGGATC-GGTTTTTTAAGTGTGATATTCGGGTCG
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCG
351142 GGCCGGGTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 27 0.79
37 7 0.21
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.39
Consensus pattern (37 bp):
GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:351355 original size:298 final size:293
Alignment explanation
Indices: 350819--351409 Score: 1040
Period size: 298 Copynumber: 2.0 Consensus size: 293
350809 CGGGTCGGGT
* *
350819 TTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGAC
1 TTTTTTAAGTGTGATATTCGGGTCAGGCCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGGAC
350884 CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTAT
66 CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC---
*
350949 ATATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGGG
128 --ATTTTTTTCAATTAAGTCACTATTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGGG
351014 TCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTCG
191 TCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTCG
351079 GGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGATCGG
256 GGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGATCGG
*
351117 TTTTTTAAGTGTGATATTCGGGTCGGGCCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGGAC
1 TTTTTTAAGTGTGATATTCGGGTCAGGCCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGGAC
351182 CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC-TT
66 CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCATT
351246 TTTTTCAATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGG
131 TTTTTCAATTAAGTCACTATTTTTATTAAATAAAAAT-ATTTTTTATTA-TT----TCGGGTCGG
351311 GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTC
190 GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTC
351376 GGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGG
255 GGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGG
351410 GAAACAAAAA
Statistics
Matches: 283, Mismatches: 4, Indels: 12
0.95 0.01 0.04
Matches are distributed among these distances:
292 38 0.13
293 11 0.04
294 2 0.01
298 232 0.82
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (293 bp):
TTTTTTAAGTGTGATATTCGGGTCAGGCCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCGGAC
CGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCATT
TTTTTCAATTAAGTCACTATTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCGGGTCGGA
TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTT
TTTAAGTGTGATATTCGGGTCGAGTCGGATCGG
Found at i:358455 original size:31 final size:33
Alignment explanation
Indices: 358392--358456 Score: 80
Period size: 36 Copynumber: 1.9 Consensus size: 33
358382 TATTGCTGAG
*
358392 CTCGACTCGACTCGAAAACTCTGAAATGGAGCTTGA
1 CTCGACTCGACTCGAAAACTCTG--A-CGAGCTTGA
358428 CTCGACTCGACTCGAAAACTC-G-CGAGCTT
1 CTCGACTCGACTCGAAAACTCTGACGAGCTT
358457 AAAATTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 6 0.21
35 1 0.04
36 21 0.75
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (33 bp):
CTCGACTCGACTCGAAAACTCTGACGAGCTTGA
Found at i:365868 original size:17 final size:17
Alignment explanation
Indices: 365846--365888 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
365836 TAACTTTATT
*
365846 TAAATTATTATTATAAA
1 TAAATTATTAATATAAA
*
365863 TAAATTTTTAATATAAA
1 TAAATTATTAATATAAA
365880 TATAATTAT
1 TA-AATTAT
365889 AAATGAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATTATTAATATAAA
Found at i:372329 original size:29 final size:29
Alignment explanation
Indices: 372286--372368 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
372276 CTCACCTAAC
372286 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
372316 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
372345 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
372369 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:377093 original size:29 final size:29
Alignment explanation
Indices: 377050--377132 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
377040 CTCACCTAAC
377050 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
377080 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
377109 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
377133 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:377505 original size:17 final size:18
Alignment explanation
Indices: 377468--377523 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
377458 CCATTAAGAT
377468 AAAA-CAAGAAAGTAAAC-
1 AAAACCAAGAAAG-AAACA
*
377485 -AAACGAAGAAA-AAACA
1 AAAACCAAGAAAGAAACA
*
377501 AAAACCCAGAAAGAAACA
1 AAAACCAAGAAAGAAACA
377519 AAAAC
1 AAAAC
377524 AAAATAAGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 15 0.47
18 10 0.31
ACGTcount: A:0.71, C:0.16, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAACCAAGAAAGAAACA
Found at i:377683 original size:2 final size:2
Alignment explanation
Indices: 377671--377700 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
377661 AGGTAGAGGC
*
377671 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
377701 TGAAGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:382070 original size:22 final size:23
Alignment explanation
Indices: 382045--382087 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
382035 TCTTATTTTC
382045 TTTCCTT-TT-TTTTCTTCAAAAT
1 TTTCCTTATTATTTT-TTCAAAAT
382067 TTTCCTTATTATTTTTTCAAA
1 TTTCCTTATTATTTTTTCAAA
382088 TGTTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTCCTTATTATTTTTTCAAAAT
Found at i:382574 original size:16 final size:16
Alignment explanation
Indices: 382553--382587 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
382543 CCATTGAATA
382553 AGATTTTCTTAAGGAT
1 AGATTTTCTTAAGGAT
382569 AGATTTTCTTAAGGAT
1 AGATTTTCTTAAGGAT
382585 AGA
1 AGA
382588 ATAATAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (16 bp):
AGATTTTCTTAAGGAT
Found at i:388810 original size:3 final size:3
Alignment explanation
Indices: 388792--388832 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
388782 ATCGAAAAAA
*
388792 TAT TAT TAAT TAAT TAT TAT TAT TAT TAG TAT TAT TAT TAT
1 TAT TAT T-AT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
388833 CTAAGTACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 28 0.80
4 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:388932 original size:12 final size:12
Alignment explanation
Indices: 388911--388944 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
388901 ACCACTCAAC
*
388911 ATTTTCTTCTAT
1 ATTTTATTCTAT
388923 ATTTTATTCTAT
1 ATTTTATTCTAT
*
388935 GTTTTATTCT
1 ATTTTATTCT
388945 TTCACTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.68
Consensus pattern (12 bp):
ATTTTATTCTAT
Found at i:390564 original size:30 final size:30
Alignment explanation
Indices: 390444--390564 Score: 104
Period size: 30 Copynumber: 4.1 Consensus size: 30
390434 ATAATAGATC
* * *
390444 TAGCAAAAACATGAACTTAAATGA-TTAAA
1 TAGCAAAAACATAAAATTAAATGACTAAAA
* * *** * *
390473 TGGTAAAAACATAAACCCAAAAGGCTAAAA
1 TAGCAAAAACATAAAATTAAATGACTAAAA
*
390503 TAGCTAAAACA-AAAATTTAAATGAC-ATAAA
1 TAGCAAAAACATAAAA-TTAAATGACTA-AAA
390533 TAGCAAAAACATAAAATTAAATGACTAAAA
1 TAGCAAAAACATAAAATTAAATGACTAAAA
390563 TA
1 TA
390565 AAATAACAGA
Statistics
Matches: 70, Mismatches: 17, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
29 21 0.30
30 44 0.63
31 5 0.07
