Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009350.1 Hibiscus syriacus cultivar Beakdansim tig00113145_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2139524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1058212 original size:21 final size:21
Alignment explanation
Indices: 1058157--1058220 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1058147 GATTCCCCTG
1058157 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTT-CCC-TCA
**
1058180 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
* *
1058201 TGGGGGGGATCGATTCCCTC
1 TGGGGGGAATCGGTTCCCTC
1058221 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.25, G:0.36, T:0.23
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:1063982 original size:21 final size:21
Alignment explanation
Indices: 1063956--1064009 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1063946 CCGTTGATCA
1063956 GGGGGAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCTAT
1063977 GGGGGAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCTAT
1063998 GGGGGAATCGGT
1 GGGGGAATCGGT
1064010 TCCCTCTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.24, G:0.39, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTAT
Found at i:1066555 original size:20 final size:20
Alignment explanation
Indices: 1066516--1066555 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1066506 TTTAATTGCG
*
1066516 AAAATTAAAAATTTTAAATT
1 AAAATTAAAAATATTAAATT
* *
1066536 AAAATTTAAAATATTCAATT
1 AAAATTAAAAATATTAAATT
1066556 CGAATTACTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTAAAAATATTAAATT
Found at i:1075539 original size:13 final size:13
Alignment explanation
Indices: 1075521--1075545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1075511 GAAGACGCTA
1075521 ATTTTTTTATTTC
1 ATTTTTTTATTTC
1075534 ATTTTTTTATTT
1 ATTTTTTTATTT
1075546 ATTATTATTT
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:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTTTTATTTC
Found at i:1077838 original size:26 final size:27
Alignment explanation
Indices: 1077786--1077843 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1077776 TAATTCTTTC
*
1077786 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
1077814 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
1077840 TTTT
1 TTTT
1077844 TTTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:1077845 original size:28 final size:28
Alignment explanation
Indices: 1077786--1077846 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
1077776 TAATTCTTTC
*
1077786 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATTTATATATATACTTATTA
* *
1077814 TTTTCATAATATTTATATGTATA-TTATTT
1 TTTTCA-AA-ATTTATATATATACTTATTA
1077843 TTTT
1 TTTT
1077847 ATATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 11 0.39
30 11 0.39
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTCAAAATTTATATATATACTTATTA
Found at i:1088524 original size:23 final size:21
Alignment explanation
Indices: 1088492--1088558 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 21
1088482 TATTATGCTT
1088492 GAAG-AAGAAAGAAAGAAAAAA
1 GAAGAAAGAAA-AAAGAAAAAA
*
1088513 GAAGAAAAGAAAAAATGAAGAAA
1 GAAG-AAAGAAAAAA-GAAAAAA
1088536 GAAGAAAGAAAAAAAAGAAAAAA
1 GAAGAAAG--AAAAAAGAAAAAA
1088559 TGTTGAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 4 0.10
22 7 0.18
23 22 0.56
24 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (21 bp):
GAAGAAAGAAAAAAGAAAAAA
Found at i:1088535 original size:30 final size:31
Alignment explanation
Indices: 1088500--1088560 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1088490 TTGAAGAAGA
*
1088500 AAGAAAGAAAAAAG-AAGAAAAGAAAAAATG
1 AAGAAAGAAAAAAGAAAAAAAAGAAAAAATG
*
1088530 AAGAAAGAAGAAAGAAAAAAAAGAAAAAATG
1 AAGAAAGAAAAAAGAAAAAAAAGAAAAAATG
1088561 TTGAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (31 bp):
AAGAAAGAAAAAAGAAAAAAAAGAAAAAATG
Found at i:1088558 original size:7 final size:7
Alignment explanation
Indices: 1088496--1088549 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
1088486 ATGCTTGAAG
1088496 AAGAAAGA
1 AAGAAA-A
1088504 AAGAAAA
1 AAGAAAA
1088511 AAGAAGAA
1 AAGAA-AA
1088519 AAGAAAA
1 AAGAAAA
*
1088526 AATGAAGA
1 AA-GAAAA
*
1088534 AAGAAGA
1 AAGAAAA
1088541 AAGAAAA
1 AAGAAAA
1088548 AA
1 AA
1088550 AAGAAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
7 23 0.55
8 19 0.45
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (7 bp):
AAGAAAA
Found at i:1088959 original size:18 final size:18
Alignment explanation
Indices: 1088932--1088966 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1088922 CAAGTTTATC
*
1088932 TTTTTGAAATTCAATTTA
1 TTTTTAAAATTCAATTTA
*
1088950 TTTTTAAAATTTAATTT
1 TTTTTAAAATTCAATTT
1088967 GTTTCACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTTAAAATTCAATTTA
Found at i:1090687 original size:23 final size:23
Alignment explanation
Indices: 1090661--1090706 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1090651 GGTTCTACGC
**
1090661 GGTCCTTTGGGATAAATCTATGT
1 GGTCCTTCAGGATAAATCTATGT
1090684 GGTCCTTCAGGATAAATCTATGT
1 GGTCCTTCAGGATAAATCTATGT
1090707 TTTCATTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (23 bp):
GGTCCTTCAGGATAAATCTATGT
Found at i:1090715 original size:23 final size:23
Alignment explanation
Indices: 1090670--1090716 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1090660 CGGTCCTTTG
*
1090670 GGATAAATCTATGTGGTCCTTCA
1 GGATAAATCTATGTGGTCATTCA
**
1090693 GGATAAATCTATGTTTTCATTCA
1 GGATAAATCTATGTGGTCATTCA
1090716 G
1 G
1090717 AACAAATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (23 bp):
GGATAAATCTATGTGGTCATTCA
Found at i:1090723 original size:23 final size:23
Alignment explanation
Indices: 1090674--1090723 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1090664 CCTTTGGGAT
* * *
1090674 AAATCTATGTGGTCCTTCAGGAT
1 AAATCTATGTGGTCATTCAGAAC
**
1090697 AAATCTATGTTTTCATTCAGAAC
1 AAATCTATGTGGTCATTCAGAAC
1090720 AAAT
1 AAAT
1090724 TCTACGCGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (23 bp):
AAATCTATGTGGTCATTCAGAAC
Found at i:1091217 original size:2 final size:2
Alignment explanation
Indices: 1091210--1091238 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1091200 ATTTTAAGTG
1091210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1091239 CAAGTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1097638 original size:24 final size:24
Alignment explanation
Indices: 1097606--1097652 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1097596 GGGAAAAATC
*
1097606 TATGTGGTCATTCGAGACAAATTA
1 TATGCGGTCATTCGAGACAAATTA
* *
1097630 TATGCGGTCCTTCGAGATAAATT
1 TATGCGGTCATTCGAGACAAATT
1097653 CTACGTGGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (24 bp):
TATGCGGTCATTCGAGACAAATTA
Found at i:1099022 original size:73 final size:74
Alignment explanation
Indices: 1098928--1099082 Score: 178
Period size: 73 Copynumber: 2.1 Consensus size: 74
1098918 TACTTGATGC
** * * *
1098928 TTGAATTC--TTTGAACTTTCATAGCTTATTTTTCTTCCTTGTCTTGATATAGA-AGGAACAATA
1 TTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCCTTGTCTTGATAT-GATAGGAACAATA
1098990 A-TCCTTTG-T
65 AGT-CTTTGCT
* * *
1098999 TTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCTTTGTCTTGGTGTGATAGGAACAATAA
1 TTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCCTTGTCTTGATATGATAGGAACAATAA
1099064 GTCTTTGCT
66 GTCTTTGCT
1099073 TT-AATTCTTT
1 TTGAATTCTTT
1099083 CAATTATCAT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
71 8 0.11
72 2 0.03
73 57 0.80
74 4 0.06
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (74 bp):
TTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCCTTGTCTTGATATGATAGGAACAATAA
GTCTTTGCT
Found at i:1099590 original size:657 final size:656
Alignment explanation
Indices: 1098334--1101036 Score: 2595
Period size: 657 Copynumber: 4.2 Consensus size: 656
1098324 GTTACAAATG
* * * *
1098334 CTTTGTTTGAATTATTTTTGAACCATCATAGCCTATTATTCCT-TATTGTCTTGGTGTGATAGGA
1 CTTTGTTTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCT-TTGTCTTGGTGTGACAGGA
*
1098398 ACAATAA-TGCTTTGCTTCT-ATTATTTGAATTATCATGGTTTATTATTCCTCCTTGTCTTGATG
65 ACAATAAGT-CTTTGCTT-TAATTCTTTGAATTATCATGGTTTATTATTCCTCCTTGTCTTGATG
* * * * * *
1098461 TTGCAGGCAGTCTTGAATGTCATTTT-AT-TTTTTTACTTATTCTTTTCGGCATTGATAATTTCG
128 TTGCAGGGAATCTTGAATGT--TTTTCATATTTTTTACTTTTTCTTTTTGGTATTGATAATTTTG
* ** * *
1098524 ACGGT-GATGGTGTCTTTTGTGAGATCAACGGCTCTAATACCAGATAGTCT-GATAGATCTGAGG
191 A-TGTAGACAGTGTCTTTTGTGAGATCAACGACTCTAATACCGGATAGTCTAG-TAGATCTGAGG
* * * *
1098587 ATCGAGTGTTGAAATTGGTGTTTTTTTATTTAATAAAATTTATTTTTAAAAAATTTGTTAAAATA
254 ATCGAGTGTTGAAATT-GTGGTTTTTGATTTAAT--AA-TT-TTTTTAAAAAAATTATTAAAATA
* * *
1098652 AAACAGAAATGAGAAAACTGGGAGAATTTTGATTTAGAGAGAATTTTATTC---GAATA-GGAAA
314 AAA-TGAAATGAGAAAACTAGAAGAATTTTGATTTAGAGAGAATTTTATTCTTTGAA-AGGGAAA
* * *
1098713 ATTAGGTTGTGCCTTACAACATAGAATTAGAGCATTTTTATAAAGAGTTCCATCATCTTTTTACA
377 ATTAGGTTGTGCCTTACAACATAAAATTAGACCATTTTTATAAAGAGTTCCATCCTCTTTTTACA
* *
1098778 ATTTAGTTCCTACTAATGGAAATGAA--ACAAATTATACAATAATTCAAAAGATAATTCATAATA
442 ATTTAGTTCCAACTAATGAAAAT-AACTA-AAATTATACAATAATTCAAAAGATAATTCATAATA
* * *
1098841 GTTTGAAATGACAAAAGG-CTAAACAATAATTTTATATAATGCTCGTCCTTTTACATTATAATGA
505 GTTTGAAATAACAAAAGGACTAAACAATAATTTTATATGATGCTCGTTCTTTTACATTATAATG-
* * * * *
1098905 GAACTCCTTTTACTACTTGATGCTTGAATTCTTTGAACTTTCATAGCTTATTTTTCTTCCTTGTC
569 GAACACCTTTTACTACTTGATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTTGTC
1098970 TTGATATAGAAGGAACAATAATC
634 TTGATATAGAAGGAACAATAATC
*
1098993 CTTTGTTTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCTTTGTCTTGGTGTGATAGGAA
1 CTTTGTTTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCTTTGTCTTGGTGTGACAGGAA
* * * * *
1099058 CAATAAGTCTTTGCTTTAATTCTTTCAATTATCATGGTTTATTTTTTCTCCTGGTGTTGATGTTG
66 CAATAAGTCTTTGCTTTAATTCTTTGAATTATCATGGTTTATTATTCCTCCTTGTCTTGATGTTG
1099123 CAGGGAATCTTGAATGTTTTTCCATATTTTTTACTTTTTCTTTTTGGTATTGATAATTTTGATGT
131 CAGGGAATCTTGAATGTTTTT-CATATTTTTTACTTTTTCTTTTTGGTATTGATAATTTTGATGT
* ** * *
1099188 AGACAGTGTCTTTTGTGAGGTCAACGACTCTAATATTGGATAGTCTAGT-GAATCTGAGGGTTGA
195 AGACAGTGTCTTTTGTGAGATCAACGACTCTAATACCGGATAGTCTAGTAG-ATCTGAGGATCGA
1099252 GTGTTGAAATTAGTGGTTTTTGATTTAATAA-TTTTTTAAAAAAATTATTAAAATAAAATGAAAT
259 GTGTTGAAATT-GTGGTTTTTGATTTAATAATTTTTTTAAAAAAATTATTAAAATAAAATGAAAT
* *
1099316 GAGAAAACTAGAAGAATTTTGATTTAGAGAGAATTTTATTCTTTGAAAGGGGAAATTAGATTGTG
323 GAGAAAACTAGAAGAATTTTGATTTAGAGAGAATTTTATTCTTTGAAAGGGAAAATTAGGTTGTG
* *
1099381 CCTTACAACATAGAATTAGAACCA-TTTTATAGAGAGTTCCATCCTCTTTTTACAATTTAGTTCC
388 CCTTACAACATAAAATTAG-ACCATTTTTATAAAGAGTTCCATCCTCTTTTTACAATTTAGTTCC
* * *
1099445 AACTAATGGAAATAACTAAAATTATACAATAATTCAAAAGATAATTCATAATGGTTTGAAATGAC
452 AACTAATGAAAATAACTAAAATTATACAATAATTCAAAAGATAATTCATAATAGTTTGAAATAAC
* * * *
1099510 TAAA-GACTAAACAATAATTTTATATGATTCTCGTTCTTTTACATTATAATGCCAACACGTTTTA
517 AAAAGGACTAAACAATAATTTTATATGATGCTCGTTCTTTTACATTATAATG-GAACACCTTTTA
* * *
1099574 CTACTTGATGCTTGAATTCTTTGTACTATCATAGCTTACTGTTCTTCCTTGTCTTGATATAGAAG
581 CTACTTGATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTTGTCTTGATATAGAAG
1099639 GAACAATAATC
646 GAACAATAATC
* * *
1099650 CTTTGATTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCTTTGTCTTGGTGTAACATGAA
1 CTTTGTTTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCTTTGTCTTGGTGTGACAGGAA
* * * *
1099715 CAATAAGTATTTTCTTTAATTCTTTGAATTATCATGATTTATTATTCCTCTTTGTCTTGATGTTG
66 CAATAAGTCTTTGCTTTAATTCTTTGAATTATCATGGTTTATTATTCCTCCTTGTCTTGATGTTG
* * * * * * *
1099780 CAAGGAATCTTAAAAGATTTTTTAATTTTTTTTACTTTTACTTTTTGGTATTTGATAATTTTGAC
131 CAGGGAATCTTGAATG--TTTTTCATATTTTTTACTTTTTCTTTTTGGTA-TTGATAATTTTGAT
* * * * * *
1099845 ATAGATAGTGTCTTTTTTGAGATCCATGACTTTAATACCGGATAGTCT-G--G---TGA--ATC-
193 GTAGACAGTGTCTTTTGTGAGATCAACGACTCTAATACCGGATAGTCTAGTAGATCTGAGGATCG
* * ** *
1099901 -----TG--A--G-GG---TCG--------A--TTGTT-GCAAAATTATTAAAATAAAACTAAAA
258 AGTGTTGAAATTGTGGTTTTTGATTTAATAATTTTTTTAAAAAAATTATTAAAATAAAA-TGAAA
* * * *
1099942 TGAGAAAACTGGGAGAATTTTGATTTGGAGAGAATTTTATTCTTTG-AATGGAGAAATTAGGTTG
322 TGAGAAAACTAGAAGAATTTTGATTTAGAGAGAATTTTATTCTTTGAAAGGGA-AAATTAGGTTG
* * ** * * *
1100006 TGCCTTACAACATAAAATTAGAGCATTTTTATAAAAAGTTGTATCTTCTATTTACAATTTGGTTC
