Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009630.1 Hibiscus syriacus cultivar Beakdansim tig00117026_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: 1249403
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1080606 original size:21 final size:22
Alignment explanation
Indices: 1080570--1080615 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1080560 TTATATATAA
1080570 AAATATAAATTATAAAATTTAT
1 AAATATAAATTATAAAATTTAT
*
1080592 AAATATCAA-TATAAAATTTAT
1 AAATATAAATTATAAAATTTAT
1080613 AAA
1 AAA
1080616 ATTAACCACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATATAAATTATAAAATTTAT
Found at i:1090488 original size:201 final size:201
Alignment explanation
Indices: 1090209--1090572 Score: 541
Period size: 201 Copynumber: 1.8 Consensus size: 201
1090199 CAAATGCATG
* * ** *
1090209 AATTGCCAAATGTAAAGAATTCGATATCGAACTTATTCAAAGTACATTCTTATAACCTGAATAAG
1 AATTGCCAAATGTAAAGAATTAGATATCGAACTTATTCAAAGCACATTCTTATAACCCAAAGAAG
* * *
1090274 CAATCTGTATACCACAAAATTCTCCTTTAAGCAACAAAGAAACCTTTTACAAACAATTTCACATG
66 AAATCTGTATACCACAAAATGCTCCTTTAACCAACAAAGAAACCTTTTACAAACAATTTCACATG
*
1090339 CTTACTCCTTTTCCATAGAAAAATATAGAAGTATATGAGACATTAAACACAAGAACGACACAAAT
131 CTTACTCCTTTTCCATAGAAAAATACAGAAGTATATGAGACATTAAACACAAGAACGACACAAAT
1090404 GTATCA
196 GTATCA
* * * * **
1090410 AATTGCCGAATGTAAGGAGTTAGATATC-ATACTTATTCAAAGCATATTCTTATCGCCCAAAGAA
1 AATTGCCAAATGTAAAGAATTAGATATCGA-ACTTATTCAAAGCACATTCTTATAACCCAAAGAA
*
1090474 GAAATCTTTATACCACAAAATGCTCCTTTAACCAACAAAGAAACCTTTTACAAACAATTTCACAT
65 GAAATCTGTATACCACAAAATGCTCCTTTAACCAACAAAGAAACCTTTTACAAACAATTTCACAT
* * *
1090539 TCTTACTCCTTTTCCCTAGAAATATACAGAAGTA
130 GCTTACTCCTTTTCCATAGAAAAATACAGAAGTA
1090573 CATTATATAC
Statistics
Matches: 143, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
200 1 0.01
201 142 0.99
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (201 bp):
AATTGCCAAATGTAAAGAATTAGATATCGAACTTATTCAAAGCACATTCTTATAACCCAAAGAAG
AAATCTGTATACCACAAAATGCTCCTTTAACCAACAAAGAAACCTTTTACAAACAATTTCACATG
CTTACTCCTTTTCCATAGAAAAATACAGAAGTATATGAGACATTAAACACAAGAACGACACAAAT
GTATCA
Found at i:1090633 original size:22 final size:20
Alignment explanation
Indices: 1090588--1090633 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1090578 TATACTTATT
*
1090588 CAAAGCACATTCTTATCACC
1 CAAAGCACATTCTTATCACA
*
1090608 CAAAGACACAATTCTTATTACA
1 CAAAG-CAC-ATTCTTATCACA
1090630 CAAA
1 CAAA
1090634 CGTAAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 3 0.14
22 14 0.64
ACGTcount: A:0.43, C:0.28, G:0.04, T:0.24
Consensus pattern (20 bp):
CAAAGCACATTCTTATCACA
Found at i:1095774 original size:799 final size:797
Alignment explanation
Indices: 1094239--1095839 Score: 2968
Period size: 799 Copynumber: 2.0 Consensus size: 797
1094229 TCTACATACC
*
1094239 CATTGATTAATAAGTTTGATCCTCCGTAACATAATGCAACATTTGAGGTCCCTTTGATGTATCTC
1 CATTGATTAATAAGTTTGATCATCCGTAACATAATGCAACATTTGAGGTCCCTTTGATGTATCTC
* *
1094304 AGGATCCTCTTTACTGTATTCCAATGCTCTTTGCATGGATTCACCATGTACCGACTAATCACTCC
66 AGAATCCTCTTTACTGTATTCCAATGCTCTTTGCATGGATTCACCATGTACCGACTAACCACTCC
*
1094369 CACTACTTGTGCAATGTCTGGTCTTGTGCATATCATAGCGAACATTAAACTTCCCACTGCATGCA
131 CACTACTTGTGCAATGTATGGTCTTGTGCATATCATAGCGAACATTAAACTTCCCACTGCATGCA
* *
1094434 TTCGGTACTCGAGACATCTTCATCCTCTCTTCTTTACTGCTAGGACTCATACTGGAGGATAATTT
196 TTCGATACTCGAGACATCTCCATCCTCTCTTCTTTACTGCTAGGACTCATACTGGAGGATAATTT
* *
1094499 GAAGTTAATAAGAAGATGGGTAGAAATTGGCTTACAATCTTGCATGTTGAATCGTGACAAGATCT
261 GAAATTAATAAGAAGAGGGGTAGAAATTGGCTTACAATCTTGCATGTTGAATCGTGACAAGATCT
*
1094564 TCTTCAAGTAATTCTTTTGTGAAAGCCAATTCTTCCTATTACTTCTGTCTCGGTGAATTTGCATC
326 TCTTCAAGTAATTCTTTTGTGAAAGCCAAATCTTCCTATTACTTCTGTCTCGGTGAATTTGCATC
*
1094629 CCCAAAATCTTGTTTACTGACCCCAAGTCCTTCATTTCAAATTCCCTAGCCAGTTGTGCCTTCAA
391 CCCAAAATATTGTTTACTGACCCCAAGTCCTTCATTTCAAATTCCCTAGCCAGTTGTGCCTTCAA
*
1094694 TTCTTCAATATGATCTTTGTTGGGTCCTGCAACCAACATGTCATCCACATACAACAACAATATAA
456 TTCTTCAATATGATCTTTGTTGGGTCATGCAACCAACATGTCATCCACATACAACAACAATATAA
* *
1094759 CACAATCGTTATCACCAGACCTCTTGAAATAAGCACAAGGGTCTGCATTAAGTCTGTTGTATCCA
521 CAAAATCGTTATCACCAGACCTCTTGAAATAAGCACAAGGGTCTGCATTAAGTCTATTGTATCCA
1094824 AGACACATAATGAAGGAATCAAATCTCTTATACCAACACCTCGGCGCCTGCTTTAGACCGTACAG
586 AGACACATAATGAAGGAATCAAATCTCTTATACCAACACCTCGGCGCCTGCTTTAGACCGTACAG
1094889 AGATTTGTTCAACCTGCAAACCAAGTTCTTCGTTTCTTTTTCTTCAAAACCTTCAGGCTGGAGCA
651 AGATTTGTTCAACCTGCAAACCAAGTTCTTCGTTTCTTTTTCTTCAAAACCTTCAGGCTGGAGCA
*
1094954 TATAAATTTATTCTTCAAGATTTCCATGACGAAAAGCTGTTTTAACATCTAGCTGCTCTAGATGT
716 TATAAATTTATTCTTCAAGATTTCCATGAAGAAAAGCTGTTTTAACATCTAGCTGCTCTAGATGT
1095019 AAGTCCAATGTAGCACA
781 AAGTCCAATGTAGCACA
*
1095036 CATTGATTAATAAGTTTGATCATCCGTAACATAATGCAATATTTGAGGTCCCTTTGATGTATCTC
1 CATTGATTAATAAGTTTGATCATCCGTAACATAATGCAACATTTGAGGTCCCTTTGATGTATCTC
*
1095101 AGAATCCTCTTTACTGTATTCCAATGCTCTTTGCCTGGATTCACCATGTACCGACTAACCACTCC
66 AGAATCCTCTTTACTGTATTCCAATGCTCTTTGCATGGATTCACCATGTACCGACTAACCACTCC
*
1095166 CACTGCTTGTGCAATGTATGGTCTTGTGCATATCATAGCGAACATTAAACTTCCCACTGCTGATG
131 CACTACTTGTGCAATGTATGGTCTTGTGCATATCATAGCGAACATTAAACTTCCCACTGC--ATG
1095231 CATTCGATACTCGAGACATCTCCATCCTCTCTTCTTTACTGCTAGGACTCATACTGGAGGATAAT
194 CATTCGATACTCGAGACATCTCCATCCTCTCTTCTTTACTGCTAGGACTCATACTGGAGGATAAT
*
1095296 TTGAAATTAATAAGAAGAGGGGTATAAATTGGCTTACAATCTTGCATGTTGAATCGTGACAAGAT
259 TTGAAATTAATAAGAAGAGGGGTAGAAATTGGCTTACAATCTTGCATGTTGAATCGTGACAAGAT
1095361 CTTCTTCAAGTAATTCTTTTGTGAAAGCCAAATCTTCCTATTACTTCTGTCTCGGTGAATTTGCA
324 CTTCTTCAAGTAATTCTTTTGTGAAAGCCAAATCTTCCTATTACTTCTGTCTCGGTGAATTTGCA
** *
1095426 TCCCCAAAATATTGTTTGTTGATCCCAAGTCCTTCATTTCAAATTCCCTAGCCAGTTGTGCCTTC
389 TCCCCAAAATATTGTTTACTGACCCCAAGTCCTTCATTTCAAATTCCCTAGCCAGTTGTGCCTTC
1095491 AATTCTTCAATATGATCTTTGTTGGGTCATGCAACCAACATGTCATCCACATACAACAACAATAT
454 AATTCTTCAATATGATCTTTGTTGGGTCATGCAACCAACATGTCATCCACATACAACAACAATAT
1095556 AACAAAATCGTTATCACCAGACCTCTTGAAATAAGCACAAGGGTCTGCATTAAGTCTATTGTATC
519 AACAAAATCGTTATCACCAGACCTCTTGAAATAAGCACAAGGGTCTGCATTAAGTCTATTGTATC
*
1095621 CAAGACACATAATGAAGGAATCAAATCTCTTATACCAACACCTCGGCGCCTGCTTTAGATCGTAC
584 CAAGACACATAATGAAGGAATCAAATCTCTTATACCAACACCTCGGCGCCTGCTTTAGACCGTAC
*
1095686 AGAGATTTGTTCAACCTGCAAACCAAGTTCTTCTTTTCTTTTTCTTCAAAACCTTCAGGCTGGAG
649 AGAGATTTGTTCAACCTGCAAACCAAGTTCTTCGTTTCTTTTTCTTCAAAACCTTCAGGCTGGAG
*
1095751 CATATAAATTTATTCTTCAAGATTTCCATGAAGAAAAGCTGTTTTAACATCTAGTTGCTCTAGAT
