Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 4 of 182
Found at i:1082056 original size:35 final size:35
Alignment explanation
Indices: 1081973--1082097 Score: 124
Period size: 35 Copynumber: 3.5 Consensus size: 35
1081963 ACATCGTCAA
* * * * * *
1081973 TCCAACCAAAATACACCAGATTCTCATCAGATCCAA
1 TCCAACCAAAACACACCA-ATGCTCATAAGAGCTAG
** * *
1082009 TCCAACTGAAACACACCAGTGCTCATGAGAGCTAG
1 TCCAACCAAAACACACCAATGCTCATAAGAGCTAG
**
1082044 TCCCTCCAAAACACACCAATGCTCATAAGAGCTAG
1 TCCAACCAAAACACACCAATGCTCATAAGAGCTAG
*
1082079 TCCAACCGAAACACACCAA
1 TCCAACCAAAACACACCAA
1082098 ACAAAGACTA
Statistics
Matches: 71, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
35 56 0.79
36 15 0.21
ACGTcount: A:0.39, C:0.34, G:0.11, T:0.16
Consensus pattern (35 bp):
TCCAACCAAAACACACCAATGCTCATAAGAGCTAG
Found at i:1083355 original size:26 final size:26
Alignment explanation
Indices: 1083318--1083394 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
1083308 ACACCAATAT
1083318 CGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* *
1083344 CGCAG-AAGAGCTTCCAGTATCAGTAA
1 CGCAGCAA-AGCTGCCAGTAACAGTAA
* * * *
1083370 AGCATCAAAGCTACCAATAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
1083395 TTTGTGGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.05
26 38 0.90
27 2 0.05
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:1086526 original size:35 final size:35
Alignment explanation
Indices: 1086443--1086567 Score: 124
Period size: 35 Copynumber: 3.5 Consensus size: 35
1086433 ACATCGTCAA
* * * * * *
1086443 TCCAACCAAAATACACCAGATTCTCATCAGATCCAA
1 TCCAACCAAAACACACCA-ATGCTCATAAGAGCTAG
** * *
1086479 TCCAACTGAAACACACCAGTGCTCATGAGAGCTAG
1 TCCAACCAAAACACACCAATGCTCATAAGAGCTAG
**
1086514 TCCCTCCAAAACACACCAATGCTCATAAGAGCTAG
1 TCCAACCAAAACACACCAATGCTCATAAGAGCTAG
*
1086549 TCCAACCGAAACACACCAA
1 TCCAACCAAAACACACCAA
1086568 ACAAAGACTA
Statistics
Matches: 71, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
35 56 0.79
36 15 0.21
ACGTcount: A:0.39, C:0.34, G:0.11, T:0.16
Consensus pattern (35 bp):
TCCAACCAAAACACACCAATGCTCATAAGAGCTAG
Found at i:1087825 original size:26 final size:26
Alignment explanation
Indices: 1087788--1087864 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
1087778 ACACCAATAT
1087788 CGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* *
1087814 CGCAG-AAGAGCTTCCAGTATCAGTAA
1 CGCAGCAA-AGCTGCCAGTAACAGTAA
* * * *
1087840 AGCATCAAAGCTACCAATAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
1087865 TTTGTGGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.05
26 38 0.90
27 2 0.05
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:1088091 original size:26 final size:26
Alignment explanation
Indices: 1088054--1088117 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
1088044 ACACCAATAT
1088054 CGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* *
1088080 CGCAG-AAGAGCTTCCAGTATCAGTAA
1 CGCAGCAA-AGCTGCCAGTAACAGTAA
* *
1088106 AGCATCAAAGCT
1 CGCAGCAAAGCT
1088118 ACCAATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 28 0.88
27 2 0.06
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:1088189 original size:27 final size:27
Alignment explanation
Indices: 1088150--1089024 Score: 809
Period size: 27 Copynumber: 32.5 Consensus size: 27
1088140 AAGCCACCAG
* * *
1088150 TAATTTTATCCATTAGGGGTACTTCGA
1 TAATTTTACCCATCAGGGGTATTTCGA
**
1088177 TAATTTTACCCATTGGGGGTATTTCGA
1 TAATTTTACCCATCAGGGGTATTTCGA
* *
1088204 TAATTTTACCTATCAAGGGTATTTCGA
1 TAATTTTACCCATCAGGGGTATTTCGA
** *
1088231 TAATTTTA-CCATTTGAGGGTATTT-TA
1 TAATTTTACCCATCAG-GGGTATTTCGA
* *
1088257 GTAATTTTACCCATCAAGGGTATTTTTG-
1 -TAATTTTACCCATCAGGGGTA-TTTCGA
* *
1088285 TAATTTTACCTATC-GAGGGTATTTTGA
1 TAATTTTACCCATCAG-GGGTATTTCGA
* *
1088312 TAATTTTACCCATC-GAGGGTATTTTGG
1 TAATTTTACCCATCAG-GGGTATTTCGA
* *
1088339 TAATGTTACCCATC-GAGGGTATTTTG-
1 TAATTTTACCCATCAG-GGGTATTTCGA
* * *
1088365 TAATTTGACCCATCGGGGGTATTT-TA
1 TAATTTTACCCATCAGGGGTATTTCGA
* * *
1088391 GTAAATTTACCCATCAAGGGTATTTTGA
1 -TAATTTTACCCATCAGGGGTATTTCGA
*
1088419 TAATTTTACCCATCAAGGGTATTTC-A
1 TAATTTTACCCATCAGGGGTATTTCGA
* * *
1088445 GTAATTTTACCCATCAGAGGTATTTTGG
1 -TAATTTTACCCATCAGGGGTATTTCGA
* * * *
1088473 CAATTTTACCCAT-TGAGGGTCTTTCAA
1 TAATTTTACCCATCAG-GGGTATTTCGA
* * *
1088500 TAATTTTACCGATCAAGGGTATTTCTA
1 TAATTTTACCCATCAGGGGTATTTCGA
*
1088527 TAATTTTACCCATCAGGGGCATTTCGA
1 TAATTTTACCCATCAGGGGTATTTCGA
* *
1088554 TAATTTTACCCATCAGGGGTATTTGGG
1 TAATTTTACCCATCAGGGGTATTTCGA
*
1088581 TAA-TTTACCCATC-GAGGGTATTTCGG
1 TAATTTTACCCATCAG-GGGTATTTCGA
1088607 TAATTTTACCCATCAGGGGTATTTCGA
1 TAATTTTACCCATCAGGGGTATTTCGA
*
1088634 TAATTTTACCCATC-GAGGGTATTT-TA
1 TAATTTTACCCATCAG-GGGTATTTCGA
*
1088660 GTAATTTTACCCATTAGGGGTATTTCGA
1 -TAATTTTACCCATCAGGGGTATTTCGA
* *
1088688 TAATTTTACCCATTAGGGGTATTTCGG
1 TAATTTTACCCATCAGGGGTATTTCGA
*
1088715 TAATTTTACCTATCAGGGGTATTTCGA
1 TAATTTTACCCATCAGGGGTATTTCGA
** *
1088742 TAATTTTACCC-TTTGAGGGTATTT-TA
1 TAATTTTACCCATCAG-GGGTATTTCGA
* *
1088768 GTAATTTTACCCATCAAGGGTATTTTG-
1 -TAATTTTACCCATCAGGGGTATTTCGA
* ** *
1088795 TAATTTGACCCATTGGGGGTATTT-TA
1 TAATTTTACCCATCAGGGGTATTTCGA
* **
1088821 GTATTTTTACCCATCAAAGGTATTTCGA
1 -TAATTTTACCCATCAGGGGTATTTCGA
* *
1088849 AAATTTTACCCATCAAGGGTATTTC-A
1 TAATTTTACCCATCAGGGGTATTTCGA
* * * * *
1088875 GTAATTTAACCGATCAGAGGTATTTTGG
1 -TAATTTTACCCATCAGGGGTATTTCGA
* * * *
1088903 TAATTTTACCCAT-GGAGGGTCTTTTGG
1 TAATTTTACCCATCAG-GGGTATTTCGA
* *
1088930 TAATTTTACCGATCAGGGGTATTTCTA
1 TAATTTTACCCATCAGGGGTATTTCGA
1088957 TAATTTTACCCATCAGGGGTATTTCGA
1 TAATTTTACCCATCAGGGGTATTTCGA
* * *
1088984 TAATTTTACCCATCGGGGGTATTTTGG
1 TAATTTTACCCATCAGGGGTATTTCGA
1089011 TAATTTTACCCATC
1 TAATTTTACCCATC
1089025 GAGGTGTAAC
Statistics
Matches: 705, Mismatches: 110, Indels: 66
0.80 0.12 0.07
Matches are distributed among these distances:
25 1 0.00
26 81 0.11
27 609 0.86
28 14 0.02
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (27 bp):
TAATTTTACCCATCAGGGGTATTTCGA
Found at i:1088521 original size:215 final size:215
Alignment explanation
Indices: 1088177--1089025 Score: 1068
Period size: 215 Copynumber: 3.9 Consensus size: 215
1088167 GGTACTTCGA
*** *
1088177 TAATTTTACCCATTGGGGGTATTTCGATAATTTTACCTATCAAGGGTATTTC-GATAATTTTA-C
1 TAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCATCAAGGGTATTTCAG-TAATTTTACC
** * ** ** * *
1088240 CATTTGAGGGTATTTTAGTAATTTTACCCATCAAGGGTATTTTTGTAATTTTACCTATCGAGGGT
65 CATCAGA-GGTATTTTGGTAATTTTACCCATTGAGGGTATTTCGGTAATTTTACCGATCAAGGGT
* * *
1088305 ATTT-TGATAATTTTACCCATC-GAGGGTATTTTGGTAATGTTACCCATCGAGGGTATTTTGTAA
129 ATTTCT-ATAATTTTACCCATCAG-GGGTATTTCGATAATTTTACCCATCGAGGGTATTTTGTAA
1088368 TTTGACCCATCGGGGGTATTTTAG
192 TTTGACCCATCGGGGGTATTTTAG
* *
1088392 TAAATTTACCCATCAAGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCC
1 TAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCC
* * **
1088457 ATCAGAGGTATTTTGGCAATTTTACCCATTGAGGGTCTTTCAATAATTTTACCGATCAAGGGTAT
66 ATCAGAGGTATTTTGGTAATTTTACCCATTGAGGGTATTTCGGTAATTTTACCGATCAAGGGTAT
* *
1088522 TTCTATAATTTTACCCATCAGGGGCATTTCGATAATTTTACCCATC-AGGGGTATTTGGGTAATT
131 TTCTATAATTTTACCCATCAGGGGTATTTCGATAATTTTACCCATCGA-GGGTATTT-TGTAATT
* **
1088586 T-ACCCATCGAGGGTATTTCGG
194 TGACCCATCGGGGGTATTTTAG
* * *
1088607 TAATTTTACCCATCAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAGTAATTTTACCC
1 TAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCC
* * * * * *
1088672 ATTAGGGGTATTTCGATAATTTTACCCATT-AGGGGTATTTCGGTAATTTTACCTATCAGGGGTA
66 ATCAGAGGTATTTTGGTAATTTTACCCATTGA-GGGTATTTCGGTAATTTTACCGATCAAGGGTA
* ** * *
1088736 TTTCGATAATTTTACCC-TTTGAGGGTATTT-TAGTAATTTTACCCATCAAGGGTATTTTGTAAT
130 TTTCTATAATTTTACCCATCAG-GGGTATTTCGA-TAATTTTACCCATCGAGGGTATTTTGTAAT
*
1088799 TTGACCCATTGGGGGTATTTTAG
193 TTGACCCATCGGGGGTATTTTAG
* * * * *
1088822 TATTTTTACCCATCAAAGGTATTTCGAAAATTTTACCCATCAAGGGTATTTCAGTAATTTAACCG
1 TAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCC
* * * *
1088887 ATCAGAGGTATTTTGGTAATTTTACCCATGGAGGGTCTTTTGGTAATTTTACCGATCAGGGGTAT
66 ATCAGAGGTATTTTGGTAATTTTACCCATTGAGGGTATTTCGGTAATTTTACCGATCAAGGGTAT
*
1088952 TTCTATAATTTTACCCATCAGGGGTATTTCGATAATTTTACCCATCGGGGGTATTTTGGTAATTT
131 TTCTATAATTTTACCCATCAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTT-GTAATTT
*
1089017 TACCCATCG
195 GACCCATCG
1089026 AGGTGTAACA
Statistics
Matches: 544, Mismatches: 75, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
214 12 0.02
215 497 0.91
216 35 0.06
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (215 bp):
TAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCC
ATCAGAGGTATTTTGGTAATTTTACCCATTGAGGGTATTTCGGTAATTTTACCGATCAAGGGTAT
TTCTATAATTTTACCCATCAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTGTAATTTG
ACCCATCGGGGGTATTTTAG
Found at i:1090808 original size:28 final size:28
Alignment explanation
Indices: 1090740--1091010 Score: 427
Period size: 28 Copynumber: 9.6 Consensus size: 28
1090730 CATGAGATTG
* * *
1090740 GCACTAAGTGTGCGGGTTTAAAT-TGCTCA
1 GCACTAAGTGTGCGAGTTTGATTATG-T-A
1090769 GCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
1090797 GCACTAAGTGTGCGAGCTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
1090825 GCACTAAGTGTGCGAGCTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
1090853 GCACTAAGTGTGCGAGCTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
1090881 GCACTAAGTGTGCGAGCTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
1090909 GCACTAAGTGTGCGAATTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
1090937 GCACTAAGTGTGCGAATTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
1090965 GCACTAAGTGTGCGAATTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
1090993 GCACTAAGTGTGCGAGTT
1 GCACTAAGTGTGCGAGTT
1091011 NNNNNNNNNN
Statistics
Matches: 234, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
28 211 0.90
29 21 0.09
30 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATGTA
Found at i:1096834 original size:27 final size:27
Alignment explanation
Indices: 1096781--1096836 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1096771 NNTGATTATG
* *
1096781 TAGCACTAAGTGTGCGAGTTGATTATA
1 TAGCACTAAGTGTGCGACTTGAATATA
*
1096808 TAGCACTGAGTGTGCGGACTT-AATATA
1 TAGCACTAAGTGTGC-GACTTGAATATA
1096835 TA
1 TA
1096837 TTCTTGAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.32
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGACTTGAATATA
Found at i:1098394 original size:27 final size:26
Alignment explanation
Indices: 1098364--1098439 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 26
1098354 GGGTGTTACA
1098364 CGAGGGTATTTCGATAATTTTACCCAT