386 TGCCTTACAACATAAAATTAGACCATTTTTATAAAGAGTTCCATCCTCTTTTTACAATTTAGTTC
* * ** * * * *
1100071 CAGCTAACGAAAATTGGCTAAATTTAAACAATAATTC-AAAGAATATTTCATAATA-TTTCAAAT
451 CAACTAATGAAAA-TAACTAAAATTATACAATAATTCAAAAG-ATAATTCATAATAGTTTGAAAT
* * * **
1100134 AACAAAATG-CTAAACAATAATTTTATATGATGCTCGTTCTTTTGCATTATAATATGAATGCC-T
514 AACAAAAGGACTAAACAATAATTTTATATGATGCTCGTTCTTTTACATTATAAT-GGAACACCTT
* * * *
1100197 TT--TAC-T-ATGCTTGAATTCTTTGAACTATCATAGCTTAATATTCCTCATTGTCTTGGTGTAG
578 TTACTACTTGATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTTGTCTTGATATAG
* *
1100258 CAGGAACATTAATC
643 AAGGAACAATAATC
*
1100272 CTTTGTTTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTC-TTGTCTTGGTGTGGCAGGAA
1 CTTTGTTTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCTTTGTCTTGGTGTGACAGGAA
* * * * *
1100336 CAATAAGCCTTTGCTTCAATTGTTTGAAATATCATGGTTTATTATTTCTCCTTGTCTTGATGTTG
66 CAATAAGTCTTTGCTTTAATTCTTTGAATTATCATGGTTTATTATTCCTCCTTGTCTTGATGTTG
* * * *
1100401 CAGGGAATCTAT-CATGGTTTTTCATACTTTCTTTTTTA-TTTTTCCTCTCTGGTCTTGATAA--
131 CAGGGAATCT-TGAAT-GTTTTTCATA-----TTTTTTACTTTTT-CTTTTTGGTATTGATAATT
* * * * * *
1100462 -T-AT-CA-ACAGTG------GTG-G-T----G--TCT--TA-TGTGAGA-TCCA-TATATTTGA
188 TTGATGTAGACAGTGTCTTTTGTGAGATCAACGACTCTAATACCG-GATAGTCTAGTAGATCTGA
* * * ** *
1100504 AGACCGAGTGTTGAATTTTGTGGTTAGTGATTTAATATAATTTGTTTTGAAAAAATTATTAAAAA
252 GGATCGAGTGTTGAA-ATTGTGGTTTTTGATTT-A-ATAATTT-TTTTAAAAAAATTATT-AAAA
* * * * *
1100569 TAGAATTGAAATGAGAAAACTA-AGAGAATTTTGATTCAAAGAAAATTTTATTCTTT-AGATGGG
312 TA-AAATGAAATGAGAAAACTAGA-AGAATTTTGATTTAGAGAGAATTTTATTCTTTGA-AAGGG
* * ** * * *
1100632 AAAATTA-G--GTCCCTTACCACATAAAATTAGAACC-TTTTTATACTGAGCTCTATCCTCCTTT
374 AAAATTAGGTTGTGCCTTACAACATAAAATTAG-ACCATTTTTATAAAGAGTTCCATCCTCTTTT
* * * * ** * * *
1100693 TATAATTTGGTTTCAGCTAATGAAAATGGCTAAAGTTATACAAATATTTCAAAAGATAATTAATA
438 TACAATTTAGTTCCAACTAATGAAAATAACTAAAATTATAC-AATAATTCAAAAGATAATTCATA
* * * *
1100758 ATAGTTTGAAATAACAAAAGGA-TGAACAATAATTTTAT-T--TG-T-TTTTTTTTGCATTATAA
502 ATAGTTTGAAATAACAAAAGGACTAAACAATAATTTTATATGATGCTCGTTCTTTTACATTATAA
* *
1100817 TTGGAACACCTTTTACAACTTCATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTT
567 -TGGAACACCTTTTACTACTTGATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTT
* * * * *
1100882 ATCTTGGTGTAGCAGGAACAATAATG
631 GTCTTGATATAGAAGGAACAATAATC
* * * *
1100908 CTTTGCTTGAATTCTTTTTAAACTATCGTAGCTTACTATTCCTCTTTGTCTTGGTGTTG-CAGGA
1 CTTTGTTTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCTTTGTCTTGGTG-TGACAGGA
* * * * * * *
1100972 AAAATAA-TGATATGCTTCAATTCTTTGAATTGTCATGGTTTATTATTCCTCCTTATCTTAATGT
65 ACAATAAGT-CTTTGCTTTAATTCTTTGAATTATCATGGTTTATTATTCCTCCTTGTCTTGATGT
1101036 T
129 T
1101037 AAGAAAATAT
Statistics
Matches: 1726, Mismatches: 226, Indels: 206
0.80 0.10 0.10
Matches are distributed among these distances:
601 3 0.00
602 5 0.00
604 2 0.00
606 4 0.00
608 2 0.00
610 1 0.00
611 1 0.00
612 2 0.00
614 2 0.00
618 5 0.00
619 2 0.00
620 10 0.01
621 84 0.05
622 105 0.06
623 2 0.00
624 14 0.01
625 14 0.01
626 28 0.02
627 184 0.11
628 32 0.02
631 20 0.01
632 5 0.00
633 3 0.00
634 15 0.01
635 83 0.05
636 145 0.08
637 80 0.05
638 56 0.03
639 8 0.00
640 1 0.00
643 1 0.00
645 2 0.00
651 1 0.00
653 3 0.00
654 44 0.03
655 24 0.01
656 5 0.00
657 393 0.23
658 32 0.02
659 192 0.11
660 110 0.06
661 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (656 bp):
CTTTGTTTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTCTTTGTCTTGGTGTGACAGGAA
CAATAAGTCTTTGCTTTAATTCTTTGAATTATCATGGTTTATTATTCCTCCTTGTCTTGATGTTG
CAGGGAATCTTGAATGTTTTTCATATTTTTTACTTTTTCTTTTTGGTATTGATAATTTTGATGTA
GACAGTGTCTTTTGTGAGATCAACGACTCTAATACCGGATAGTCTAGTAGATCTGAGGATCGAGT
GTTGAAATTGTGGTTTTTGATTTAATAATTTTTTTAAAAAAATTATTAAAATAAAATGAAATGAG
AAAACTAGAAGAATTTTGATTTAGAGAGAATTTTATTCTTTGAAAGGGAAAATTAGGTTGTGCCT
TACAACATAAAATTAGACCATTTTTATAAAGAGTTCCATCCTCTTTTTACAATTTAGTTCCAACT
AATGAAAATAACTAAAATTATACAATAATTCAAAAGATAATTCATAATAGTTTGAAATAACAAAA
GGACTAAACAATAATTTTATATGATGCTCGTTCTTTTACATTATAATGGAACACCTTTTACTACT
TGATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTTGTCTTGATATAGAAGGAACA
ATAATC
Found at i:1100347 original size:72 final size:71
Alignment explanation
Indices: 1100207--1100404 Score: 218
Period size: 72 Copynumber: 2.8 Consensus size: 71
1100197 TTTACTATGC
* * *
1100207 TTGAATTCTTTGAACTATCATAGCTTAATATTCCTCATTGTCTTGGTGTAGCAGGAACATTAATC
1 TTGAATTCTTTGAACCATCATAGCTTAATATTCCTCATTGTCTTGGTGTAGCAGGAACAATAAGC
1100272 CTTTGT
66 CTTTGT
* *
1100278 TTGAATTCTTTTTGAACCATCATAGCTTACTATTCCTC-TTGTCTTGGTGTGGCAGGAACAATAA
1 TTGAATTC--TTTGAACCATCATAGCTTAATATTCCTCATTGTCTTGGTGTAGCAGGAACAATAA
*
1100342 GCCTTTGC
64 GCCTTTGT
* * ** * * * * * * *
1100350 TTCAATTGTTTGAAATATCATGGTTTATTATTTCTCCTTGTCTTGATGTTGCAGG
1 TTGAATTCTTTGAACCATCATAGCTTAATATTCCTCATTGTCTTGGTGTAGCAGG
1100405 GAATCTATCA
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
70 22 0.20
71 24 0.22
72 36 0.33
73 26 0.24
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (71 bp):
TTGAATTCTTTGAACCATCATAGCTTAATATTCCTCATTGTCTTGGTGTAGCAGGAACAATAAGC
CTTTGT
Found at i:1100923 original size:71 final size:71
Alignment explanation
Indices: 1100839--1101030 Score: 240
Period size: 73 Copynumber: 2.7 Consensus size: 71
1100829 TTACAACTTC
*
1100839 ATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTTATCTTGGTGTAGCAGGAACAAT
1 ATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTTATCTTGGTGTAGCAGGAAAAAT
*
1100904 AATGCT
66 AATGAT
* * * * * *
1100910 TTGCTTGAATTCTTTTTAAACTATCGTAGCTTACTATTCCTCTTTGTCTTGGTGTTGCAGGAAAA
1 ATGCTTGAATTC--TTTGAACTATCATAGCTTACTATTCCTCCTTATCTTGGTGTAGCAGGAAAA
1100975 ATAATGAT
64 ATAATGAT
* * * * * *
1100983 ATGCTTCAATTCTTTGAATTGTCATGGTTTATTATTCCTCCTTATCTT
1 ATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTTATCTT
1101031 AATGTTAAGA
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
71 38 0.38
73 62 0.62
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (71 bp):
ATGCTTGAATTCTTTGAACTATCATAGCTTACTATTCCTCCTTATCTTGGTGTAGCAGGAAAAAT
AATGAT
Found at i:1102175 original size:4 final size:4
Alignment explanation
Indices: 1102166--1102190 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1102156 TAGATCCCAA
1102166 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1102191 GGAATAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1103963 original size:44 final size:44
Alignment explanation
Indices: 1103891--1104007 Score: 198
Period size: 44 Copynumber: 2.7 Consensus size: 44
1103881 TGTCATATAC
* *
1103891 AATTGTCCAGAAGGACCACATATATGTCCTGATGGACCGCGTAG
1 AATTGTCCCGAAGGACCACATATATGTCCTGAAGGACCGCGTAG
*
1103935 AATTATCCCGAAGGACCACATATATGTCCTGAAGGACCGCGTAG
1 AATTGTCCCGAAGGACCACATATATGTCCTGAAGGACCGCGTAG
*
1103979 AATTGTCCCAAAGGACCACATATATGTCC
1 AATTGTCCCGAAGGACCACATATATGTCC
1104008 CGAATAACCT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (44 bp):
AATTGTCCCGAAGGACCACATATATGTCCTGAAGGACCGCGTAG
Found at i:1103992 original size:23 final size:23
Alignment explanation
Indices: 1103915--1103995 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
1103905 ACCACATATA
* *
1103915 TGTCCTGATGGACCGCGTAGAAT
1 TGTCCCGAAGGACCGCGTAGAAT
* * * *
1103938 TATCCCGAAGGACCACATA-TA-
1 TGTCCCGAAGGACCGCGTAGAAT
*
1103959 TGTCCTGAAGGACCGCGTAGAAT
1 TGTCCCGAAGGACCGCGTAGAAT
*
1103982 TGTCCCAAAGGACC
1 TGTCCCGAAGGACC
1103996 ACATATATGT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
21 15 0.35
22 2 0.05
23 26 0.60
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
TGTCCCGAAGGACCGCGTAGAAT
Found at i:1104008 original size:21 final size:21
Alignment explanation
Indices: 1103894--1104011 Score: 92
Period size: 21 Copynumber: 5.4 Consensus size: 21
1103884 CATATACAAT
*
1103894 TGTCCAGAAGGACCACATATA
1 TGTCCCGAAGGACCACATATA
* * * * *
1103915 TGTCCTGATGGACCGCGTAGAA
1 TGTCCCGAAGGACCACATA-TA
*
1103937 TTATCCCGAAGGACCACATATA
1 -TGTCCCGAAGGACCACATATA
* * * *
1103959 TGTCCTGAAGGACCGCGTAGAA
1 TGTCCCGAAGGACCACATA-TA
*
1103981 TTGTCCCAAAGGACCACATATA
1 -TGTCCCGAAGGACCACATATA
1104003 TGTCCCGAA
1 TGTCCCGAA
1104012 TAACCTTGTA
Statistics
Matches: 71, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
21 38 0.54
22 4 0.06
23 29 0.41
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:1105086 original size:17 final size:17
Alignment explanation
Indices: 1105064--1105097 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1105054 TTGGAAATTT
*
1105064 AAACTTTTATTAACATA
1 AAACTTGTATTAACATA
*
1105081 AAACTTGTATTTACATA
1 AAACTTGTATTAACATA
1105098 CTGAAGTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (17 bp):
AAACTTGTATTAACATA
Found at i:1105789 original size:32 final size:32
Alignment explanation
Indices: 1105739--1105822 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
1105729 GGACCTATCA
* * * *
1105739 ATATGTTCTGAAGAACATAGGTAAACTTGTCC
1 ATATGTCCCGAAGGACATAGGTAAACCTGTCC
*
1105771 ATATGTCCCGAAGGACATAGGTAATCCTGTCC
1 ATATGTCCCGAAGGACATAGGTAAACCTGTCC
1105803 ATATGTCCCGAAGGACATAG
1 ATATGTCCCGAAGGACATAG
1105823 TTATCCCTCG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (32 bp):
ATATGTCCCGAAGGACATAGGTAAACCTGTCC
Found at i:1109740 original size:69 final size:69
Alignment explanation
Indices: 1109623--1109753 Score: 208
Period size: 69 Copynumber: 1.9 Consensus size: 69
1109613 GCTTTAGCAT
* * *
1109623 GATTTACAACTTCTTGAAATAAGCACAAGTTAAGCACAATTAACATTTCTTTCAACCTCGGGCAC
1 GATTTACAACTTCTTGAAATAAGAACAAGTTAAACACAATCAACATTTCTTTCAACCTCGGGCAC
1109688 ACTC
66 ACTC
* * *
1109692 GATTTACAACTTCTTGAAATGAGAACAAGTTAAACACAATCAATATTTCTTTCAAGCTCGGG
1 GATTTACAACTTCTTGAAATAAGAACAAGTTAAACACAATCAACATTTCTTTCAACCTCGGG
1109754 TGCAAGCCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 56 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (69 bp):
GATTTACAACTTCTTGAAATAAGAACAAGTTAAACACAATCAACATTTCTTTCAACCTCGGGCAC
ACTC
Found at i:1111819 original size:20 final size:19
Alignment explanation
Indices: 1111794--1111867 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 19
1111784 CCTTTGAAGA
1111794 GGTATCGATACCCACTATAG
1 GGTATCGATACCCAC-ATAG
*
1111814 GGTATCAGTACTACCCTAGATGAG
1 GGTATC-G-A-TACCC-ACAT-AG
*
1111838 GGTATCGATACCTACAT-G
1 GGTATCGATACCCACATAG
*
1111856 GGTATCGGTACC
1 GGTATCGATACC
1111868 AAAATTACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
18 12 0.27
20 9 0.20
21 5 0.11
22 2 0.04
23 8 0.18
24 9 0.20
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (19 bp):
GGTATCGATACCCACATAG
Found at i:1117242 original size:21 final size:21
Alignment explanation
Indices: 1117218--1117290 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
1117208 AAATTGTCAT
*
1117218 GAAGGACCGCATATATGTCCC
1 GAAGGACCACATATATGTCCC
* * *
1117239 GAAGGACCTCATAGAATTGTCTC
1 GAAGGACCACATA-TA-TGTCCC
*
1117262 GAAGAACCACATATATGTCCC
1 GAAGGACCACATATATGTCCC
1117283 GAAGGACC
1 GAAGGACC
1117291 TCGTAGAACC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 24 0.57
22 2 0.05
23 16 0.38
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (21 bp):
GAAGGACCACATATATGTCCC
Found at i:1117257 original size:44 final size:44
Alignment explanation
Indices: 1117209--1117298 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 44
1117199 TGCCATATAA
* *
1117209 AATTGTCAT-GAAGGACCGCATATATGTCCCGAAGGACCTCATAG
1 AATTGTC-TCGAAGAACCACATATATGTCCCGAAGGACCTCATAG
*
1117253 AATTGTCTCGAAGAACCACATATATGTCCCGAAGGACCTCGTAG
1 AATTGTCTCGAAGAACCACATATATGTCCCGAAGGACCTCATAG
1117297 AA
1 AA
1117299 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (44 bp):
AATTGTCTCGAAGAACCACATATATGTCCCGAAGGACCTCATAG
Found at i:1118702 original size:19 final size:19
Alignment explanation
Indices: 1118678--1118715 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1118668 AGGTACAGTG
1118678 GTATCGATA-CTATATTTCA
1 GTATCGATACCTA-ATTTCA
1118697 GTATCGATACCTAATTTCA
1 GTATCGATACCTAATTTCA
1118716 ATTCTGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
GTATCGATACCTAATTTCA
Found at i:1124946 original size:19 final size:19
Alignment explanation
Indices: 1124922--1124962 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1124912 TTGCTTAGAA
1124922 ATTGAACTATAAGGAGGAG
1 ATTGAACTATAAGGAGGAG
*
1124941 ATTGAACTCTAAGGAGGAG
1 ATTGAACTATAAGGAGGAG
1124960 ATT
1 ATT
1124963 TTCTTACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.24