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.21
Consensus pattern (30 bp):
TAGCAAAAACATAAAATTAAATGACTAAAA
Found at i:391247 original size:283 final size:284
Alignment explanation
Indices: 390720--391446 Score: 939
Period size: 283 Copynumber: 2.5 Consensus size: 284
390710 GTTGATGTGA
* * * ** * *
390720 TGCCGT-G-CCACCGTCCGATTGTCCTGAAATATCAGTATGTTGTTCGTG-TTGACCTCACGCAA
1 TGCCGTCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATACTGTTTGTGCTAG-CCTCACGCAA
* *
390782 CTTTTGACCGTTCGGAATATTGATCGGAGTTCCCGATCACCGAG-GAGAGGCCAAAAACCGTCAG
65 CTTTTGACCGTTCGGAATGTTGATCGGAGATCCCGATCACCG-GCGAGAGGCCAAAAACCGTCA-
* * **
390846 GATTTGTTTTCTACGATTCACCACCGTCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTC
128 GATTT-TTTTCTCCGATTCACCACCGT----CG-CCGATCATCATGAAATTTCAGTATACTGTTC
* *
390911 GTGTTGACATGACACAACTTTTTACCGTTTGAAATATTGATCGGAGATCCCGATCGCC-AGCAAG
187 GTGTTGACATGACACAACTTTTCACCGTTTGAAATATTGATCGGAGATCCCGATCGCCGA-CAAA
* *
390975 AGACTAAAAACCGTTTGGCTTATTTTCTTCGATC
251 AGACTAAAAACCGTTCGGCTTATTTTCTCCGATC
* * * * *
391009 TGCCGTCGTCCACCGTCCGATCGTCCTGAATTTTTAGTATACTGTTTTTGCTGGTCTCATGCAAC
1 TGCCGTCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATACTGTTTGTGCTAGCCTCACGCAAC
*
391074 TTTTGACCGTTCGGACTGTTGATCGGA-AGTCCCGATCACCGGCGAGAGGCCAAAAACCGTCCAG
66 TTTTGACCGTTCGGAATGTTGATCGGAGA-TCCCGATCACCGGCGAGAGGCCAAAAACCGT-CAG
391138 ATTTTTTTCTCCGATTCACCACCGT-G-CGATCATCATGAAATTTCAGTATACTGTTCGTGTTGA
129 ATTTTTTTCTCCGATTCACCACCGTCGCCGATCATCATGAAATTTCAGTATACTGTTCGTGTTGA
* *
391201 CATGACACAACTTTTCACTGTTTGAAATATTGATCGGAGATCCCGATCGCCGACAAAAGGCTAAA
194 CATGACACAACTTTTCACCGTTTGAAATATTGATCGGAGATCCCGATCGCCGACAAAAGACTAAA
391266 AACCGTTCGGCTTATTTTCTCCGATC
259 AACCGTTCGGCTTATTTTCTCCGATC
* * **
391292 TGCCGTCGTCCACTGTCCGATCGTCTTGAATTTTCAGTATGTTGTTTGTGCTAGCCTCACGCAAC
1 TGCCGTCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATACTGTTTGTGCTAGCCTCACGCAAC
* * * * * *
391357 TTTTGACCGTTCGGAATGTTGATCAGAGATTCCGATCGCAGGCAAGAGGCCAAAAACCGTTCGGA
66 TTTTGACCGTTCGGAATGTTGATCGGAGATCCCGATCACCGGCGAGAGGCCAAAAACCG-TCAGA
* * *
391422 TTATTTTCTCCGATCCACCGCCGTC
130 TTTTTTTCTCCGATTCACCACCGTC
391447 CACCGTCTGA
Statistics
Matches: 385, Mismatches: 43, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
283 248 0.64
284 3 0.01
285 1 0.00
289 6 0.02
290 22 0.06
291 101 0.26
292 4 0.01
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (284 bp):
TGCCGTCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATACTGTTTGTGCTAGCCTCACGCAAC
TTTTGACCGTTCGGAATGTTGATCGGAGATCCCGATCACCGGCGAGAGGCCAAAAACCGTCAGAT
TTTTTTCTCCGATTCACCACCGTCGCCGATCATCATGAAATTTCAGTATACTGTTCGTGTTGACA
TGACACAACTTTTCACCGTTTGAAATATTGATCGGAGATCCCGATCGCCGACAAAAGACTAAAAA
CCGTTCGGCTTATTTTCTCCGATC
Found at i:391533 original size:145 final size:144
Alignment explanation
Indices: 390721--391531 Score: 719
Period size: 145 Copynumber: 5.6 Consensus size: 144
390711 TTGATGTGAT
* * * *
390721 GCCGTGCCACCGTCCGATTGTCCTGAAATATCAGTATGTTGTTCGTGTTGACCTCACGCAACTTT
1 GCCGT-CCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTGTGGA-CTCACGCAACTTT
* *
390786 TGACCGTTCGGAATATTGATCGGAGTTCCCGATCACCGAGG--AGAGGCCAAAAACCG-TCAGGA
64 TGACCGTTCGGAATATTGATCGGAGATCCCGATC-GC-AGGCAAGAGGCCAAAAACCGTTC-GGA
* * *
390848 TTTGTTTTCTACGATTCACC
126 -TTATTTTCTCCGATCCACC
* * * *
390868 ACCGTCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTGTTGACATGACACAACTTTT
1 GCCGTCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTGTGGAC-TCACGCAACTTTT
* * * * * * *
390933 TACCGTTTGAAATATTGATCGGAGATCCCGATCGCCA-GCAAGAGACTAAAAACCGTTTGGCTTA
65 GACCGTTCGGAATATTGATCGGAGATCCCGATCG-CAGGCAAGAGGCCAAAAACCGTTCGGATTA
* **
390997 TTTTCTTCGATCTGCC
129 TTTTCTCCGATCCACC
* * * * ** ** * *
391013 GTCGTCCACCGTCCGATCGTCCTGAATTTTTAGTATACTGTTTTTGCTGGTCTCATGCAACTTTT
1 GCCGTCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTG-TGGACTCACGCAACTTTT
* * * * * * * *
391078 GACCGTTCGGACTGTTGATCGGA-AGTCCCGATCACCGGCGAGAGGCCAAAAACCGTCCAGATTT
65 GACCGTTCGGAATATTGATCGGAGA-TCCCGATCGCAGGCAAGAGGCCAAAAACCGTTCGGATTA
*
391142 TTTTCTCCGATTCA--
129 TTTTCTCCGATCCACC
* * ** * * *
391156 -----CCACCGTGCGATCATCATGAAATTTCAGTATACTGTTCGTGTTGACATGACACAACTTTT
1 GCCGTCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTGTGGAC-TCACGCAACTTTT
* * * * * * * * *
391216 CACTGTTTGAAATATTGATCGGAGATCCCGATCGCCGACAAAAGGCTAAAAACCGTTCGGCTTAT
65 GACCGTTCGGAATATTGATCGGAGATCCCGATCGCAGGCAAGAGGCCAAAAACCGTTCGGATTAT
**
391281 TTTCTCCGATCTGCC
130 TTTCTCCGATCCACC
* * * * * * *
391296 GTCGTCCACTGTCCGATCGTCTTGAATTTTCAGTATGTTGTTTGTGCTAGCCTCACGCAACTTTT
1 GCCGTCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTG-TGGACTCACGCAACTTTT
* * *
391361 GACCGTTCGGAATGTTGATCAGAGATTCCGATCGCAGGCAAGAGGCCAAAAACCGTTCGGATTAT
65 GACCGTTCGGAATATTGATCGGAGATCCCGATCGCAGGCAAGAGGCCAAAAACCGTTCGGATTAT
391426 TTTCTCCGATCCACC
130 TTTCTCCGATCCACC
* * * **
391441 GCCGTCCACCGTCTGATCGTCATGAATTTTCAGTATGTTGTTCGTGATGGTCTTGCGCAACTTTT
1 GCCGTCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTG-TGGACTCACGCAACTTTT
* * *
391506 GACAGTTCAGAATATTGATCGTAGAT
65 GACCGTTCGGAATATTGATCGGAGAT
391532 TCTGATCACT
Statistics
Matches: 522, Mismatches: 124, Indels: 38
0.76 0.18 0.06
Matches are distributed among these distances:
137 3 0.01
138 102 0.20
139 1 0.00
144 3 0.01
145 304 0.58
146 104 0.20
147 5 0.01
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (144 bp):
GCCGTCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTGTGGACTCACGCAACTTTTG
ACCGTTCGGAATATTGATCGGAGATCCCGATCGCAGGCAAGAGGCCAAAAACCGTTCGGATTATT
TTCTCCGATCCACC
Found at i:391548 original size:428 final size:429
Alignment explanation
Indices: 390744--391526 Score: 964
Period size: 428 Copynumber: 1.8 Consensus size: 429
390734 CCGATTGTCC
** * * * *
390744 TGAAATATCAGTATGTTGTTCGTGTTGACCTCACGCAACTTTTGACCGTTCGGAATATTGATCGG
1 TGAAATATCAGTATACTGTTCGTGTTGACATCACACAACTTTTCACCGTTCGAAATATTGATCGG
* ** * * *
390809 AGTTCCCGATCACCGAGGAGAGGCCAAAAACCGTCAGGATTTGTTTTCTACGATTCACCACCGTC
66 AGATCCCGATCACCGACAAAAGGCCAAAAACCGTCAGGACTTATTTTCTACGATTCACCACCGTC
* * *
390874 CACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTGTTGACATGACACAACTTTTTACCGT
131 CACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTGTAGACATCACACAACTTTTGACCGT
* * * * * *
390939 TTGAAATATTGATCGGAGATCCCGATCGCCAGCAAGAGACTAAAAACCGTTTGGCTTATTTTCTT
196 TCGAAATATTGATCAGAGATCCCGATCGCCAGCAAGAGACCAAAAACCGTTCGGATTATTTTCTC
** * * * ** * *
391004 CGATCTGCCGTCGTCCACCGTCCGATCGTCCTGAATTTTTAGTATACTGTTTTTGCTGGTCTCAT
261 CGATCCACCGCCGTCCACCGTCCGATCGTCATGAATTTTCAGTATACTGTTCGTGATGGTCTCAC
* * * *
391069 GCAACTTTTGACCGTTCGGACTGTTGATCGGAAGTCCCGATCACCGGCGAGAGGCCAAAAACCGT
326 GCAACTTTTGACAGTTCAGAATATTGATCGGAAGTCCCGATCACCGGCGAGAGGCCAAAAACCGT
391134 CCAGATTTTTTTCTCCGATTCACCACCGTGCGATCATCA
391 CCAGATTTTTTTCTCCGATTCACCACCGTGCGATCATCA
* * * *
391173 TGAAATTTCAGTATACTGTTCGTGTTGACATGACACAACTTTTCACTGTTTGAAATATTGATCGG
1 TGAAATATCAGTATACTGTTCGTGTTGACATCACACAACTTTTCACCGTTCGAAATATTGATCGG
* * * * **
391238 AGATCCCGATCGCCGACAAAAGGCTAAAAACCGTTC-GG-CTTATTTTCTCCGA-TCTGCCGTCG
66 AGATCCCGATCACCGACAAAAGGCCAAAAACCG-TCAGGACTTATTTTCTACGATTC-ACCACCG
* * * * * *
391300 TCCACTGTCCGATCGTCTTGAATTTTCAGTATGTTGTTTGTGCTAG-CCTCACGCAACTTTTGAC
129 TCCACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTG-TAGACATCACACAACTTTTGAC
* * * *
391364 CGTTCGGAATGTTGATCAGAGATTCCGATCG-CAGGCAAGAGGCCAAAAACCGTTCGGATTATTT