714 CATATAAATTTATTCTTCAAGATTTCCATGAAGAAAAGCTGTTTTAACATCTAGCTGCTCTAGAT
1095816 GTAAGTCCAATGTAGCACA
779 GTAAGTCCAATGTAGCACA
1095835 CATTG
1 CATTG
1095840 CCAAAACTAC
Statistics
Matches: 778, Mismatches: 24, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
797 183 0.24
799 595 0.76
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (797 bp):
CATTGATTAATAAGTTTGATCATCCGTAACATAATGCAACATTTGAGGTCCCTTTGATGTATCTC
AGAATCCTCTTTACTGTATTCCAATGCTCTTTGCATGGATTCACCATGTACCGACTAACCACTCC
CACTACTTGTGCAATGTATGGTCTTGTGCATATCATAGCGAACATTAAACTTCCCACTGCATGCA
TTCGATACTCGAGACATCTCCATCCTCTCTTCTTTACTGCTAGGACTCATACTGGAGGATAATTT
GAAATTAATAAGAAGAGGGGTAGAAATTGGCTTACAATCTTGCATGTTGAATCGTGACAAGATCT
TCTTCAAGTAATTCTTTTGTGAAAGCCAAATCTTCCTATTACTTCTGTCTCGGTGAATTTGCATC
CCCAAAATATTGTTTACTGACCCCAAGTCCTTCATTTCAAATTCCCTAGCCAGTTGTGCCTTCAA
TTCTTCAATATGATCTTTGTTGGGTCATGCAACCAACATGTCATCCACATACAACAACAATATAA
CAAAATCGTTATCACCAGACCTCTTGAAATAAGCACAAGGGTCTGCATTAAGTCTATTGTATCCA
AGACACATAATGAAGGAATCAAATCTCTTATACCAACACCTCGGCGCCTGCTTTAGACCGTACAG
AGATTTGTTCAACCTGCAAACCAAGTTCTTCGTTTCTTTTTCTTCAAAACCTTCAGGCTGGAGCA
TATAAATTTATTCTTCAAGATTTCCATGAAGAAAAGCTGTTTTAACATCTAGCTGCTCTAGATGT
AAGTCCAATGTAGCACA
Found at i:1119789 original size:18 final size:18
Alignment explanation
Indices: 1119747--1119781 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1119737 ACCGGTCACA
*
1119747 ACCCGACCCGACTCGTTC
1 ACCCGACCCGACCCGTTC
1119765 ACCCGACCCGACCCGTT
1 ACCCGACCCGACCCGTT
1119782 GACTCGACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.51, G:0.17, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTC
Found at i:1121146 original size:18 final size:18
Alignment explanation
Indices: 1121120--1121160 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1121110 ATTGTTCGAA
*
1121120 AAGACTGAAGTAAATGAT
1 AAGACTGAAGTAAATAAT
* *
1121138 AAGATTGAATTAAATAAT
1 AAGACTGAAGTAAATAAT
1121156 AAGAC
1 AAGAC
1121161 CGGATGGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (18 bp):
AAGACTGAAGTAAATAAT
Found at i:1122383 original size:24 final size:24
Alignment explanation
Indices: 1122247--1122380 Score: 207
Period size: 24 Copynumber: 5.6 Consensus size: 24
1122237 TGAATATTTT
1122247 ATCTGATACTTGACATGGATTCTG
1 ATCTGATACTTGACATGGATTCTG
1122271 ATCTGATACTTGACATGGATTCTG
1 ATCTGATACTTGACATGGATTCTG
*
1122295 ATCTGATA-TCTGACATAGATTCTG
1 ATCTGATACT-TGACATGGATTCTG
*
1122319 ATCTGATACTTGACTTGGATTCTG
1 ATCTGATACTTGACATGGATTCTG
* *
1122343 ATCTGATACTTGACCTGGATTTTG
1 ATCTGATACTTGACATGGATTCTG
*
1122367 ATATGATACTTGAC
1 ATCTGATACTTGAC
1122381 CTGATTTATG
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
23 1 0.01
24 100 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
ATCTGATACTTGACATGGATTCTG
Found at i:1122601 original size:2 final size:2
Alignment explanation
Indices: 1122594--1122646 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1122584 TGGATGAGGG
1122594 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
1122636 TA TA TA TA TA T
1 TA TA TA TA TA T
1122647 GTTTTAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1127603 original size:8 final size:8
Alignment explanation
Indices: 1127592--1127629 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
1127582 CAATATTGCA
1127592 AAATAATT
1 AAATAATT
1127600 AAATAATT
1 AAATAATT
1127608 AAATAATCT
1 AAATAAT-T
1127617 AAATAA-T
1 AAATAATT
1127624 AAATAA
1 AAATAA
1127630 ATAGGCTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (8 bp):
AAATAATT
Found at i:1128475 original size:2 final size:2
Alignment explanation
Indices: 1128470--1128508 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1128460 GTATATATAT
1128470 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1128509 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1146596 original size:24 final size:24
Alignment explanation
Indices: 1146569--1146614 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1146559 GTGACGTGAT
*
1146569 TTTTCTCTACTCTTGTGGCACGCG
1 TTTTCTCTACTCTTGTGCCACGCG
**
1146593 TTTTCTCTGTTCTTGTGCCACG
1 TTTTCTCTACTCTTGTGCCACG
1146615 ATCCTCATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.07, C:0.28, G:0.20, T:0.46
Consensus pattern (24 bp):
TTTTCTCTACTCTTGTGCCACGCG
Found at i:1147951 original size:17 final size:18
Alignment explanation
Indices: 1147931--1147972 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1147921 AATAAGGACT
1147931 TAATTAAAAAAATA-ATA
1 TAATTAAAAAAATATATA
*
1147948 TAATTTTAAAAAATATATA
1 TAA-TTAAAAAAATATATA
*
1147967 TTATTA
1 TAATTA
1147973 TCCATGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 3 0.15
18 12 0.60
19 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATTAAAAAAATATATA
Found at i:1148697 original size:16 final size:16
Alignment explanation
Indices: 1148678--1148708 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1148668 GAGAATTTAA
1148678 AATATTCAATATTTTT
1 AATATTCAATATTTTT
1148694 AATATTCAATATTTT
1 AATATTCAATATTTT
1148709 ACTATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATTCAATATTTTT
Found at i:1148768 original size:16 final size:17
Alignment explanation
Indices: 1148733--1148769 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1148723 TATGGGATGA
1148733 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
1148750 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
1148766 AAAA
1 AAAA
1148770 TAATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:1148866 original size:17 final size:17
Alignment explanation
Indices: 1148844--1148876 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1148834 CGCTACCATA
*
1148844 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
1148861 ATATTATATTTTATAT
1 ATATTATATTTTATAT
1148877 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:1149690 original size:48 final size:48
Alignment explanation
Indices: 1149595--1149693 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
1149585 TGAATGATAC
*
1149595 TGATAGGAATGTTTAATTTTTGATTTTAATCGAATTAATCGATAGAAT
1 TGATAGGAATGTTTAATTTTTGATTTTAACCGAATTAATCGATAGAAT
1149643 TGATAGGAATGTTTAATTTTTGATTTTAACCGAATTAATCGATAGAAT
1 TGATAGGAATGTTTAATTTTTGATTTTAACCGAATTAATCGATAGAAT
1149691 TGA
1 TGA
1149694 ATTAATTTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.42
Consensus pattern (48 bp):
TGATAGGAATGTTTAATTTTTGATTTTAACCGAATTAATCGATAGAAT