1 CGAGGGTATTTC-ATAATTTTACCCAT
1098391 CGAGGGTATTTCAGTAATTTTACCCAT
1 CGAGGGTATTTCA-TAATTTTACCCAT
1098418 CGAGGGTATTTCAATAATTTTA
1 CGAGGGTATTTC-ATAATTTTA
1098440 GAGGCCCATT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.02
27 45 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (26 bp):
CGAGGGTATTTCATAATTTTACCCAT
Found at i:1120240 original size:39 final size:40
Alignment explanation
Indices: 1120145--1120406 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
1120135 TTGAATGATG
*
1120145 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
1120183 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
1120224 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
1120263 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1120302 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
1120341 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
1120380 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
1120407 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:1122857 original size:9 final size:10
Alignment explanation
Indices: 1122841--1122865 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1122831 TTCAAGTCTC
1122841 GTTTTTTTAT
1 GTTTTTTTAT
1122851 GTTTTTTTAT
1 GTTTTTTTAT
1122861 GTTTT
1 GTTTT
1122866 CAAGTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.12, T:0.80
Consensus pattern (10 bp):
GTTTTTTTAT
Found at i:1126626 original size:20 final size:20
Alignment explanation
Indices: 1126601--1126640 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1126591 CGTAAAATAA
*
1126601 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1126621 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1126641 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1126630 original size:34 final size:35
Alignment explanation
Indices: 1126586--1126652 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1126576 CAGTAAAATG
* *
1126586 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
* *
1126620 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTT
1126653 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
Found at i:1126834 original size:22 final size:24
Alignment explanation
Indices: 1126809--1126859 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
1126799 TTATTTATAA
1126809 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
1126829 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
1126855 ATAAA
1 ATAAA
1126860 AGCATTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:1129172 original size:462 final size:463
Alignment explanation
Indices: 1128307--1129230 Score: 1805
Period size: 462 Copynumber: 2.0 Consensus size: 463
1128297 CAATGCCAAG
1128307 TTTTATACAACAAGTTCAACAGCAGTTTGCAGCAAAACTTATGCAAGTAAAGCGCCAACATAATG
1 TTTTATACAACAAGTTCAACAGCAGTTTGCAGCAAAACTTATGCAAGTAAAGCGCCAACATAATG
*
1128372 TCGCACCCCACAAAGATGATAATGATTACATAGGTTCATGCCAACACATTTAAAAACTAATAAAA
66 CCGCACCCCACAAAGATGATAATGATTACATAGGTTCATGCCAACACATTTAAAAACTAATAAAA
1128437 ATGCCTAAAAGTGCTACAATGAGCCAACACAATAATACTCCAGAAAGATAAAATGCAATGATGCA
131 ATGCCTAAAAGTGCTACAATGAGCCAACACAATAATACTCCAGAAAGATAAAATGCAATGATGCA
1128502 ATTCCCCAAACGATTCTAATGAAAAATCACCTACCACAAGAAGTACACAGGAGGCAGTGTACCTG
196 ATTCCCCAAACGATTCTAATGAAAAATCACCTACCACAAGAAGTACACAGGAGGCAGTGTACCTG
1128567 AGCTAAGCGACATGTAAGCAGATCAGGAATTAGGCTGACATGAATGAGGCAGAAGTTATCTTTCC
261 AGCTAAGCGACATGTAAGCAGATCAGGAATTAGGCTGACATGAATGAGGCAGAAGTTATCTTTCC
1128632 CTGAGGAAGAAAATGAAAATTATTATGACACATGAGGATTAATATCCAAATATACCAAATAGATT
326 CTGAGGAAGAAAATGAAAATTATTATGACACATGAGGATTAATATCCAAATATACCAAATAGATT
*
1128697 GATATAGTCTCTTTGAACCACTCCATAAATGTAGAATCAAATGTTCTAGATTGAGGTTTAACAGA
391 GATATAGTCTCTTTGAACCACTCCATAAATGCAGAATCAAATGTTCTAGATTGAGGTTTAACAGA
1128762 ATGGGAAT
456 ATGGGAAT
*
1128770 TTTTATACGACAAGTTCAACAGCAGTTTGCAGCAAAACTTATGCAAGTAAAGCGCCAACATAATG
1 TTTTATACAACAAGTTCAACAGCAGTTTGCAGCAAAACTTATGCAAGTAAAGCGCCAACATAATG
1128835 CCGCACCCCACAAAGATGATAATGATTACATAGGTTCATGCCAACACATTTAAAAACTAATAAAA
66 CCGCACCCCACAAAGATGATAATGATTACATAGGTTCATGCCAACACATTTAAAAACTAATAAAA
1128900 ATG-CTAAAAGTGCTACAATGAGCCAACACAATAATACTCCAGAAAGATAAAATGCAATGATGCA
131 ATGCCTAAAAGTGCTACAATGAGCCAACACAATAATACTCCAGAAAGATAAAATGCAATGATGCA
1128964 ATTCCCCAAACGATTCTAATGAAAAATCACCTACCACAAGAAGTACACAGGAGGCAGTGTACCTG
196 ATTCCCCAAACGATTCTAATGAAAAATCACCTACCACAAGAAGTACACAGGAGGCAGTGTACCTG
1129029 AGCTAAGCGACATGTAAGCAGATCAGGAATTAGGCTGACATGAATGAGGCAGAAGTTATCTTTCC
261 AGCTAAGCGACATGTAAGCAGATCAGGAATTAGGCTGACATGAATGAGGCAGAAGTTATCTTTCC
1129094 CTGAGGAAGAAAATGAAAATTATTATGACACATGAGGATTAATATCCAAATATACCAAATAGATT
326 CTGAGGAAGAAAATGAAAATTATTATGACACATGAGGATTAATATCCAAATATACCAAATAGATT
*
1129159 GATATAGTCTCTTTGAACCACTCCATAGATGCAGAATCAAATGTTCTAGATTGAGGTTTAACAGA
391 GATATAGTCTCTTTGAACCACTCCATAAATGCAGAATCAAATGTTCTAGATTGAGGTTTAACAGA
1129224 ATGGGAA
456 ATGGGAA
1129231 CGGCTACAAG
Statistics
Matches: 457, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
462 326 0.71
463 131 0.29
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (463 bp):
TTTTATACAACAAGTTCAACAGCAGTTTGCAGCAAAACTTATGCAAGTAAAGCGCCAACATAATG
CCGCACCCCACAAAGATGATAATGATTACATAGGTTCATGCCAACACATTTAAAAACTAATAAAA
ATGCCTAAAAGTGCTACAATGAGCCAACACAATAATACTCCAGAAAGATAAAATGCAATGATGCA
ATTCCCCAAACGATTCTAATGAAAAATCACCTACCACAAGAAGTACACAGGAGGCAGTGTACCTG
AGCTAAGCGACATGTAAGCAGATCAGGAATTAGGCTGACATGAATGAGGCAGAAGTTATCTTTCC
CTGAGGAAGAAAATGAAAATTATTATGACACATGAGGATTAATATCCAAATATACCAAATAGATT
GATATAGTCTCTTTGAACCACTCCATAAATGCAGAATCAAATGTTCTAGATTGAGGTTTAACAGA
ATGGGAAT
Found at i:1137081 original size:22 final size:21
Alignment explanation
Indices: 1137033--1137083 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1137023 GGACAAGCCA
* *
1137033 CCACATAATTGCTAATACCGG
1 CCACATAATTGCAAATAACGG
*
1137054 CCACATAATTGCAAATAAACTG
1 CCACATAATTGCAAAT-AACGG
1137076 CCACATAA
1 CCACATAA
1137084 CTTCCACCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (21 bp):
CCACATAATTGCAAATAACGG
Found at i:1139982 original size:30 final size:30
Alignment explanation
Indices: 1139948--1140017 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
1139938 GCGTGTGACT
***
1139948 TGGCCGTGTGAAGCACATGGCTAGGCGACA
1 TGGCCGTGTGAAGCACACAACTAGGCGACA
* *
1139978 TGGCCGTGTGAGGCACACAACTGGGCGACA
1 TGGCCGTGTGAAGCACACAACTAGGCGACA
*
1140008 CGGCCGTGTG
1 TGGCCGTGTG
1140018 TCATATGTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.39, T:0.16
Consensus pattern (30 bp):
TGGCCGTGTGAAGCACACAACTAGGCGACA
Found at i:1159028 original size:500 final size:501
Alignment explanation
Indices: 1158087--1159091 Score: 2003
Period size: 500 Copynumber: 2.0 Consensus size: 501
1158077 AAAGTAATTC
1158087 CCTTATTCAAGTAAACTGTTAAAAGATAAAATAAAATATTACTAAAAAATCTTAATTGATTATTC
1 CCTTATTCAAGTAAACTGTTAAAAGATAAAATAAAATATTACTAAAAAATCTTAATTGATTATTC
1158152 TAGGATTTATCTACCTAAATAATTTTTAAAAATATCTCAAAATATATGGGGCTTCAACATTTATT
66 TAGGATTTATCTACCTAAATAATTTTTAAAAATATCTCAAAATATATGGGGCTTCAACATTTATT
1158217 TCAATACCTCCCTCAAGTTGGTGCATATATATCAATCATACCCAACTTGCTTACGAGAAAATCGA
131 TCAATACCTCCCTCAAGTTGGTGCATATATATCAATCATACCCAACTTGCTTACGAGAAAATCGA
1158282 AACTTCTCTTAGAGAGCCCTTTGGTGAGTACATCAACAATCTGTTGTTCTGAAGGAGCAAACGGT
196 AACTTCTCTTAGAGAGCCCTTTGGTGAGTACATCAACAATCTGTTGTTCTGAAGGAGCAAACGGT
1158347 GTGCACACATGGTCTTTCTTCATTCTTCTCCTTGATAAAGTGTCTATCAATCTCAACATGTTTAG
261 GTGCACACATGGTCTTTCTTCATTCTTCTCCTTGATAAAGTGTCTATCAATCTCAACATGTTTAG
1158412 TTTTGTCATGCTAGACTGGGTTGTGAATCTAAAACATTGCTTCTTCATGTTCCTCCCTTGGGGAG
326 TTTTGTCATGCTAGACTGGGTTGTGAATCTAAAACATTGCTTCTTCATGTTCCTCCCTTGGGGAG
1158477 TGCATAAATTGACTTGATAAGCTTACTACAAAAGCTATGTCTGGCCTTATATGTGATAAGTAGAT
391 TGCATAAATTGACTTGATAAGCTTACTACAAAAGCTATGTCTGGCCTTATATGTGATAAGTAGAT
1158542 TAACTTACCAACTAATCTCTAGTATTGCCCTTTATCAATTGG-TTT
456 TAACTTACCAACTAATCTCTAGTATTGCCCTTTATCAATTGGTTTT
1158587 CCTTATTCAAGTAAACTGTTAAAAGATAAAATAAAATATTACTAAAAAATCTTAATTGATTATTC
1 CCTTATTCAAGTAAACTGTTAAAAGATAAAATAAAATATTACTAAAAAATCTTAATTGATTATTC
1158652 TAGGATTTATCTACCTAAATAATTTTTAAAAATATCTCAAAATATATGGGGCTTCAACATTTATT
66 TAGGATTTATCTACCTAAATAATTTTTAAAAATATCTCAAAATATATGGGGCTTCAACATTTATT
1158717 TCAATACCTCCCTCAAGTTGGTGCATATATATCAATCATACCCAACTTGCTTACGAGAAAATCGA
131 TCAATACCTCCCTCAAGTTGGTGCATATATATCAATCATACCCAACTTGCTTACGAGAAAATCGA
1158782 AACTTCTCTTAGAGAGCCCTTTGGTGAGTACATCAACAATCTGTTGTTCTGAAGGAGCAAACGGT
196 AACTTCTCTTAGAGAGCCCTTTGGTGAGTACATCAACAATCTGTTGTTCTGAAGGAGCAAACGGT
1158847 GTGCACACATGGTCTTTCTTCATTCTTCTCCTTGATAAAGTGTCTATCAATCTCAACATGTTTAG
261 GTGCACACATGGTCTTTCTTCATTCTTCTCCTTGATAAAGTGTCTATCAATCTCAACATGTTTAG
1158912 TTTTGTCATGCTAGACTGGGTTGTGAATCTAAAACATTGCTTCTTCATGTTCCTCCCTTGGGGAG
326 TTTTGTCATGCTAGACTGGGTTGTGAATCTAAAACATTGCTTCTTCATGTTCCTCCCTTGGGGAG
1158977 TGCATAAATTGACTTGATAAGCTTACTACAAAAGCTATGTCTGGCCTTATATGTGATAAGTAGAT
391 TGCATAAATTGACTTGATAAGCTTACTACAAAAGCTATGTCTGGCCTTATATGTGATAAGTAGAT
1159042 TAACTTACCAACTAATCTCTAGTATTGCCCTTTATCAATTGGTTTT
456 TAACTTACCAACTAATCTCTAGTATTGCCCTTTATCAATTGGTTTT
1159088 CCTT
1 CCTT
1159092 TGTTTTCGAA
Statistics
Matches: 504, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
500 497 0.99
501 7 0.01
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (501 bp):
CCTTATTCAAGTAAACTGTTAAAAGATAAAATAAAATATTACTAAAAAATCTTAATTGATTATTC
TAGGATTTATCTACCTAAATAATTTTTAAAAATATCTCAAAATATATGGGGCTTCAACATTTATT
TCAATACCTCCCTCAAGTTGGTGCATATATATCAATCATACCCAACTTGCTTACGAGAAAATCGA
AACTTCTCTTAGAGAGCCCTTTGGTGAGTACATCAACAATCTGTTGTTCTGAAGGAGCAAACGGT
GTGCACACATGGTCTTTCTTCATTCTTCTCCTTGATAAAGTGTCTATCAATCTCAACATGTTTAG
TTTTGTCATGCTAGACTGGGTTGTGAATCTAAAACATTGCTTCTTCATGTTCCTCCCTTGGGGAG
TGCATAAATTGACTTGATAAGCTTACTACAAAAGCTATGTCTGGCCTTATATGTGATAAGTAGAT
TAACTTACCAACTAATCTCTAGTATTGCCCTTTATCAATTGGTTTT
Found at i:1167192 original size:21 final size:21
Alignment explanation
Indices: 1167163--1167202 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1167153 GAAAAAATGG
*
1167163 AAAAGAAAAAGAAAAGAAATC
1 AAAAAAAAAAGAAAAGAAATC
*
1167184 AAAAAAAAAAGAAAGGAAA
1 AAAAAAAAAAGAAAAGAAA
1167203 AAATAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAGAAAAGAAATC
Found at i:1167203 original size:16 final size:16
Alignment explanation
Indices: 1167162--1167205 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1167152 GGAAAAAATG
*
1167162 GAAAAGAAAAAGAAAA
1 GAAAAGAAAAAAAAAA
**
1167178 GAAATCAAAAAAAAAA
1 GAAAAGAAAAAAAAAA
*
1167194 GAAAGGAAAAAA
1 GAAAAGAAAAAA
1167206 TAATTTAGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (16 bp):
GAAAAGAAAAAAAAAA
Found at i:1170925 original size:35 final size:35
Alignment explanation
Indices: 1170877--1170945 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
1170867 AAGTCTACCT
* *