Consensus pattern (19 bp):
ATTGAACTATAAGGAGGAG
Found at i:1127258 original size:27 final size:27
Alignment explanation
Indices: 1127228--1127279 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
1127218 AAATGTTAAA
1127228 GAGTAGTTGATTCTTTTGATATTCTGT
1 GAGTAGTTGATTCTTTTGATATTCTGT
1127255 GAGTAGTTGATTCTTTTGATATTCT
1 GAGTAGTTGATTCTTTTGATATTCT
1127280 ATGAACTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.08, G:0.21, T:0.52
Consensus pattern (27 bp):
GAGTAGTTGATTCTTTTGATATTCTGT
Found at i:1128544 original size:134 final size:134
Alignment explanation
Indices: 1128338--1128852 Score: 635
Period size: 134 Copynumber: 3.8 Consensus size: 134
1128328 GTGAAACATG
* *
1128338 TCCCTCTCTTTCAAGATTTGATATTCTCTGAGTGACAGCGGAACAAGTCTGCCTCGATTCAATCT
1 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCACGATTCAATCT
* * * *
1128403 TCCCTGAGTGACAGTGGAATGAATCAACGT-CTCCAGATCTGATATTCCC-TCTAGAAGAAGCGG
66 TCCCTGAGTGACAGCGGAATGGATCAAC-TCCCCCAGATCTGATATTCCCTTC-AGAAGAAGCAG
* *
1128466 AATAGA
129 AACAAA
** *
1128472 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAATGGAACAAATCTGTCC-CGATTCAATC
1 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTG-CCACGATTCAATC
* * * ** * *
1128536 TTCACTGAGTGACAACAGAATGGATCAACTCCTTCAGATCTGATATTCCTTTCAGAAGAAGAAGA
65 TTCCCTGAGTGACAGCGGAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAAGAAGCAGA
*
1128601 ACATA
130 ACAAA
* * *
1128606 TCCCTCT-TTTCCAAGATTTGATATTCCCTAAGTGACAGTGGAACAAGGCTGCCACGATTCAATC
1 TCCCTCTCTTT-CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCACGATTCAATC
* * * * *
1128670 TTCCCTAAGTGACATCGGAATGCATCAACTCCCCCAAATATGATATTCCCTTCAGAAGAAGCAGA
65 TTCCCTGAGTGACAGCGGAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAAGAAGCAGA
1128735 ACAAA
130 ACAAA
* * * * *
1128740 TCCCTTTCTTCCAATATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTCAATCT
1 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCACGATTCAATCT
* * *
1128805 TCCTTGAGTGACAGCGAAATGGATCAACAT-CCCCATATCTGATATTCC
66 TCCCTGAGTGACAGCGGAATGGATCAAC-TCCCCCAGATCTGATATTCC
1128853 GTGAGTGACA
Statistics
Matches: 328, Mismatches: 46, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
133 6 0.02
134 315 0.96
135 7 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (134 bp):
TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCACGATTCAATCT
TCCCTGAGTGACAGCGGAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAAGAAGCAGAA
CAAA
Found at i:1128798 original size:268 final size:267
Alignment explanation
Indices: 1128302--1128852 Score: 704
Period size: 268 Copynumber: 2.1 Consensus size: 267
1128292 TTTTAATTTG
* * * * *
1128302 CAGATCAGATATTTCATTTAGAAGAAGTGAAACATGTCCCTCTCTTTCAAGATTTGATATTCTCT
1 CAGATCTGATA-TTCCTTTAGAAGAAGAGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCT
* * * *
1128367 GAGTGACAGCGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACG
65 AAGTGACAGCGGAACAAGGCTGCCACGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACG
* * * * * * *
1128432 TCTCCAGATCTGATATTCCCTCTAGAAGAAGCGGAATAGATCCCTCTCTTTCAAGATTTGATATT
130 TCCCCAAATATGATATTCCCTCTAGAAGAAGCAGAACAAATCCCTCTCTTCCAAGATTTGATATT
* **
1128497 CCCTGAGTGACAATGGAACAAATCTGTCCCGATTCAATCTTCAC-TGAGTGACAAC-AGAATGGA
195 CCCTGAGTGACAACGGAACAAATCTACCCCGATTCAATCTTC-CTTGAGTGACAACGA-AATGGA
*
1128560 TCAAC-TCCTT
258 TCAACATCC-C
1128570 CAGATCTGATATTCCTTTCAGAAGAAGA-AGAACATATCCCTCT-TTTCCAAGATTTGATATTCC
1 CAGATCTGATATTCCTTT-AGAAGAAGAGA-AACATATCCCTCTCTTT-CAAGATTTGATATTCC
* *
1128633 CTAAGTGACAGTGGAACAAGGCTGCCACGATTCAATCTTCCCTAAGTGACA-TCGGAATGCATCA
63 CTAAGTGACAGCGGAACAAGGCTGCCACGATTCAATCTTCCCTAAGTGACAGT-GGAATGAATCA
* *
1128697 AC-TCCCCCAAATATGATATTCCCT-TCAGAAGAAGCAGAACAAATCCCTTTCTTCCAATATTTG
127 ACGT-CCCCAAATATGATATTCCCTCT-AGAAGAAGCAGAACAAATCCCTCTCTTCCAAGATTTG
* * *
1128760 ATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCTTGAGTGACAGCGAAAT
190 ATATTCCCTGAGTGACAACGGAACAAATCTACCCCGATTCAATCTTCCTTGAGTGACAACGAAAT
1128825 GGATCAACATCCC
255 GGATCAACATCCC
*
1128838 CATATCTGATATTCC
1 CAGATCTGATATTCC
1128853 GTGAGTGACA
Statistics
Matches: 246, Mismatches: 28, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
267 14 0.06
268 228 0.93
269 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (267 bp):
CAGATCTGATATTCCTTTAGAAGAAGAGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTA
AGTGACAGCGGAACAAGGCTGCCACGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGT
CCCCAAATATGATATTCCCTCTAGAAGAAGCAGAACAAATCCCTCTCTTCCAAGATTTGATATTC
CCTGAGTGACAACGGAACAAATCTACCCCGATTCAATCTTCCTTGAGTGACAACGAAATGGATCA
ACATCCC
Found at i:1129477 original size:4 final size:4
Alignment explanation
Indices: 1129468--1129492 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1129458 TCCCGAATAA
1129468 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1129493 GGAATAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1131043 original size:28 final size:27
Alignment explanation
Indices: 1131012--1131099 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 27
1131002 TTTATTTTAA
1131012 TTTTGGTATGTTAGTTTGATTATTTATG
1 TTTT-GTATGTTAGTTTGATTATTTATG
*
1131040 TTTTAGTCCCACT-TCTA-TTTTATT-TTTAT-
1 TTTT-GT---A-TGT-TAGTTTGATTATTTATG
*
1131069 TTTTGCATGTTAGTTTGATTATTTATG
1 TTTTGTATGTTAGTTTGATTATTTATG
1131096 TTTT
1 TTTT
1131100 AGTCCTACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 19
0.67 0.06 0.27
Matches are distributed among these distances:
24 3 0.06
25 8 0.17
26 5 0.11
27 4 0.09
28 7 0.15
29 4 0.09
30 5 0.11
31 8 0.17
32 3 0.06
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (27 bp):
TTTTGTATGTTAGTTTGATTATTTATG
Found at i:1131079 original size:56 final size:56
Alignment explanation
Indices: 1130995--1131140 Score: 242
Period size: 56 Copynumber: 2.6 Consensus size: 56
1130985 TCCTTTGTAT
* * *
1130995 ACTT-TATTTTATTTTAATTTTGGTATGTTAGTTTGATTATTTATGTTTTAGTCCC
1 ACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTGATTATTTATGTTTTAGTCCC
*
1131050 ACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTGATTATTTATGTTTTAGTCCT
1 ACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTGATTATTTATGTTTTAGTCCC
1131106 ACTTCTATTTTATTTTTATTTTTGCATGTTA-TTTG
1 ACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTG
1131141 CATATAGTTC
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
55 8 0.09
56 78 0.91
ACGTcount: A:0.18, C:0.08, G:0.11, T:0.62
Consensus pattern (56 bp):
ACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTGATTATTTATGTTTTAGTCCC
Found at i:1131118 original size:28 final size:28
Alignment explanation
Indices: 1131031--1131120 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
1131021 GTTAGTTTGA
*
1131031 TTATTTATGTTTTAGTCCCACTTCTATT
1 TTATTTATGTTTTAGTCCTACTTCTATT
* * * * * *
1131059 TTATTTTTATTTTTG-CAT-GTTAGT-TT
1 TTATTTATGTTTTAGTCCTACTT-CTATT
1131085 GATTATTTATGTTTTAGTCCTACTTCTATT
1 --TTATTTATGTTTTAGTCCTACTTCTATT
1131115 TTATTT
1 TTATTT
1131121 TTATTTTTGC
Statistics
Matches: 43, Mismatches: 13, Indels: 12
0.63 0.19 0.18
Matches are distributed among these distances:
26 4 0.09
27 2 0.05
28 30 0.70
29 3 0.07
30 4 0.09
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (28 bp):
TTATTTATGTTTTAGTCCTACTTCTATT
Found at i:1131156 original size:56 final size:55
Alignment explanation
Indices: 1130994--1131162 Score: 227
Period size: 56 Copynumber: 3.0 Consensus size: 55
1130984 GTCCTTTGTA
* * *
1130994 TACTT-TATTTTATTTTAATTTTGGTATGTTAGTTTGATTATTTATGTTTTAGTCC
1 TACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTGATTATTTA-GTTTTAGTCC
*
1131049 CACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTGATTATTTATGTTTTAGTCC
1 TACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTGATTATTTA-GTTTTAGTCC
*
1131105 TACTTCTATTTTATTTTTATTTTTGCATGTTA-TTTGCATATAGTTCA-TTTTAGTCC
1 TACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTG-AT-TA-TTTAGTTTTAGTCC
1131161 TA
1 TA
1131163 ATTAATTTCG
Statistics
Matches: 104, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
55 8 0.08
56 91 0.88
57 2 0.02
58 3 0.03
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.60
Consensus pattern (55 bp):
TACTTCTATTTTATTTTTATTTTTGCATGTTAGTTTGATTATTTAGTTTTAGTCC
Found at i:1138209 original size:23 final size:23
Alignment explanation
Indices: 1138178--1138246 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1138168 CACCACAGCT
*
1138178 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCTAAGTGCCA
* * *
1138201 CTTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCTAAGTGCCA
*
1138224 CGTAGAATTACACCGT-AGTGCCA
1 CGTAGAATTGCACC-TAAGTGCCA
1138247 TATAATAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCTAAGTGCCA
Found at i:1138387 original size:103 final size:103
Alignment explanation
Indices: 1138262--1138479 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1138252 TAATGTCCAT
* *
1138262 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1138327 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1138365 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
*
1138430 GACCTCACACATGTTTCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1138468 AAGGACCACATA
1 AAGGACCACATA
1138480 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1138981 original size:20 final size:20
Alignment explanation
Indices: 1138956--1138996 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1138946 CTTTTTTTAT
*
1138956 TATGGGGGAATCGGTTCCCC
1 TATGGGGGAATCGATTCCCC
*
1138976 TATGGGGGTATCGATTCCCC
1 TATGGGGGAATCGATTCCCC
1138996 T
1 T
1138997 CTAGCATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (20 bp):
TATGGGGGAATCGATTCCCC
Found at i:1139047 original size:21 final size:21
Alignment explanation
Indices: 1139023--1139065 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1139013 TCATATTCGT
* *
1139023 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCAATTCCCC
*
1139044 TTGAATGGGTATCAATTCCCC
1 TTGAAGGGGTATCAATTCCCC
1139065 T
1 T
1139066 AGCCTAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCAATTCCCC
Found at i:1140464 original size:18 final size:18
Alignment explanation
Indices: 1140441--1140478 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1140431 AATAAGGTCA
1140441 CTATAAAGAACAAATATC
1 CTATAAAGAACAAATATC
1140459 CTATAAAGAACAAATATC
1 CTATAAAGAACAAATATC
1140477 CT
1 CT
1140479 CTTCCGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (18 bp):
CTATAAAGAACAAATATC
Found at i:1144025 original size:19 final size:19
Alignment explanation
Indices: 1144001--1144078 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 19
1143991 AGCTAATTTA
*
1144001 GGTATCGATACAATAAGAG
1 GGTATCGATACCATAAGAG
* * *
1144020 GGTATCAATACCCTAATATG
1 GGTATCGATACCATAAGA-G
1144040 GTAGTATCGATACCATAAGGAG
1 G--GTATCGATACCATAA-GAG
1144062 GGATATCGATACC-TAAG
1 GG-TATCGATACCATAAG
1144079 GGCCAAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
19 15 0.32
20 6 0.13
21 10 0.21
22 15 0.32
23 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (19 bp):
GGTATCGATACCATAAGAG
Found at i:1144590 original size:22 final size:23
Alignment explanation
Indices: 1144534--1144591 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
1144524 ATTTCTGGCC
1144534 CTTA-GGTATCGATA-T-CCCTA
1 CTTAGGGTATCGATACTACCCTA
*
1144554 CTTATGGTATCGATACTACCCTA
1 CTTAGGGTATCGATACTACCCTA
*
1144577 -TTAGGGTATTGATAC
1 CTTAGGGTATCGATAC
1144592 CCTCTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.12
21 10 0.30
22 14 0.42
23 5 0.15
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (23 bp):
CTTAGGGTATCGATACTACCCTA
Found at i:1149601 original size:127 final size:130
Alignment explanation
Indices: 1149372--1149626 Score: 336
Period size: 127 Copynumber: 2.0 Consensus size: 130
1149362 ACTGTGCTGT
* * * * * * *
1149372 TATTTTTTTTACATTGCATTGTTCGAATCTATTGTGTATTTTTCTGCACTGTTCGAACCAAAACA
1 TATTTTTTATACACTGCATTGTTCAAATCTACTCTGAATTTTTCTGCAATGTTCGAACCAAAACA
* * * *
1149437 ATTTTGTTTTGTACTGTTTTGTTCTAACTTTTCTGCACAATTCGAACCAAATCTGTTTTTTTCAC
66 AGTTTGTTTTGCACTGTTTTGTTCGAACTTTTCTGCACAATTCGAACCAAATCTATTTTTTTCAC
* * *
1149502 TATTTTTTATGCACTGCATTGTTCAAATCTGCTCTGAATTTTT-TGCAATGTTCGAACCAAATC-
1 TATTTTTTATACACTGCATTGTTCAAATCTACTCTGAATTTTTCTGCAATGTTCGAACCAAAACA
* * *