Found at i:1151782 original size:21 final size:21
Alignment explanation
Indices: 1151756--1151805 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1151746 TAAGGTTTCG
1151756 AAACCCCTAAGGATGGCTTTA
1 AAACCCCTAAGGATGGCTTTA
1151777 AAACCCCTAAGGATGGCTTTA
1 AAACCCCTAAGGATGGCTTTA
1151798 AAACCCCT
1 AAACCCCT
1151806 GCCTAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (21 bp):
AAACCCCTAAGGATGGCTTTA
Found at i:1152603 original size:21 final size:21
Alignment explanation
Indices: 1152577--1152619 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1152567 ATTCTGGGTT
* *
1152577 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
1152598 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
1152619 A
1 A
1152620 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:1152680 original size:66 final size:69
Alignment explanation
Indices: 1152599--1152750 Score: 211
Period size: 67 Copynumber: 2.2 Consensus size: 69
1152589 ACCCATTCAA
* *
1152599 GGGGAACCGATACCCCTTCAACGAATATG-AATTCCAGAATGCTAGAGGGGAATCGGTACCC-CA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
1152662 -GGG
66 GGGG
* * * * *
1152665 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCATA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
1152730 GGGG
66 GGGG
*
1152734 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1152751 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
66 26 0.35
67 29 0.39
68 1 0.01
69 19 0.25
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
GGGG
Found at i:1153087 original size:29 final size:29
Alignment explanation
Indices: 1153053--1153124 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1153043 CATATTATGA
**
1153053 TACATGACATGAATTTGTATTAAAGGTAT
1 TACATGACATGAATTCATATTAAAGGTAT
* *
1153082 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAAGGTAT
1153111 TACATGACATGAAT
1 TACATGACATGAAT
1153125 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAAGGTAT
Found at i:1153181 original size:30 final size:31
Alignment explanation
Indices: 1153139--1153198 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1153129 AGAAAACGTT
*
1153139 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGAAAATG
*
1153170 ATATGC-CTATGTGTTAAAGGTATGAAAAT
1 ATATGCACTATGTGATAAAGGTATGAAAAT
1153199 ACTATGGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGAAAATG
Found at i:1153492 original size:22 final size:22
Alignment explanation
Indices: 1153418--1153484 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
1153408 TTATGGACAT
*
1153418 AATTCTACGGGGACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1153440 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1153462 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1153484 A
1 A
1153485 TTTATACGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1159546 original size:21 final size:21
Alignment explanation
Indices: 1159520--1159562 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1159510 ATTCTGGGTT
* *
1159520 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
1159541 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
1159562 A
1 A
1159563 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:1159639 original size:69 final size:69
Alignment explanation
Indices: 1159542--1159696 Score: 213
Period size: 69 Copynumber: 2.2 Consensus size: 69
1159532 ACCCATTCAA
* * *
1159542 GGGGAACCGATACCCCTTCAACGAATATG-AATTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
1159606 GGGGG
66 -GGGG
* * * * *
1159611 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCATA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
1159676 GGGG
66 GGGG
*
1159680 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1159697 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
69 46 0.61
70 30 0.39
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
GGGG
Found at i:1160034 original size:29 final size:29
Alignment explanation
Indices: 1160000--1160071 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1159990 CATATTATGA
**
1160000 TACATGACATGAATTTGTATTAAAGGTAT
1 TACATGACATGAATTCATATTAAAGGTAT
* *
1160029 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAAGGTAT
1160058 TACATGACATGAAT
1 TACATGACATGAAT
1160072 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAAGGTAT
Found at i:1160128 original size:30 final size:30
Alignment explanation
Indices: 1160086--1160144 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1160076 AGAAAACGTT
1160086 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATG-AAATG
*
1160117 ATATGC-CTATGTGTTAAAGGTATGAAAT
1 ATATGCACTATGTGATAAAGGTATGAAAT
1160145 ACTATGGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 17 0.63
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (30 bp):
ATATGCACTATGTGATAAAGGTATGAAATG
Found at i:1160436 original size:22 final size:22
Alignment explanation
Indices: 1160362--1160428 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
1160352 TTATGGACAT
*
1160362 AATTCTACGGGGACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1160384 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1160406 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1160428 A
1 A
1160429 TTTATACGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1186076 original size:14 final size:14
Alignment explanation
Indices: 1186042--1186084 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
1186032 CCGAAATACA
1186042 GAAATCAGATATCAG
1 GAAATCA-ATATCAG
1186057 GAAATCAATATTCAG
1 GAAATCAATA-TCAG
1186072 G-AATCAAGTATCA
1 GAAATCAA-TATCA
1186085 TGTATCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (14 bp):
GAAATCAATATCAG
Found at i:1186766 original size:29 final size:29
Alignment explanation
Indices: 1186734--1186831 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 29
1186724 CATTTTACAG
* * *
1186734 AAATAACACCCTTTTAAAAATAATTACTA
1 AAATAGCACCCTTTTCAAATTAATTACTA
* * *
1186763 AAATATCACTCATTTCAAATTAATTACTA
1 AAATAGCACCCTTTTCAAATTAATTACTA
* *
1186792 AAATAGCA-CATATTTCGAATTAATTACTA
1 AAATAGCACCCT-TTTCAAATTAATTACTA
1186821 AAATAGCACCC
1 AAATAGCACCC
1186832 GATCAACGGT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 55 0.98
30 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAATTAATTACTA
Found at i:1186861 original size:13 final size:13
Alignment explanation