1170877 CAATGGCTGTTCGGGAACTCCAATTGACAAAGCTC
1 CAATGACTATTCGGGAACTCCAATTGACAAAGCTC
*
1170912 CAATGACTATTCGGGAACTCCAATTGTCAAAGCT
1 CAATGACTATTCGGGAACTCCAATTGACAAAGCT
1170946 GATTAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (35 bp):
CAATGACTATTCGGGAACTCCAATTGACAAAGCTC
Found at i:1173978 original size:27 final size:27
Alignment explanation
Indices: 1173947--1174011 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1173937 ACTATGAATA
**
1173947 GCCTTTGTGGTGAACTTTGAATGGGAT-
1 GCCTTTGTGGCAAACTTTGAAT-GGATC
*
1173974 GCCTTTGTGGCAAATTTTGAATGGATC
1 GCCTTTGTGGCAAACTTTGAATGGATC
*
1174001 GCCTTAGTGGC
1 GCCTTTGTGGC
1174012 GTGCTTTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.35
Consensus pattern (27 bp):
GCCTTTGTGGCAAACTTTGAATGGATC
Found at i:1174778 original size:14 final size:14
Alignment explanation
Indices: 1174759--1174785 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1174749 CCGAAACTAG
1174759 AAAGAAAAAAAAAC
1 AAAGAAAAAAAAAC
1174773 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
1174786 TGCTCATCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.04, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAC
Found at i:1175958 original size:39 final size:40
Alignment explanation
Indices: 1175863--1176124 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
1175853 TTGAATGATG
*
1175863 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
1175901 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
1175942 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
1175981 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1176020 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
1176059 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
1176098 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
1176125 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:1185120 original size:62 final size:61
Alignment explanation
Indices: 1185050--1185172 Score: 210
Period size: 62 Copynumber: 2.0 Consensus size: 61
1185040 GGCAGAACGG
*
1185050 TTTCTGGATTTCCTGTTCCGACTTTGGAAATTCATTATAAATCAACCAGAGACAATTAGGA
1 TTTCTGGATTCCCTGTTCCGACTTTGGAAATTCATTATAAATCAACCAGAGACAATTAGGA
* *
1185111 NTTTCTGGATTCCCTGTTCCGACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGGA
1 -TTTCTGGATTCCCTGTTCCGACTTTGGAAATTCATTATAAATCAACCAGAGACAATTAGGA
1185173 GTCATACCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (61 bp):
TTTCTGGATTCCCTGTTCCGACTTTGGAAATTCATTATAAATCAACCAGAGACAATTAGGA
Found at i:1193658 original size:18 final size:18
Alignment explanation
Indices: 1193635--1193670 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1193625 TTTTTTAAAG
1193635 TTATTTAGGTAGAGAAAT
1 TTATTTAGGTAGAGAAAT
*
1193653 TTATTTAGGTAGATAAAT
1 TTATTTAGGTAGAGAAAT
1193671 CTTAGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (18 bp):
TTATTTAGGTAGAGAAAT
Found at i:1202821 original size:19 final size:19
Alignment explanation
Indices: 1202797--1202841 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1202787 TAGAATAACA
1202797 TCAGTGGCCAACTCTTGGC
1 TCAGTGGCCAACTCTTGGC
*
1202816 TCAGTGGCTAACTCTTGGC
1 TCAGTGGCCAACTCTTGGC
1202835 TCAGTGG
1 TCAGTGG
1202842 AAATCCAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (19 bp):
TCAGTGGCCAACTCTTGGC
Found at i:1205926 original size:15 final size:14
Alignment explanation
Indices: 1205901--1205930 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1205891 ACCCGACAAC
1205901 AACCTTTATAGTAG
1 AACCTTTATAGTAG
1205915 AACCTATTATAGTAG
1 AACCT-TTATAGTAG
1205930 A
1 A
1205931 TGTATGACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (14 bp):
AACCTTTATAGTAG
Found at i:1212524 original size:22 final size:21
Alignment explanation
Indices: 1212464--1212524 Score: 50
Period size: 22 Copynumber: 2.8 Consensus size: 21
1212454 AGTGATCAGA
* *
1212464 ATGGCTAAGAGCCGTAAACAGG
1 ATGGCT-ATAGCCATAAACAGG
** *
1212486 ACAGCTATACGCTATAAACAGG
1 ATGGCTATA-GCCATAAACAGG
1212508 ATGGCTACTAGCCATAA
1 ATGGCTA-TAGCCATAA
1212525 GTATAGTAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
21 2 0.07
22 25 0.86
23 2 0.07
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (21 bp):
ATGGCTATAGCCATAAACAGG
Found at i:1212570 original size:32 final size:32
Alignment explanation
Indices: 1212529--1212625 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
1212519 CCATAAGTAT
*
1212529 AGTAATATGATTGGCACAAAGCCATCAGTAGC
1 AGTAATATGATCGGCACAAAGCCATCAGTAGC
* * * *
1212561 AGTGATATGATCGGCACACA-CCCTACAGTAAC
1 AGTAATATGATCGGCACAAAGCCAT-CAGTAGC
* * *
1212593 GGTAATATGATCGACACAAAGCCATCAGCAGC
1 AGTAATATGATCGGCACAAAGCCATCAGTAGC
1212625 A
1 A
1212626 TCGCAGCAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
31 3 0.06
32 44 0.88
33 3 0.06
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19
Consensus pattern (32 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAGC
Found at i:1212695 original size:27 final size:27
Alignment explanation
Indices: 1212658--1212725 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
1212648 AGTACCGCAA
* *
1212658 CAAAGCTACCAGTAACAGT-ATATGTAG
1 CAAAGCCACCAGTAACAGTGAT-GGTAG
* * *
1212685 CTAAGCCACCAGTAATAGTGATGGTGG
1 CAAAGCCACCAGTAACAGTGATGGTAG
1212712 CAAAGCCACCAGTA
1 CAAAGCCACCAGTA
1212726 CAATATTTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (27 bp):
CAAAGCCACCAGTAACAGTGATGGTAG
Found at i:1212826 original size:24 final size:24
Alignment explanation
Indices: 1212794--1212875 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
1212784 CCATGCTCAG
*
1212794 AATCAGTCATACAATTCACAGAAA
1 AATCAGTCATACAATTCACAGACA
* *
1212818 AATTAGTCATAC-CTATCACAGACA
1 AATCAGTCATACAAT-TCACAGACA
** *
1212842 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATACAATTCACAGACA
1212866 AATCAGTCAT
1 AATCAGTCAT
1212876 TTACATCTCG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.24
Consensus pattern (24 bp):
AATCAGTCATACAATTCACAGACA
Found at i:1212876 original size:24 final size:24
Alignment explanation
Indices: 1212832--1212903 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
1212822 AGTCATACCT
1212832 ATCACAGACAAATCAGTCATTTAA
1 ATCACAGACAAATCAGTCATTTAA
*
1212856 ATCACAGACAAATCAGTCATTTAC
1 ATCACAGACAAATCAGTCATTTAA
* * *
1212880 ATCTCGGACAAATCAATCATTTAA
1 ATCACAGACAAATCAGTCATTTAA
1212904 CCTCGAGGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.26
Consensus pattern (24 bp):
ATCACAGACAAATCAGTCATTTAA
Found at i:1213005 original size:26 final size:27
Alignment explanation
Indices: 1212969--1213064 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
1212959 TAATAGAGGT
* *
1212969 ATTACAATCATTTTA-CCTACAAGGGC
1 ATTACGATCATTTTACCCTACAGGGGC
* *
1212995 ATCACGATCATTTTACCCTACAGGGGA
1 ATTACGATCATTTTACCCTACAGGGGC
* *
1213022 ATTACGGTCATTTTACCCTATAGGGGC
1 ATTACGATCATTTTACCCTACAGGGGC
1213049 ATTAC-AGTCATTTTAC
1 ATTACGA-TCATTTTAC
1213065 AAATATTAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
26 13 0.22
27 46 0.78
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (27 bp):
ATTACGATCATTTTACCCTACAGGGGC
Found at i:1215003 original size:178 final size:178
Alignment explanation
Indices: 1214704--1215049 Score: 692
Period size: 178 Copynumber: 1.9 Consensus size: 178
1214694 AACGTCAGAC
1214704 TTGTAACACCCCAAACCCGAGACCGTCACCGGAGTCGAATACGAGGTGTTGACAGACTTTTAAAA
1 TTGTAACACCCCAAACCCGAGACCGTCACCGGAGTCGAATACGAGGTGTTGACAGACTTTTAAAA
1214769 ATTTTTCCAGACACTGTCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAA
66 ATTTTTCCAGACACTGTCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAA
1214834 CTCGAAAATCAGTTTTGTGATTTTTCCCTGAAACTAGATACCAATCAA
131 CTCGAAAATCAGTTTTGTGATTTTTCCCTGAAACTAGATACCAATCAA
1214882 TTGTAACACCCCAAACCCGAGACCGTCACCGGAGTCGAATACGAGGTGTTGACAGACTTTTAAAA
1 TTGTAACACCCCAAACCCGAGACCGTCACCGGAGTCGAATACGAGGTGTTGACAGACTTTTAAAA
1214947 ATTTTTCCAGACACTGTCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAA
66 ATTTTTCCAGACACTGTCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAA
1215012 CTCGAAAATCAGTTTTGTGATTTTTCCCTGAAACTAGA
131 CTCGAAAATCAGTTTTGTGATTTTTCCCTGAAACTAGA
1215050 CTCATGTCCC
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 168 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (178 bp):
TTGTAACACCCCAAACCCGAGACCGTCACCGGAGTCGAATACGAGGTGTTGACAGACTTTTAAAA
ATTTTTCCAGACACTGTCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAA
CTCGAAAATCAGTTTTGTGATTTTTCCCTGAAACTAGATACCAATCAA
Found at i:1216308 original size:40 final size:40
Alignment explanation
Indices: 1216260--1216467 Score: 353
Period size: 40 Copynumber: 5.2 Consensus size: 40
1216250 GCAAACACAT
* * *
1216260 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
1216300 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
1216340 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
1216380 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
1216420 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1216460 TTGCCTTC
1 TTGCCTTC
1216468 TTTTGACTAA
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 162 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:1216909 original size:27 final size:27
Alignment explanation
Indices: 1216878--1216932 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1216868 GCCCAAATAC
*
1216878 TTAGCCTCCAAAGCTACACTTAATTTA
1 TTAGCCTCCAAAGCTACACCTAATTTA
1216905 TTAGCCTCCAAAGCTACACCTAATTTA
1 TTAGCCTCCAAAGCTACACCTAATTTA
1216932 T
1 T
1216933 GATATTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (27 bp):
TTAGCCTCCAAAGCTACACCTAATTTA
Found at i:1220430 original size:20 final size:20
Alignment explanation
Indices: 1220384--1220442 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
1220374 CATAGATGCA
* *
1220384 AAACAGGGGCACATACGTGC
1 AAACAGGGGCACAGAAGTGC
** *
1220404 AGTCAGGGGCACCGAAGTGC
1 AAACAGGGGCACAGAAGTGC
* *
1220424 AAACAGGGACACTGAAGTG
1 AAACAGGGGCACAGAAGTG
1220443 TATTTAGGGG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.34, T:0.10
Consensus pattern (20 bp):
AAACAGGGGCACAGAAGTGC
Found at i:1221360 original size:12 final size:12
Alignment explanation
Indices: 1221343--1221367 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1221333 GGACACACAT
1221343 CTGTGTTCTAGC
1 CTGTGTTCTAGC
1221355 CTGTGTTCTAGC
1 CTGTGTTCTAGC
1221367 C
1 C
1221368 CCTGTTCTTA
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:0.08, C:0.28, G:0.24, T:0.40
Consensus pattern (12 bp):
CTGTGTTCTAGC
Found at i:1228301 original size:60 final size:59
Alignment explanation
Indices: 1228231--1228434 Score: 214
Period size: 60 Copynumber: 3.4 Consensus size: 59
1228221 AAAAATCGCA
* ** * *
1228231 ATGGTTGTCACCATCCTTTTCCATTGTTCGATAGCTGAAGCTATCCCTTTTCTTATTTTG