193 CGTTCGAAATATTGATCAGAGATCCCGATCGCCA-GCAAGAGACCAAAAACCGTTCGGATTATTT
* **
391428 TCTCCGATCCACCGCCGTCCACCGTCTGATCGTCATGAATTTTCAGTATGTTGTTCGTGATGGTC
257 TCTCCGATCCACCGCCGTCCACCGTCCGATCGTCATGAATTTTCAGTATACTGTTCGTGATGGTC
**
391493 TTGCGCAACTTTTGACAGTTCAGAATATTGATCG
322 TCACGCAACTTTTGACAGTTCAGAATATTGATCG
391527 TAGATTCTGA
Statistics
Matches: 291, Mismatches: 59, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
427 4 0.01
428 199 0.68
429 86 0.30
430 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (429 bp):
TGAAATATCAGTATACTGTTCGTGTTGACATCACACAACTTTTCACCGTTCGAAATATTGATCGG
AGATCCCGATCACCGACAAAAGGCCAAAAACCGTCAGGACTTATTTTCTACGATTCACCACCGTC
CACCGTCCGATCGTCATGAAATTTCAGTATGTTGTTCGTGTAGACATCACACAACTTTTGACCGT
TCGAAATATTGATCAGAGATCCCGATCGCCAGCAAGAGACCAAAAACCGTTCGGATTATTTTCTC
CGATCCACCGCCGTCCACCGTCCGATCGTCATGAATTTTCAGTATACTGTTCGTGATGGTCTCAC
GCAACTTTTGACAGTTCAGAATATTGATCGGAAGTCCCGATCACCGGCGAGAGGCCAAAAACCGT
CCAGATTTTTTTCTCCGATTCACCACCGTGCGATCATCA
Found at i:391880 original size:3 final size:3
Alignment explanation
Indices: 391867--391924 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
391857 TTAGGTATAG
*
391867 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
391913 TATT TAA TAA TA
1 TA-A TAA TAA TA
391925 TTTTTTTGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 44 0.90
4 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:392137 original size:40 final size:41
Alignment explanation
Indices: 392093--392276 Score: 126
Period size: 40 Copynumber: 4.3 Consensus size: 41
392083 ACACGACCCA
*
392093 TACGTGATGAGGA-GATCTGGTCGAGA-GATGACACGGTTCC
1 TACGTGATGAGGACGA-CTGGTCGAGAGGATAACACGGTTCC
* * *
392133 TACGTGATGAGGACGACATGCCATCTTTACGGATGATAACACGGTTCC
1 TACGTGATGAGGACGAC-TG--GTC--GA--GAGGATAACACGGTTCC
* * * *
392181 TACGTGATGAGGACGACTGGTTATCTA-AGGTTGACACGGCTCC
1 TACGTGATGAGGACGACTGG---TCGAGAGGATAACACGGTTCC
* * *
392224 TACGTGATGAAGA-GATATGGTCGAG-GGATAACACAGTTCC
1 TACGTGATGAGGACGA-CTGGTCGAGAGGATAACACGGTTCC
392264 TACGTGATGAGGA
1 TACGTGATGAGGA
392277 TGACAGACCA
Statistics
Matches: 114, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
40 40 0.35
41 4 0.04
42 2 0.02
43 29 0.25
45 1 0.01
46 2 0.02
47 4 0.04
48 32 0.28
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (41 bp):
TACGTGATGAGGACGACTGGTCGAGAGGATAACACGGTTCC
Found at i:392380 original size:36 final size:36
Alignment explanation
Indices: 392333--392478 Score: 188
Period size: 35 Copynumber: 4.1 Consensus size: 36
392323 CAAATGATGC
* *
392333 TTCAAGAGAAACTGTCTCAAAAGAGATAAAATATGT
1 TTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGT
* **
392369 TTCAAGGGAAACTGTCTCATGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGT
* * *
392405 TTCAAGA-AAAATGTCTCAAAAGATACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGT
*
392440 TTCAAGAG-AACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAGAGAAACTGTCTCAAAAGAGACAAAA-TTTGT
392476 TTC
1 TTC
392479 GTGGATGGCC
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 48 0.52
36 45 0.48
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGT
Found at i:392427 original size:71 final size:72
Alignment explanation
Indices: 392333--392478 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 72
392323 CAAATGATGC
* * * *
392333 TTCAAGAGAAACTGTCTCAAAAGAGATAAAATATGTTTCAAGGGAAACTGTCTCATGAGAGACAA
1 TTCAAGAGAAAATGTCTCAAAAGAGACAAAATATGTTTCAAGAG-AACTGTCTCAAGAGAGACAA
392398 AA-TTTGT
65 AACTTTGT
* * *
392405 TTCAAGA-AAAATGTCTCAAAAGATACGAAATTTGTTTCAAGAGAACTGTCTCAAGAGAGACAAA
1 TTCAAGAGAAAATGTCTCAAAAGAGACAAAATATGTTTCAAGAGAACTGTCTCAAGAGAGACAAA
392469 ACTTTGT
66 ACTTTGT
392476 TTC
1 TTC
392479 GTGGATGGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
70 21 0.32
71 38 0.58
72 7 0.11
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (72 bp):
TTCAAGAGAAAATGTCTCAAAAGAGACAAAATATGTTTCAAGAGAACTGTCTCAAGAGAGACAAA
ACTTTGT
Found at i:393008 original size:120 final size:120
Alignment explanation
Indices: 392790--393010 Score: 295
Period size: 120 Copynumber: 1.8 Consensus size: 120
392780 CCGTGGATGT
* * * * **
392790 GTGGGCACGATATCCTTCGTCGTGGAGTTGAAATCGTGGATGGTCCCTTCGTCGTGAAGTTGAGC
1 GTGGACACGATATCCTTCGTCGTGAAGTTAAAACCGTGGATGACCCCTTCGTCGTGAAGTTGAGC
392855 CTTGACTTGAATATCCTTCGTCGTGAAATTGAAATCCAAGTATTGTATGTTGTGG
66 CTTGACTTGAATATCCTTCGTCGTGAAATTGAAATCCAAGTATTGTATGTTGTGG
* *
392910 GTGGACACGAT-TCCCTTCGTCGTGAAGTTAAAACCGTGGATGACCCCTTCGTTGTGAAGTT-TG
1 GTGGACACGATAT-CCTTCGTCGTGAAGTTAAAACCGTGGATGACCCCTTCGTCGTGAAGTTGAG
* * *
392973 TCTTCGAGTT-AGATATCCTTCGTCGTGAATTTGAAATC
65 CCTT-GACTTGA-ATATCCTTCGTCGTGAAATTGAAATC
393011 TACTCTCGAG
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
119 6 0.07
120 81 0.93
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (120 bp):
GTGGACACGATATCCTTCGTCGTGAAGTTAAAACCGTGGATGACCCCTTCGTCGTGAAGTTGAGC
CTTGACTTGAATATCCTTCGTCGTGAAATTGAAATCCAAGTATTGTATGTTGTGG
Found at i:393538 original size:32 final size:32
Alignment explanation
Indices: 393453--393539 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
393443 TTGCATCAGG
* *
393453 ATGTTGAATCCCTAAATATGCCCCAATATTCA
1 ATGTTGAATCTCTAAATATGCCCCAACATTCA
* **
393485 ATGTTGAATCTCCAAATATGCCCCAACATTTG
1 ATGTTGAATCTCTAAATATGCCCCAACATTCA
* * *
393517 TTGTTGAATCTTTAAAGATGCCC
1 ATGTTGAATCTCTAAATATGCCC
393540 ATTGTTCCTC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (32 bp):
ATGTTGAATCTCTAAATATGCCCCAACATTCA
Found at i:397846 original size:30 final size:30
Alignment explanation
Indices: 397725--397846 Score: 113
Period size: 30 Copynumber: 4.1 Consensus size: 30
397715 ATAATTGATC
* * *
397725 TAGCAAAAACATGAACTTAAAGGA-TTAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
* * * * *
397754 TGGTAAAAACATAAACTAAAAAAGGCTAAAA
1 TAGCAAAAACATAAACT-TAAATGACTAAAA
* * *
397785 TAGCTAAAACAGAAATTTAAATGAC-ATAAA
1 TAGCAAAAACATAAACTTAAATGACTA-AAA
397815 TAGCAAAAACATAAACTTAAATGACTAAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
397845 TA
1 TA
397847 AAATAAGAGA
Statistics
Matches: 71, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
29 15 0.21
30 39 0.55
31 17 0.24
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (30 bp):
TAGCAAAAACATAAACTTAAATGACTAAAA
Found at i:398356 original size:145 final size:144
Alignment explanation
Indices: 398207--398811 Score: 544
Period size: 145 Copynumber: 4.2 Consensus size: 144
398197 TTGACATGAC
* * * * * * * *
398207 ACAACTTTTCACCATTTGAAATATTGATTGGAGATCACAATCGCTAGCAAGAGACTAAAAACCGT
1 ACAACTTTTGACCGTTCGAAATATTGATCGGAGATCTCGATCGCTGGCAAGAGGCTAAAAACCGT
* *
398272 TCGGCTTATTTTCTTTGATCTGCCGTCGTCCAGTGTCCGATCGTCCTAAATTTTCAGTATGCTGT
66 TCGGCTTATTTTCTCTGATCTGCCGTCGTCCACTGTCCGATCGTCCTAAATTTTCAGTATGCTGT
*
398337 TTTTGCTGGTCTCGT
131 TTGTG-TGGTCTCGT
* * * * **
398352 ACAACTTTTTGACCGTTCGGAATATTGATCGGAGGTTTCGATCACTGGTGAGAGGCTAAAAACCG
1 ACAAC-TTTTGACCGTTCGAAATATTGATCGGAGATCTCGATCGCTGGCAAGAGGCTAAAAACCG
* * * * * * * *
398417 TCCGGATTTGTTTTCTC-CA-AT----TC-ACCACAGTCCGATCGTCATGAAATTTT-AGTATGC
65 TTCGG-CTTATTTTCTCTGATCTGCCGTCGTCCACTGTCCGATCGTCCT-AAATTTTCAGTATGC
* * * *
398474 TGTTCGTGTTGACAT-GAC
128 TGTTTGTGTGGTC-TCG-T
* * * * *
398492 ACAACTTTTAACCGTTTGAAATATTGATCGGATATCCCGATCGCTGGTAAGAGGCTAAAAACCGT
1 ACAACTTTTGACCGTTCGAAATATTGATCGGAGATCTCGATCGCTGGCAAGAGGCTAAAAACCGT
* * * * * * *
398557 TCAGCTTATTTTCTCCGATCTGCCATCATCCACTGTCCGATCGTCTTGAATTTTCAGTATGTTGT
66 TCGGCTTATTTTCTCTGATCTGCCGTCGTCCACTGTCCGATCGTCCTAAATTTTCAGTATGCTGT