1149565 AGTTT-TTTTGCACTGTTTTGTTCGAACTTTTTTGCACAGTTCGAACCAAGTCTATTTTTTTC
66 AGTTTGTTTTGCACTGTTTTGTTCGAACTTTTCTGCACAATTCGAACCAAATCTATTTTTTTC
1149627 TGAATTATCC
Statistics
Matches: 108, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
127 51 0.47
128 4 0.04
129 18 0.17
130 35 0.32
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (130 bp):
TATTTTTTATACACTGCATTGTTCAAATCTACTCTGAATTTTTCTGCAATGTTCGAACCAAAACA
AGTTTGTTTTGCACTGTTTTGTTCGAACTTTTCTGCACAATTCGAACCAAATCTATTTTTTTCAC
Found at i:1149855 original size:6 final size:6
Alignment explanation
Indices: 1149844--1149881 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1149834 AAATTAAATC
* *
1149844 ATAAAA ATAAAA TTGAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
1149882 TGAACAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (6 bp):
ATAAAA
Found at i:1149864 original size:12 final size:12
Alignment explanation
Indices: 1149847--1149885 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1149837 TTAAATCATA
1149847 AAAATAAAATTG
1 AAAATAAAATTG
* *
1149859 AAAATAAAAATA
1 AAAATAAAATTG
1149871 AAAATAAAAATTG
1 AAAAT-AAAATTG
1149884 AA
1 AA
1149886 CAAACGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (12 bp):
AAAATAAAATTG
Found at i:1149865 original size:18 final size:18
Alignment explanation
Indices: 1149821--1149873 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1149811 AAAAATCAAA
* *
1149821 GAAAATTAAAACAAAATT
1 GAAAATAAAAATAAAATT
1149839 -AAATCATAAAAATAAAATT
1 GAAA--ATAAAAATAAAATT
1149858 GAAAATAAAAATAAAA
1 GAAAATAAAAATAAAA
1149874 ATAAAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 12 0.40
20 3 0.10
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (18 bp):
GAAAATAAAAATAAAATT
Found at i:1149879 original size:11 final size:11
Alignment explanation
Indices: 1149810--1149879 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
1149800 CAACGTACCT
*
1149810 TAAAAATCAAA
1 TAAAAATAAAA
* *
1149821 GAAAATTAAAA
1 TAAAAATAAAA
* *
1149832 CAAAATTAAATCA
1 TAAAAATAAA--A
1149845 TAAAAATAAAA
1 TAAAAATAAAA
*
1149856 TTGAAAATAAAAA
1 -TAAAAAT-AAAA
1149869 TAAAAATAAAA
1 TAAAAATAAAA
1149880 ATTGAACAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
11 22 0.47
12 12 0.26
13 13 0.28
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:1152759 original size:12 final size:12
Alignment explanation
Indices: 1152744--1152782 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1152734 ATAAAATTTA
*
1152744 AAATAAAAAACT
1 AAATAAAAAAAT
1152756 AAATAAAAAAAT
1 AAATAAAAAAAT
* *
1152768 AAATATAAATAT
1 AAATAAAAAAAT
1152780 AAA
1 AAA
1152783 GGTGAGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:1154304 original size:120 final size:120
Alignment explanation
Indices: 1154067--1154297 Score: 292
Period size: 120 Copynumber: 2.0 Consensus size: 120
1154057 TATTAATTTC
* * * * *
1154067 TATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATTAGAAAAGGACTTCTAGGTGCCT
1 TATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACCT
* * *
1154130 TAAGACAGCTCTTTTCTTCTATATTAAAAAATAAATAATTAATTAAAACAATTAA
66 TAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
* * **
1154185 TATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTATT
1 TATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTACC
* *
1154250 TTAAGACTGC-CCTTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
65 TTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
1154298 TGATTAAAAT
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 14 0.15
119 24 0.25
120 40 0.42
121 18 0.19
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (120 bp):
TATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACCT
TAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:1154379 original size:21 final size:20
Alignment explanation
Indices: 1154322--1154380 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
1154312 TAAAAATAAT
*
1154322 TAAATAATAT-TTTAATAAA
1 TAAATAATATATTTATTAAA
*
1154341 TAAAATAAATATTATTTATTATA
1 T-AAAT-AATA-TATTTATTAAA
1154364 TAAATATATATATTTAT
1 TAAATA-ATATATTTAT
1154381 GGCTAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 12 0.36
22 8 0.24
23 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATAATATATTTATTAAA
Found at i:1155776 original size:3 final size:3
Alignment explanation
Indices: 1155768--1155858 Score: 114
Period size: 3 Copynumber: 29.7 Consensus size: 3
1155758 AATTATTTTT
1155768 TAA TAA TAA TAA T-A TATA TAA TAA TATA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TA-A TAA TAA TAA TAA TAA
* *
1155815 TAA TAG TAA TAA TTA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
1155859 TTCAAATGAA
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.05
3 63 0.80
4 12 0.15
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1156262 original size:112 final size:111
Alignment explanation
Indices: 1156097--1157121 Score: 1638
Period size: 112 Copynumber: 9.2 Consensus size: 111
1156087 TTGAATAATC
* * **
1156097 TCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTAG
1 TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-G
** * * * * *
1156162 AAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGT
64 AACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
* * *
1156210 TCTTCTCATTATGAACTTCTTCTTATTCTTCAGATGAGTTCTTTTCATTATGAACTCTAACTGGC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-GA
*
1156275 ACTGCTGATCCACC-AGTGATGAATTTAAGCAAAAAGTTGAACAAGT
65 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
* * *
1156321 TCTTCTCATTATGTACTTCTTCTTCTTCTTCAGATGAATTCTTCTCATTATGAACTCTAACTGGC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-GA
* *
1156386 ACTGTTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAACT
65 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
*
1156433 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-GA
1156498 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
65 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
*
1156545 TCTTCTCATTATGAACTTTTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGAC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGA-
*
1156610 ACTGTTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
65 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
* * * *
1156657 TCTTCTCATTATGAACTTTTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTAATTGGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-GA
* *
1156722 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAATTTGAACATGT
65 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
*
1156769 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTAACTGAC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGA-
*
1156834 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTAAACAAGT
65 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
* *
1156881 TCTTCTCATTATGAAGTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAGTATGAACTCTAACTGAC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGA-
*
1156946 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAATTTGAACAAGT
65 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
*
1156993 TCTTCTCATTATGAACTTATTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGAC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGA-
1157058 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
65 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
1157105 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
1157122 CTAACTGGAA
Statistics
Matches: 858, Mismatches: 50, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
111 107 0.12
112 727 0.85
113 24 0.03
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (111 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGAA
CTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
Found at i:1158318 original size:19 final size:17
Alignment explanation
Indices: 1158290--1158338 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
1158280 AAAATAAAAG
*
1158290 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
1158309 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
1158325 AATAAATTGAATTT
1 AATAAATTGAATTT
1158339 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:1158704 original size:8 final size:8
Alignment explanation
Indices: 1158691--1158766 Score: 50
Period size: 8 Copynumber: 9.2 Consensus size: 8
1158681 CTTGACCCAT
1158691 TTTTTTTC
1 TTTTTTTC
1158699 TTTTTTTTC
1 -TTTTTTTC
*
1158708 ATTTTTTC
1 TTTTTTTC
1158716 TTCATTTTT-
1 TT--TTTTTC
1158725 TATTTTTT-
1 T-TTTTTTC
1158733 TATTTTTT-
1 T-TTTTTTC
* *
1158741 TATTTTTA
1 TTTTTTTC
1158749 TTTTTTTC
1 TTTTTTTC
*
1158757 ATTTTTTC
1 TTTTTTTC
1158765 TT
1 TT
1158767 CAAGCATAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
7 5 0.09
8 36 0.64
9 9 0.16
10 6 0.11
ACGTcount: A:0.09, C:0.08, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1158746 original size:22 final size:23
Alignment explanation
Indices: 1158700--1158763 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 23
1158690 TTTTTTTTCT
1158700 TTTTTTTCATTTTTTCTTCATTTTTTA
1 TTTTTTTCA-TTTTT-TT-A-TTTTTA
1158727 TTTTTTT-ATTTTTTTATTTTTA
1 TTTTTTTCATTTTTTTATTTTTA
1158749 TTTTTTTCATTTTTT
1 TTTTTTTCATTTTTT
1158764 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
22 13 0.36
23 8 0.22
24 2 0.06
25 5 0.14
26 1 0.03
27 7 0.19
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTTTTCATTTTTTTATTTTTA
Found at i:1158768 original size:11 final size:10
Alignment explanation
Indices: 1158688--1158768 Score: 66
Period size: 9 Copynumber: 8.2 Consensus size: 10
1158678 CAACTTGACC
1158688 CATTTTTTTT
1 CATTTTTTTT
1158698 C-TTTTTTTT
1 CATTTTTTTT
1158707 CATTTTTTCTT
1 CATTTTTT-TT
1158718 CATTTTTTATT
1 CATTTTTT-TT
1158729 --TTTTTATTT
1 CATTTTT-TTT
1158738 --TTTTATTTT
1 CATTTT-TTTT
*
1158747 TA-TTTTTTT
1 CATTTTTTTT
1158756 CATTTTTTCTT
1 CATTTTTT-TT
1158767 CA
1 CA
1158769 AGCATAATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
9 28 0.46
10 17 0.28
11 16 0.26
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (10 bp):
CATTTTTTTT
Found at i:1162174 original size:9 final size:9
Alignment explanation
Indices: 1162157--1162195 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
1162147 GAAATAAATG
1162157 AATGT-AAA
1 AATGTAAAA
1162165 AATGTAAAA
1 AATGTAAAA
1162174 AATGTAAAA
1 AATGTAAAA
*
1162183 AATGTAAAG
1 AATGTAAAA
1162192 AATG
1 AATG
1162196 ATTGCCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (9 bp):
AATGTAAAA
Found at i:1169899 original size:20 final size:19
Alignment explanation
Indices: 1169849--1169890 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1169839 TTTCTTCGAT
*
1169849 ATTAAAAAATAAATAAATA
1 ATTAAAAAATTAATAAATA
*
1169868 ATTAAAACAATTAATATATA
1 ATTAAAA-AATTAATAAATA
1169888 ATT
1 ATT
1169891 TATAAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATTAATAAATA
Found at i:1170022 original size:20 final size:20
Alignment explanation
Indices: 1169987--1170026 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1169977 TAAATAAATT
*
1169987 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
1170008 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
1170027 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:1170040 original size:23 final size:22
Alignment explanation
Indices: 1169977--1170040 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
1169967 TATTGAAAAA
*
1169977 TAAATAA-ATTTTAAAACATGAT
1 TAAATAAGATTTTAAAA-ATAAT
1169999 TAAAATAAG---TTAAAAATAAT
1 T-AAATAAGATTTTAAAAATAAT
1170019 TAAATAAGATTTTAATAAATAA
1 TAAATAAGATTTTAA-AAATAA
1170041 AATAAATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
19 7 0.20
20 5 0.14
21 6 0.17
22 5 0.14
23 12 0.34
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (22 bp):
TAAATAAGATTTTAAAAATAAT
Found at i:1170091 original size:3 final size:3
Alignment explanation
Indices: 1170083--1170118 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1170073 TTTATGGCTA
*
1170083 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1170119 TAAAAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1171512 original size:9 final size:9
Alignment explanation
Indices: 1171497--1171575 Score: 52
Period size: 8 Copynumber: 9.8 Consensus size: 9
1171487 TTTTTTAATA