1 ATGGTCGTCACCATCCTTTT-CATAATTCGATAGCTGAAGCTATCCCTTTTCATAATTTG
* * *
1228291 ATGGTTGTCACCATCCCTTTTCATAATTTGATAGCCGAAGCTATCCCTTTTCATAATTTG
1 ATGGTCGTCACCAT-CCTTTTCATAATTCGATAGCTGAAGCTATCCCTTTTCATAATTTG
* * * * *
1228351 ATAGCCG-AAGCTATCCTTTTTCATAATTCGATAG-TCGAAGCTATCCCTTTTCATAGTTTG
1 ATGGTCGTCA-CCATCC-TTTTCATAATTCGATAGCT-GAAGCTATCCCTTTTCATAATTTG
*
1228411 ATGGTCATCACCATCGCTTTTCAT
1 ATGGTCGTCACCATC-CTTTTCAT
1228435 TGTTGATGGT
Statistics
Matches: 119, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
59 3 0.03
60 108 0.91
61 8 0.07
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (59 bp):
ATGGTCGTCACCATCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTTTCATAATTTG
Found at i:1228337 original size:30 final size:30
Alignment explanation
Indices: 1228267--1228580 Score: 230
Period size: 30 Copynumber: 10.5 Consensus size: 30
1228257 TTCGATAGCT
* * * *
1228267 GAAGCTATCCCTTTTCTTATTTTGATGGTT
1 GAAGCTATCCCTTTTCATAATTTGATAGTC
* * *
1228297 GTCA-CCATCCCTTTTCATAATTTGATAGCC
1 G-AAGCTATCCCTTTTCATAATTTGATAGTC
*
1228327 GAAGCTATCCCTTTTCATAATTTGATAGCC
1 GAAGCTATCCCTTTTCATAATTTGATAGTC
* *
1228357 GAAGCTATCCTTTTTCATAATTCGATAGTC
1 GAAGCTATCCCTTTTCATAATTTGATAGTC
* *
1228387 GAAGCTATCCCTTTTCATAGTTTGATGGTC
1 GAAGCTATCCCTTTTCATAATTTGATAGTC
* * *
1228417 -ATCA-CCATCGCTTTTCAT--TGTTGATGGTC
1 GA--AGCTATCCCTTTTCATAAT-TTGATAGTC
* * * *
1228446 GTCA-CCATCCCCTTTCATAATTTGATA-AC
1 G-AAGCTATCCCTTTTCATAATTTGATAGTC
* **
1228475 TGAAGCTATCTCTTTTCATAATTCAATAGTC
1 -GAAGCTATCCCTTTTCATAATTTGATAGTC
* *** *
1228506 AAAGCTATCCCTTTTCATTGGTCGATAGTC
1 GAAGCTATCCCTTTTCATAATTTGATAGTC
* * * *
1228536 AAAGCTATCCCTTTTTATTGA-TCGATAGTC
1 GAAGCTATCCCTTTTCA-TAATTTGATAGTC
1228566 GAAGCTATCCCTTTT
1 GAAGCTATCCCTTTT
1228581 TATTTATCGA
Statistics
Matches: 231, Mismatches: 40, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
28 1 0.00
29 26 0.11
30 199 0.86
31 5 0.02
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (30 bp):
GAAGCTATCCCTTTTCATAATTTGATAGTC
Found at i:1228444 original size:29 final size:30
Alignment explanation
Indices: 1228393--1228471 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 30
1228383 AGTCGAAGCT
1228393 ATCCCTTTTCATAGTTTGATGGTCATCACC
1 ATCCCTTTTCATAGTTTGATGGTCATCACC
* * *
1228423 ATCGCTTTTCATTG-TTGATGGTCGTCACC
1 ATCCCTTTTCATAGTTTGATGGTCATCACC
* *
1228452 ATCCCCTTTCATAATTTGAT
1 ATCCCTTTTCATAGTTTGAT
1228472 AACTGAAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTTGATGGTCATCACC
Found at i:1228578 original size:119 final size:118
Alignment explanation
Indices: 1228300--1228579 Score: 298
Period size: 119 Copynumber: 2.3 Consensus size: 118
1228290 GATGGTTGTC
* * *
1228300 ACCATCCCTTTTCATAAT-TTGATAGCCGAAGCTATCCCTTTTCATAATTTGATAGCCGAAGCTA
1 ACCATCCCTTTTCAT--TGTCGATAGTCGAAGCTATCCC-TTTCATAATTTGATAACCGAAGCTA
* * * * * *
1228364 TCCTTTTTCATAATTCGATAGTCGAAGCTATCCCTTTTCATAGTTTGATGGTCATC
63 TCCTTTTTCATAATTCAATAGTCAAAGCTATCCCTTTTCATAGGTCGATAGTCATA
* * * * * *
1228420 ACCATCGCTTTTCATTGTTGATGGTCGTCA-CCATCCCCTTTCATAATTTGATAACTGAAGCTAT
1 ACCATCCCTTTTCATTGTCGATAGTCG-AAGCTAT-CCCTTTCATAATTTGATAACCGAAGCTAT
*
1228484 -CTCTTTTCATAATTCAATAGTCAAAGCTATCCCTTTTCATTGGTCGATAGTCA-A
64 CCT-TTTTCATAATTCAATAGTCAAAGCTATCCCTTTTCATAGGTCGATAGTCATA
* *
1228538 AGCTATCCCTTTTTATTGATCGATAGTCGAAGCTATCCCTTT
1 A-CCATCCCTTTTCATTG-TCGATAGTCGAAGCTATCCCTTT
1228580 TTATTTATCG
Statistics
Matches: 132, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
118 4 0.03
119 99 0.75
120 29 0.22
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.39
Consensus pattern (118 bp):
ACCATCCCTTTTCATTGTCGATAGTCGAAGCTATCCCTTTCATAATTTGATAACCGAAGCTATCC
TTTTTCATAATTCAATAGTCAAAGCTATCCCTTTTCATAGGTCGATAGTCATA
Found at i:1228580 original size:149 final size:149
Alignment explanation
Indices: 1228245--1228585 Score: 404
Period size: 149 Copynumber: 2.3 Consensus size: 149
1228235 TTGTCACCAT
* *
1228245 CCTTTTCCATTGTTCGATAG-CTGAAGCTATCCCTTTTCTTATTTTGATGGTTGTCACCATCCCT
1 CCTTTT-CATTGTTCGATAGTC-GAAGCTATCCCTTTTC-TATTTTGATGGTCGTCACCATCCCC
* ** * *
1228309 TTTCATAATTTGATAGCCGAAGCTATCCCTTTTCATAATTTGATAGCCGAAGCTATCCTTTTTCA
63 TTTCATAATTTGATAACCGAAGCTATCCCTTTTCATAATTCAATAGCCAAAGCTATCCCTTTTCA
* *
1228374 TAATTCGATAGTCGAAGCTATC
128 TAAGTCGATAGTCAAAGCTATC
* * * * *
1228396 CCTTTTCATAGTTTGATGGTC-ATCA-CCATCGCTTTTC-ATTGTTGATGGTCGTCACCATCCCC
1 CCTTTTCATTGTTCGATAGTCGA--AGCTATCCCTTTTCTATT-TTGATGGTCGTCACCATCCCC
* * *
1228458 TTTCATAATTTGATAACTGAAGCTATCTCTTTTCATAATTCAATAGTCAAAGCTATCCCTTTTCA
63 TTTCATAATTTGATAACCGAAGCTATCCCTTTTCATAATTCAATAGCCAAAGCTATCCCTTTTCA
**
1228523 TTGGTCGATAGTCAAAGCTATC
128 TAAGTCGATAGTCAAAGCTATC
* *
1228545 CCTTTTTATTGATCGATAGTCGAAGCTATCCCTTTT-TATTT
1 CCTTTTCATTGTTCGATAGTCGAAGCTATCCCTTTTCTATTT
1228586 ATCGATGATC
Statistics
Matches: 157, Mismatches: 26, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
148 5 0.03
149 123 0.78
150 21 0.13
151 8 0.05
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (149 bp):
CCTTTTCATTGTTCGATAGTCGAAGCTATCCCTTTTCTATTTTGATGGTCGTCACCATCCCCTTT
CATAATTTGATAACCGAAGCTATCCCTTTTCATAATTCAATAGCCAAAGCTATCCCTTTTCATAA
GTCGATAGTCAAAGCTATC
Found at i:1228581 original size:30 final size:30
Alignment explanation
Indices: 1228500--1228591 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
1228490 TCATAATTCA
* *
1228500 ATAGTCAAAGCTATCCCTTTTCATTGGTCG
1 ATAGTCAAAGCTATCCCTTTTTATTGATCG
1228530 ATAGTCAAAGCTATCCCTTTTTATTGATCG
1 ATAGTCAAAGCTATCCCTTTTTATTGATCG
* *
1228560 ATAGTCGAAGCTATCCCTTTTTATTTATCG
1 ATAGTCAAAGCTATCCCTTTTTATTGATCG
1228590 AT
1 AT
1228592 GATCATAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (30 bp):
ATAGTCAAAGCTATCCCTTTTTATTGATCG
Found at i:1236594 original size:50 final size:51
Alignment explanation
Indices: 1236535--1236662 Score: 170
Period size: 50 Copynumber: 2.5 Consensus size: 51
1236525 AAAGTGATGG
* * *
1236535 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAGT-ATAGA
* * * *
1236585 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAGTATAGA
1236636 TCACATGTGTAGTACTATGTGCAGGCT
1 TCACATGTGTAGTACTATGTGCAGGCT
1236663 CATATGTGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 38 0.56
51 29 0.43
52 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAGTATAGA
Found at i:1236728 original size:45 final size:45
Alignment explanation
Indices: 1236672--1236766 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
1236662 TCATATGTGA
* * *
1236672 ACCGAACATCATTGATTAGTAAAGTGGTTGCTATGTGTTGATTCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
* * *
1236717 ACCGGACATCATTGATTAATAAGGTGGTTGTTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
1236762 ACCGA
1 ACCGA
1236767 GTATCTGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
Found at i:1242312 original size:39 final size:40
Alignment explanation
Indices: 1242260--1242354 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 40
1242250 GAGTTATCGG
* *
1242260 AGTATAAACAGGGGCACAAAAGTGCATTCA-AAGTACTGA
1 AGTACAAATAGGGGCACAAAAGTGCATTCATAAGTACTGA
** * ** *
1242299 AGTACAAATAGGGGCACGTATGTGCATTCATGGGTACTTA
1 AGTACAAATAGGGGCACAAAAGTGCATTCATAAGTACTGA
*
1242339 AGTACCAATAGGGGCA
1 AGTACAAATAGGGGCA
1242355 TGTATGTGCT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 25 0.54
40 21 0.46
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (40 bp):
AGTACAAATAGGGGCACAAAAGTGCATTCATAAGTACTGA
Found at i:1242349 original size:40 final size:40
Alignment explanation
Indices: 1242292--1242369 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
1242282 TGCATTCAAA
1242292 GTACTGAAGTACAAATAGGGGCACGTATGTGCATTCATGG
1 GTACTGAAGTACAAATAGGGGCACGTATGTGCATTCATGG
* * * *
1242332 GTACTTAAGTACCAATAGGGGCATGTATGTGCTTTCAT
1 GTACTGAAGTACAAATAGGGGCACGTATGTGCATTCAT
1242370 ACAACAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (40 bp):
GTACTGAAGTACAAATAGGGGCACGTATGTGCATTCATGG
Found at i:1250298 original size:20 final size:20
Alignment explanation
Indices: 1250275--1250317 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1250265 GCAGTAAGAA
*
1250275 GCACCAAAGTGCAAATAGGG
1 GCACCAAAGTGCAAACAGGG
* *
1250295 GCACCAATGTGCGAACAGGG
1 GCACCAAAGTGCAAACAGGG
1250315 GCA
1 GCA
1250318 TCGAAGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.33, T:0.09
Consensus pattern (20 bp):
GCACCAAAGTGCAAACAGGG
Found at i:1256143 original size:20 final size:20
Alignment explanation
Indices: 1256118--1256158 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1256108 TTCCATTGGC
1256118 TTAGATTCT-TTCTTTAGGTT
1 TTAGATT-TATTCTTTAGGTT
*
1256138 TTAGATTTATTCTTTTGGTT
1 TTAGATTTATTCTTTAGGTT
1256158 T
1 T
1256159 CTTAGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (20 bp):
TTAGATTTATTCTTTAGGTT
Found at i:1258204 original size:53 final size:53
Alignment explanation
Indices: 1258124--1258226 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
1258114 TTTAACTTAC
*
1258124 TTAATTACTAAACCTATCTCACATATTCCTATGTTCAACAGACTCAAAATAAA
1 TTAATTACTAAACCTATCTCACATATTCCTATATTCAACAGACTCAAAATAAA
* *
1258177 TTAATTACTAAACCTATTTCACGTATTCCTATATTCAACAGACTCAAAAT
1 TTAATTACTAAACCTATCTCACATATTCCTATATTCAACAGACTCAAAAT
1258227 TTTATAAGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (53 bp):
TTAATTACTAAACCTATCTCACATATTCCTATATTCAACAGACTCAAAATAAA
Found at i:1260268 original size:104 final size:104
Alignment explanation
Indices: 1260088--1260290 Score: 379
Period size: 104 Copynumber: 2.0 Consensus size: 104
1260078 TCCTAAATCC
*
1260088 GTTTATGGATTTATTCACTTGTGACGTTCATAGTGTGGCATACTTAAATCCTAACTGAATGACGG
1 GTTTATGGATTTATTCACTTGTGACGTTCATAGTGTGGCATACTTAAATCCTAACTGAATGACAG
1260153 GCTATGTATGCATGACTCATATACTTTGATGTAAAATTT
66 GCTATGTATGCATGACTCATATACTTTGATGTAAAATTT
1260192 GTTTATGGATTTATTCACTTGTGACGTTCATAGTGTGGCATACTTAAATCCTAACTGAATGACAG
1 GTTTATGGATTTATTCACTTGTGACGTTCATAGTGTGGCATACTTAAATCCTAACTGAATGACAG
**
1260257 GCTATGTATGCATGACTTGTATACTTTGATGTAA
66 GCTATGTATGCATGACTCATATACTTTGATGTAA
1260291 GTAAAAGCTT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (104 bp):
GTTTATGGATTTATTCACTTGTGACGTTCATAGTGTGGCATACTTAAATCCTAACTGAATGACAG
GCTATGTATGCATGACTCATATACTTTGATGTAAAATTT
Found at i:1276600 original size:13 final size:13
Alignment explanation
Indices: 1276582--1276606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1276572 ACCATATTAA
1276582 TAAAACACATAAT
1 TAAAACACATAAT
1276595 TAAAACACATAA
1 TAAAACACATAA
1276607 CTAATTTAAA
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:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAACACATAAT
Found at i:1277447 original size:48 final size:48
Alignment explanation
Indices: 1277279--1277436 Score: 217