398622 TTGTGTTGGTCTCGT
131 TTGTG-TGGTCTCGT
* * * *
398637 GCAACTTTTGACCGTTCGGAATATTGATCGGAGATCTCGATCGCCGGCAAGAGGCCAAAAACCGT
1 ACAACTTTTGACCGTTCGAAATATTGATCGGAGATCTCGATCGCTGGCAAGAGGCTAAAAACCGT
** * * * * * *
398702 TCGGCTTATTTTCTCTGATCCACCGCCGTCCACCGTCTGATCGTCCTGAATTTTTAGTATGTTGT
66 TCGGCTTATTTTCTCTGATCTGCCGTCGTCCACTGTCCGATCGTCCTAAATTTTCAGTATGCTGT
* * * *
398767 TCGTGATGGTTTTGC
131 TTGTG-TGGTCTCGT
* *
398782 GCAACTTTTGACCGTTCGAAATGTTGATCG
1 ACAACTTTTGACCGTTCGAAATATTGATCG
398812 TAATATCCGA
Statistics
Matches: 365, Mismatches: 80, Indels: 30
0.77 0.17 0.06
Matches are distributed among these distances:
138 9 0.02
139 58 0.16
140 35 0.10
141 9 0.02
144 8 0.02
145 184 0.50
146 54 0.15
147 8 0.02
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (144 bp):
ACAACTTTTGACCGTTCGAAATATTGATCGGAGATCTCGATCGCTGGCAAGAGGCTAAAAACCGT
TCGGCTTATTTTCTCTGATCTGCCGTCGTCCACTGTCCGATCGTCCTAAATTTTCAGTATGCTGT
TTGTGTGGTCTCGT
Found at i:398596 original size:285 final size:285
Alignment explanation
Indices: 398062--398701 Score: 888
Period size: 285 Copynumber: 2.2 Consensus size: 285
398052 TGACCTCGCG
* *
398062 CAACTTTTGACCGTTCGGAATGTTGATCGGAGGTCCCGATCAACGGCGAGAGGCCAAAAACCGTC
1 CAACTTTTGACCGTTCGGAATATTGATCGGAGGTCTCGATC-ACGGCGAGAGGCCAAAAACCGTC
* *
398127 CGGATTTGTTTTCTCCTATTCACCACCTTCCACCGTCCGATCGTCATGAAATTTCAGTATATTGT
65 CGGATTTGTTTTCTCCAATTCACCA----CCA-CGTCCGATCGTCATGAAATTTCAGTATACTGT
* *
398192 TCGTGTTGACATGACACAACTTTTCACCATTTGAAATATTGATTGGAGATCACAATCGCTAGCAA
125 TCGTGTTGACATGACACAACTTTTAACCATTTGAAATATTGATCGGAGATCACAATCGCTAGCAA
* ** * * *
398257 GAGACTAAAAACCGTTCGGCTTATTTTCTTTGATCTGCCGTCGTCCAGTGTCCGATCGTCCTAAA
190 GAGACTAAAAACCGTTCAGCTTATTTTCTCCGATCTGCCATCATCCACTGTCCGATCGTCCTAAA
*
398322 TTTTCAGTATGCTGTTTTTGCTGGTCTCGTA
255 TTTTCAGTATGCTGTTTGTGCTGGTCTCGTA
* * *
398353 CAACTTTTTGACCGTTCGGAATATTGATCGGAGGTTTCGATCACTGGTGAGAGGCTAAAAACCGT
1 CAAC-TTTTGACCGTTCGGAATATTGATCGGAGGTCTCGATCAC-GGCGAGAGGCCAAAAACCGT
* *
398418 CCGGATTTGTTTTCTCCAATTCACCA-CA-GTCCGATCGTCATGAAATTTTAGTATGCTGTTCGT
64 CCGGATTTGTTTTCTCCAATTCACCACCACGTCCGATCGTCATGAAATTTCAGTATACTGTTCGT
* * * * * * *
398481 GTTGACATGACACAACTTTTAACCGTTTGAAATATTGATCGGATATCCCGATCGCTGGTAAGAGG
129 GTTGACATGACACAACTTTTAACCATTTGAAATATTGATCGGAGATCACAATCGCTAGCAAGAGA
* *
398546 CTAAAAACCGTTCAGCTTATTTTCTCCGATCTGCCATCATCCACTGTCCGATCGTCTTGAATTTT
194 CTAAAAACCGTTCAGCTTATTTTCTCCGATCTGCCATCATCCACTGTCCGATCGTCCTAAATTTT
* * *
398611 CAGTATGTTGTTTGTGTTGGTCTCGTG
259 CAGTATGCTGTTTGTGCTGGTCTCGTA
* * *
398638 CAACTTTTGACCGTTCGGAATATTGATCGGAGATCTCGATCGCCGGCAAGAGGCCAAAAACCGT
1 CAACTTTTGACCGTTCGGAATATTGATCGGAGGTCTCGATC-ACGGCGAGAGGCCAAAAACCGT
398702 TCGGCTTATT
Statistics
Matches: 310, Mismatches: 36, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
284 52 0.17
285 173 0.56
287 2 0.01
291 6 0.02
292 77 0.25
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (285 bp):
CAACTTTTGACCGTTCGGAATATTGATCGGAGGTCTCGATCACGGCGAGAGGCCAAAAACCGTCC
GGATTTGTTTTCTCCAATTCACCACCACGTCCGATCGTCATGAAATTTCAGTATACTGTTCGTGT
TGACATGACACAACTTTTAACCATTTGAAATATTGATCGGAGATCACAATCGCTAGCAAGAGACT
AAAAACCGTTCAGCTTATTTTCTCCGATCTGCCATCATCCACTGTCCGATCGTCCTAAATTTTCA
GTATGCTGTTTGTGCTGGTCTCGTA
Found at i:398823 original size:145 final size:143
Alignment explanation
Indices: 398005--398829 Score: 535
Period size: 145 Copynumber: 5.7 Consensus size: 143
397995 TGCTGCACTG
* * * ** *
398005 TCGTGCCACCGTCTGATTGTTCTG-ATATTTCAGTATGTTGTTCGTGTTGACCTCGCGCAACTTT
1 TCGT-CCACCGTCCGATCGTCCTGAAT-TTTCAGTATGTTGTTCGTG-TGGTCTCGCACAACTTT
* * * ** * * * * *
398069 TGACCGTTCGGAATGTTGATCGGAGGTCCCGATCAACGGCGAGAGGCCAAAAACCGTCCGGATTT
63 TGACCGTTCGAAATATTGATCGAATAT-CCGATCACCGGCAAGAGGCTAAAAACCGTTCGG-CTT
* *
398134 GTTTTCTCCT-ATTCACCA
126 ATTTTCT-CTGATCCACCA
* * * * * * *
398152 CCTTCCACCGTCCGATCGTCATGAAATTTCAGTATATTGTTCGTGTTGACAT-GACACAACTTTT
1 TCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATGTTGTTCGTGTGGTC-TCG-CACAACTTTT
* * * * * * * * ** *
398216 CACCATTTGAAATATTGATTGGAGATCACAATCGCTAGCAAGAGACTAAAAACCGTTCGGCTTAT
64 GACCGTTCGAAATATTGATCGAATATC-CGATCACCGGCAAGAGGCTAAAAACCGTTCGGCTTAT
* ** *
398281 TTTCTTTGATCTGCCG
128 TTTCTCTGATCCACCA
** * * ** *
398297 TCGTCCAGTGTCCGATCGTCCTAAATTTTCAGTATGCTGTTTTTGCTGGTCTCGTACAACTTTTT
1 TCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATGTTGTTCGTG-TGGTCTCGCACAAC-TTTT
* * * * ** * *
398362 GACCGTTCGGAATATTGATCGGAGGT-TTCGATCACTGGTGAGAGGCTAAAAACCGTCCGGATT-
64 GACCGTTCGAAATATTGATC-GA-ATATCCGATCACCGGCAAGAGGCTAAAAACCGTTCGGCTTA
398425 TGTTT-TC---TCCA--A
127 T-TTTCTCTGATCCACCA
* * * * * *
398437 TTC-ACCACAGTCCGATCGTCATGAAATTTT-AGTATGCTGTTCGTGTTGACAT-GACACAACTT
1 -TCGTCCACCGTCCGATCGTCCTG-AATTTTCAGTATGTTGTTCGTGTGGTC-TCG-CACAACTT
* * * * * * *
398499 TTAACCGTTTGAAATATTGATCGGATATCCCGATCGCTGGTAAGAGGCTAAAAACCGTTCAGCTT
62 TTGACCGTTCGAAATATTGATCGAATAT-CCGATCACCGGCAAGAGGCTAAAAACCGTTCGGCTT
* **
398564 ATTTTCTCCGATCTGCCA
126 ATTTTCTCTGATCCACCA
* * * * **
398582 TCATCCACTGTCCGATCGTCTTGAATTTTCAGTATGTTGTTTGTGTTGGTCTCGTGCAACTTTTG
1 TCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATGTTGTTCGTG-TGGTCTCGCACAACTTTTG
* * * * *
398647 ACCGTTCGGAATATTGATCGGAGATCTCGATCGCCGGCAAGAGGCCAAAAACCGTTCGGCTTATT
65 ACCGTTCGAAATATTGATCGAATATC-CGATCACCGGCAAGAGGCTAAAAACCGTTCGGCTTATT
*
398712 TTCTCTGATCCACCG
129 TTCTCTGATCCACCA
* * * * * *
398727 CCGTCCACCGTCTGATCGTCCTGAATTTTTAGTATGTTGTTCGTGATGGTTTTGCGCAACTTTTG
1 TCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATGTTGTTCGTG-TGGTCTCGCACAACTTTTG
*
398792 ACCGTTCGAAATGTTGATCGTAATATCCGATCACCGGC
65 ACCGTTCGAAATATTGATCG-AATATCCGATCACCGGC
398830 GAGAATCCAG
Statistics
Matches: 518, Mismatches: 130, Indels: 62
0.73 0.18 0.09
Matches are distributed among these distances:
137 1 0.00
138 2 0.00
139 58 0.11
140 37 0.07
141 8 0.02
142 2 0.00
143 2 0.00
144 10 0.02
145 247 0.48
146 146 0.28
147 5 0.01
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (143 bp):
TCGTCCACCGTCCGATCGTCCTGAATTTTCAGTATGTTGTTCGTGTGGTCTCGCACAACTTTTGA
CCGTTCGAAATATTGATCGAATATCCGATCACCGGCAAGAGGCTAAAAACCGTTCGGCTTATTTT
CTCTGATCCACCA
Found at i:399153 original size:3 final size:3
Alignment explanation
Indices: 399140--399194 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
399130 TTAGGTATAG
* * *
399140 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAG TAA TATT
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
399187 TAA TAA TA
1 TAA TAA TA
399195 TTTTTTCGAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 39 0.89
4 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:400772 original size:60 final size:60
Alignment explanation
Indices: 400668--400791 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
400658 TATATCTATG
* * ** **
400668 TCCTCAAACTATGATCCTATTTTTAAATTAGTCTCTAAGTTTTTGAATATTTTAATTTTA
1 TCCTCAAACTATGATACTATTTCTAAATTAGTCTCTAAACTTTTGAATATTCCAATTTTA
*
400728 TCCTCAAACTATGATATTCA-TTCTAAATTAGT-TCTTAAACTTTTGAATATTCCAATTTTA
1 TCCTCAAACTATGATACT-ATTTCTAAATTAGTCTC-TAAACTTTTGAATATTCCAATTTTA
400788 TCCT
1 TCCT
400792 TGAACTGACC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.04
60 52 0.95
61 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.48
Consensus pattern (60 bp):
TCCTCAAACTATGATACTATTTCTAAATTAGTCTCTAAACTTTTGAATATTCCAATTTTA
Found at i:401615 original size:3 final size:3
Alignment explanation