1171497 ATAATA-AT
1 ATAATATAT
1171505 AT-ATATA-
1 ATAATATAT
1171512 ATAATATAT
1 ATAATATAT
1171521 ATAATA-AT
1 ATAATATAT
*
1171529 -TATTAT-T
1 ATAATATAT
1171536 ATAAT-TATT
1 ATAATATA-T
1171545 ATAAT-TAT
1 ATAATATAT
*
1171553 A-ATTATA-
1 ATAATATAT
*
1171560 ATAATATAA
1 ATAATATAT
1171569 ATAATAT
1 ATAATAT
1171576 TCAAATGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
7 14 0.25
8 22 0.39
9 21 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATAATATAT
Found at i:1171514 original size:12 final size:13
Alignment explanation
Indices: 1171497--1171567 Score: 89
Period size: 12 Copynumber: 5.8 Consensus size: 13
1171487 TTTTTTAATA
1171497 ATAATAATATA-T
1 ATAATAATATATT
1171509 ATAATAATATA-T
1 ATAATAATATATT
1171521 ATAATAAT-TATT
1 ATAATAATATATT
*
1171533 ATTATAAT-TATT
1 ATAATAATATATT
*
1171545 ATAATTATA-ATT
1 ATAATAATATATT
1171557 ATAATAATATA
1 ATAATAATATA
1171568 AATAATATTC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
11 2 0.04
12 49 0.94
13 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATAATATATT
Found at i:1171514 original size:15 final size:14
Alignment explanation
Indices: 1171492--1171574 Score: 76
Period size: 15 Copynumber: 5.6 Consensus size: 14
1171482 AATTATTTTT
1171492 TAATAATAATAATA
1 TAATAATAATAATA
1171506 TATATAATAATATATA
1 TA-ATAATAATA-ATA
* *
1171522 TAATAATTATTATTA
1 TAATAA-TAATAATA
* *
1171537 TAATTATTATAATTA
1 TAATAATAATAA-TA
*
1171552 TAATTATAATAATA
1 TAATAATAATAATA
1171566 TAAATAATA
1 T-AATAATA
1171575 TTCAAATGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
14 8 0.14
15 39 0.70
16 9 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:1174180 original size:45 final size:45
Alignment explanation
Indices: 1174116--1174304 Score: 204
Period size: 45 Copynumber: 4.0 Consensus size: 45
1174106 ATTCCGTCTC
1174116 TTCCGCACATATCAACTAATTTTACTATTCCGAGTTCTCAATCTG
1 TTCCGCACATATCAACTAATTTTACTATTCCGAGTTCTCAATCTG
* *
1174161 TTCCGCACATATCAACTAATTTTACCATTCCGAGTTATCAATCTATACTATCG
1 TTCCGCACATATCAACTAATTTTACTATTCCGAG-T-TC--TC-A-A-TCT-G
* *
1174214 ATATCGGC-CATAT-AGACT-ATTTTACTATTCCGAGTTCTCAATCTA
1 -T-TCCGCACATATCA-ACTAATTTTACTATTCCGAGTTCTCAATCTG
* *
1174259 TTCCGCACATATCAACTAGTTTTACTAGTCCGAGTTCTCAATCTG
1 TTCCGCACATATCAACTAATTTTACTATTCCGAGTTCTCAATCTG
1174304 T
1 T
1174305 ACTATCAATA
Statistics
Matches: 120, Mismatches: 10, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
43 4 0.03
44 9 0.08
45 59 0.49
46 3 0.03
47 3 0.03
48 1 0.01
49 4 0.03
50 1 0.01
51 3 0.03
52 3 0.03
53 17 0.14
54 9 0.08
55 4 0.03
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (45 bp):
TTCCGCACATATCAACTAATTTTACTATTCCGAGTTCTCAATCTG
Found at i:1174308 original size:98 final size:98
Alignment explanation
Indices: 1174134--1174322 Score: 315
Period size: 98 Copynumber: 1.9 Consensus size: 98
1174124 ATATCAACTA
* *
1174134 ATTTTACTATTCCGAGTTCTCAATCTGTTCCGCACATATCAACTAATTTTACCATTCCGAGTTAT
1 ATTTTACTATTCCGAGTTCTCAATCTATTCCGCACATATCAACTAATTTTACCAGTCCGAGTTAT
*
1174199 CAATCTATACTATCGATATCGGCCATATAGACT
66 CAATCTATACTATCAATATCGGCCATATAGACT
* * *
1174232 ATTTTACTATTCCGAGTTCTCAATCTATTCCGCACATATCAACTAGTTTTACTAGTCCGAGTTCT
1 ATTTTACTATTCCGAGTTCTCAATCTATTCCGCACATATCAACTAATTTTACCAGTCCGAGTTAT
*
1174297 CAATCTGTACTATCAATATCGGCCAT
66 CAATCTATACTATCAATATCGGCCAT
1174323 TAGTGTGGAG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.37
Consensus pattern (98 bp):
ATTTTACTATTCCGAGTTCTCAATCTATTCCGCACATATCAACTAATTTTACCAGTCCGAGTTAT
CAATCTATACTATCAATATCGGCCATATAGACT
Found at i:1176566 original size:24 final size:24
Alignment explanation
Indices: 1176521--1176571 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1176511 CAGCTTGTAT
* **
1176521 AATTGCATCGAAGTACCGCATAGA
1 AATTGCACCGAAGTACAACATAGA
*
1176545 AATTGCACCGAAGTGCAACATAGA
1 AATTGCACCGAAGTACAACATAGA
1176569 AAT
1 AAT
1176572 GTCCTGAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (24 bp):
AATTGCACCGAAGTACAACATAGA
Found at i:1176615 original size:46 final size:46
Alignment explanation
Indices: 1176565--1176661 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 46
1176555 AAGTGCAACA
* * * *
1176565 TAGAAATGTCCTGAAGGAGCACATAGTATTGTCTCGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCGCG
*
1176611 TAGAAATGTCCCGAAGGACCACGTAGAATTGTCCCGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCGCG
1176657 TAGAA
1 TAGAA
1176662 CCCTCGACTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.19
Consensus pattern (46 bp):
TAGAAATGTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCGCG
Found at i:1176658 original size:23 final size:23
Alignment explanation
Indices: 1176565--1176661 Score: 113
Period size: 23 Copynumber: 4.2 Consensus size: 23
1176555 AAGTGCAACA
* * *
1176565 TAGAAATGTCCTGAAGGAGCACA
1 TAGAAATGTCCCGAAGGACCACG
* * * *
1176588 TAGTATTGTCTCGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACG
1176611 TAGAAATGTCCCGAAGGACCACG
1 TAGAAATGTCCCGAAGGACCACG
* *
1176634 TAGAATTGTCCCGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACG
1176657 TAGAA
1 TAGAA
1176662 CCCTCGACTC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.19
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCACG
Found at i:1176913 original size:17 final size:16
Alignment explanation
Indices: 1176900--1176949 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
1176890 CTCATGTATC
1176900 CACATAGATCATGTAA
1 CACATAGATCATGTAA
*
1176916 CACATAGAATAACATATAA
1 CACATAG-AT--CATGTAA
*
1176935 CACATAGCTCATGTA
1 CACATAGATCATGTA
1176950 TAACAGTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 12 0.43
17 2 0.07
18 1 0.04
19 13 0.46
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (16 bp):
CACATAGATCATGTAA
Found at i:1185227 original size:53 final size:53
Alignment explanation
Indices: 1185164--1185279 Score: 182
Period size: 53 Copynumber: 2.2 Consensus size: 53
1185154 TTATGTGTAC
*
1185164 TTTCGACACTATGTGTGCATCCATG-GTATTCACAATGAGTTTGTGAATT-TCCA
1 TTTCGACACTATGTGTGCATCCATGAAT-TTCACAATGAGTTTGTGAATTAT-CA
*
1185217 TTTCGACACTATGTGTGCATCCATGAATTTCATAATGAGTTTGTGAATTATCA
1 TTTCGACACTATGTGTGCATCCATGAATTTCACAATGAGTTTGTGAATTATCA
1185270 TTTCGACACT
1 TTTCGACACT
1185280 TAGGTGCAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
53 57 0.97
54 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (53 bp):
TTTCGACACTATGTGTGCATCCATGAATTTCACAATGAGTTTGTGAATTATCA
Found at i:1187675 original size:19 final size:21
Alignment explanation
Indices: 1187653--1187697 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
1187643 TAAAATAAAT
1187653 AATAATAAAT-ATA-ATGTAA
1 AATAATAAATAATAGATGTAA
*
1187672 AATAATAAATAATAGTTGTAA
1 AATAATAAATAATAGATGTAA
1187693 AATAA
1 AATAA
1187698 AAGGGGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (21 bp):
AATAATAAATAATAGATGTAA
Found at i:1187685 original size:10 final size:10
Alignment explanation
Indices: 1187635--1187685 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
1187625 TGAAAAGATT
1187635 TAATAAAATAA
1 TAAT-AAATAA
1187646 -AATAAATAA
1 TAATAAATAA
1187655 TAATAAAT-A
1 TAATAAATAA
*
1187664 TAATGTAA-AA
1 TAAT-AAATAA
1187674 TAATAAATAA
1 TAATAAATAA
1187684 TA
1 TA
1187686 GTTGTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 13 0.38
10 21 0.62
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
TAATAAATAA
Found at i:1187685 original size:22 final size:21
Alignment explanation
Indices: 1187649--1187697 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1187639 AAAATAAAAT
1187649 AAATAATAATAAATA-TAATGTA
1 AAATAATAATAAATAGT--TGTA
1187671 AAATAATAA-ATAATAGTTGTA
1 AAATAATAATA-AATAGTTGTA
1187692 AAATAA
1 AAATAA
1187698 AAGGGGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 11 0.44
22 13 0.52
23 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (21 bp):
AAATAATAATAAATAGTTGTA
Found at i:1187698 original size:26 final size:26
Alignment explanation
Indices: 1187637--1187699 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
1187627 AAAAGATTTA
1187637 ATAAAATAAAATAAATAATAATAAAT
1 ATAAAATAAAATAAATAATAATAAAT
** **
1187663 ATAATGTAAAAT-AATAAATAATAGTT
1 ATAAAATAAAATAAAT-AATAATAAAT
*
1187689 GTAAAATAAAA
1 ATAAAATAAAA
1187700 GGGGATTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (26 bp):
ATAAAATAAAATAAATAATAATAAAT
Found at i:1188487 original size:25 final size:24
Alignment explanation
Indices: 1188440--1188487 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1188430 AAATCCAAAT
** *
1188440 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
1188464 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
1188488 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:1190223 original size:5 final size:5
Alignment explanation
Indices: 1190213--1190325 Score: 97
Period size: 5 Copynumber: 22.8 Consensus size: 5
1190203 TTTTCAGAGA
* * * *
1190213 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT -AAAT ATAAT GAAAAT AAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
** * * * *
1190263 TTACT AAAA- AATAT AATA- AAAAT AAAAT GAAAT AAAAT GAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
1190312 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
1190326 AATTGAACGA
Statistics
Matches: 86, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
4 10 0.12
5 67 0.78
6 9 0.10
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:1190305 original size:21 final size:21
Alignment explanation
Indices: 1190213--1190326 Score: 92
Period size: 21 Copynumber: 5.5 Consensus size: 21
1190203 TTTTCAGAGA
* *
1190213 AAAAT-AAAATAAAATTAATT
1 AAAATAAAAATAAAATAAAAT
*
1190233 AAAAT-AAAAT-AAATATAAT
1 AAAATAAAAATAAAATAAAAT
** *
1190252 GAAAATAAAGTTTACTAA-AAAAT
1 -AAAATAAA-AATA-AAATAAAAT
* *
1190275 ATAATAAAAATAAAATGAAAT
1 AAAATAAAAATAAAATAAAAT
*
1190296 AAAATGAAAATAAAATAAAAT
1 AAAATAAAAATAAAATAAAAT
1190317 AAAATAAAAA
1 AAAATAAAAA
1190327 ATTGAACGAA
Statistics
Matches: 72, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
19 6 0.08
20 17 0.24
21 35 0.49
22 8 0.11
23 4 0.06
24 2 0.03
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAATAAAAATAAAATAAAAT
Found at i:1195827 original size:19 final size:19
Alignment explanation
Indices: 1195810--1195868 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 19
1195800 TGAAAAGATT
1195810 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
*
1195830 TAATAAATAAAA-GGA-AA
1 TAATAAATAAAATAGATAA
1195847 -AAT-AATAAAATA-ATAAA
1 TAATAAATAAAATAGAT-AA
1195864 TAATA
1 TAATA
1195869 GTAGTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
15 8 0.25
16 3 0.09
17 4 0.12
18 5 0.16
19 8 0.25
20 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:1195883 original size:27 final size:26
Alignment explanation
Indices: 1195811--1195883 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 26
1195801 GAAAAGATTT
*
1195811 AATAAAA--TAAAATAGATAATAATA
1 AATAAAAGGTAAAATAGAAAATAATA
* *
1195835 AATAAAAGGAAAAATAATAAAATAATA
1 AATAAAAGGTAAAAT-AGAAAATAATA
*
1195862 AATAATAGTAGTAAAATA-AAAA
1 AATAAAAG--GTAAAATAGAAAA
1195884 GGGGGTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 7 0.18
26 5 0.13
27 20 0.51
28 1 0.03
29 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (26 bp):
AATAAAAGGTAAAATAGAAAATAATA
Found at i:1210804 original size:13 final size:13
Alignment explanation
Indices: 1210786--1210817 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1210776 GTCATAAATC
1210786 TATGACACGCATT
1 TATGACACGCATT
1210799 TATGACACGCATT
1 TATGACACGCATT
1210812 TATGAC
1 TATGAC
1210818 TTACATTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:1217583 original size:44 final size:45
Alignment explanation
Indices: 1217511--1217604 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
1217501 CATTTCTTAT
* *
1217511 CAATAAATTTATCATTTATTCCATAAGCTCATAAGCTTATTTTAC
1 CAATAAATTTACCATTTAATCCATAAGCTCATAAGCTTATTTTAC
* * *
1217556 CAATACATTTACCA-TTAATCCATAAGCTCGTAAGTTTATTTTAC
1 CAATAAATTTACCATTTAATCCATAAGCTCATAAGCTTATTTTAC
1217600 CAATA
1 CAATA
1217605 TACTTGCCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 32 0.73
45 12 0.27
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.39
Consensus pattern (45 bp):
CAATAAATTTACCATTTAATCCATAAGCTCATAAGCTTATTTTAC
Found at i:1217615 original size:44 final size:44