Period size: 48 Copynumber: 3.3 Consensus size: 48
1277269 TGATTTGTAC
* * * *
1277279 AAAAATGGACAACATTTAAGCACCAATTTGGACAGCATTAATAAACTA
1 AAAAATGGACAACAATTAAGCATCAATTTGGACAACATTAATATACTA
* * * * *
1277327 AAAAATGGGCAGCAATTAAGCATAAATTTGGATAACATTAATATACTC
1 AAAAATGGACAACAATTAAGCATCAATTTGGACAACATTAATATACTA
* *
1277375 AAAAATGGACAGCAATTAAGCATCAATGTGGACAACATTAATATACTA
1 AAAAATGGACAACAATTAAGCATCAATTTGGACAACATTAATATACTA
1277423 AAAAATGGACAACA
1 AAAAATGGACAACA
1277437 TCTTATCATC
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 95 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (48 bp):
AAAAATGGACAACAATTAAGCATCAATTTGGACAACATTAATATACTA
Found at i:1278079 original size:42 final size:43
Alignment explanation
Indices: 1278012--1278097 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
1278002 ACATGTTATA
* *
1278012 ATATATCGATGCCACTGTCCCAAACAGGGTCTTACACGAAATC
1 ATATATCGATGCCAATGTCACAAACAGGGTCTTACACGAAATC
* *
1278055 ATATA-CGATGTCAATGTCACAAACATGGTCTTACACGAAATC
1 ATATATCGATGCCAATGTCACAAACAGGGTCTTACACGAAATC
1278097 A
1 A
1278098 CACCTCGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 34 0.87
43 5 0.13
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (43 bp):
ATATATCGATGCCAATGTCACAAACAGGGTCTTACACGAAATC
Found at i:1280824 original size:50 final size:51
Alignment explanation
Indices: 1280764--1280903 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 51
1280754 TATCATTTGA
* * * * *
1280764 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAA-CTTTTCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCAG
*
1280814 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCAG
* *
1280865 TACACAT-GTAGCCTGCACATAGTACTACACATGTGACCA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1280904 TTATCTATCG
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 70 0.88
51 10 0.12
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCAG
Found at i:1288568 original size:51 final size:50
Alignment explanation
Indices: 1288448--1288736 Score: 258
Period size: 51 Copynumber: 5.7 Consensus size: 50
1288438 ATCATTCGAG
* * * *
1288448 ACACGTAGTAGCCTTCACATAATACTACACACGTGATCAAACTTTCCGGT
1 ACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAACCTTCCGGT
* * *
1288498 TCACGTAGTAGCCTGCACATAGTACTACACACGTTACCAAAGCCTTCCGGT
1 ACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAA-CCTTCCGGT
* * * * * * *
1288549 ACACATAGTGGCCTACACATAGTACTAAACATGTGACCATTATCTAT-CGAT
1 ACACGTAGTAGCCTACACATAGTACTACACACGTGACCA-AACCT-TCCGGT
* * * *
1288600 ACACGTAGTAACCTGCACTTAGTACTACACACGTTACCAAAGCCTTCCGGT
1 ACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAA-CCTTCCGGT
* * * * * * *
1288651 ACACATAGTGGCCTACACATAGTACTAAACATGTGACCATTATCTAT-CGAT
1 ACACGTAGTAGCCTACACATAGTACTACACACGTGACCA-AACCT-TCCGGT
* * *
1288702 ACACGTAGTAACCTGCACTTAGTACTACACACGTG
1 ACACGTAGTAGCCTACACATAGTACTACACACGTG
1288737 TTTATAGGCA
Statistics
Matches: 187, Mismatches: 45, Indels: 13
0.76 0.18 0.05
Matches are distributed among these distances:
50 38 0.20
51 145 0.78
52 4 0.02
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (50 bp):
ACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAACCTTCCGGT
Found at i:1288675 original size:102 final size:102
Alignment explanation
Indices: 1288499--1288735 Score: 456
Period size: 102 Copynumber: 2.3 Consensus size: 102
1288489 CTTTCCGGTT
* *
1288499 CACGTAGTAGCCTGCACATAGTACTACACACGTTACCAAAGCCTTCCGGTACACATAGTGGCCTA
1 CACGTAGTAACCTGCACTTAGTACTACACACGTTACCAAAGCCTTCCGGTACACATAGTGGCCTA
1288564 CACATAGTACTAAACATGTGACCATTATCTATCGATA
66 CACATAGTACTAAACATGTGACCATTATCTATCGATA
1288601 CACGTAGTAACCTGCACTTAGTACTACACACGTTACCAAAGCCTTCCGGTACACATAGTGGCCTA
1 CACGTAGTAACCTGCACTTAGTACTACACACGTTACCAAAGCCTTCCGGTACACATAGTGGCCTA
1288666 CACATAGTACTAAACATGTGACCATTATCTATCGATA
66 CACATAGTACTAAACATGTGACCATTATCTATCGATA
1288703 CACGTAGTAACCTGCACTTAGTACTACACACGT
1 CACGTAGTAACCTGCACTTAGTACTACACACGT
1288736 GTTTATAGGC
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 133 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (102 bp):
CACGTAGTAACCTGCACTTAGTACTACACACGTTACCAAAGCCTTCCGGTACACATAGTGGCCTA
CACATAGTACTAAACATGTGACCATTATCTATCGATA
Found at i:1296467 original size:12 final size:12
Alignment explanation
Indices: 1296450--1296475 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1296440 CTATGAGGAT
1296450 GAATGATCAGTA
1 GAATGATCAGTA
1296462 GAATGATCAGTA
1 GAATGATCAGTA
1296474 GA
1 GA
1296476 TCACCTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.27, T:0.23
Consensus pattern (12 bp):
GAATGATCAGTA
Found at i:1303184 original size:21 final size:20
Alignment explanation
Indices: 1303139--1303184 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1303129 TTGTTGGAAT
1303139 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
1303158 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
1303179 GGTTGA
1 GGTTGA
1303185 TTGTATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:1308316 original size:50 final size:50
Alignment explanation
Indices: 1308199--1308439 Score: 254
Period size: 50 Copynumber: 4.8 Consensus size: 50
1308189 GATAATAACA
* ** * *
1308199 TGCCAAAT-CCATGTCCCAGACATGGTTTTACATGGGATGTTTCATGTAC--
1 TGCC-AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * ** *
1308248 TGCCAATGCCATATCCCAGATATGGACTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
1308298 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
1308348 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
1308398 AGCCAATGCCATGTCCCATACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1308440 TTACCCAAAT
Statistics
Matches: 159, Mismatches: 30, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
48 4 0.03
49 35 0.22
50 120 0.75
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:1318678 original size:22 final size:22
Alignment explanation
Indices: 1318650--1318717 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
1318640 AAACCGACAA
1318650 TAAGCCTGAATAACATCGGCAC
1 TAAGCCTGAATAACATCGGCAC
*
1318672 TAAGCCTG-----C-TAGGCAC
1 TAAGCCTGAATAACATCGGCAC
1318688 TAAGCCTGAATAACA-CTGGCAC
1 TAAGCCTGAATAACATC-GGCAC
1318710 TAAGCCTG
1 TAAGCCTG
1318718 CTAGGCACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
16 14 0.38
17 1 0.03
21 1 0.03
22 21 0.57
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (22 bp):
TAAGCCTGAATAACATCGGCAC
Found at i:1318688 original size:16 final size:16
Alignment explanation
Indices: 1318667--1318733 Score: 71
Period size: 16 Copynumber: 3.8 Consensus size: 16
1318657 GAATAACATC
1318667 GGCACTAAGCCTGCTA
1 GGCACTAAGCCTGCTA
*
1318683 GGCACTAAGCCTGAATAACA
1 GGCACTAAGCCTG-CT---A
1318703 CTGGCACTAAGCCTGCTA
1 --GGCACTAAGCCTGCTA
1318721 GGCACTAAGCCTG
1 GGCACTAAGCCTG
1318734 AATAACAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
16 26 0.60
17 1 0.02
18 1 0.02
20 1 0.02
21 1 0.02
22 13 0.30
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (16 bp):
GGCACTAAGCCTGCTA
Found at i:1318701 original size:38 final size:38
Alignment explanation
Indices: 1318650--1318740 Score: 166
Period size: 38 Copynumber: 2.4 Consensus size: 38
1318640 AAACCGACAA
1318650 TAAGCCTGAATAACA-TCGGCACTAAGCCTGCTAGGCAC
1 TAAGCCTGAATAACACT-GGCACTAAGCCTGCTAGGCAC
1318688 TAAGCCTGAATAACACTGGCACTAAGCCTGCTAGGCAC
1 TAAGCCTGAATAACACTGGCACTAAGCCTGCTAGGCAC
1318726 TAAGCCTGAATAACA
1 TAAGCCTGAATAACA
1318741 ATACGATTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 51 0.98
39 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (38 bp):
TAAGCCTGAATAACACTGGCACTAAGCCTGCTAGGCAC
Found at i:1321810 original size:335 final size:335
Alignment explanation
Indices: 1321194--1321866 Score: 1130
Period size: 335 Copynumber: 2.0 Consensus size: 335
1321184 AGAATACACA
*
1321194 GTCGATTATCAAAATACATCATACCATTGTCACTCATAATGAATCCCGTAGTCGAATCACTCTGG
1 GTCGATTATCAAAATACATCATACCATTGTCACTCATAATGAATCCCATAGTCGAATCACTCTGG
* * *
1321259 ATCAGCTCTCGTTTGGCTACTAACTTCAGGTCATCACTTCGTAATTCTCGAATTCGCTGAAGAAA
66 ATCAGCTCTCGTTTGGCTACTAACTTCAGGTCATCACTTCGTAATTCCCAAATTCACTGAAGAAA
1321324 TAACGACCTAGCCCTAAGCTTAGCTATAACAGAACCATCACTCTCCAAGGATAAATGTGCGTTCA
131 TAACGACCTAGCCCTAAGCTTAGCTATAACAGAACCATCACTCTCCAAGGATAAATGTGCGTTCA
* *
1321389 TTGTTCTTAAAGCAAACAATCATTTACAGCTTAAATCATCTGCAACAACATTTACCTTCCTAGGA
196 TTGTTCTTAAAGCAAACAATCATTTACAGCTTAAAGCATCTGCAACAACATTTACCTTCCCAGGA
* * * *
1321454 TGGTAATTAATCACGAGGTCATAATCTTTCAATAGCTCTAACCACTGTCGCTGTCTCAGATTCAG
261 TGGTAATCAATCACAAGGTCATAATCTTTCAATAGCTCTAACCACCGTCACTGTCTCAGATTCAG
*
1321519 TTCCTTCTAT
326 TTCCCTCTAT
*
1321529 GTCGATTATGAAAATACATCATACCATTGTCACTCATAATGAATCCCATAGTCGAATCACTCTGG
1 GTCGATTATCAAAATACATCATACCATTGTCACTCATAATGAATCCCATAGTCGAATCACTCTGG
*
1321594 ATCAGCTCTCGTTTGGCTACTAACTTCAGGTCATCACTTTGTAATTCCCAAATTCACTGAAGAAA
66 ATCAGCTCTCGTTTGGCTACTAACTTCAGGTCATCACTTCGTAATTCCCAAATTCACTGAAGAAA
* * * *
1321659 TAACGGCCTAGCCCTAAGCTTAGCTATAATAGAACCATCACTCTCTAGGGATAAATGTGCGTTCA
131 TAACGACCTAGCCCTAAGCTTAGCTATAACAGAACCATCACTCTCCAAGGATAAATGTGCGTTCA
* * *** *
1321724 TTGTTCTTAAAGTAAACAATGATTTGTGGCTTAAAGCATTTGCAACAACATTTACCTTCCCAGGA
196 TTGTTCTTAAAGCAAACAATCATTTACAGCTTAAAGCATCTGCAACAACATTTACCTTCCCAGGA
*
1321789 TGGTAATCAATCACAAGGTCATAATCTTTCAATAGCTCTAACCACCGTTACTGTCTCAGATTCAG
261 TGGTAATCAATCACAAGGTCATAATCTTTCAATAGCTCTAACCACCGTCACTGTCTCAGATTCAG
1321854 TTCCCTCTAT
326 TTCCCTCTAT
1321864 GTC
1 GTC
1321867 ATCAAATACT
Statistics
Matches: 314, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
335 314 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (335 bp):
GTCGATTATCAAAATACATCATACCATTGTCACTCATAATGAATCCCATAGTCGAATCACTCTGG
ATCAGCTCTCGTTTGGCTACTAACTTCAGGTCATCACTTCGTAATTCCCAAATTCACTGAAGAAA
TAACGACCTAGCCCTAAGCTTAGCTATAACAGAACCATCACTCTCCAAGGATAAATGTGCGTTCA
TTGTTCTTAAAGCAAACAATCATTTACAGCTTAAAGCATCTGCAACAACATTTACCTTCCCAGGA
TGGTAATCAATCACAAGGTCATAATCTTTCAATAGCTCTAACCACCGTCACTGTCTCAGATTCAG
TTCCCTCTAT
Found at i:1329645 original size:38 final size:38
Alignment explanation
Indices: 1329581--1329678 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 38
1329571 TTATTACACC
** *
1329581 GGCAATAAGCCTGAATAACATTGGCACTAAGCTTGCTA
1 GGCAATAAGCCTGAATAACACCGGCACTAAGCCTGCTA
* *
1329619 GGCACTATGCCTGAATAACACCGGCACTAAGCCTGCTA
1 GGCAATAAGCCTGAATAACACCGGCACTAAGCCTGCTA
1329657 GGCAATAAGCCTGAATAACACC
1 GGCAATAAGCCTGAATAACACC
1329679 AACACCAAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (38 bp):
GGCAATAAGCCTGAATAACACCGGCACTAAGCCTGCTA
Found at i:1329745 original size:98 final size:98
Alignment explanation
Indices: 1329587--1329774 Score: 286
Period size: 98 Copynumber: 1.9 Consensus size: 98
1329577 CACCGGCAAT