Indices: 401607--401664 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
401597 AACAAGTTGC
401607 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
401655 ATT ATT ATT A
1 ATT ATT ATT A
401665 GTGGACGGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:402235 original size:30 final size:30
Alignment explanation
Indices: 402167--402287 Score: 120
Period size: 30 Copynumber: 4.1 Consensus size: 30
402157 ATAATAGATC
* * *
402167 TAGCAAAAACATGAACTTAAAGGA-TTAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
* * * * *
402196 TGGTAAAAACATAAACTCAAAAGGCTAAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
* * *
402226 TAGCTAAAACAGAAATTTAAATGAC-ATAAA
1 TAGCAAAAACATAAACTTAAATGACTA-AAA
402256 TAGCAAAAACATAAACTTAAATGACTAAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
402286 TA
1 TA
402288 AAATAACAGA
Statistics
Matches: 71, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
29 19 0.27
30 51 0.72
31 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.11, T:0.21
Consensus pattern (30 bp):
TAGCAAAAACATAAACTTAAATGACTAAAA
Found at i:402300 original size:29 final size:29
Alignment explanation
Indices: 402231--402301 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
402221 TAAAATAGCT
*
402231 AAAACAGAAATTTAAATGACATAAATAGCA
1 AAAACAGAAACTTAAATGACATAAATA-CA
*
402261 AAAACATAAACTTAAATGAC-TAAAATA-A
1 AAAACAGAAACTTAAATGACAT-AAATACA
402289 AATAACAGAAACT
1 AA-AACAGAAACT
402302 AAAGTGTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 10 0.28
30 23 0.64
ACGTcount: A:0.62, C:0.11, G:0.07, T:0.20
Consensus pattern (29 bp):
AAAACAGAAACTTAAATGACATAAATACA
Found at i:402966 original size:145 final size:144
Alignment explanation
Indices: 402456--402952 Score: 528
Period size: 145 Copynumber: 3.4 Consensus size: 144
402446 CGTGCCACAC
* * ** * *
402456 TCCGATTGTCCTGAAATTTCATTATGTTGTTCGTGTTGACCTCGCGCAACTTTTGACCGTTCGAA
1 TCCGATCGTCCTGAAATTTCAGTATGTTGTTCGTG-TGGTCTCACACAACTTTTGACCGTTCGAA
* * * * * * * *
402521 ATGTTGATCGGAAGTCCCGATCACCGGCGAGAGGCCAAAAA-TCGTCCGGATTTGTTTTCTACGA
65 ATATTGATCGGAAATCCCGATCGCCGGCAAGAGGCCAAAAACT-GTTCGG-CTTATTTTCTCCGA
*
402585 TTCACCACCGTCCACCG
128 TCCACCACCGTCCACCG
* * * * * * * *
402602 TCCGATCGTCATGAAATTTCAGTATGCTGTTCGTGTTGACATGACACAACTTTTCACTGTTTGAA
1 TCCGATCGTCCTGAAATTTCAGTATGTTGTTCGTGTGGTC-TCACACAACTTTTGACCGTTCGAA
* * * * *
402667 ATATTGATCGGAGATCCCGATCGCCAGCAAGAGGCTAAAAACCGTTTGGCTTATTTTCTCCGATC
65 ATATTGATCGGAAATCCCGATCGCCGGCAAGAGGCCAAAAACTGTTCGGCTTATTTTCTCCGATC
* ** * *
402732 TACCGTCATCCACTG
130 CACCACCGTCCACCG
* * * * * *
402747 TCCGATCGTCTTGAATTTTCAGTATGTTGTTTGTGCTGGTCTCGCACAACTTTTGACCATTCGGA
1 TCCGATCGTCCTGAAATTTCAGTATGTTGTTCGTG-TGGTCTCACACAACTTTTGACCGTTCGAA
402812 ATATTGATCGGAAATCCCGATCGCCGGCAAGAGGCCAAAAACTGTTCGGCTTATTTTCTCCGATC
65 ATATTGATCGGAAATCCCGATCGCCGGCAAGAGGCCAAAAACTGTTCGGCTTATTTTCTCCGATC
402877 CACCACCGTCCACCG
130 CACCACCGTCCACCG
* * * * * *
402892 TCTGATCGTCCTGAATTTTTAGTATGTTGTTCGTGATGGTCTTACGCAACTTTTGAGCGTT
1 TCCGATCGTCCTGAAATTTCAGTATGTTGTTCGTG-TGGTCTCACACAACTTTTGACCGTT
402953 TGGAATGGTG
Statistics
Matches: 283, Mismatches: 65, Indels: 7
0.80 0.18 0.02
Matches are distributed among these distances:
145 193 0.68
146 90 0.32
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (144 bp):
TCCGATCGTCCTGAAATTTCAGTATGTTGTTCGTGTGGTCTCACACAACTTTTGACCGTTCGAAA
TATTGATCGGAAATCCCGATCGCCGGCAAGAGGCCAAAAACTGTTCGGCTTATTTTCTCCGATCC
ACCACCGTCCACCG
Found at i:403301 original size:3 final size:3
Alignment explanation
Indices: 403293--403357 Score: 94
Period size: 3 Copynumber: 21.0 Consensus size: 3
403283 TGGTTTAGGT
*
403293 ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
403339 ATA ATA ATA TTTA ATA ATA
1 ATA ATA ATA -ATA ATA ATA
403358 TTTTTTCGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 51 0.91
4 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:405822 original size:3 final size:3
Alignment explanation
Indices: 405814--405853 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
405804 AACAAGTTGC
405814 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
405854 GTGGACGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:406296 original size:20 final size:20
Alignment explanation
Indices: 406257--406296 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
406247 ATTTTGGTCC
*
406257 GTTTTAATTTCTAAACTTTA
1 GTTTTAATTTCTAAAATTTA
406277 GTTTTAATTT-TCAAAATTTA
1 GTTTTAATTTCT-AAAATTTA
406297 ACATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
GTTTTAATTTCTAAAATTTA
Found at i:407390 original size:10 final size:10
Alignment explanation
Indices: 407377--407406 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
407367 CAAACGGATG
407377 TAAACGAACA
1 TAAACGAACA
*
407387 TAAACGAACG
1 TAAACGAACA
407397 TAAACGAACA
1 TAAACGAACA
407407 CAGATGGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (10 bp):
TAAACGAACA
Found at i:407435 original size:24 final size:24
Alignment explanation
Indices: 407390--407435 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
407380 ACGAACATAA
* *
407390 ACGAACGTAAACGAACACAGATGG
1 ACGAACATAAACGAAAACAGATGG
* *
407414 ACGAACATAAATGAAAATAGAT
1 ACGAACATAAACGAAAACAGAT
407436 TTTTTTTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.52, C:0.15, G:0.20, T:0.13
Consensus pattern (24 bp):
ACGAACATAAACGAAAACAGATGG
Found at i:407645 original size:24 final size:24
Alignment explanation
Indices: 407596--407651 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
407586 GATTGAGCTA
* * *
407596 AACATAAATGAGCGCACATAATCG
1 AACATAAATGAACGAACATAAACG
* *
407620 AATATAAATGAACGAACGTAAACG
1 AACATAAATGAACGAACATAAACG
407644 AACATAAA
1 AACATAAA
407652 CAAACATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.16, G:0.14, T:0.16
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:410285 original size:32 final size:32
Alignment explanation
Indices: 410210--410333 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
410200 CCCTAAGGGA
*
410210 ACATCTTAGGGCC-TGAGAGCCTACCCAAGAT
1 ACATCTTAGGGCCGTGAGAGCCTACCCAAGAC
* * *
410241 AGAT-TTCGGGGCCGTGAGA-CCTACCTAAGAAC
1 ACATCTT-AGGGCCGTGAGAGCCTACCCAAG-AC
* * *
410273 ACATCTTAGGGCCG-CAGGGCCTACCCGAGA-
1 ACATCTTAGGGCCGTGAGAGCCTACCCAAGAC
* * * *
410303 ATGATCTCAGGGCCG-CAGAGCCTACCTAAGA
1 A-CATCTTAGGGCCGTGAGAGCCTACCCAAGA
410334 GTCACATTAG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 3 0.04
31 44 0.61
32 23 0.32
33 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (32 bp):
ACATCTTAGGGCCGTGAGAGCCTACCCAAGAC
Found at i:410316 original size:63 final size:63
Alignment explanation
Indices: 410210--410333 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
410200 CCCTAAGGGA
* * *
410210 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGACCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAG-CCTACCTAAGAAC
* *
410273 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
410334 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 48 0.91
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:411341 original size:61 final size:59
Alignment explanation
Indices: 411211--411346 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 59
411201 CATTCAAAAA
* * *
411211 TTCCCAAAATGTCA-CATTTTTCAAAATAATTCTCAAAATGTCACTTTTTTCGAAATAT
1 TTCCCAGAATGTCACCATTTTTCAAAAAAATTCTCAAAATATCACTTTTTTCGAAATAT
** *
411269 TTCTAAGAATGTCACCTTTTTTTCAAAAAAATTC-CTAAAATATCACCTTTTTTCGAAATAT