Alignment explanation
Indices: 1217530--1217617 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
1217520 TATCATTTAT
*
1217530 TCCATAAGCTCATAAGCTTATTTTACCAATACATTTACCATTAA
1 TCCATAAGCTCATAAGCTTATTTTACCAATACACTTACCATTAA
* * * *
1217574 TCCATAAGCTCGTAAGTTTATTTTACCAATATACTTGCCATTAA
1 TCCATAAGCTCATAAGCTTATTTTACCAATACACTTACCATTAA
1217618 CCTCATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.38
Consensus pattern (44 bp):
TCCATAAGCTCATAAGCTTATTTTACCAATACACTTACCATTAA
Found at i:1217783 original size:59 final size:58
Alignment explanation
Indices: 1217716--1217874 Score: 137
Period size: 59 Copynumber: 2.7 Consensus size: 58
1217706 CTCTATCTGG
* *
1217716 AAAATCATACGC-TTAGTATGCCTCCCCTT-TCATTTTAGCACATGAAGTGCCCTATTCA
1 AAAATCATAC-CATTAGTATG-ATCCCCTTATCATTTTAGCACATGAAATGCCCTATTCA
**** *
1217774 AAAATTCATACCATTAGTATGATTTTGTTATCATTTTAGCACATGAAATGCCCTATGT-G
1 AAAA-TCATACCATTAGTATGATCCCCTTATCATTTTAGCACATGAAATGCCCTAT-TCA
* * **
1217833 AAAATCCATACCAATAATATGATTTCCTTATC-TTTGTAGCAC
1 AAAAT-CATACCATTAGTATGATCCCCTTATCATTT-TAGCAC
1217875 CCTTAGTGCT
Statistics
Matches: 84, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
58 12 0.14
59 71 0.85
60 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (58 bp):
AAAATCATACCATTAGTATGATCCCCTTATCATTTTAGCACATGAAATGCCCTATTCA
Found at i:1217897 original size:59 final size:59
Alignment explanation
Indices: 1217834--1218158 Score: 214
Period size: 59 Copynumber: 5.5 Consensus size: 59
1217824 CCCTATGTGA
1217834 AAATCCATACCAAT-AATATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGG
1 AAATCCATA-CAATCAATATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGG
* * * * * * * **
1217893 AAATCCATACACTCAGTATGATTCCCTTACCATTT-TAGCA-CATCAAATGCCCTATCTGG
1 AAATCCATACAATCAATATGATTTCCTTATC-TTTGTAGCACCCT-TAGTGCTTTATCTGG
*** *
1217952 AAATCCATATTTTCAATATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTAG
1 AAATCCATACAATCAATATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGG
* * * * * * * * ** *
1218011 AAATCCATGCACTCAGTATGATTCCCTTACCATTT-TAGCA-CATAAAATGCCCTATCTAG
1 AAATCCATACAATCAATATGATTTCCTTATC-TTTGTAGCACCCT-TAGTGCTTTATCTGG
*** * * * ** *
1218070 AAATCCATATTTTCAATATGATTTCCTTATCATT-TAACACACC-CAGTGCTCCATATGG
1 AAATCCATACAATCAATATGATTTCCTTATCTTTGTAGCAC-CCTTAGTGCTTTATCTGG
** * *
1218128 AAATCTTTACACTCAGTATGATTTCCTTATC
1 AAATCCATACAATCAATATGATTTCCTTATC
1218159 ATTTTAACAC
Statistics
Matches: 202, Mismatches: 55, Indels: 19
0.73 0.20 0.07
Matches are distributed among these distances:
58 50 0.25
59 143 0.71
60 9 0.04
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (59 bp):
AAATCCATACAATCAATATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGG
Found at i:1217914 original size:118 final size:118
Alignment explanation
Indices: 1217805--1218169 Score: 495
Period size: 118 Copynumber: 3.1 Consensus size: 118
1217795 ATTTTGTTAT
* * ***
1217805 CATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCAAT-AATATGATTTCCTTATCTTTG
1 CATTTTAGCACATAAAATGCCCTATCTGAAAATCCATA-TTTTCAATATGATTTCCTTATCTTTG
1217869 TAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTAC
65 TAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTAC
* *
1217923 CATTTTAGCACATCAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCTTTGT
1 CATTTTAGCACATAAAATGCCCTATCTGAAAATCCATATTTTCAATATGATTTCCTTATCTTTGT
* *
1217988 AGCACCCTTAGTGCTTTATCTAGAAATCCATGCACTCAGTATGATTCCCTTAC
66 AGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTAC
*
1218041 CATTTTAGCACATAAAATGCCCTATCT-AGAAATCCATATTTTCAATATGATTTCCTTATCATT-
1 CATTTTAGCACATAAAATGCCCTATCTGA-AAATCCATATTTTCAATATGATTTCCTTATCTTTG
* * ** * ** * *
1218104 TAACACACC-CAGTGCTCCATATGGAAATCTTTACACTCAGTATGATTTCCTTAT
65 TAGCAC-CCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTAC
*
1218158 CATTTTAACACA
1 CATTTTAGCACA
1218170 CACAATTCCA
Statistics
Matches: 221, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
117 52 0.24
118 169 0.76
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (118 bp):
CATTTTAGCACATAAAATGCCCTATCTGAAAATCCATATTTTCAATATGATTTCCTTATCTTTGT
AGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTAC
Found at i:1221805 original size:30 final size:30
Alignment explanation
Indices: 1221728--1221817 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
1221718 TCTTTAAGTT
* * * * *
1221728 TTTTTTATCAAAATAAGTACCTAAACTTATT
1 TTTTTGATCAAAATAGGTACATAAA-GTATA
* * * *
1221759 TTTTTGGTTAATATAGGTACTTAAAGTATA
1 TTTTTGATCAAAATAGGTACATAAAGTATA
1221789 TTTTTGATCAAAATAGGTACATAAAGTAT
1 TTTTTGATCAAAATAGGTACATAAAGTAT
1221818 TCAATATTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 28 0.60
31 19 0.40
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (30 bp):
TTTTTGATCAAAATAGGTACATAAAGTATA
Found at i:1223081 original size:50 final size:50
Alignment explanation
Indices: 1223022--1223142 Score: 233
Period size: 50 Copynumber: 2.4 Consensus size: 50
1223012 GTTTTAACTC
1223022 TAATTCCTAATAAAATAATAATAACTAAAAATATTGTTTTAACCCAACCT
1 TAATTCCTAATAAAATAATAATAACTAAAAATATTGTTTTAACCCAACCT
*
1223072 TAATTCCTAATAAAATAATTATAACTAAAAATATTGTTTTAACCCAACCT
1 TAATTCCTAATAAAATAATAATAACTAAAAATATTGTTTTAACCCAACCT
1223122 TAATTCCTAATAAAATAATAA
1 TAATTCCTAATAAAATAATAA
1223143 ATCTGATCCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.35
Consensus pattern (50 bp):
TAATTCCTAATAAAATAATAATAACTAAAAATATTGTTTTAACCCAACCT
Found at i:1224056 original size:21 final size:21
Alignment explanation
Indices: 1224030--1224071 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1224020 GAGTGAATGG
1224030 ATCGATTATAAGCAAACTCAA
1 ATCGATTATAAGCAAACTCAA
1224051 ATCGATTATAAGCAAACTCAA
1 ATCGATTATAAGCAAACTCAA
1224072 CAAAAGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (21 bp):
ATCGATTATAAGCAAACTCAA
Found at i:1228932 original size:18 final size:17
Alignment explanation
Indices: 1228911--1228945 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1228901 TTTTGGCTTC
1228911 TTTTT-TTTTTTGCTTTT
1 TTTTTGTTTTTTG-TTTT
1228928 TTTTTGTTTTTTGTTTT
1 TTTTTGTTTTTTGTTTT
1228945 T
1 T
1228946 GAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.89
Consensus pattern (17 bp):
TTTTTGTTTTTTGTTTT
Found at i:1229755 original size:43 final size:48
Alignment explanation
Indices: 1229691--1229796 Score: 132
Period size: 50 Copynumber: 2.3 Consensus size: 48
1229681 ATAACTAGAG
*
1229691 AATAAAATAATAATAAATT-AAACA-TGTTTTAA-C-TC-TAATTCCT
1 AATAAAATAATAATAAATTAAAACATTGTTTTAACCACCTTAATTCCT
* *
1229734 AATAAAATAATAATAACTTAAAATATTGTTTTAACCCAACCTTAATTCCT
1 AATAAAATAATAATAAATTAAAACATTGTTTTAA-CC-ACCTTAATTCCT
1229784 AATAAAATAATAA
1 AATAAAATAATAA
1229797 ATCTGATCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
43 18 0.34
44 4 0.08
45 8 0.15
47 1 0.02
49 1 0.02
50 21 0.40
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (48 bp):
AATAAAATAATAATAAATTAAAACATTGTTTTAACCACCTTAATTCCT
Found at i:1230568 original size:148 final size:147
Alignment explanation
Indices: 1230296--1230591 Score: 486
Period size: 148 Copynumber: 2.0 Consensus size: 147
1230286 TATCATATGT
*
1230296 TTGCATTTACATCTTATGATATGCTTATCAAATATTCATCATTCATTATGTTTAATGATATACAT
1 TTGCATTTACA-CTTATGATATGCTTATCAAATATTCATCATTCATCATGTTTAATGATATACAT
* * * * *
1230361 TGATGTGACTCATCATACAAGAACCTAGAAGAATTCTCTAGTGGACCTATGACATGAGCTAGGGC
65 TGATGTGACTCATCAGACAAGAACCCAGAAGAATTCTATAGTGGACCTATGAAACGAGCTAGGGC
1230426 AAGGAAATTCCAAGTAAC
130 AAGGAAATTCCAAGTAAC
* *
1230444 TTGCATTTAC-CTTATACGATATGCTTATCAAATGTTCATCATTCATCATGTTTAATGATATGCA
1 TTGCATTTACACTTAT--GATATGCTTATCAAATATTCATCATTCATCATGTTTAATGATATACA
1230508 TTGATGTGACTCATCAGACAAGAACCCAGAAGAATTCTATAGTGGACCTATGAAACGAGCTAGGG
64 TTGATGTGACTCATCAGACAAGAACCCAGAAGAATTCTATAGTGGACCTATGAAACGAGCTAGGG
1230573 CAAGGAAATTCCAAGTAAC
129 CAAGGAAATTCCAAGTAAC
1230592 CATGGAAAGC
Statistics
Matches: 138, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
146 5 0.04
148 133 0.96
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (147 bp):
TTGCATTTACACTTATGATATGCTTATCAAATATTCATCATTCATCATGTTTAATGATATACATT
GATGTGACTCATCAGACAAGAACCCAGAAGAATTCTATAGTGGACCTATGAAACGAGCTAGGGCA
AGGAAATTCCAAGTAAC
Found at i:1230855 original size:17 final size:17
Alignment explanation
Indices: 1230835--1230873 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1230825 AGTTCACTGG
* *
1230835 TTAAATTAGTTCATTCA
1 TTAAAATAGTTCATTAA
*
1230852 TTAAAATGGTTCATTAA
1 TTAAAATAGTTCATTAA
1230869 TTAAA
1 TTAAA
1230874 CTAGCTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (17 bp):
TTAAAATAGTTCATTAA
Found at i:1235479 original size:82 final size:81
Alignment explanation
Indices: 1235326--1235587 Score: 228
Period size: 82 Copynumber: 3.2 Consensus size: 81
1235316 TTTAGTGATG
* * * * * *
1235326 TTTTTATATAAACGCCGCTAAAGACTATATTTTAGTGGC-TTTTTATACAAATGGCGCTATAGAC
1 TTTTTATACAAACGCCGCTAAATACTATATTTTAGTGGCGTTTTTATACAAACGCCACTAAAGAC
*
1235390 TCATACTTTAATGG-T
66 TCATACTTTAATGGCA
* *
1235405 TTTTTCATACAAACGCCGCTAAATACTCATATTTTAGTTGCGTTTTTATACAAACGCCACTAAAT
1 TTTTT-ATACAAACGCCGCTAAATACT-ATATTTTAGTGGCGTTTTTATACAAACGCCACTAAAG
* *
1235470 ACTCGTACTTTAGTGGCA
64 ACTCATACTTTAATGGCA
* * * * * ** * *
1235488 TTTTTATAGAAAAGTCTCTAAATACTTGTACGTTAGTGGCGTTTTTAAACAAACGCC-GTAATAG
1 TTTTTATACAAACGCCGCTAAATAC-TATATTTTAGTGGCGTTTTTATACAAACGCCACTAA-A-
* *
1235552 GACACATA-TATAATGGCA
63 GACTCATACTTTAATGGCA
*
1235570 TTTTTGA-AAAAACGCCGC
1 TTTTT-ATACAAACGCCGC
1235588 AAGAGATTCA
Statistics
Matches: 145, Mismatches: 30, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
79 5 0.03
80 19 0.13
81 15 0.10
82 94 0.65
83 12 0.08
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (81 bp):
TTTTTATACAAACGCCGCTAAATACTATATTTTAGTGGCGTTTTTATACAAACGCCACTAAAGAC
TCATACTTTAATGGCA
Found at i:1235509 original size:41 final size:41
Alignment explanation
Indices: 1235316--1235540 Score: 159
Period size: 41 Copynumber: 5.5 Consensus size: 41
1235306 ATACTCATTT
** * * * * * *
1235316 TTTAGTGATGTTTTTATATAAACGCCGCTAAAGACT-ATAT
1 TTTAGTGGCGTTTTTATACAAAAGCCACTAAATACTCGTAC
* * * * * *
1235356 TTTAGTGGC-TTTTTATACAAATGGCGCTATAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAAAGCCACTAAATACTCGTAC
* * * * * *
1235396 TTTAATGG-TTTTTTCATACAAACGCCGCTAAATACTCATAT
1 TTTAGTGGCGTTTTT-ATACAAAAGCCACTAAATACTCGTAC
* *
1235437 TTTAGTTGCGTTTTTATACAAACGCCACTAAATACTCGTAC
1 TTTAGTGGCGTTTTTATACAAAAGCCACTAAATACTCGTAC
* * * * *
1235478 TTTAGTGGCATTTTTATAGAAAAGTCTCTAAATACTTGTAC
1 TTTAGTGGCGTTTTTATACAAAAGCCACTAAATACTCGTAC
* *
1235519 GTTAGTGGCGTTTTTAAACAAA
1 TTTAGTGGCGTTTTTATACAAA
1235541 CGCCGTAATA
Statistics
Matches: 151, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
39 22 0.15
40 22 0.15
41 102 0.68
42 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAAAGCCACTAAATACTCGTAC
Found at i:1235794 original size:20 final size:20
Alignment explanation
Indices: 1235771--1235820 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1235761 ATCTGATGTT
*
1235771 TCTTCGCCGATATCACTTTC
1 TCTTCGCCGATATAACTTTC
* * *
1235791 TCTTGGCTGATCTAACTTTC
1 TCTTCGCCGATATAACTTTC
1235811 TCTTCGCCGA
1 TCTTCGCCGA
1235821 ATCTGCTGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.32, G:0.14, T:0.40
Consensus pattern (20 bp):
TCTTCGCCGATATAACTTTC
Found at i:1236889 original size:17 final size:17
Alignment explanation
Indices: 1236864--1236897 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1236854 TTTAATTAAC
* *
1236864 TATTTAAATTTAAAATT
1 TATTCAAATTCAAAATT
1236881 TATTCAAATTCAAAATT
1 TATTCAAATTCAAAATT
1236898 AACATGATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTCAAATTCAAAATT
Found at i:1237744 original size:26 final size:25
Alignment explanation
Indices: 1237698--1237746 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1237688 TAAAAAAATA
* *
1237698 AAAACAAAAAAATAAAGAAATAAAG
1 AAAACAAAAAAAAAAACAAATAAAG
1237723 AAAACAAAAAAAAATAACAAATAA
1 AAAACAAAAAAAAA-AACAAATAA
1237747 TAATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.82, C:0.06, G:0.04, T:0.08
Consensus pattern (25 bp):
AAAACAAAAAAAAAAACAAATAAAG
Found at i:1237770 original size:38 final size:36
Alignment explanation
Indices: 1237667--1237808 Score: 96
Period size: 38 Copynumber: 3.9 Consensus size: 36
1237657 AACATAATGG
* * *