* * * * *
1329587 AAGCCTGAATAACATTGGCACTAAGCTTGCTAGGCACTATGCCTGAATAACACCGGCACTAAGCC
1 AAGCATGAATAACATTGGCACTAAGCGTGCTAGGCACTAAGCCTGAATAACACCAGCACTAAGCA
1329652 TGCTAGGCAATAAGCCTGAATAACACCAACACC
66 TGCTAGGCAATAAGCCTGAATAACACCAACACC
* * *
1329685 AAGCATGAATAGCATTGGCATTAAGCGTGCTAGGCACTAAGCCTGAATAACACCAGCACTAGGCA
1 AAGCATGAATAACATTGGCACTAAGCGTGCTAGGCACTAAGCCTGAATAACACCAGCACTAAGCA
* *
1329750 TGTTAGGCACTAAGCCTGAATAACA
66 TGCTAGGCAATAAGCCTGAATAACA
1329775 ATACGATTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 80 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (98 bp):
AAGCATGAATAACATTGGCACTAAGCGTGCTAGGCACTAAGCCTGAATAACACCAGCACTAAGCA
TGCTAGGCAATAAGCCTGAATAACACCAACACC
Found at i:1331569 original size:18 final size:19
Alignment explanation
Indices: 1331543--1331579 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1331533 AATTTTGGAA
1331543 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
1331561 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
1331580 ATGTGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:1333305 original size:35 final size:35
Alignment explanation
Indices: 1333259--1333326 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1333249 CAGTTCCTTA
1333259 ATCTTCTTTTCTGTAGTGGCTTTGTCATGACATCC
1 ATCTTCTTTTCTGTAGTGGCTTTGTCATGACATCC
1333294 ATCTTCTTTTCTGTAGTGGCTTTGTCATGACAT
1 ATCTTCTTTTCTGTAGTGGCTTTGTCATGACAT
1333327 TCTTGTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (35 bp):
ATCTTCTTTTCTGTAGTGGCTTTGTCATGACATCC
Found at i:1352032 original size:69 final size:68
Alignment explanation
Indices: 1351921--1352057 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 68
1351911 AGCATTGTAA
1351921 TGCTTACTCCGTGTACTTTGTTTCCTCTGTTTTATAGATCTCATTTGGAAGCTACAGGCTCGCGG
1 TGCTTACTCCGTGTACTTTGTTTCCTCTGTTTTATAGATCTCATTTGGAAGCTACAGGCTCGCGG
1351986 ATC
66 ATC
*
1351989 NTGCTTACTCCGTGTACTTTGTTTCCTCTGTTTTATAGATCTCATTTGGAAGCTACAGGCTCGGG
1 -TGCTTACTCCGTGTACTTTGTTTCCTCTGTTTTATAGATCTCATTTGGAAGCTACAGGCTCGCG
1352054 GATC
65 GATC
1352058 ATCAGCAACT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.39
Consensus pattern (68 bp):
TGCTTACTCCGTGTACTTTGTTTCCTCTGTTTTATAGATCTCATTTGGAAGCTACAGGCTCGCGG
ATC
Found at i:1352892 original size:40 final size:40
Alignment explanation
Indices: 1352835--1353144 Score: 521
Period size: 40 Copynumber: 7.8 Consensus size: 40
1352825 GAGTGAAATG
* *
1352835 TCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*
1352875 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*
1352915 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
* *
1352955 TCCGGGCTAAGTTTCAAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*
1352995 TCCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*
1353035 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
* *
1353075 TCCGGGCTAAGTTTCAAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*
1353115 TCCGGGCTAAGTTTCGAAGAGCATTCGTGC
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGC
1353145 AGAGCATTCG
Statistics
Matches: 257, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 257 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:1353150 original size:13 final size:13
Alignment explanation
Indices: 1353132--1353157 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1353122 TAAGTTTCGA
1353132 AGAGCATTCGTGC
1 AGAGCATTCGTGC
1353145 AGAGCATTCGTGC
1 AGAGCATTCGTGC
1353158 TAGTGATATA
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:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
AGAGCATTCGTGC
Found at i:1353186 original size:53 final size:53
Alignment explanation
Indices: 1353092--1353193 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
1353082 TAAGTTTCAA
* **** *
1353092 AGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTTCGAAGAGCATTCGTGC
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAACCCCGAAGAACATTCGTGC
*
1353145 AGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAACATTC
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAACCCCGAAGAACATTC
1353194 ATGCTGGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (53 bp):
AGAGCATTCGTGCTAGTGATATATCCGGGCTAAACCCCGAAGAACATTCGTGC
Found at i:1353208 original size:40 final size:40
Alignment explanation
Indices: 1353149--1353243 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
1353139 TCGTGCAGAG
* * *
1353149 CATTCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAA
1 CATTCATGCTGGTGATATATCCGGGCTAAACCCCGAAGAA
* *** *
1353189 CATTCATGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAG
1 CATTCATGCTGGTGATATATCCGGGCTAAACCCCGAAGAA
*
1353229 CAATCATGCTGGTGA
1 CATTCATGCTGGTGA
1353244 CGTGTATTCG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (40 bp):
CATTCATGCTGGTGATATATCCGGGCTAAACCCCGAAGAA
Found at i:1353211 original size:93 final size:93
Alignment explanation
Indices: 1353052--1353230 Score: 223
Period size: 93 Copynumber: 1.9 Consensus size: 93
1353042 TAAGTTCCGA
* **** * * *
1353052 AGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTTCAAAGAGCATTCGTGCTAGTGATGTATC
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAACCCCAAAGAACATTCATGCTAGTGATATATC
**
1353117 CGGGCTAAGTTTCGAAGAGCATTCGTGC
66 CGGGCTAAGTCCCGAAGAGCATTCGTGC
* * * *
1353145 AGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAACATTCATGCTGGTGTTATATC
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAACCCCAAAGAACATTCATGCTAGTGATATATC
*
1353210 CGGGCTAGGTCCCGAAGAGCA
66 CGGGCTAAGTCCCGAAGAGCA
1353231 ATCATGCTGG
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (93 bp):
AGAGCATTCGTGCTAGTGATATATCCGGGCTAAACCCCAAAGAACATTCATGCTAGTGATATATC
CGGGCTAAGTCCCGAAGAGCATTCGTGC
Found at i:1366212 original size:25 final size:23
Alignment explanation
Indices: 1366156--1366213 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
1366146 ATTTGGGCTA
1366156 TAACAGGAAGCTCATAAGAGCCT
1 TAACAGGAAGCTCATAAGAGCCT
* * *
1366179 AAATTAGGAAGCTCATAAAGAGCTTT
1 TAA-CAGGAAGCTCAT-AAGAGC-CT
1366205 TAACAGGAA
1 TAACAGGAA
1366214 ACTCCAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 2 0.07
24 11 0.41
25 11 0.41
26 3 0.11
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.21
Consensus pattern (23 bp):
TAACAGGAAGCTCATAAGAGCCT
Found at i:1368192 original size:19 final size:20
Alignment explanation
Indices: 1368154--1368192 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1368144 TGATTTTTGG
* *
1368154 GAAAATTAATTTTGATCAAA
1 GAAAATTAATATTAATCAAA
1368174 GAAAATTAA-ATTAATCAAA
1 GAAAATTAATATTAATCAAA
1368193 TTGATTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (20 bp):
GAAAATTAATATTAATCAAA
Found at i:1372189 original size:27 final size:27
Alignment explanation
Indices: 1372159--1372225 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
1372149 GACTACCCCA
* * *
1372159 TGTTTAGTGTCTGGGCAGACCA-CCTCG
1 TGTTTACTGTCTCGACAGACCACCCT-G
*
1372186 TGTTTACTGTCCCGACAGACCACCCTG
1 TGTTTACTGTCTCGACAGACCACCCTG
1372213 TGTTTACTGTCTC
1 TGTTTACTGTCTC
1372226 TGTGAACTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 31 0.91
28 3 0.09
ACGTcount: A:0.15, C:0.30, G:0.22, T:0.33
Consensus pattern (27 bp):
TGTTTACTGTCTCGACAGACCACCCTG
Found at i:1380273 original size:22 final size:22
Alignment explanation
Indices: 1380248--1380290 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1380238 TATATATTGT
1380248 AATAATTAGATATAAA-ATAAAA
1 AATAATTA-ATATAAATATAAAA
1380270 AATAATTAATATAAATATAAA
1 AATAATTAATATAAATATAAA
1380291 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAATTAATATAAATATAAAA
Found at i:1380698 original size:12 final size:12
Alignment explanation
Indices: 1380683--1380720 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1380673 ATATTTAATA
1380683 TTTATATAATTT
1 TTTATATAATTT
1380695 TTTATA-AATTT
1 TTTATATAATTT
1380706 ATTTA-ATAATTT
1 -TTTATATAATTT
1380718 TTT
1 TTT
1380721 TGCACGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTATATAATTT
Found at i:1389314 original size:40 final size:42
Alignment explanation
Indices: 1389262--1389360 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 42
1389252 GTTTATTTAA
* *
1389262 AAAAACTCCGCTAAA-A-GTGACCTTTAGCGGCGCTTCTCCC
1 AAAAACGCCGCTAAAGACATGACCTTTAGCGGCGCTTCTCCC
* *
1389302 ACAAACGCCGCTAAAGATCATTACCTTTAGCGGCGCTTCTCCC
1 AAAAACGCCGCTAAAGA-CATGACCTTTAGCGGCGCTTCTCCC
* *
1389345 AAAAATGTCGCTAAAG
1 AAAAACGCCGCTAAAG
1389361 GTCATAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 13 0.27
41 1 0.02
43 35 0.71
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACATGACCTTTAGCGGCGCTTCTCCC
Found at i:1389331 original size:43 final size:43
Alignment explanation
Indices: 1389281--1389365 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
1389271 GCTAAAAGTG
*
1389281 ACCTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGATCATT
1 ACCTTTAGCGGCGCTTCTCCCAAAAACGCCGCTAAAGATCATT
* * *
1389324 ACCTTTAGCGGCGCTTCTCCCAAAAATGTCGCTAAAGGTCAT
1 ACCTTTAGCGGCGCTTCTCCCAAAAACGCCGCTAAAGATCAT
1389366 AAAATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.25
Consensus pattern (43 bp):
ACCTTTAGCGGCGCTTCTCCCAAAAACGCCGCTAAAGATCATT
Found at i:1391080 original size:29 final size:30
Alignment explanation
Indices: 1391038--1391099 Score: 117
Period size: 29 Copynumber: 2.1 Consensus size: 30
1391028 TTTTATACCG
1391038 GAATAACATTGACTACATTAAAAAATT-CT
1 GAATAACATTGACTACATTAAAAAATTGCT
1391067 GAATAACATTGACTACATTAAAAAATTGCT
1 GAATAACATTGACTACATTAAAAAATTGCT
1391097 GAA
1 GAA
1391100 ATCCAGACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (30 bp):
GAATAACATTGACTACATTAAAAAATTGCT
Found at i:1394547 original size:6 final size:7
Alignment explanation
Indices: 1394465--1394564 Score: 78
Period size: 7 Copynumber: 14.0 Consensus size: 7
1394455 ACTAATTAAT
1394465 CTAAACC
1 CTAAACC
1394472 CTAAACC
1 CTAAACC
*
1394479 TCTTAACTC
1 -CTAAAC-C
*
1394488 CT-ATCC
1 CTAAACC
*
1394494 CATAAACA
1 C-TAAACC
*
1394502 CTAAACA
1 CTAAACC
*
1394509 CTTAACC
1 CTAAACC
1394516 CTAAACC
1 CTAAACC
* *
1394523 CTTACCC
1 CTAAACC
*
1394530 CTTAAACT
1 C-TAAACC
1394538 CT-AACC
1 CTAAACC
1394544 CTAAACC
1 CTAAACC
1394551 CTAAACC
1 CTAAACC
1394558 CTAAACC
1 CTAAACC
1394565 ATAATATCTA
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
6 7 0.09
7 52 0.70
8 14 0.19
9 1 0.01
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:1394551 original size:35 final size:36
Alignment explanation
Indices: 1394465--1394559 Score: 104
Period size: 35 Copynumber: 2.6 Consensus size: 36
1394455 ACTAATTAAT
* *
1394465 CTAAACCCTAAACCTCTTAACTCC-TATCCCATAAACA
1 CTAAACCCTAAACC-CTAAAC-CCTTACCCCATAAACA
* * * *
1394502 CTAAACACTTAACCCTAAACCCTTACCCCTTAAACT