Indices: 1186843--1186868 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1186833 ATCAACGGTT
1186843 AACGGGTCGGGTC
1 AACGGGTCGGGTC
1186856 AACGGGTCGGGTC
1 AACGGGTCGGGTC
1186869 GGGTTGTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
AACGGGTCGGGTC
Found at i:1193402 original size:29 final size:28
Alignment explanation
Indices: 1193364--1193519 Score: 186
Period size: 29 Copynumber: 5.4 Consensus size: 28
1193354 CATTTTACAG
*
1193364 AAATAGCACCCTTTTAAAAATAATTACTA
1 AAATAGCACCCTTTT-AAATTAATTACTA
* *
1193393 AAATATCACCCATTTTGAATTAATTACTA
1 AAATAGCACCC-TTTTAAATTAATTACTA
* *
1193422 AAATAGCACCTATTTTTTAATTAATTACTA
1 AAATAGCACC--CTTTTAAATTAATTACTA
*
1193452 AAATAGCACCCATTTTGAATTAATTACTA
1 AAATAGCACCC-TTTTAAATTAATTACTA
**
1193481 AAATAGCACATATTTTAAATTAATTACTA
1 AAATAGCAC-CCTTTTAAATTAATTACTA
1193510 AAATAGCACC
1 AAATAGCACC
1193520 AGATCAACGG
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
29 80 0.73
30 30 0.27
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.35
Consensus pattern (28 bp):
AAATAGCACCCTTTTAAATTAATTACTA
Found at i:1193455 original size:59 final size:58
Alignment explanation
Indices: 1193375--1193519 Score: 236
Period size: 59 Copynumber: 2.5 Consensus size: 58
1193365 AATAGCACCC
* * *
1193375 TTTTAAAAATAATTACTAAAATATCACCCATTTTGAATTAATTACTAAAATAGCACCTA
1 TTTT-AAATTAATTACTAAAATAGCACCCATTTTGAATTAATTACTAAAATAGCACATA
*
1193434 TTTTTTAATTAATTACTAAAATAGCACCCATTTTGAATTAATTACTAAAATAGCACATA
1 -TTTTAAATTAATTACTAAAATAGCACCCATTTTGAATTAATTACTAAAATAGCACATA
1193493 TTTTAAATTAATTACTAAAATAGCACC
1 TTTTAAATTAATTACTAAAATAGCACC
1193520 AGATCAACGG
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
58 26 0.32
59 50 0.62
60 4 0.05
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.37
Consensus pattern (58 bp):
TTTTAAATTAATTACTAAAATAGCACCCATTTTGAATTAATTACTAAAATAGCACATA
Found at i:1195427 original size:2 final size:2
Alignment explanation
Indices: 1195420--1195451 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1195410 ACACCTTTCA
1195420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1195452 GTTTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1196647 original size:165 final size:165
Alignment explanation
Indices: 1196085--1196745 Score: 869
Period size: 165 Copynumber: 4.0 Consensus size: 165
1196075 AATGAAAAGA
* * *
1196085 AAGAGGATCATATCGGCGTCGTAGTGCCCGGACCAGATGAGAGGGTGGAAGTAAGAGTAGATAGT
1 AAGAGGATCATATCGGTGTCATAGTGCCCGGACCAGATGAGAGGTTGGAAGTAAGAGTAGATAGT
* * * *
1196150 GGAAGTGATGACGATGTGATTGTAGAAAATGATAAGAACGAGGGGTCAAAGGAAGATCATTGTTT
66 GGAAGTGAGGACAATGTGGTTGTAGAAAATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTT
* *
1196215 GGGTATTAATGGAGTTGGTTCGGTTAAGAGGATAC
131 GGGGATTAATGGAGTTGATTCGGTTAAGAGGATAC
** * * *
1196250 AAGAGGATTGTACCGGTGTCATAGTGCCCGGACCATATGAGAGGTTGGAAGTAAGACTAGATAGT
1 AAGAGGATCATATCGGTGTCATAGTGCCCGGACCAGATGAGAGGTTGGAAGTAAGAGTAGATAGT
* * * *
1196315 GGAAGTGAGGACAATGTGGCTGTAGAAAATGATAAG---GAGGGATCGAAGAAAGATCATTGTTT
66 GGAAGTGAGGACAATGTGGTTGTAGAAAATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTT
* *
1196377 GGAGATTAATGGAGTTGATTCGATTAAGAGGATAC
131 GGGGATTAATGGAGTTGATTCGGTTAAGAGGATAC
** * * * * *
1196412 AAGAGGATTTTAATCGGTGTCGTAGTGGCTGGATCAGAGGAGAGGTTGGAAGTAAGAGTAGATAG
1 AAGAGGATCAT-ATCGGTGTCATAGTGCCCGGACCAGATGAGAGGTTGGAAGTAAGAGTAGATAG
*
1196477 TGGAAGTGGGGACAATGTGGTTGTAGAAAATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTT
65 TGGAAGTGAGGACAATGTGGTTGTAGAAAATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTT
* *
1196542 CGGGGATTAATGGAGTTGATTCGGTTAAGGGGATAC
130 TGGGGATTAATGGAGTTGATTCGGTTAAGAGGATAC
* * ** * * *
1196578 GAGAGGATCATATTGGTGTCATAGTGGTCGGATCAGATGAGAGGTTGGGAGTAAGAGTGGATAGT
1 AAGAGGATCATATCGGTGTCATAGTGCCCGGACCAGATGAGAGGTTGGAAGTAAGAGTAGATAGT
* * * * * * *
1196643 GGAAGTGAGGGCGACGTGGATGTAGAACATGCTAAGAATGAGGGGTCAATGGAAGATCATTGTTT
66 GGAAGTGAGGACAATGTGGTTGTAGAAAATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTT
* * *
1196708 GGGGGTTAATGGGGTTGATTCTGTTAAGAGGATAC
131 GGGGATTAATGGAGTTGATTCGGTTAAGAGGATAC
1196743 AAG
1 AAG
1196746 TTTCTGGAGA
Statistics
Matches: 431, Mismatches: 61, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
162 64 0.15
163 80 0.19
165 225 0.52
166 62 0.14
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.25
Consensus pattern (165 bp):
AAGAGGATCATATCGGTGTCATAGTGCCCGGACCAGATGAGAGGTTGGAAGTAAGAGTAGATAGT
GGAAGTGAGGACAATGTGGTTGTAGAAAATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTT
GGGGATTAATGGAGTTGATTCGGTTAAGAGGATAC
Found at i:1199573 original size:49 final size:48
Alignment explanation
Indices: 1199544--1199645 Score: 150
Period size: 49 Copynumber: 2.1 Consensus size: 48
1199534 TTATAAAATT
*
1199544 TTAAGAGGATAAGAATAAATTATCAATAAAAATTAAAAAAATATTTAAA
1 TTAAGAGGATAAGAATAAATTATCAAT-AAAATTAAAAAAATATTAAAA
* *
1199593 TTAAGAGGATAAGAATAAATTATCAATAAAAATAAAAATAAATATTTAAA
1 TTAAGAGGATAAGAATAAATTATCAAT-AAAATTAAAA-AAATATTAAAA
1199643 TTA
1 TTA
1199646 TATGAAAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 37 0.73
50 14 0.27
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (48 bp):
TTAAGAGGATAAGAATAAATTATCAATAAAATTAAAAAAATATTAAAA
Found at i:1200494 original size:20 final size:19
Alignment explanation
Indices: 1200471--1200515 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1200461 TAATTTAAAA
*
1200471 AAAATATTTTTAAAAAATAT
1 AAAATATATTT-AAAAATAT
*
1200491 AAAAAATATTTAAAAATAT
1 AAAATATATTTAAAAATAT
*
1200510 TAAATA
1 AAAATA
1200516 AAAAAACCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATATTTAAAAATAT
Found at i:1200505 original size:10 final size:10
Alignment explanation
Indices: 1200480--1200513 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1200470 AAAAATATTT
1200480 TTAAAAAATA
1 TTAAAAAATA
1200490 -TAAAAAATA
1 TTAAAAAATA
*
1200499 TTTAAAAATA
1 TTAAAAAATA
1200509 TTAAA
1 TTAAA
1200514 TAAAAAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:1200956 original size:30 final size:27
Alignment explanation
Indices: 1200922--1200983 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
1200912 CCTTAATTTT
*
1200922 AATTATTAGTATT-TTATTAACATAATATTA
1 AATTATTA-TATTAATATTAA-AT-ATA-TA
1200952 AATTATTATATTAATATTAAATATATA
1 AATTATTATATTAATATTAAATATATA
1200979 AATTA
1 AATTA
1200984 ATATTACTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 3 0.10