1237667 ATAAAACAAAGATAAA-GAACATAAA-AAAATAAA-A
1 ATAAAATAAAAATAAATAAACATAAATAAAA-AAAGA
* * * * *
1237701 ACAAAAAAATAAAGAAATAAAGA-AAACAAAAAAA-A
1 ATAAAATAA-AAATAAATAAACATAAATAAAAAAAGA
* * *
1237736 ATAACAAATAATAATATATATACAATAAATAAAAACAAGA
1 AT-A-AAATAAAAATAAATAAAC-ATAAATAAAAA-AAGA
1237776 ATAAAATAAAAATAAATAAACATAAATAAAAAA
1 ATAAAATAAAAATAAATAAACATAAATAAAAAA
1237809 TATAAAGAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
34 7 0.09
35 13 0.16
36 16 0.20
37 17 0.21
38 23 0.28
39 3 0.04
40 3 0.04
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.15
Consensus pattern (36 bp):
ATAAAATAAAAATAAATAAACATAAATAAAAAAAGA
Found at i:1237794 original size:10 final size:10
Alignment explanation
Indices: 1237779--1237928 Score: 59
Period size: 9 Copynumber: 15.0 Consensus size: 10
1237769 AACAAGAATA
1237779 AAATAAAAAT
1 AAATAAAAAT
*
1237789 AAATAAACAT
1 AAATAAAAAT
1237799 AAATAAAAA-
1 AAATAAAAAT
* *
1237808 ATATAAAGA-
1 AAATAAAAAT
*
1237817 AAAGAAAAA-
1 AAATAAAAAT
*
1237826 AAAGAAAGAA-
1 AAATAAA-AAT
*
1237836 AAA-AAAAGT
1 AAATAAAAAT
* *
1237845 AATATATATAT
1 AA-ATAAAAAT
*
1237856 ATAATAAAATGT
1 A-AATAAAA-AT
1237868 AAAATAAAATATT
1 -AAATAAAA-A-T
1237881 AGAA-AAAAAT
1 A-AATAAAAAT
1237891 -AA-AAAAAT
1 AAATAAAAAT
1237899 AAA-AAAAAT
1 AAATAAAAAT
1237908 AAAATAAACAAT
1 -AAATAAA-AAT
1237920 AAA-AAAAAT
1 AAATAAAAAT
1237929 TAAAAGACCA
Statistics
Matches: 112, Mismatches: 15, Indels: 27
0.73 0.10 0.18
Matches are distributed among these distances:
8 9 0.08
9 36 0.32
10 30 0.27
11 15 0.13
12 18 0.16
13 4 0.04
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1237843 original size:14 final size:14
Alignment explanation
Indices: 1237812--1237841 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1237802 TAAAAAATAT
1237812 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
1237826 AAAG-AAAGAAAAA
1 AAAGAAAAGAAAAA
1237839 AAA
1 AAA
1237842 AGTAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAA
Found at i:1237891 original size:18 final size:17
Alignment explanation
Indices: 1237868--1237914 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
1237858 AATAAAATGT
*
1237868 AAAATAAAATATTAGAAA
1 AAAATAAAATAATA-AAA
*
1237886 AAAATAAAAAAATAAAA
1 AAAATAAAATAATAAAA
1237903 AAAATAAAATAA
1 AAAATAAAATAA
1237915 ACAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAATAAAATAATAAAA
Found at i:1237897 original size:9 final size:9
Alignment explanation
Indices: 1237883--1237933 Score: 59
Period size: 10 Copynumber: 5.3 Consensus size: 9
1237873 AAAATATTAG
1237883 AAAAAAAT-
1 AAAAAAATA
1237891 AAAAAAATA
1 AAAAAAATA
1237900 AAAAAAATAA
1 AAAAAAAT-A
1237910 AATAAACAATA
1 AA-AAA-AATA
1237921 AAAAAAATTA
1 AAAAAAA-TA
1237931 AAA
1 AAA
1237934 GACCAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.21
9 10 0.26
10 11 0.29
11 6 0.16
12 3 0.08
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1237911 original size:14 final size:14
Alignment explanation
Indices: 1237587--1237933 Score: 79
Period size: 14 Copynumber: 22.9 Consensus size: 14
1237577 AATTAGGGAA
*
1237587 AAAAACAAATGAAAT
1 AAAAA-AAATAAAAT
*
1237602 AAAGAAAATAAAAT
1 AAAAAAAATAAAAT
*
1237616 AAAGAAAATAAAAAGAT
1 AAA-AAAA-ATAAA-AT
1237633 AAAGAAAAA-AAAGAT
1 AAA-AAAAATAAA-AT
*
1237648 -AAAAAAGTAAACAT
1 AAAAAAAATAAA-AT
* *
1237662 AATGGATAAAACAAAGAT
1 AA---AAAAAATAAA-AT
*
1237680 AAAGAACATAAAAAAAT
1 AAA-AA-A-AATAAAAT
1237697 AAAAACAAA-AAAAT
1 AAAAA-AAATAAAAT
*
1237711 -AAAGAAATAAAGA-
1 AAAAAAAATAAA-AT
1237724 AAACAAAAA-AAAAT
1 AAA-AAAAATAAAAT
* *
1237738 AACAAATAATAATAT
1 AA-AAAAAATAAAAT
* * *
1237753 ATATACAAT-AAAT
1 AAAAAAAATAAAAT
1237766 AAAAACAAGAATAAAAT
1 -AAAA-AA-AATAAAAT
1237783 AAAAATAAATAAACAT
1 AAAAA-AAATAAA-AT
*
1237799 AAATAAAAAATATAAAG
1 -AA-AAAAAATA-AAAT
*
1237816 AAAAGAAAA-AAAAG
1 AAAA-AAAATAAAAT
1237830 AAAGAAAAA-AAAAGT
1 AAA-AAAAATAAAA-T
* * *
1237845 AATATATATATATAAT
1 AA-A-AAAAATAAAAT
1237861 AAAATGTAAAATAAAAT
1 AAAA---AAAATAAAAT
** *
1237878 ATTAGAAA-AAAAT
1 AAAAAAAATAAAAT
1237891 -AAAAAAATAAAA-
1 AAAAAAAATAAAAT
1237903 AAAATAAAATAAACAAT
1 AAAA-AAAAT-AA-AAT
1237920 AAAAAAAATTAAAA
1 AAAAAAAA-TAAAA
1237934 GACCAAAACA
Statistics
Matches: 252, Mismatches: 38, Indels: 84
0.67 0.10 0.22
Matches are distributed among these distances:
12 7 0.03
13 26 0.10
14 66 0.26
15 46 0.18
16 41 0.16
17 45 0.18
18 21 0.08
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (14 bp):
AAAAAAAATAAAAT
Found at i:1237922 original size:21 final size:23
Alignment explanation
Indices: 1237886--1237933 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
1237876 ATATTAGAAA
1237886 AAAATAAAAAAATAAAAAAAA-T
1 AAAATAAAAAAATAAAAAAAATT
*
1237908 AAAAT-AAACAATAAAAAAAATT
1 AAAATAAAAAAATAAAAAAAATT
1237930 AAAA
1 AAAA
1237934 GACCAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAATAAAAAAATAAAAAAAATT
Found at i:1237923 original size:17 final size:17
Alignment explanation
Indices: 1237762--1237925 Score: 62
Period size: 17 Copynumber: 8.9 Consensus size: 17
1237752 TATATACAAT
* *
1237762 AAATAAAAACAAGAATA
1 AAATAAAAAAAAAAATA
*
1237779 AAATAAAAATAAATAAACA
1 AAATAAAAA-AAA-AAATA
* *
1237798 TAAATAAAAAATATAAAGA
1 -AAATAAAAAA-AAAAATA
* *
1237817 AAAGAAAAAAAAGAAAGA
1 AAATAAAAAAAA-AAATA
1237835 AAA-AAAAAGTAATATATATATA
1 AAATAAAAA--AA-A-A-A-ATA
* ***
1237857 TAATAAAATGTAAAATA
1 AAATAAAAAAAAAAATA
* *
1237874 AAATATTAGAAAAAAATA
1 AAATA-AAAAAAAAAATA
1237892 AAA-AAATAAAAAAAATA
1 AAATAAA-AAAAAAAATA
1237909 AAATAAACAATAAAAAA
1 AAATAAA-AA-AAAAAA
1237926 AATTAAAAGA
Statistics
Matches: 110, Mismatches: 22, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
16 1 0.01
17 35 0.32
18 35 0.32
19 17 0.15
20 13 0.12
21 1 0.01
22 4 0.04
23 4 0.04
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (17 bp):
AAATAAAAAAAAAAATA
Found at i:1237935 original size:101 final size:99
Alignment explanation
Indices: 1237687--1237927 Score: 235
Period size: 101 Copynumber: 2.4 Consensus size: 99
1237677 GATAAAGAAC
* *
1237687 ATAAAAAAATAAAAACAAAAAAATAAAGAAATAAAGAAAACAAAA-AAAAATAACAAATAATAAT
1 ATAAAAAAATAAAAA-AAAAAAATAAA-AAATAAAAAAAAAAAAAGAAAAATAACAAATAATAAT
1237751 ATATATACAATAAATAAAAACAAGAATAAAATAAAA
64 ATATATACAATAAATAAAAACAAGAATAAAATAAAA
* * * *
1237787 ATAAATAAACATAAATAAAAAATATAAAGAAA-AGAAAAAAAAGAAAGAAAAA-AA-AAGTAAT-
1 ATAAA-AAA-ATAAAAAAAAAAAATAAA-AAATA-AAAAAAAAAAAAGAAAAATAACAAATAATA
* * *
1237848 ATATATATATAATAAAATGTAAAATAA-AATATTAGAA-AAAA
62 ATATATATACAAT-AAAT-AAAAACAAGAATA--A-AATAAAA
*
1237889 ATAAAAAAATAAAAAAAATAAAATAAACAATAAAAAAAA
1 ATAAAAAAATAAAAAAAA-AAAATAAAAAATAAAAAAAA
1237928 TTAAAAGACC
Statistics
Matches: 118, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
99 12 0.10
100 38 0.32
101 45 0.38
102 21 0.18
103 2 0.02
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.17
Consensus pattern (99 bp):
ATAAAAAAATAAAAAAAAAAAATAAAAAATAAAAAAAAAAAAAGAAAAATAACAAATAATAATAT
ATATACAATAAATAAAAACAAGAATAAAATAAAA
Found at i:1237952 original size:13 final size:13
Alignment explanation
Indices: 1237934--1237958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1237924 AAAATTAAAA
1237934 GACCAAAACAAAT
1 GACCAAAACAAAT
1237947 GACCAAAACAAA
1 GACCAAAACAAA
1237959 GTTATTGTAA
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:0.24, G:0.08, T:0.04
Consensus pattern (13 bp):
GACCAAAACAAAT
Found at i:1239749 original size:171 final size:170
Alignment explanation
Indices: 1239437--1240900 Score: 1405
Period size: 171 Copynumber: 8.5 Consensus size: 170
1239427 TTAAGCTATA
* * * * * * *
1239437 CTGCAAATGTGACATGCCCTTGAGCGGAGTGTAATCGAACTTGAAGGTCTTGGCTGACAGATAGC
1 CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTCTTGGTTGACAGATAAC
* * * * * *
1239502 CCTTCTCGCCTTGAGCTATGATGTAAATTTGATTTGCC-TCGAAGTTGAGTGTAATCAAACTCGA
66 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTAG-AGCTGAGTGTAATCGAACTCGA
* *
1239566 GGGTCTTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATG
130 AGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* * * * *
1239607 CTGCAAATTTGATATGCCTTTGAGCTAAGTGTAATCGAACTAGAAGGTCTTTTGATGACAAATAG
1 CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTC-TTGGTTGACAGATAA
* * * * * * *
1239672 CCCTACTCGCCTTGAGATATGCTATAAATTTCATGTGCCTCAGAGCTGAGTGTAATCGAACTCTA
65 CCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTAGAGCTGAGTGTAATCGAACTCGA
* * * ** *
1239737 GGGTCCTGGTTGATAGATAACCCTTCTCGTTTTGAGTTATA
130 AGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* * * *
1239778 CTGCAAATTTGACATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAGATAG
1 CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTC-TTGGTTGACAGATA-
* * ** *
1239843 A-CCTTCTCGCCTTGAGCTATGATGTAAATTTGATGTGCATGTGTTAGAGTTGAGTGTAATCGAA
64 ACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGA--T--ATGCCTTAGAGCTGAGTGTAATCGAA
* * *
1239907 CTTGAGGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTATG
125 CTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* * *
1239953 CTGCAAATTTTATATACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAAC
1 CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTCTTGGTTGACAGATAAC
* * * * *
1240018 CCTTCTCACCTTGAGTTATGCTGCAAAATTGATATTCCTTAGAG-TAGAGTGTAATCAAACTCGA
66 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTAGAGCT-GAGTGTAATCGAACTCGA
* * * *
1240082 AGGTCTT-TTAATGACATATAACCCTTCTCGCCTTGAGCTATA
130 AGGTCTTGGT--TGACAGATAACCCTTCTCGCCTTGAGTTATG
** * * ** * * * * *
1240124 CTATAAATTTGATGTGTCTCGGAGCTGAGTGTAATCAAACTCGAGGGTCTTGGTTGACAAATAAA
1 CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTCTTGGTTGACAGATAAC
* * * *
1240189 CCTTCTCGTCTTGAGTTATG-TTTCAAATTTGATATTCCTTTGAGCTGAGTGTAATCGAACTCGA
66 CCTTCTCGCCTTGAGTTATGCTGT-AAATTTGATATGCCTTAGAGCTGAGTGTAATCGAACTCGA
* * * * *
1240253 AGGTCTTTTGATGACAGATAACCCTTCTTGCCTTAAGTTATT
130 AGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
** ** ** * * *
1240295 CTATAAATTTGACGTGCCTAGGAGCTGAGTGTAATCGAACTAGAGGGTATTGGTTGAGAGATAAC
1 CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTCTTGGTTGACAGATAAC
* * ** * * * *
1240360 CATTCTCACCTTGAGTTATGCTACAAATTTTATATGCCTTAAAGTTTAGTGTAATCGAACTCGAA
66 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTAGAGCTGAGTGTAATCGAACTCGAA
* * * * *
1240425 GGTCTTTTGATGACAAATAGA-CCTTCTCTCCTTGAGCTATG
131 GGTC-TTGGTTGACAGATA-ACCCTTCTCGCCTTGAGTTATG
* * *** * * *
1240466 ATGTAAATTTGATATGCATGCGTCAAAGCTAAGTGTAATCGAACTCA-AGGGTCTTGGTTGATAG
1 CTGCAAATTTGATATGC---C-TTTGAGCTGAGTGTAATCGAACT-AGAAGGTCTTGGTTGACAG
* * *** * * *
1240530 ATAACCCTTTTCTCCTTGAGTTATGCAACAAATTTGATATACCTTTGAGCTGAGTCTAATCGAAC
61 ATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTAGAGCTGAGTGTAATCGAAC
*
1240595 TCGAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGTTATG
126 TCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* * * * * *
1240640 TTGCAAATTTGATATGCCTTTGAGCTTAGTGTAATCGAACTCGAAGGTCTTTTGATGACAAATAA
1 CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTC-TTGGTTGACAGATAA
** * * *
1240705 CCCTTCTCGCCTTGAGCCATGTTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
65 CCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTAGAGCTGAGTGTAATCGAACTCGA
* * * * *
1240770 AGGTCTTTTGTTGATAGATAACCCTTATTGCCTTAAGTTATG
130 AGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* * * * * *
1240812 CTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGACAGATAG
1 CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTC-TTGGTTGACAGATAA
*
1240877 CTCTTCTCGCCTTGAGCTTA-GCTG
65 CCCTTCTCGCCTTGAG-TTATGCTG
1240901 AACTTGATTC
Statistics
Matches: 1077, Mismatches: 190, Indels: 52
0.82 0.14 0.04
Matches are distributed among these distances:
169 2 0.00
170 98 0.09
171 576 0.53
172 111 0.10
173 4 0.00
174 84 0.08
175 201 0.19
176 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (170 bp):
CTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTCTTGGTTGACAGATAAC
CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTAGAGCTGAGTGTAATCGAACTCGAA
GGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
Found at i:1240266 original size:431 final size:428
Alignment explanation
Indices: 1239456--1240900 Score: 1672
Period size: 431 Copynumber: 3.4 Consensus size: 428
1239446 TGACATGCCC
* * * *
1239456 TTGAGCGGAGTGTAATCGAACTTGAAGGTCTTGGCTGACAGATAGCCCTTCTCGCCTTGAGCTAT