1 TTCCCAGAATGTCACC-ATTTTTCAAAAAAATTCTC-AAAATATCA-CTTTTTTCGAAATAT
411330 TTCCCAGAATGTCACCA
1 TTCCCAGAATGTCACCA
411347 GGTCGGGTCG
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
58 11 0.17
59 2 0.03
60 23 0.35
61 29 0.45
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (59 bp):
TTCCCAGAATGTCACCATTTTTCAAAAAAATTCTCAAAATATCACTTTTTTCGAAATAT
Found at i:411345 original size:30 final size:30
Alignment explanation
Indices: 411209--411345 Score: 136
Period size: 29 Copynumber: 4.6 Consensus size: 30
411199 CACATTCAAA
*
411209 AATTCCCAAAATGTCA-CATTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTTCAAAAT
* *
411238 AATTCTCAAAATGTCA-CTTTTTTCGAAAT
1 AATTCCCAAAATGTCACCTTTTTTCAAAAT
* * *
411267 -ATTTCTAAGAATGTCACCTTTTTTTCAAAAA
1 AATTCCCAA-AATGTCACC-TTTTTTCAAAAT
* * *
411298 AATTCCTAAAATATCACCTTTTTTCGAAAT
1 AATTCCCAAAATGTCACCTTTTTTCAAAAT
* *
411328 ATTTCCCAGAATGTCACC
1 AATTCCCAAAATGTCACC
411346 AGGTCGGGTC
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
28 5 0.06
29 33 0.38
30 25 0.28
31 18 0.20
32 7 0.08
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (30 bp):
AATTCCCAAAATGTCACCTTTTTTCAAAAT
Found at i:411368 original size:13 final size:13
Alignment explanation
Indices: 411350--411374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
411340 GTCACCAGGT
411350 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
411363 CGGGTCGGGTCA
1 CGGGTCGGGTCA
411375 GACCAATCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:418600 original size:29 final size:29
Alignment explanation
Indices: 418559--418747 Score: 193
Period size: 29 Copynumber: 6.6 Consensus size: 29
418549 CATATTCGAA
* *
418559 AATTCTCAAAATGTCACATTTTTCAAAAG
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
418588 AATTCCCAGAATGTCACCTTTTTCGAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
418617 ATTTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* **
418646 AATTCTCAAAATGT--CATTTTTTGAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
418673 ATTTCCCAAAATGTCACCTTTTTCAAAAA
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* **
418702 AATTCCCAAACTGTCACATTTTTTGAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* *
418731 ATTTCCCAGAATGTCAC
1 AATTCCCAAAATGTCAC
418748 CGGGTCGGGT
Statistics
Matches: 130, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
27 22 0.17
29 108 0.83
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (29 bp):
AATTCCCAAAATGTCACATTTTTCAAAAT
Found at i:418641 original size:58 final size:56
Alignment explanation
Indices: 418568--418748 Score: 256
Period size: 58 Copynumber: 3.2 Consensus size: 56
418558 AAATTCTCAA
* * *
418568 AATGTCACATTTTTCAAAAGAATTCCCAGAATGTCACCTTTTTCGAAATATTTCCCAG
1 AATGTCACCTTTTTCAAAAAAATTCCCA-AATGTCA-CTTTTTTGAAATATTTCCCAG
* * *
418626 AATGTCACCTTTTTCAAAATAATTCTCAAAATGTCA-TTTTTTGAAATATTTCCCAA
1 AATGTCACCTTTTTCAAAAAAATTC-CCAAATGTCACTTTTTTGAAATATTTCCCAG
418682 AATGTCACCTTTTTCAAAAAAATTCCCAAACTGTCACATTTTTTGAAATATTTCCCAG
1 AATGTCACCTTTTTCAAAAAAATTCCCAAA-TGTCAC-TTTTTTGAAATATTTCCCAG
418740 AATGTCACC
1 AATGTCACC
418749 GGGTCGGGTC
Statistics
Matches: 111, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
55 4 0.04
56 47 0.42
58 58 0.52
59 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (56 bp):
AATGTCACCTTTTTCAAAAAAATTCCCAAATGTCACTTTTTTGAAATATTTCCCAG
Found at i:418708 original size:85 final size:86
Alignment explanation
Indices: 418559--418724 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 86
418549 CATATTCGAA
* * * *
418559 AATTCTCAAAATGTCACATTTTTCAAAAGAATTCCCAGAATGTCACCTTTTTCGAAATATTTCCC
1 AATTCTCAAAATGT-ACATTTTTCAAAAGAATTCCCAAAATGTCACCTTTTTCAAAAAAATTCCC
*
418624 AGAA-TGTCACCTTTTTCAAAAT
65 A-AACTGTCACATTTTTCAAAAT
** * *
418646 AATTCTCAAAATGT-CATTTTTTGAAATATTTCCCAAAATGTCACCTTTTTCAAAAAAATTCCCA
1 AATTCTCAAAATGTACATTTTTCAAAAGAATTCCCAAAATGTCACCTTTTTCAAAAAAATTCCCA
418710 AACTGTCACATTTTT
66 AACTGTCACATTTTT
418725 TGAAATATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 2 0.03
85 53 0.77
87 14 0.20
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (86 bp):
AATTCTCAAAATGTACATTTTTCAAAAGAATTCCCAAAATGTCACCTTTTTCAAAAAAATTCCCA
AACTGTCACATTTTTCAAAAT
Found at i:420863 original size:15 final size:14
Alignment explanation
Indices: 420833--420883 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 14
420823 TATCAAACGT
420833 AATAATAAAA-TAA
1 AATAATAAAATTAA
420846 AATAATAATAATTAA
1 AATAATAA-AATTAA
420861 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
420876 AAGTAATA
1 AA-TAATA
420884 TTATTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 8 0.25
14 2 0.06
15 17 0.53
16 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:422837 original size:76 final size:76
Alignment explanation
Indices: 422326--422810 Score: 900
Period size: 76 Copynumber: 6.4 Consensus size: 76
422316 GGTCTTAAAA
* * *
422326 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
422390 AGGCTTTTTGG
66 AGGCTTTTTGG
*
422401 AAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
422466 AGGCTTTTTGG
66 AGGCTTTTTGG
*
422477 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
422542 AGGCTTTTTGG
66 AGGCTTTTTGG
422553 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
422618 AGGCTTTTTGG
66 AGGCTTTTTGG
*
422629 AAACATCATGCACTGCAGGACTTACAGATGATCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
422694 AGGCTTTTTGG
66 AGGCTTTTTGG
422705 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
422770 AGGCATTTTGG
66 AGGCTTTTTGG
422781 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
422811 TGGGAAATAG
Statistics
Matches: 399, Mismatches: 10, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
75 35 0.09
76 364 0.91
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:423107 original size:187 final size:185
Alignment explanation
Indices: 422751--423116 Score: 660
Period size: 187 Copynumber: 2.0 Consensus size: 185
422741 AGGCTTTGAA
422751 AACATCAAAAAGCTCCCGAAGGCATTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCATTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
*
422816 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTTATTTTTAG
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
*
422881 AAAAGATTAAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
131 AAAAGATTAAATGAGAAACTATGGAAATCATTTTCTCATTATGTTTCAAAGTAAC
*
422936 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCATTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
423001 AATAGTTTACTAAGTAAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTT
66 AATAGTTTACTAAGT--AAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTT
* * *
423066 AGAAAAGATTGAATGAGAAACTTTGGAAATCGTTTTCTCATTATGTTTCAA
129 AGAAAAGATTAAATGAGAAACTATGGAAATCATTTTCTCATTATGTTTCAA
423117 GATAACCTGT
Statistics
Matches: 173, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
185 79 0.46
187 94 0.54
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (185 bp):
AACATCAAAAAGCTCCCGAAGGCATTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
AAAAGATTAAATGAGAAACTATGGAAATCATTTTCTCATTATGTTTCAAAGTAAC
Found at i:423274 original size:166 final size:167
Alignment explanation
Indices: 422998--423325 Score: 543
Period size: 166 Copynumber: 2.0 Consensus size: 167
422988 TACAGATGTG
*
422998 GGAAATAGTTTACTAAGTAAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATT
1 GGAAATAGTTTACTAAGT-AAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATT
** * * *
423063 TTTAGAAAAGATTGAATGAGAAACTTTGGAAATCGTTTTCTCATTATG-TTTCAAGATAACCTGT
65 TTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTCAA-ATAACATAT
423127 TGATTGGGTAACATGCCCCAATCTCAAGATAAGGTTGTT
129 TGATTGGGTAACATGCCCCAATCTCAAGATAAGGTTGTT
*
423166 GGAAATAGTTTACTAAGT-AAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAGTTTCATTT
1 GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTT
*
423230 TTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTTGAAATAACATATT
66 TTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATG-TTTTCAAATAACATATT
423295 GATTGGGTAACATGCCCCAATCTCAAGATAA
130 GATTGGGTAACATGCCCCAATCTCAAGATAA
423326 TGCTCATTCT
Statistics
Matches: 150, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
166 88 0.59
167 39 0.26
168 23 0.15
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (167 bp):
GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTT
TTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTCAAATAACATATTG
ATTGGGTAACATGCCCCAATCTCAAGATAAGGTTGTT
Found at i:423857 original size:22 final size:22
Alignment explanation
Indices: 423832--423930 Score: 155
Period size: 22 Copynumber: 4.5 Consensus size: 22
423822 AATAAAGCTT
423832 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
423854 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
423876 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
423898 TCATCTTTGAAAA-AGGAGTCTA
1 TCATCTTTGAAAAGA-GAATCTA
423920 TCATCTTTGAA
1 TCATCTTTGAA
423931 GAGTGTAGAT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
21 1 0.01
22 72 0.99
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:431490 original size:14 final size:14
Alignment explanation
Indices: 431473--431511 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
431463 TAAAAGTATG
431473 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
431487 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
431502 AATG-AAAATG
1 AATGCAAAATG
431512 CATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:434506 original size:137 final size:137
Alignment explanation
Indices: 434245--434495 Score: 328
Period size: 137 Copynumber: 1.8 Consensus size: 137
434235 TAATTTTAAG
* *
434245 AAAAAATATTAATATATAAATAAGATATTTACTTATTTAGAAATATCAGAAAATGGCTTCTAGGT
1 AAAAAATATTAATATATAAATAAAACATTTACTTATTTAGAAATATCAGAAAATGGCTTCTAGGT
* * ** * *
434310 GCTTTAAGACAGCTCTTTTCTTTGATATTAATGAATAATAAATGTTAATAAAACATTTATCTAAA
66 ACTTTAAGACAGCTCTTTTCTTAGATATTAAAAAATAATAAATATCAATAAAACATTTATCTAAA
434375 AATAATT
131 AATAATT
* * *
434382 AAAATATATTGATATATGAAA-AAAACATTTATTTATTTA-AGAATATCAGAAAA-GGACTTCTA
1 AAAAAATATTAATATAT-AAATAAAACATTTACTTATTTAGA-AATATCAGAAAATGG-CTTCTA
* *
434444 GGTATTTTAAGACAGCTCTTTTCTTAGATATTAAAAAATAAATACATATCAA
63 GGTACTTTAAGACAGCTCTTTTCTTAGATATTAAAAAAT-AATAAATATCAA
434496 AATATGTTTA
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
136 3 0.03
137 82 0.85
138 12 0.12
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (137 bp):
AAAAAATATTAATATATAAATAAAACATTTACTTATTTAGAAATATCAGAAAATGGCTTCTAGGT
ACTTTAAGACAGCTCTTTTCTTAGATATTAAAAAATAATAAATATCAATAAAACATTTATCTAAA
AATAATT
Found at i:434696 original size:15 final size:14
Alignment explanation
Indices: 434666--434725 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
434656 TATCAAACGT
434666 AATAATAAAA-TAA
1 AATAATAAAATTAA
434679 AATAATAATAATTAA
1 AATAATAA-AATTAA
434694 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
434709 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
434724 AA
1 AA
434726 ACTAATGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:435451 original size:3 final size:3
Alignment explanation
Indices: 435422--435530 Score: 112
Period size: 3 Copynumber: 36.0 Consensus size: 3
435412 TTGGGTTTTG
* * * * *
435422 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
435469 TTA TAA TAA TAA TAA TAA TTA TTA TTA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
435516 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
435531 ATTTAAATTT
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.02
3 88 0.92
4 6 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:446915 original size:2 final size:2
Alignment explanation
Indices: 446908--446940 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
446898 AGAAACCATA
*
446908 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
446941 TCTAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:448475 original size:11 final size:11
Alignment explanation
Indices: 448459--448483 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
448449 AGAGGCGGCC
448459 GATGCGGCGTT
1 GATGCGGCGTT
448470 GATGCGGCGTT
1 GATGCGGCGTT
448481 GAT
1 GAT
448484 TCTGCATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.16, G:0.44, T:0.28
Consensus pattern (11 bp):
GATGCGGCGTT
Found at i:448612 original size:22 final size:22
Alignment explanation
Indices: 448578--448637 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
448568 ATGTTTATTT
448578 TATTTAAAGTTTTAATGTTTCAA
1 TATTT-AAGTTTTAATGTTTCAA
448601 TATTTAAGTTTTAATGTTTCAA
1 TATTTAAGTTTTAATGTTTCAA
**
448623 TATTTGTGTTTTAAT
1 TATTTAAGTTTTAAT
448638 CCTGTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 30 0.86
23 5 0.14
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (22 bp):
TATTTAAGTTTTAATGTTTCAA
Found at i:449050 original size:30 final size:30
Alignment explanation
Indices: 449016--449101 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
449006 TTGTAACTTT
* *
449016 TATTTTAGTCCTTAAAGTTTCTGTTTGTGC
1 TATTTTAGTCCTTAAAATTTATGTTTGTGC
* * * *
449046 TATTTTAGTCCTTTAACTTTATATTTTTGC
1 TATTTTAGTCCTTAAAATTTATGTTTGTGC
*
449076 TATTTT-GATCCTTAAAATTTTTGTTT
1 TATTTTAG-TCCTTAAAATTTATGTTT
449102 CTCTATATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
29 1 0.02
30 45 0.98
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (30 bp):
TATTTTAGTCCTTAAAATTTATGTTTGTGC
Found at i:450172 original size:257 final size:257
Alignment explanation
Indices: 449714--450234 Score: 925
Period size: 257 Copynumber: 2.0 Consensus size: 257
449704 GTTAATTTAT
**
449714 GATTCATTTATTGAAGTTTGTAATTGCTTCATTTTTTGTTATACTAACATTTGAATGTTTGTTTT
1 GATTCATTTATTGAAGTTTGTAATTGCTTCATTTTTTGTTATACTAACATTTGAATGTTTACTTT
*
449779 CAGATCTTTTCAAGATGATCGAGTTTCGTTTTCCTTTTGAGTCAAAGGGCTGAATGTTCCTCCTC
66 CAGATCTTTTCAAGATGATCGAGTTTCGTTTTCCATTTGAGTCAAAGGGCTGAATGTTCCTCCTC
* *
449844 ACACACATCACGAGCATTTGCATAACATAAGCGCTATACCCGAGCTTCGAACCCTTTCTAAGTGG
131 ACACACATCACGAGCATTTGCATAACATAAGCGCTATACCCGAGCTCCGAACCCTTTCTAAGTGA
* *
449909 GGGTAAAAGCGACGTCTTCGTGAGAATTTATTCTCTGCATAGGCCTAGCAAGTAACCTTCGG
196 GGGTAAAAGCGACGTCTTCGTGAGAATTTATTATCTGCATAGGCCTAGCAAGTAACCTTCAG
*
449971 GATTCATTTATTGAAGTTTGTAATTGCTTTATTTTTTGTTATACTAACATTTGAATGTTTACTTT
1 GATTCATTTATTGAAGTTTGTAATTGCTTCATTTTTTGTTATACTAACATTTGAATGTTTACTTT
*
450036 CAGATCTTTTCAAGATGATCGAGTTTCGTTTTCCATTTGAGTCAAAGGGTTGAATGTTCCTCCTC
66 CAGATCTTTTCAAGATGATCGAGTTTCGTTTTCCATTTGAGTCAAAGGGCTGAATGTTCCTCCTC
* * * *
450101 ACACACATCACTAGTATTTGCATAACATAAGCTCTATACCCGAGCTCCGAACCCTTTTTAAGTGA
131 ACACACATCACGAGCATTTGCATAACATAAGCGCTATACCCGAGCTCCGAACCCTTTCTAAGTGA
450166 GGGTAAAAGCGACGTCTTCGTGAGAATTTATTATCTGCATAGGCCTAGCAAGTAACCTTCAG
196 GGGTAAAAGCGACGTCTTCGTGAGAATTTATTATCTGCATAGGCCTAGCAAGTAACCTTCAG
450228 GATTCAT
1 GATTCAT