29 6 0.20
30 14 0.47
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
AATTATTATATTAATATTAAATATATA
Found at i:1200958 original size:24 final size:27
Alignment explanation
Indices: 1200931--1200983 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
1200921 TAATTATTAG
*
1200931 TATTTTATTAACA-T-AATAT-TAAAT
1 TATTATATTAACATTAAATATATAAAT
*
1200955 TATTATATTAATATTAAATATATAAAT
1 TATTATATTAACATTAAATATATAAAT
1200982 TA
1 TA
1200984 ATATTACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 1 0.04
26 5 0.21
27 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTATATTAACATTAAATATATAAAT
Found at i:1200983 original size:19 final size:19
Alignment explanation
Indices: 1200935--1200989 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1200925 TATTAGTATT
1200935 TTATTAACA-TAATATTAAA
1 TTATTAA-ATTAATATTAAA
*
1200954 TTATTATATTAATATTAAA
1 TTATTAAATTAATATTAAA
1200973 -TATATAAATTAATATTA
1 TTAT-TAAATTAATATTA
1200990 CTCATTGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.12
19 28 0.88
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATTAAATTAATATTAAA
Found at i:1201122 original size:19 final size:18
Alignment explanation
Indices: 1201098--1201141 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1201088 GAGTACATAT
1201098 TAATATAATATTAAAAATA
1 TAATAT-ATATTAAAAATA
*
1201117 TAATAT-TATTAAAATTA
1 TAATATATATTAAAAATA
*
1201134 TATTATAT
1 TAATATAT
1201142 GTATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATATATTAAAAATA
Found at i:1201173 original size:16 final size:15
Alignment explanation
Indices: 1201150--1201217 Score: 54
Period size: 16 Copynumber: 4.6 Consensus size: 15
1201140 ATGTATATTA
1201150 AATA-TTTTAATAATT
1 AATATTTTTAATAA-T
*
1201165 AATATTTTTATTAA-
1 AATATTTTTAATAAT
1201179 AATATTAATTTAATAAT
1 AATATT--TTTAATAAT
* *
1201196 AA-ATGTATAA-AAT
1 AATATTTTTAATAAT
1201209 AATATTTTT
1 AATATTTTT
1201218 GAATGCTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
13 5 0.12
14 14 0.33
15 4 0.10
16 17 0.40
17 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
AATATTTTTAATAAT
Found at i:1211980 original size:14 final size:14
Alignment explanation
Indices: 1211958--1211987 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1211948 AAAAGTATTC
1211958 ATATGTGTCTTAAA
1 ATATGTGTCTTAAA
*
1211972 ATATTTGTCTTAAA
1 ATATGTGTCTTAAA
1211986 AT
1 AT
1211988 TAAATGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
ATATGTGTCTTAAA
Found at i:1216683 original size:2 final size:2
Alignment explanation
Indices: 1216676--1216725 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1216666 CACAGATTAC
1216676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1216718 AT AT AT AT
1 AT AT AT AT
1216726 TAAAATTCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1223254 original size:35 final size:34
Alignment explanation
Indices: 1223214--1223291 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
1223204 AACATAATCC
*
1223214 TCAATTTCATTCTAAACTAC-AAATTTCAAAATAAT
1 TCAATTT-ATTCTAAAC-ACTAAATTTAAAAATAAT
* * *
1223249 TCAATTATATTTTAAACCCTAAATTTAAAAATACT
1 TCAATT-TATTCTAAACACTAAATTTAAAAATAAT
1223284 TCAATTTA
1 TCAATTTA
1223292 GGGTTTAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 3 0.08
35 33 0.89
36 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (34 bp):
TCAATTTATTCTAAACACTAAATTTAAAAATAAT
Found at i:1223362 original size:33 final size:35
Alignment explanation
Indices: 1223286--1223376 Score: 132
Period size: 33 Copynumber: 2.7 Consensus size: 35
1223276 AAAATACTTC
* *
1223286 AATTTAGGGTTTAGAATGTAATTAAAATATTTTTG
1 AATTTGGGGTTTAGAATGTAATTAAAATATTTTGG
* *
1223321 AATTTGGGGTTTAGAATGTAATT-GAA-GTTTTGG
1 AATTTGGGGTTTAGAATGTAATTAAAATATTTTGG
1223354 AATTTGGGGTTTAGAATGTAATT
1 AATTTGGGGTTTAGAATGTAATT
1223377 CAAAGTTAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 28 0.54
34 2 0.04
35 22 0.42
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
AATTTGGGGTTTAGAATGTAATTAAAATATTTTGG
Found at i:1224920 original size:23 final size:23
Alignment explanation
Indices: 1224894--1224941 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1224884 ATAAAGTACA
*
1224894 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
1224917 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1224940 AT
1 AT
1224942 TTACCTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1225358 original size:23 final size:23
Alignment explanation
Indices: 1225332--1225394 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1225322 ATATAACCAC
1225332 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1225355 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1225378 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1225395 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1225791 original size:23 final size:23
Alignment explanation
Indices: 1225765--1225827 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1225755 ATATAACCAC
1225765 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1225788 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1225811 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1225828 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1226251 original size:23 final size:22
Alignment explanation
Indices: 1226189--1226260 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
1226179 ACACTTTACA
*
1226189 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
1226212 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
1226234 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
1226257 ATAT
1 ATAT
1226261 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 20 0.45
23 24 0.55
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:1226351 original size:434 final size:433
Alignment explanation
Indices: 1225273--1226471 Score: 2357
Period size: 433 Copynumber: 2.8 Consensus size: 433
1225263 TCTTAATTCA
1225273 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTA
1 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTA
1225338 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
66 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
1225403 ATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATT
131 ATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATT
1225468 TATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