1 TTGAGCTGAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTAT
* * * * * * * *
1239521 GATGTAAATTTGATTTGCC-TCGAAGTTGAGTGTAATCAAACTCGAGGGTC-TTGGTTGATAGAT
66 GCTGCAAATTTGATATGCCTTTG-AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGACAGAT
* * *
1239584 AACCCTTCTCGCCTTGAGTTATGCTGCAAATTTGATATGCCTTTGAGCTAAGTGTAATCGAACTA
130 AACCCTTCTCGCCTTGAGTTATGCTGCAAATTTGATATTCCTTAGAGCTAAGTGTAATCGAACTC
* * *
1239649 GAAGGTCTTTTGATGACAAATAGCCCTACTCGCCTTGAGATATGCTATAAATTTCATGTGCCTCA
195 GAAGGTCTTTT-ATGACAAATAACCCTTCTCGCCTTGAGATATGCTATAAATTTGATGTGCCTCA
* * * * **
1239714 GAGCTGAGTGTAATCGAACTCTAGGGTCCTGGTTGATAGATAACCCTTCTCGTTTTGAGTTATAC
259 GAGCTGAGTGTAATCGAACTCGAGGGTCTTGGTTGACAGATAACCCTTCTCGTCTTGAGTTATGT
*
1239779 TGCAAATTTGACATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAGATAGA
324 TGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAGATA-A
1239844 -CCTTCTCGCCTTGAGCTATGATGTAAATTTGATGTGCATGTG
388 CCCTTCTCGCCTTGAGCTATGATGTAAATTTGATGTGC-T-TG
* * *
1239886 TTAGAGTTGAGTGTAATCGAACTTGAGGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTA
1 TT-GAGCTGAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTA
* * *
1239951 TGCTGCAAATTTTATATACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTC-TTGGTTGACAGAT
65 TGCTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGACAGAT
* * *
1240015 AACCCTTCTCACCTTGAGTTATGCTGCAAAATTGATATTCCTTAGAG-TAGAGTGTAATCAAACT
130 AACCCTTCTCGCCTTGAGTTATGCTGCAAATTTGATATTCCTTAGAGCTA-AGTGTAATCGAACT
* * * *
1240079 CGAAGGTCTTTTAATGACATATAACCCTTCTCGCCTTGAGCTATACTATAAATTTGATGTGTCTC
194 CGAAGGTCTTTT-ATGACAAATAACCCTTCTCGCCTTGAGATATGCTATAAATTTGATGTGCCTC
* * * *
1240144 GGAGCTGAGTGTAATCAAACTCGAGGGTCTTGGTTGACAAATAAACCTTCTCGTCTTGAGTTATG
258 AGAGCTGAGTGTAATCGAACTCGAGGGTCTTGGTTGACAGATAACCCTTCTCGTCTTGAGTTATG
* *
1240209 TTTCAAATTTGATATTCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAGATAA
323 TTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAGATAA
* * * ** * * *
1240274 CCCTTCTTGCCTTAAGTTATTCTATAAATTTGACGTGCCTAG
388 CCCTTCTCGCCTTGAGCTATGATGTAAATTTGATGTG-CTTG
* * * * * *
1240316 --GAGCTGAGTGTAATCGAACTAGAGGGTATTGGTTGAGAGATAACCATTCTCACCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTAT
* * ** * * * * *
1240379 GCTACAAATTTTATATGCCTTAAAGTTTAGTGTAATCGAACTCGAAGGTCTTTTGATGACAAATA
66 GCTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGACAGATA
* * * * * * *
1240444 GA-CCTTCTCTCCTTGAGCTATGATGTAAATTTGATATGCATGCGTCAAAGCTAAGTGTAATCGA
131 -ACCCTTCTCGCCTTGAGTTATGCTGCAAATTTGATAT---T-CCTTAGAGCTAAGTGTAATCGA
* * * * * * * * * *
1240508 ACTC-AAGGGTCTTGGT-TGATAGATAACCCTTTTCTCCTTGAGTTATGCAACAAATTTGATATA
191 ACTCGAA-GGTCTT-TTATGACAAATAACCCTTCTCGCCTTGAGATATGCTATAAATTTGATGTG
** * * **
1240571 CCTTTGAGCTGAGTCTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGT
254 CCTCAGAGCTGAGTGTAATCGAACTCGAGGGTCTTGGTTGACAGATAACCCTTCTCGTCTTGAGT
* *
1240636 TATGTTGCAAATTTGATATGCCTTTGAGCTTAGTGTAATCGAACTCGAAGGTCTTTTGATGACAA
319 TATGTTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAG
* * *
1240701 ATAACCCTTCTCGCCTTGAGCCATGTTGTAAATTTGATGTGCCT-
384 ATAACCCTTCTCGCCTTGAGCTATGATGTAAATTTGATGTGCTTG
* * * * * *
1240745 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTATTGCCTTAAGTTA
1 TTGAGCTGAGTGTAATCGAACTTGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTA
* * * * *
1240810 TGCTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGACAGAT
65 TGCTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGACAGAT
* *
1240875 AGCTCTTCTCGCCTTGAGCTTA-GCTG
130 AACCCTTCTCGCCTTGAG-TTATGCTG
1240901 AACTTGATTC
Statistics
Matches: 855, Mismatches: 141, Indels: 36
0.83 0.14 0.03
Matches are distributed among these distances:
427 99 0.12
428 41 0.05
429 1 0.00
430 7 0.01
431 577 0.67
432 125 0.15
433 5 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (428 bp):
TTGAGCTGAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTAT
GCTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGACAGATA
ACCCTTCTCGCCTTGAGTTATGCTGCAAATTTGATATTCCTTAGAGCTAAGTGTAATCGAACTCG
AAGGTCTTTTATGACAAATAACCCTTCTCGCCTTGAGATATGCTATAAATTTGATGTGCCTCAGA
GCTGAGTGTAATCGAACTCGAGGGTCTTGGTTGACAGATAACCCTTCTCGTCTTGAGTTATGTTG
CAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAGATAACCC
TTCTCGCCTTGAGCTATGATGTAAATTTGATGTGCTTG
Found at i:1240654 original size:602 final size:601
Alignment explanation
Indices: 1239437--1240889 Score: 1991
Period size: 602 Copynumber: 2.4 Consensus size: 601
1239427 TTAAGCTATA
* * * * * *
1239437 CTGC-AAATGTGACATGCCCTT-GAGCGGAGTGTAATCGAACTTGAAGGTC-TTGGCTGACAGAT
1 CTGCAAAAT-TGATATG-CCTTAGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAAAT
* * * *
1239499 AGCCCTTCTCGCCTTGAGCTATGATGTAAATTTGATTTGCCTCGAAGTTGAGTGTAATCAAACTC
64 AACCCTTCTCGCCTTGAGCTAT-ATGTAAATTTGATGTGCCTCGGAGCTGAGTGTAATCAAACTC
* *
1239564 GAGGGTCTTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTTGATATGCCTTTG
128 GAGGGTCTTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATGTTTCAAATTTGATATGCCTTTG
* * * *
1239629 AGCTAAGTGTAATCGAACTAGAAGGTCTTTTGATGACAAATAGCCCTACTCGCCTTGAGATATGC
193 AGCTGAGTGTAATCGAACTAGAAGGTCTTTTGATGACAGATAGCCCTTCTCGCCTTAAGATATGC
* ** * *
1239694 TATAAATTTCATGTGCCTCAGAGCTGAGTGTAATCGAACTCTAGGGTCCTGGTTGATAGATAACC
258 TATAAATTTCACGTGCCTCAGAGCTGAGTGTAATCGAACTAGAGGGTACTGGTTGAGAGATAACC
* *** * **
1239759 CTTCTCGTTTTGAGTTATACTGCAAATTTGACATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
323 ATTCTCACCTTGAGTTATACTACAAATTTGACATGCCTTAAAGCTGAGTGTAATCGAACTCGAAG
* * * *
1239824 GTCTTTTGATGACAGATAGACCTTCTCGCCTTGAGCTATGATGTAAATTTGATGTGCATGTGTTA
388 GTCTTTTGATGACAAATAGACCTTCTCGCCTTGAGCTATGATGTAAATTTGATATGCATGCGTCA
* * * **
1239889 GAGTTGAGTGTAATCGAACTTGAGGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTATGC
453 AAGCTAAGTGTAATCGAACTCAAGGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTATGC
** * * *
1239954 TGCAAATTTTATATACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACC
518 AACAAATTTGATATACCTTTGAGCTGAGTCTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
1240019 CTTCTCACCTTGAGTTATG
583 CTTCTCACCTTGAGTTATG
* * * *
1240038 CTGCAAAATTGATATTCCTTAGAG-TAGAGTGTAATCAAACTCGAAGGTCTTTTAATGACATATA
1 CTGCAAAATTGATATGCCTTAGAGCT-GAGTGTAATCGAACTCGAAGGTCTTTTGATGACAAATA
* *
1240102 ACCCTTCTCGCCTTGAGCTATACTATAAATTTGATGTGTCTCGGAGCTGAGTGTAATCAAACTCG
65 ACCCTTCTCGCCTTGAGCTATA-TGTAAATTTGATGTGCCTCGGAGCTGAGTGTAATCAAACTCG
* * * * *
1240167 AGGGTCTTGGTTGACAAATAAACCTTCTCGTCTTGAGTTATGTTTCAAATTTGATATTCCTTTGA
129 AGGGTCTTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATGTTTCAAATTTGATATGCCTTTGA
* * * * *
1240232 GCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAGATAACCCTTCTTGCCTTAAGTTATTCT
194 GCTGAGTGTAATCGAACTAGAAGGTCTTTTGATGACAGATAGCCCTTCTCGCCTTAAGATATGCT
* *
1240297 ATAAATTTGACGTGCCT-AGGAGCTGAGTGTAATCGAACTAGAGGGTATTGGTTGAGAGATAACC
259 ATAAATTTCACGTGCCTCA-GAGCTGAGTGTAATCGAACTAGAGGGTACTGGTTGAGAGATAACC
* * * * *
1240361 ATTCTCACCTTGAGTTATGCTACAAATTTTATATGCCTTAAAGTTTAGTGTAATCGAACTCGAAG
323 ATTCTCACCTTGAGTTATACTACAAATTTGACATGCCTTAAAGCTGAGTGTAATCGAACTCGAAG
*
1240426 GTCTTTTGATGACAAATAGACCTTCTCTCCTTGAGCTATGATGTAAATTTGATATGCATGCGTCA
388 GTCTTTTGATGACAAATAGACCTTCTCGCCTTGAGCTATGATGTAAATTTGATATGCATGCGTCA
* *
1240491 AAGCTAAGTGTAATCGAACTCAAGGGTCTTGGTTGATAGATAACCCTTTTCTCCTTGAGTTATGC
453 AAGCTAAGTGTAATCGAACTCAAGGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTATGC
1240556 AACAAATTTGATATACCTTTGAGCTGAGTCTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
518 AACAAATTTGATATACCTTTGAGCTGAGTCTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
1240621 CTTCTCACCTTGAGTTATG
583 CTTCTCACCTTGAGTTATG
* * * *
1240640 TTGCAAATTTGATATGCCTTTGAGCTTAGTGTAATCGAACTCGAAGGTCTTTTGATGACAAATAA
1 CTGCAAAATTGATATGCCTTAGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAAATAA
* * ** *
1240705 CCCTTCTCGCCTTGAGCCATGTTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
66 CCCTTCTCGCCTTGAGCTAT-ATGTAAATTTGATGTGCCTCGGAGCTGAGTGTAATCAAACTCGA
* * * * * * * *
1240770 AGGTCTTTTGTTGATAGATAACCCTTATTGCCTTAAGTTATGCTGT-AAATTCGATGTGCCTTTG
130 GGGTC-TTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATG-TTTCAAATTTGATATGCCTTTG
* * *
1240834 AGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGACAGATAGCTCTTCTCGCCTT
193 AGCTGAGTGTAATCGAACTAGAAGGTCTTTTGATGACAGATAGCCCTTCTCGCCTT
1240890 GAGCTTAGCT
Statistics
Matches: 742, Mismatches: 100, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
600 4 0.01
601 35 0.05
602 606 0.82
603 95 0.13
604 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (601 bp):
CTGCAAAATTGATATGCCTTAGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAAATAA
CCCTTCTCGCCTTGAGCTATATGTAAATTTGATGTGCCTCGGAGCTGAGTGTAATCAAACTCGAG
GGTCTTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATGTTTCAAATTTGATATGCCTTTGAGC
TGAGTGTAATCGAACTAGAAGGTCTTTTGATGACAGATAGCCCTTCTCGCCTTAAGATATGCTAT
AAATTTCACGTGCCTCAGAGCTGAGTGTAATCGAACTAGAGGGTACTGGTTGAGAGATAACCATT
CTCACCTTGAGTTATACTACAAATTTGACATGCCTTAAAGCTGAGTGTAATCGAACTCGAAGGTC
TTTTGATGACAAATAGACCTTCTCGCCTTGAGCTATGATGTAAATTTGATATGCATGCGTCAAAG
CTAAGTGTAATCGAACTCAAGGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTATGCAAC
AAATTTGATATACCTTTGAGCTGAGTCTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTT
CTCACCTTGAGTTATG
Found at i:1241994 original size:99 final size:99
Alignment explanation
Indices: 1241812--1242005 Score: 262
Period size: 99 Copynumber: 2.0 Consensus size: 99
1241802 GACAACTCAA
* * * *
1241812 TATTATGATCACCTTTATCAGGCTAGCTAAATCTTATCCATAAAGTCGGGGCATTTAACCAATTT
1 TATTATAATCACCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCAGGGCATTTAACCAATTG
* * *
1241877 CCTTATAGAGATAGCTCAAGCTTTATTGTAAATG
66 CCTTAGAGAGACAACTCAAGCTTTATTGTAAATG
* * * *
1241911 TATTATAATCACCTTTATCAGGTTAGTTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCAGGGCATTTAACCAATTG
* * *
1241976 CTTTAGAGGGACAACTCAAGTTTTATTGTA
66 CCTTAGAGAGACAACTCAAGCTTTATTGTA
1242006 TATATATAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
99 81 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (99 bp):
TATTATAATCACCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCAGGGCATTTAACCAATTG
CCTTAGAGAGACAACTCAAGCTTTATTGTAAATG
Found at i:1244798 original size:15 final size:18
Alignment explanation
Indices: 1244764--1244799 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
1244754 GATAAAACAA
1244764 AAATAAAGAACATGAAAG
1 AAATAAAGAACATGAAAG
1244782 AAATAAA-AA-AT-AAAG
1 AAATAAAGAACATGAAAG
1244797 AAA
1 AAA
1244800 ACAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.39
16 2 0.11
17 2 0.11
18 7 0.39
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (18 bp):
AAATAAAGAACATGAAAG
Found at i:1244826 original size:20 final size:19
Alignment explanation
Indices: 1244777--1244875 Score: 55
Period size: 18 Copynumber: 5.3 Consensus size: 19
1244767 TAAAGAACAT
1244777 GAAAGAAATAA-AAAATAAA
1 GAAA-AAATAATAAAATAAA
* *
1244796 GAAAACA-AATAAAATAAC
1 GAAAAAATAATAAAATAAA
* *
1244814 GAAAATAATAATAATATATA
1 GAAAA-AATAATAAAATAAA
* * *
1244834 TACAATA-AATAAAA-AAA
1 GAAAAAATAATAAAATAAA
*
1244851 GAAAAGATAA-AAAGATAAA
1 GAAAAAATAATAAA-ATAAA
*
1244870 TAAAAA
1 GAAAAA
1244876 GAAAGAGAAT
Statistics
Matches: 58, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
17 11 0.19
18 23 0.40
19 13 0.22
20 11 0.19
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (19 bp):
GAAAAAATAATAAAATAAA
Found at i:1244872 original size:12 final size:13
Alignment explanation
Indices: 1244846--1244879 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1244836 CAATAAATAA
1244846 AAAAAGAAAAGAT
1 AAAAAGAAAAGAT
*
1244859 AAAAAGATAA-AT
1 AAAAAGAAAAGAT
1244871 AAAAAGAAA
1 AAAAAGAAA
1244880 GAGAATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAAGAT
Found at i:1244923 original size:12 final size:12
Alignment explanation
Indices: 1244908--1244949 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
1244898 AATAAAATGT
1244908 ATAAACAAAAAA
1 ATAAACAAAAAA
1244920 ATAAA-AAACAAA
1 ATAAACAAA-AAA
1244932 ATAAACAATAAAA
1 ATAAACAA-AAAA
1244945 ATAAA
1 ATAAA
1244950 AATTTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.11
12 13 0.48
13 10 0.37
14 1 0.04
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (12 bp):
ATAAACAAAAAA
Done.