1 CTAAACCCTAAACCCTAAACCCTTACCCCATAAACA
1394538 CT-AACCCTAAACCCTAAACCCT
1 CTAAACCCTAAACCCTAAACCCT
1394560 AAACCATAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 20 0.41
36 17 0.35
37 12 0.24
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (36 bp):
CTAAACCCTAAACCCTAAACCCTTACCCCATAAACA
Found at i:1394559 original size:28 final size:27
Alignment explanation
Indices: 1394465--1394563 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 27
1394455 ACTAATTAAT
*
1394465 CTAAACCCTAAACCTCTTAACTCCT-ATCC
1 CTAAACCCTAAA-CTC-TAAC-CCTAAACC
* *
1394494 CATAAACACTAAACACTTAACCCTAAACC
1 C-TAAACCCTAAACTC-TAACCCTAAACC
* *
1394523 CTTACCCCTTAAACTCTAACCCTAAACC
1 CTAAACCC-TAAACTCTAACCCTAAACC
1394551 CTAAACCCTAAAC
1 CTAAACCCTAAAC
1394564 CATAATATCT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
27 5 0.09
28 25 0.43
29 18 0.31
30 10 0.17
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.22
Consensus pattern (27 bp):
CTAAACCCTAAACTCTAACCCTAAACC
Found at i:1394660 original size:14 final size:14
Alignment explanation
Indices: 1394617--1394668 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1394607 AATTAACTCC
* *
1394617 TAAACCTTAAACCC
1 TAAACCATAAACCT
* * *
1394631 TAAATCATATATCT
1 TAAACCATAAACCT
1394645 TAAACCATAAACCT
1 TAAACCATAAACCT
*
1394659 TAAACTATAA
1 TAAACCATAA
1394669 TGATAATTAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:1395026 original size:41 final size:41
Alignment explanation
Indices: 1394833--1395034 Score: 237
Period size: 41 Copynumber: 4.9 Consensus size: 41
1394823 GTTATATGAC
* * *
1394833 TTTTAGCGGCGTTTTAGCAAAAGCGTCGCTAATACTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
1394874 TTTTAGCGGCGCTTTACCAAAAGCGCAGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * **
1394915 TTTTAGCGGCGCTTTACCGAAAGCGTAGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
** *
1394956 TTTTAGCGGCGTTTTACCGAAAA-ATCCGCTATTGCTCT-GT
1 TTTTAGCGGCGTTTTACC-AAAAGCGCCGCTAATGCTCTGGT
* * *
1394996 TTTTAGCGGCGTTTTAGCAAAAAACGCCGCTATTGCTCT
1 TTTTAGCGGCGTTTTA-CCAAAAGCGCCGCTAATGCTCT
1395035 ATATTTTACA
Statistics
Matches: 141, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 22 0.16
41 116 0.82
42 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.33
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:1398802 original size:24 final size:24
Alignment explanation
Indices: 1398768--1398836 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
1398758 TTTCTAGAAA
* *
1398768 ATTTAATATTTATTAGCGTAATAT
1 ATTTAACATTTATTAGCATAATAT
* *
1398792 ATTTAGCATTTATTAACATAATAT
1 ATTTAACATTTATTAGCATAATAT
*
1398816 ATTTAACATTTATTAGTATAA
1 ATTTAACATTTATTAGCATAA
1398837 AAATATTTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTTAACATTTATTAGCATAATAT
Found at i:1400465 original size:10 final size:10
Alignment explanation
Indices: 1400438--1400476 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1400428 TTAAATTCTA
1400438 AAAGATAAAT
1 AAAGATAAAT
1400448 ACAA-ATAAAT
1 A-AAGATAAAT
*
1400458 AAAGATAATT
1 AAAGATAAAT
1400468 AAAGATAAA
1 AAAGATAAA
1400477 CGATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:1400520 original size:13 final size:12
Alignment explanation
Indices: 1400504--1400536 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1400494 ATTAAATCTA
1400504 AATAATAATCCTT
1 AATAATAATCC-T
1400517 AATAATAATCCT
1 AATAATAATCCT
1400529 AAT-ATAAT
1 AATAATAAT
1400537 TAAACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAATAATCCT
Found at i:1402089 original size:19 final size:19
Alignment explanation
Indices: 1402037--1402089 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1402027 GAAGAATAGT
*
1402037 AAATAATAAAAT-AAAGTA
1 AAATAATAAAATAAAAGAA
*
1402055 AAATAA-AAAAGAAAAAGAA
1 AAATAATAAAA-TAAAAGAA
*
1402074 AAATAATAAATTAAAA
1 AAATAATAAAATAAAA
1402090 TAAATTAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 15 0.54
20 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (19 bp):
AAATAATAAAATAAAAGAA
Found at i:1403049 original size:25 final size:25
Alignment explanation
Indices: 1402989--1403039 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1402979 TCCAGTTAGA
1402989 AACATAGTCTACTCAAGAATTATAT
1 AACATAGTCTACTCAAGAATTATAT
1403014 AACATAGTCTACTCAAGAATTATAT
1 AACATAGTCTACTCAAGAATTATAT
1403039 A
1 A
1403040 TACGTTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (25 bp):
AACATAGTCTACTCAAGAATTATAT
Found at i:1409783 original size:10 final size:10
Alignment explanation
Indices: 1409756--1409795 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1409746 TTAAATTCTA
1409756 AAAGATAAAT
1 AAAGATAAAT
1409766 ACAA-ATAAAT
1 A-AAGATAAAT
*
1409776 AAAGATAATT
1 AAAGATAAAT
1409786 AAAGATAAAT
1 AAAGATAAAT
1409796 GGTAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:1409838 original size:13 final size:12
Alignment explanation
Indices: 1409822--1409854 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1409812 ATTAAATCTA
1409822 AATAATAATCCTT
1 AATAATAATCC-T
1409835 AATAATAATCCT
1 AATAATAATCCT
1409847 AAT-ATAAT
1 AATAATAAT
1409855 TAAACACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAATAATCCT
Found at i:1411980 original size:21 final size:21
Alignment explanation
Indices: 1411956--1412005 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 21
1411946 TATGAAAAGA
1411956 AATAA-TAAATATATTTATACT
1 AATAACTAAATATA-TTATACT
1411977 AATAAATGCTAAATATATTATACT
1 AAT-AA--CTAAATATATTATACT
1412001 AATAA
1 AATAA
1412006 AAAGCTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.12
22 2 0.08
23 2 0.08
24 10 0.40
25 8 0.32
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (21 bp):
AATAACTAAATATATTATACT
Found at i:1412002 original size:24 final size:26
Alignment explanation
Indices: 1411961--1412015 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
1411951 AAAGAAATAA
*
1411961 TAAATATATTTATACTAAT-AAATGC
1 TAAATATATTTATACTAATAAAAAGC
1411986 TAAATATA-TTATACTAATAAAAAGC
1 TAAATATATTTATACTAATAAAAAGC
1412011 TAAAT
1 TAAAT
1412016 CTTCTAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (26 bp):
TAAATATATTTATACTAATAAAAAGC
Found at i:1421500 original size:25 final size:23
Alignment explanation
Indices: 1421451--1421500 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1421441 AATAACAAAG
** *
1421451 ATATTTATACTAATAAATGCTAA
1 ATATTTATACTAATAAAAACCAA
1421474 ATATATTATACTAATAAAAAACCAA
1 ATAT-TTATACTAAT-AAAAACCAA
1421499 AT
1 AT
1421501 CTTCTAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.18
24 10 0.45
25 8 0.36
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (23 bp):
ATATTTATACTAATAAAAACCAA
Found at i:1424236 original size:16 final size:17
Alignment explanation
Indices: 1424215--1424254 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1424205 ATTTGTCAAA
1424215 AAAATAAA-AATAAAA-T
1 AAAATAAAGAA-AAAATT
1424231 AAAATAAAGAAAAAATT
1 AAAATAAAGAAAAAATT
1424248 AAAATAA
1 AAAATAA
1424255 CACACAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAATAAAGAAAAAATT
Found at i:1429653 original size:46 final size:48
Alignment explanation
Indices: 1429549--1429668 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
1429539 TGTCTTCGAC
** * * *
1429549 ATGGACTTACATGAATTATTCTTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
* * *
1429597 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATA-A-CTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
*
1429643 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
1429669 CTGTCCTGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 27 0.44
47 1 0.02
48 34 0.55
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
Found at i:1431370 original size:28 final size:28
Alignment explanation
Indices: 1431338--1431463 Score: 123
Period size: 29 Copynumber: 4.4 Consensus size: 28
1431328 TACATACATG
**
1431338 CATATGGCCCA-CTAGGTCCAATCTCATT
1 CATATGGCCCATC-AGACCCAATCTCATT
* * *
1431366 TATATGGCCCATCCGGCCCAAT-TCATGTT
1 CATATGGCCCATCAGACCCAATCTCA--TT
*
1431395 CATATGGCCCATCAGACCCAATTCACATT
1 CATATGGCCCATCAGACCCAA-TCTCATT
1431424 CATATGGCCCA-CTAGACCCAATCTCATT
1 CATATGGCCCATC-AGACCCAATCTCATT
*
1431452 CACATGGCCCAT
1 CATATGGCCCAT
1431464 TCGGCCCAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
27 3 0.04
28 34 0.41
29 42 0.51
30 1 0.01
31 2 0.02
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.26
Consensus pattern (28 bp):
CATATGGCCCATCAGACCCAATCTCATT
Found at i:1431471 original size:28 final size:28
Alignment explanation
Indices: 1431338--1431472 Score: 123
Period size: 28 Copynumber: 4.8 Consensus size: 28
1431328 TACATACATG
* *
1431338 CATATGGCCCACTAGGTCCAATCTCATT
1 CATATGGCCCACTCGGCCCAATCTCATT
*
1431366 TATATGGCCCA-TCCGGCCCAAT-TCATGTT
1 CATATGGCCCACT-CGGCCCAATCTCA--TT
* *
1431395 CATATGGCCCA-TCAGACCCAATTCACATT
1 CATATGGCCCACTC-GGCCCAA-TCTCATT
* *
1431424 CATATGGCCCACTAGACCCAATCTCATT
1 CATATGGCCCACTCGGCCCAATCTCATT
* *
1431452 CACATGGCCCATTCGGCCCAA
1 CATATGGCCCACTCGGCCCAA
1431473 ATCACATTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
27 4 0.05
28 41 0.47
29 39 0.44
30 2 0.02
31 2 0.02
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.25
Consensus pattern (28 bp):
CATATGGCCCACTCGGCCCAATCTCATT
Found at i:1440261 original size:28 final size:29
Alignment explanation
Indices: 1440173--1440305 Score: 114
Period size: 28 Copynumber: 4.7 Consensus size: 29
1440163 ATGGACCACT
* * *
1440173 AGGCCCAA-TCTCATTTATATGGCCCATC
1 AGGCCCAATTCACATTCATATGGCCCATA
* ** *
1440201 CGGCTAAATTCACATTCATATGGCCTATA
1 AGGCCCAATTCACATTCATATGGCCCATA
*
1440230 AGG-CCAATTCACATTCATATGACCCACT-
1 AGGCCCAATTCACATTCATATGGCCCA-TA
* * *
1440258 AGGCCCAA-TCTCATTCACATGGCCCATC
1 AGGCCCAATTCACATTCATATGGCCCATA
*
1440286 AGGCCCAAATCACATT-ATAT
1 AGGCCCAATTCACATTCATAT
1440306 TCATGGTCAC
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
27 1 0.01
28 53 0.64
29 29 0.35
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (29 bp):
AGGCCCAATTCACATTCATATGGCCCATA
Found at i:1453698 original size:93 final size:93
Alignment explanation
Indices: 1453586--1453757 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
1453576 GCCCATAAGT
* *
1453586 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1453651 CGAGCTT-GGATGCCTAGTTACATCTCTC
66 CGAG-TTCGGATGCCTAGTTACATCTCTC
*
1453679 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1453744 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
1453758 CAAATATCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCTC
Found at i:1453753 original size:46 final size:46
Alignment explanation
Indices: 1453578--1453753 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