196 TATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
1225533 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
261 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1225598 CAACATTAAATATATATCGTAACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAAAA
326 CAACATTAAATATATATCGTAACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAAAA
1225663 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCC
391 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCC
1225706 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTA
1 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTA
1225771 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
66 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
1225836 ATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATT
131 ATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATT
1225901 TATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
196 TATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
1225966 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
261 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1226031 CAACATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAA
326 CAACATTAAATATATATCGTAACGTAAAAAAT-AATCATTAGACGCCTATAATTACTAAATTAAA
1226096 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCC
390 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCC
1226140 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTA
1 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTA
1226205 TTACATTATAT-AACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
66 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
*
1226269 ATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATT
131 ATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATT
1226334 TATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
196 TATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
*
1226399 TTTGCAC-AAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
261 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1226463 CAACATTAA
326 CAACATTAA
1226472 CCAAAGATAA
Statistics
Matches: 763, Mismatches: 2, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
432 65 0.09
433 546 0.72
434 152 0.20
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (433 bp):
ACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTA
TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
ATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATT
TATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
CAACATTAAATATATATCGTAACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAAAA
TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCC
Found at i:1226732 original size:39 final size:39
Alignment explanation
Indices: 1226678--1226763 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
1226668 CAAGTTGTAG
*
1226678 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
1226717 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
1226756 ATTTTGAT
1 ATTTTGAT
1226764 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:1227042 original size:18 final size:18
Alignment explanation
Indices: 1227019--1227055 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1227009 CGAAATATAT
1227019 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1227037 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1227055 A
1 A
1227056 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1227509 original size:28 final size:26
Alignment explanation
Indices: 1227477--1227538 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 26
1227467 GATAGATACT
*
1227477 TTACAATATATTATATAAGCGCTACCTA
1 TTACAATATATTATA-AA-CGATACCTA
1227505 TTAC-AT-TA-TATAAACGATACCTA
1 TTACAATATATTATAAACGATACCTA
*
1227528 TTACATTATAT
1 TTACAATATAT
1227539 ACTTGTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 12 0.41
24 3 0.10
25 6 0.21
26 2 0.07
27 2 0.07
28 4 0.14
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (26 bp):
TTACAATATATTATAAACGATACCTA
Found at i:1227516 original size:23 final size:23
Alignment explanation
Indices: 1227486--1227539 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1227476 TTTACAATAT
* *
1227486 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGATACCTATTAC
1227509 ATTATATAAACGATACCTATTAC
1 ATTATATAAACGATACCTATTAC
1227532 ATTATATA
1 ATTATATA
1227540 CTTGTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.37
Consensus pattern (23 bp):
ATTATATAAACGATACCTATTAC
Found at i:1230463 original size:182 final size:183
Alignment explanation
Indices: 1230018--1231004 Score: 1797
Period size: 182 Copynumber: 5.4 Consensus size: 183
1230008 CGACACATTT
* * * *
1230018 TAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1230083 ATTACATTATAATTAT-GGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
1230147 TTTTCTTCCAATATGGACAT-AAGTACCGACACAATATTAAAAAGTGTCGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
1230199 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1230264 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
*
1230329 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTTGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
1230382 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1230447 ATTACATTAT-ATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
1230511 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
1230564 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
*
1230629 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACA-ATTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
*
1230693 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTTGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
1230746 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1230811 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
1230876 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCG--A
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
* * * * * *
1230927 TAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATTTACCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
**
1230992 ATTTTATTATAAT
66 ATTACATTATAAT
1231005 ATGTTGAAAG
Statistics
Matches: 784, Mismatches: 18, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
181 148 0.19
182 429 0.55
183 207 0.26
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