450235 ATACCTTATG
Statistics
Matches: 251, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
257 251 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (257 bp):
GATTCATTTATTGAAGTTTGTAATTGCTTCATTTTTTGTTATACTAACATTTGAATGTTTACTTT
CAGATCTTTTCAAGATGATCGAGTTTCGTTTTCCATTTGAGTCAAAGGGCTGAATGTTCCTCCTC
ACACACATCACGAGCATTTGCATAACATAAGCGCTATACCCGAGCTCCGAACCCTTTCTAAGTGA
GGGTAAAAGCGACGTCTTCGTGAGAATTTATTATCTGCATAGGCCTAGCAAGTAACCTTCAG
Found at i:450660 original size:49 final size:48
Alignment explanation
Indices: 450604--450734 Score: 183
Period size: 49 Copynumber: 2.7 Consensus size: 48
450594 GAAAAATTAT
* * *
450604 TTCGGGTAGATAGCAGGACCGGGTATGAGTGTTATTTAATTAAAGCATG
1 TTCGGGTAGATAACATGACCGGGTA-GAGTGTTATTTAATTAAAACATG
*
450653 TTCGGGTAGATAACATGTCCGGGTAGGAGTGTTATTTAATTAAAACATG
1 TTCGGGTAGATAACATGACCGGGTA-GAGTGTTATTTAATTAAAACATG
* *
450702 TTCGGGTAGATATCATGACAGGGTAG-GTGTTAT
1 TTCGGGTAGATAACATGACCGGGTAGAGTGTTAT
450735 ATTCATCTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
47 7 0.09
48 1 0.01
49 66 0.89
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.32
Consensus pattern (48 bp):
TTCGGGTAGATAACATGACCGGGTAGAGTGTTATTTAATTAAAACATG
Found at i:452159 original size:2 final size:2
Alignment explanation
Indices: 452152--452222 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
452142 TTTGTTTCAT
452152 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
452194 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 T
452223 CCCTTGTTGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:458687 original size:23 final size:24
Alignment explanation
Indices: 458661--458705 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
458651 TAAATGAACA
458661 TAAACGAACACA-ATAAACGAATG
1 TAAACGAACACAGATAAACGAATG
*
458684 TAAACGAACACAGATGAACGAA
1 TAAACGAACACAGATAAACGAA
458706 CATAAATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.56, C:0.18, G:0.16, T:0.11
Consensus pattern (24 bp):
TAAACGAACACAGATAAACGAATG
Found at i:458711 original size:24 final size:24
Alignment explanation
Indices: 458612--458711 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
458602 CATTTAAATG
* * *
458612 ATAAACGGACACAAATGAAAGAAC
1 ATAAACGAACACAGATGAACGAAC
* * *
458636 ATAAA-TAA-ACGGATGTAAATGAAC
1 ATAAACGAACACAGATG--AACGAAC
* *
458660 ATAAACGAACACA-ATAAACGAAT
1 ATAAACGAACACAGATGAACGAAC
*
458683 GTAAACGAACACAGATGAACGAAC
1 ATAAACGAACACAGATGAACGAAC
458707 ATAAA
1 ATAAA
458712 TGAAAAATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
22 5 0.09
23 18 0.32
24 28 0.49
25 4 0.07
26 2 0.04
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (24 bp):
ATAAACGAACACAGATGAACGAAC
Found at i:458919 original size:34 final size:34
Alignment explanation
Indices: 458880--458945 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
458870 GATTGGGCTA
* *
458880 AACATAAATGAGCGCACATAAACAAACATAAACG
1 AACATAAATGAACGAACATAAACAAACATAAACG
* *
458914 AACATAAATGAACGAACGTAAACGAACATAAA
1 AACATAAATGAACGAACATAAACAAACATAAA
458946 TGTATGAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (34 bp):
AACATAAATGAACGAACATAAACAAACATAAACG
Found at i:458940 original size:24 final size:24
Alignment explanation
Indices: 458908--459001 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
458898 TAAACAAACA
458908 TAAACGAACATAAATGAACGAACG
1 TAAACGAACATAAATGAACGAACG
* * *
458932 TAAACGAACATAAATGTATGAACA
1 TAAACGAACATAAATGAACGAACG
* *
458956 TAAACGAACAT--ATTATCGAACG
1 TAAACGAACATAAATGAACGAACG
** **
458978 TTCACGAATGTAAATGAACGAACG
1 TAAACGAACATAAATGAACGAACG
459002 AGCCCTCTGT
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
22 13 0.24
24 41 0.76
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (24 bp):
TAAACGAACATAAATGAACGAACG
Found at i:462694 original size:30 final size:30
Alignment explanation
Indices: 462626--462746 Score: 120
Period size: 30 Copynumber: 4.1 Consensus size: 30
462616 ATAATAGATC
* * *
462626 TAGCAAAAACATGAACTTAAAGGA-TTAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
* * * * *
462655 TGGTAAAAACATAAACTCAAAAGGCTAAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
* * *
462685 TAGCTAAAACAGAAATTTAAATGAC-ATAAA
1 TAGCAAAAACATAAACTTAAATGACTA-AAA
462715 TAGCAAAAACATAAACTTAAATGACTAAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
462745 TA
1 TA
462747 AAATAACAGA
Statistics
Matches: 71, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
29 19 0.27
30 51 0.72
31 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.11, T:0.21
Consensus pattern (30 bp):
TAGCAAAAACATAAACTTAAATGACTAAAA
Found at i:462759 original size:29 final size:29
Alignment explanation
Indices: 462690--462760 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
462680 TAAAATAGCT
*
462690 AAAACAGAAATTTAAATGACATAAATAGCA
1 AAAACAGAAACTTAAATGACATAAATA-CA
*
462720 AAAACATAAACTTAAATGAC-TAAAATA-A
1 AAAACAGAAACTTAAATGACAT-AAATACA
462748 AATAACAGAAACT
1 AA-AACAGAAACT
462761 AAAGTGTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 10 0.28
30 23 0.64
ACGTcount: A:0.62, C:0.11, G:0.07, T:0.20
Consensus pattern (29 bp):
AAAACAGAAACTTAAATGACATAAATACA
Found at i:463425 original size:145 final size:143
Alignment explanation
Indices: 462917--463417 Score: 511
Period size: 145 Copynumber: 3.4 Consensus size: 143
462907 TGCCACTGTT
* * ** *
462917 CGATTGTCCTGAAATTTCATTATGTTGTTCGTGTTGACCTCCCGCAACTTTTGACCGTTCGGAAT
1 CGATCGTCCTGAAATTTCAGTATGTTGTTCGTG-TGGTCTCACGCAACTTTTGACCGTTCGGAAT
* * * * * * *
462982 ATTGATCGGA-AGTCCCGATCAACGGCGAGAGGCCAAAAACCGTCCGGATTTGTTTTCTACAATT
65 ATTGATCGGAGA-TCCCGATC-GCGGCAAGAGGCCAAAAACCGTTCGG-CTTATTTTCTCCGATT
*
463046 CACCACCGTCCACCGTC
127 CACCGCCGTCCACCGTC
* * * * * * * * ** * *
463063 CAATCGTCATGAAATTTCAGTATGCTGTTCGTGTTGACATGACACAACTTTTCACTATTTGAAAT
1 CGATCGTCCTGAAATTTCAGTATGTTGTTCGTGTGGTC-TCACGCAACTTTTGACCGTTCGGAAT
* * * * *
463128 ATTGATCGGAGATTCCGATCGCCAGCAAGAGGCTAAAAACCATTTGGCTTATTTTCTCCGA-TCT
65 ATTGATCGGAGATCCCGATCG-CGGCAAGAGGCCAAAAACCGTTCGGCTTATTTTCTCCGATTC-
* * * *
463192 GCCGTCATCCACTGTC
128 ACCGCCGTCCACCGTC
* * ** * *
463208 CGATCGTCTTGAATTTTCAGTATGTTGTTTTTTCTGGTCTCGCGCAACTTTTGACCGTTCGGAAT
1 CGATCGTCCTGAAATTTCAGTATGTTG-TTCGTGTGGTCTCACGCAACTTTTGACCGTTCGGAAT
463273 ATTGATCGGAGATCCCGATCGCTGGCAAGAGGCCAAAAACCGTTCGGCTTATTTTCTCCGATTCA
65 ATTGATCGGAGATCCCGATCGC-GGCAAGAGGCCAAAAACCGTTCGGCTTATTTTCTCCGATTCA
463338 CCGCCGTCCACCGTC
129 CCGCCGTCCACCGTC
* * *
463353 CGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTTACGCAACTTTTGACCGTTAGGAAT
1 CGATCGTCCTGAAATTTCAGTATGTTGTTCGTG-TGGTCTCACGCAACTTTTGACCGTTCGGAAT
463418 GGTGATCGTA
Statistics
Matches: 281, Mismatches: 66, Indels: 17
0.77 0.18 0.05
Matches are distributed among these distances:
144 6 0.02
145 184 0.65
146 90 0.32
147 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (143 bp):
CGATCGTCCTGAAATTTCAGTATGTTGTTCGTGTGGTCTCACGCAACTTTTGACCGTTCGGAATA
TTGATCGGAGATCCCGATCGCGGCAAGAGGCCAAAAACCGTTCGGCTTATTTTCTCCGATTCACC
GCCGTCCACCGTC
Found at i:463768 original size:3 final size:3
Alignment explanation
Indices: 463755--463815 Score: 86
Period size: 3 Copynumber: 19.7 Consensus size: 3
463745 TTAGGTATAG
*
463755 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
463801 TAA TATT TAA TAA TA
1 TAA TA-A TAA TAA TA
463816 TTTTTTTGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 47 0.90
4 5 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Done.