1453568 TGTAACCCGC
* * *
1453578 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
1453624 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGC-A--T
* ***
1453670 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1453717 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1453754 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 69 0.63
47 31 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:1457272 original size:56 final size:57
Alignment explanation
Indices: 1457169--1457281 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
1457159 ACTTAATAAG
1457169 TATAAGAAAAAAATAATAAAAACAACCAAAAACAACAATAAACATAAACATAAACAT
1 TATAAGAAAAAAATAATAAAAACAACCAAAAACAACAATAAACATAAACATAAACAT
1457226 TATAAGAAAAAAATAATAAAAACAACCAAAAACAAC-ATAAACATAAACATAAACAT
1 TATAAGAAAAAAATAATAAAAACAACCAAAAACAACAATAAACATAAACATAAACAT
1457282 AAACATAAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 20 0.36
57 36 0.64
ACGTcount: A:0.70, C:0.14, G:0.02, T:0.14
Consensus pattern (57 bp):
TATAAGAAAAAAATAATAAAAACAACCAAAAACAACAATAAACATAAACATAAACAT
Found at i:1457315 original size:6 final size:6
Alignment explanation
Indices: 1457259--1457314 Score: 103
Period size: 6 Copynumber: 9.3 Consensus size: 6
1457249 AACCAAAAAC
1457259 AACATA AACATA AACATA AACATA AACATA AACATA AACATA AACATA
1 AACATA AACATA AACATA AACATA AACATA AACATA AACATA AACATA
*
1457307 AAAATA AA
1 AACATA AA
1457315 ACAAATAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (6 bp):
AACATA
Found at i:1463182 original size:46 final size:47
Alignment explanation
Indices: 1462956--1463182 Score: 175
Period size: 50 Copynumber: 4.8 Consensus size: 47
1462946 TAATGCCAAT
* * * *
1462956 GCCATGTCCCAGACATGGTCTTACACTTGC-T-CATCCATC-AAGTCGAT
1 GCCATGTCCCAGACAT-GTCTTACACTGGCTTACAT-C-TCGTAGCCGAC
* ** **
1463003 GCCATGTCCCAAACATGGTCTTACACTAAC-TATCGAAATCG-AGGCCGAC
1 GCCATGTCCCAGACAT-GTCTTACACTGGCTTA-C-ATCTCGTA-GCCGAC
* * *
1463052 GCCATGTCCTAGACATGTTCTTAAACTGGCTCTCACATCTCTGT-GCCGAT
1 GCCATGTCCCAGACATG-TCTTACACTGGCT-T-ACATCTC-GTAGCCGAC
1463102 GCCATGTCCCAGACATGGTCTTACACTGGC--ACATCTCGTAGCCGAC
1 GCCATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGTAGCCGAC
1463148 G-CATGTCCCAGACATGTCTTACACTGGCTTACATC
1 GCCATGTCCCAGACATGTCTTACACTGGCTTACATC
1463183 ACGAGGCTGA
Statistics
Matches: 147, Mismatches: 18, Indels: 31
0.75 0.09 0.16
Matches are distributed among these distances:
44 13 0.09
45 16 0.11
46 18 0.12
47 28 0.19
48 4 0.03
49 28 0.19
50 35 0.24
51 4 0.03
52 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.26
Consensus pattern (47 bp):
GCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTAGCCGAC
Found at i:1468514 original size:18 final size:18
Alignment explanation
Indices: 1468491--1468526 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1468481 TTGTTGAGCT
1468491 GTCAGTAGTCTATGCACA
1 GTCAGTAGTCTATGCACA
1468509 GTCAGTAGTCTATGCACA
1 GTCAGTAGTCTATGCACA
1468527 ATCTCATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
GTCAGTAGTCTATGCACA
Found at i:1469481 original size:90 final size:92
Alignment explanation
Indices: 1469319--1469536 Score: 296
Period size: 90 Copynumber: 2.4 Consensus size: 92
1469309 TTTGACATGA
* * * * * *
1469319 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGCTGTCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTATCACGCTGCCATGGTATCTTTCAAC
* * *
1469384 CATGGTCTTATTCTTTTCATGTCACGT
66 CATGGTCTTATACATTTCATATCACGT
* *
1469411 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTC-ATCACGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTATCACGCTGCCATGGTATCTTTCAAC
*
1469474 CATGGTCTTATACATTTCATATCATGT
66 CATGGTCTTATACATTTCATATCACGT
* *
1469501 TGTCATGGTATCTTTCAACCATGGTCTTACACATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTT
1469537 CATTTCAGAG
Statistics
Matches: 110, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
90 74 0.67
91 8 0.07
92 28 0.25
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTATCACGCTGCCATGGTATCTTTCAAC
CATGGTCTTATACATTTCATATCACGT
Found at i:1469492 original size:21 final size:21
Alignment explanation
Indices: 1469467--1469538 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
1469457 CCATGGTATC
1469467 TTTCAACCATGGTCTTATACA
1 TTTCAACCATGGTCTTATACA
*
1469488 TTTCATATCATGTTGTCATGGTAT-C-
1 TTTCA-ACCATG--GTC-T--TATACA
*
1469513 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTATACA
1469534 TTTCA
1 TTTCA
1469539 TTTCAGAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.20
24 8 0.20
25 6 0.15
26 1 0.03
27 3 0.08
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (21 bp):
TTTCAACCATGGTCTTATACA
Found at i:1469537 original size:46 final size:46
Alignment explanation
Indices: 1469319--1469539 Score: 268
Period size: 46 Copynumber: 4.8 Consensus size: 46
1469309 TTTGACATGA
* * * * * * *
1469319 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCACGT
* * *
1469365 TGTCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
*
1469411 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTC--ATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
* *
1469455 TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
* **
1469501 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
1469540 TTCAGAGAGC
Statistics
Matches: 157, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
44 41 0.26
45 4 0.03
46 112 0.71
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
Found at i:1475153 original size:51 final size:49
Alignment explanation
Indices: 1475079--1475211 Score: 158
Period size: 51 Copynumber: 2.7 Consensus size: 49
1475069 TATTGTGAGG
* * *
1475079 TCACATGTGTAGTACTAACTGCAGGCTACTATGCGTACCCAAAAACTGTGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAA-T-TGA
* * ** * *
1475130 TCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAATTGA
*
1475179 TCACGTGTGTAGTACTAAGTGCAAGCTACTACG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACG
1475212 TGCATAGGAT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 33 0.46
50 1 0.01
51 37 0.52
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAATTGA
Found at i:1475207 original size:49 final size:49
Alignment explanation
Indices: 1475077--1475258 Score: 193
Period size: 49 Copynumber: 3.7 Consensus size: 49
1475067 TCTATTGTGA
* * * ** *
1475077 GGTCACATGTGTAGTACTAACTGCAGGCTACTATGCGTACCCAAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-T
* **
1475128 GATCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * * ** *
1475177 GGTCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGCATAGGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
1475226 GGTCGCATGTGTAGTACTATGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
1475259 TGCGTACCAA
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 72 0.65
50 1 0.01
51 38 0.34
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:1478310 original size:30 final size:30
Alignment explanation
Indices: 1478274--1478342 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
1478264 TATCGTATCT
*
1478274 TGGGTTTCTTTA-CTCTGGGTTTCTTTATTC
1 TGGGTTTCTTTATCT-TGGATTTCTTTATTC
*
1478304 TGGGTTTCTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTTATCTTGGATTTCTTTATTC
*
1478334 -GGTTTTCTT
1 TGGGTTTCTT
1478343 GTTATCTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.21
30 25 0.74
31 2 0.06
ACGTcount: A:0.07, C:0.16, G:0.19, T:0.58
Consensus pattern (30 bp):
TGGGTTTCTTTATCTTGGATTTCTTTATTC
Found at i:1478342 original size:14 final size:15
Alignment explanation
Indices: 1478274--1478342 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
1478264 TATCGTATCT
*
1478274 TGGGTTTCTTTACTC
1 TGGGTTTCTTTATTC
1478289 TGGGTTTCTTTATTC
1 TGGGTTTCTTTATTC
*
1478304 TGGGTTTCTCTA-TC
1 TGGGTTTCTTTATTC
*
1478318 TTGGATTTCTTTATTC
1 -TGGGTTTCTTTATTC
*
1478334 -GGTTTTCTT
1 TGGGTTTCTT
1478343 GTTATCTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.21
15 35 0.74
16 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.19, T:0.58
Consensus pattern (15 bp):
TGGGTTTCTTTATTC
Found at i:1480648 original size:49 final size:49
Alignment explanation
Indices: 1480482--1480706 Score: 288
Period size: 49 Copynumber: 4.5 Consensus size: 49
1480472 TGAGGTCGCA
* * * * * *
1480482 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACG
* * ** *
1480533 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCACG
1480583 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* * *
1480632 TGTGTAGTACTAAGTGCAGGCTACTACGAGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
*
1480681 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
1480707 TGCGTACCAG
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 78 0.50
50 45 0.29
51 33 0.21
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
Found at i:1485360 original size:240 final size:241
Alignment explanation
Indices: 1484667--1485393 Score: 1323
Period size: 241 Copynumber: 3.0 Consensus size: 241
1484657 ATGAATTAAT
* *
1484667 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACATT
1 TTTATTACCATGTAGCTTGCTTGTTCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
1484732 ATTTTAAATATTTTAAAGATTCAAAGTATATAAGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
1484797 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
*
1484862 AAAAAGAC-TTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTTG-AAAAAGTTCTATCGATCTCATTTACTATTGAATA
* * *
1484908 TTTATTACCATGTAGCTTGCTTGTTCATTAAAATTTCAACAGTAGCTGACCTTCTCTCTAACCTT
1 TTTATTACCATGTAGCTTGCTTGTTCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
1484973 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGAGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
1485038 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
*
1485103 AAAAAGACTTGGAAAAAGTTCTATCGATCTCATTTACTATTGAATA
196 AAAAAGACTTTGAAAAAGTTCTATCGATCTCATTTACTATTGAATA
*
1485149 TTTATTACCATGTAGCTTGCTTGTTCATTAAAATTACACCAATAGCTGACCTTC-CTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTTCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1485213 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
1485278 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
* *
1485343 AAAAAAACTTTGAAAAAGTTATATCGATCTCATTTACTATTGAATA
196 AAAAAGACTTTGAAAAAGTTCTATCGATCTCATTTACTATTGAATA
1485389 TTTAT
1 TTTAT
1485394 ATAACCTTAA
Statistics
Matches: 468, Mismatches: 17, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
240 186 0.40
241 280 0.60
242 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTTCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
AAAAAGACTTTGAAAAAGTTCTATCGATCTCATTTACTATTGAATA
Done.