Found at i:1232475 original size:3 final size:3
Alignment explanation
Indices: 1232467--1232541 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
1232457 ACTTGTTTGG
* * * ** * *
1232467 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1232515 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1232542 GTCAGCTTCA
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1232484 original size:12 final size:12
Alignment explanation
Indices: 1232471--1232553 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
1232461 GTTTGGATCA
*
1232471 TCATCTTCATCA
1 TCATCTTCATCG
* * *
1232483 TCATCATCGTCA
1 TCATCTTCATCG
1232495 TCATCTTCATCG
1 TCATCTTCATCG
* *
1232507 CCAGCTTCATCG
1 TCATCTTCATCG
*
1232519 TCATCATCATCG
1 TCATCTTCATCG
1232531 TCATCTTCATCG
1 TCATCTTCATCG
*
1232543 TCAGCTTCATC
1 TCATCTTCATC
1232554 TTCTGCGACC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1232515 original size:36 final size:36
Alignment explanation
Indices: 1232475--1232553 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
1232465 GGATCATCAT
*
1232475 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
1232511 CTTCATCGTCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
1232547 CTTCATC
1 CTTCATC
1232554 TTCTGCGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:1232554 original size:18 final size:18
Alignment explanation
Indices: 1232495--1232556 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
1232485 ATCATCGTCA
*
1232495 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
1232513 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCT
1232531 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
1232549 TCATCTTC
1 TCATCTTC
1232557 TGCGACCGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:1232556 original size:6 final size:6
Alignment explanation
Indices: 1232471--1232556 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
1232461 GTTTGGATCA
* * * * * * * *
1232471 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
1232519 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
1232557 TGCGACCGCT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:1234445 original size:195 final size:197
Alignment explanation
Indices: 1234006--1235271 Score: 2342
Period size: 196 Copynumber: 6.5 Consensus size: 197
1233996 TTTAAATTAG
1234006 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACA-AAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1234070 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1234135 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1234200 AA
196 AA
1234202 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1234267 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1234331 CGACAC-TTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTTTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1234395 AA
196 AA
1234397 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1234462 ATTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1234526 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1234591 AA
196 AA
1234593 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1234658 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1234723 CGACATTTTTTATATATGGATCGACACTTTATGGGTGCA-CCTGTTTTCCATTCATTCTGG-AAT
131 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1234786 AAA
195 AAA
1234789 TATCG--ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAAACC-GTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACAT-AAAACCGGTAT
1234851 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
1234915 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
*
1234980 AAAA
194 TAAA
*
1234984 TATCGACATAAACTATATTAGTGTCG--ACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1235047 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1235112 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1235177 AA
196 AA
* *
1235179 TATCGACACAAACTATATTAGTATCGACACATTATTTAGACATATTCTCACATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1235244 ATTGTACCGGTTAGATTG-AAAATTACAT
66 ATTGTACCGGTTAGATTGAAAAATTACAT
1235272 CCTTTTGGCC
Statistics
Matches: 1044, Mismatches: 11, Indels: 30
0.96 0.01 0.03
Matches are distributed among these distances:
192 6 0.01
193 75 0.07
194 98 0.09
195 284 0.27
196 402 0.39
197 173 0.17
198 6 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
AA
Found at i:1234847 original size:391 final size:391
Alignment explanation
Indices: 1234006--1235271 Score: 2307
Period size: 391 Copynumber: 3.2 Consensus size: 391
1233996 TTTAAATTAG
1234006 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACA-AAAACCGGTATA
1 TATCGA-ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1234070 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGAT
1234135 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
129 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1234200 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
194 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
1234265 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
259 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
1234329 ATCGACACTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTTTGGAAAT
324 ATCGACATTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1234394 AAA
389 AAA
1234397 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGA-ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1234462 ATTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTCGATGATTTTGGGATC
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTCGATGATTTTGGGATC
1234527 GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
130 GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
1234592 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
195 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
1234657 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
260 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
1234722 TCGACATTTTTTATATATGGATCGACACTTTATGGGTGCA-CCTGTTTTCCATTCATTCTGG-AA
325 TCGACA-TTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAA
1234785 TAAA
388 TAAA
1234789 TATCG-ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAAACC-GTATA
1 TATCGAACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACAT-AAAACCGGTATA
*
1234852 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGGTTCGATGATTTTGGGATC
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTCGATGATTTTGGGATC
*
1234917 GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAA
130 GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAATA
*
1234982 AATATCGACATAAACTATATTAGTGTCG--ACATTATTTAGACATATTCTCACATAAAACCGGTA
194 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
1235045 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
259 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
1235110 ATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAA
324 ATCGACA-TTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAA
*
1235175 AAAA
388 TAAA
* *
1235179 TATCGACACAAACTATATTAGTATCGACACATTATTTAGACATATTCTCACATAAAACTGGTATA
1 TATCGA-ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1235244 ATTGTACCGGTTAGATTG-AAAATTACAT
65 ATTGTACCGGTTAGATTGAAAAATTACAT
1235272 CCTTTTGGCC
Statistics
Matches: 853, Mismatches: 11, Indels: 22
0.96 0.01 0.02
Matches are distributed among these distances:
388 6 0.01
389 154 0.18
390 183 0.21
391 273 0.32
392 186 0.22
393 45 0.05
394 6 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (391 bp):
TATCGAACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTCGATGATTTTGGGATCG
ACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAA
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACATTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
A
Found at i:1235442 original size:19 final size:17
Alignment explanation
Indices: 1235401--1235434 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1235391 TTCACAAACG
1235401 AAAA-TATAAATCGTAT
1 AAAATTATAAATCGTAT
*
1235417 AAAATTATAAATCTTAT
1 AAAATTATAAATCGTAT
1235434 A
1 A
1235435 CAAAATTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAATTATAAATCGTAT
Found at i:1237345 original size:21 final size:21
Alignment explanation
Indices: 1237305--1237369 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1237295 CCCCTTATGC
* *
1237305 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1237326 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
1237347 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
1237368 CT
1 CT
1237370 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1239618 original size:20 final size:19
Alignment explanation
Indices: 1239572--1239618 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1239562 ATCCGGATCA
1239572 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1239591 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1239612 TTTTACC
1 TTTTACC
1239619 TGTATATCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1239762 original size:20 final size:20
Alignment explanation
Indices: 1239736--1239781 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1239726 CACGTTTAAA
1239736 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1239755 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1239776 TTTACC
1 TTTACC
1239782 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1240262 original size:229 final size:225
Alignment explanation
Indices: 1239847--1240293 Score: 752
Period size: 229 Copynumber: 2.0 Consensus size: 225
1239837 TTATAACTGC
1239847 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
1239912 TTAATTAATAATTTAATTTACACAAAATTTTATTTGATGTTTTGATATTTTATAAAATATTATTT
66 TTAATTAATAATTTAATTTACACAAAAAATTATTTGATGTTTTGATATTTTATAAAATATTATTT
* *
1239977 AGAATTTAAATTTAACAATATTAACCAAATATAATAATAATATGTTTTCAACAGTGAAATAAGTA
131 AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAATATATTTTCAACAGTGAAATAAGTA
*
1240042 TGAACACTTTTATAAAAATGATATATACTT
196 TGAACACTTTTATAAAAAGGATATATACTT
*
1240072 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAA
1 TTTT-AAAGTTATGTAATTTATGTTTCAA-TTTATTTAATAGTGTTTCATGTTTTCCACCTACAA
*
1240137 TATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATT
64 TATTAA-TTAATAATTTAATTTACACAAAAAATTATTTGA-TGTTTTGATATTTTATAAAATATT
* *
1240202 ATTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAAT
127 ATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT-AATATATTTTCAACAGTGAAAT
*
1240266 AAGTATGGACACTTTTATAAAAAGGATA
191 AAGTATGAACACTTTTATAAAAAGGATA
1240294 GATAATTTAC
Statistics
Matches: 207, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
225 4 0.02
226 24 0.12
227 40 0.19
228 30 0.14
229 99 0.48
230 10 0.05
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (225 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTAATAATTTAATTTACACAAAAAATTATTTGATGTTTTGATATTTTATAAAATATTATTT
AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAATATATTTTCAACAGTGAAATAAGTA
TGAACACTTTTATAAAAAGGATATATACTT
Found at i:1240679 original size:33 final size:31
Alignment explanation
Indices: 1240634--1240716 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
1240624 TTTAATTATT
* *
1240634 AAATA-AACTAATGGCATGTTTTTACATAAAAG
1 AAATATAATTAATGACATGTTTTT--ATAAAAG
1240666 AAATATAATTAATGACATG-TTTTATAAAAG
1 AAATATAATTAATGACATGTTTTTATAAAAG
1240696 AAATATAATTAATGACATGTT
1 AAATATAATTAATGACATGTT
1240717 GAATTATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
30 26 0.55
31 1 0.02
32 9 0.19
33 11 0.23
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (31 bp):
AAATATAATTAATGACATGTTTTTATAAAAG
Found at i:1242460 original size:21 final size:20
Alignment explanation
Indices: 1242411--1242460 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
1242401 AAAAAAATTC
* *
1242411 ACATATTTTATTTTTATAAA
1 ACATATTTTAATTTTACAAA
* *
1242431 ATATTTTTTAAATTTTACAAA
1 ACATATTTT-AATTTTACAAA
1242452 ACATATTTT
1 ACATATTTT
1242461 CTCTAATATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (20 bp):
ACATATTTTAATTTTACAAA
Found at i:1243113 original size:40 final size:39
Alignment explanation
Indices: 1243059--1243154 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 39
1243049 GATATAACAA
* *
1243059 TCCCTATCCTTATCCCCA-TTGAGCTTTGGGGATAAAACT
1 TCCCCATCCCTATCCCCATTTGAGCTTT-GGGATAAAACT
*
1243098 TCCCCCATCTCTATCCCCATTTGAGCTTTGGGATAAAACT
1 T-CCCCATCCCTATCCCCATTTGAGCTTTGGGATAAAACT
*
1243138 TCTCCATCCCTATCCCC
1 TCCCCATCCCTATCCCC
1243155 GTGGGTGAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
39 15 0.30
40 26 0.52
41 9 0.18
ACGTcount: A:0.21, C:0.35, G:0.11, T:0.32
Consensus pattern (39 bp):
TCCCCATCCCTATCCCCATTTGAGCTTTGGGATAAAACT
Done.