Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008211.1 Hibiscus syriacus cultivar Beakdansim tig00110833_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: 2208279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1350579 original size:16 final size:17
Alignment explanation
Indices: 1350543--1350587 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1350533 TATTTACGAG
*
1350543 GGAATTGGAATCTGTGAA
1 GGAATTGGAATC-GCGAA
1350561 GGAATTGGAATC-CGAA
1 GGAATTGGAATCGCGAA
*
1350577 GGAATTAGAAT
1 GGAATTGGAAT
1350588 TAGAATCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.52
18 12 0.48
ACGTcount: A:0.38, C:0.07, G:0.31, T:0.24
Consensus pattern (17 bp):
GGAATTGGAATCGCGAA
Found at i:1351210 original size:28 final size:29
Alignment explanation
Indices: 1351152--1351219 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
1351142 GAATATCACA
*
1351152 TTTAAAAAAACCGACCCGAACCCGATTTTT
1 TTTAAAAAAA-TGACCCGAACCCGATTTTT
* * *
1351182 TTTTAAAAAATGACCCGATCCTGA-TTTT
1 TTTAAAAAAATGACCCGAACCCGATTTTT
1351210 TTTAAAAAAA
1 TTTAAAAAAA
1351220 CCCGACCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 13 0.39
29 11 0.33
30 9 0.27
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (29 bp):
TTTAAAAAAATGACCCGAACCCGATTTTT
Found at i:1351218 original size:29 final size:29
Alignment explanation
Indices: 1351152--1351234 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
1351142 GAATATCACA
*
1351152 TTTAAAAAAACCGACCCGAACCCGATTTT
1 TTTAAAAAAAACGACCCGAACCCGATTTT
** * * *
1351181 TTTTTAAAAAATGACCCGATCCTGATTTT
1 TTTAAAAAAAACGACCCGAACCCGATTTT
*
1351210 TTTAAAAAAACCCGACCCG-ACCCGA
1 TTTAAAAAAA-ACGACCCGAACCCGA
1351235 ATATCAAACT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
29 35 0.85
30 6 0.15
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.27
Consensus pattern (29 bp):
TTTAAAAAAAACGACCCGAACCCGATTTT
Found at i:1359591 original size:3 final size:3
Alignment explanation
Indices: 1359583--1359646 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
1359573 TCAAAAACAC
*
1359583 AAG AAG AAG AAG AAG CAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1359631 AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG A
1359647 TACCGTTGAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1360178 original size:21 final size:21
Alignment explanation
Indices: 1360136--1360179 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1360126 CGGTAAAAAA
**
1360136 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATTAACATTT
*
1360157 TTACCTAAAACATTAACGTTT
1 TTACCTAAAACATTAACATTT
1360178 TT
1 TT
1360180 TAAAATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
TTACCTAAAACATTAACATTT
Found at i:1360842 original size:59 final size:59
Alignment explanation
Indices: 1360747--1360879 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 59
1360737 TAAAGTATAT
* * * *
1360747 AAATGGTCCCCTAATTATAGGGTATTGCTTTGTTGAGTCCCATGACTATCAAAAGTTACA
1 AAATGGTCCCC-AATTATAGGATATTGATTTATTGAGTCCCATAACTATCAAAAGTTACA
* *
1360807 AAATGGTCCCCAATTATAGGATATTGATTTATTGAGTCCCCTAACTATTAAAAGTTACA
1 AAATGGTCCCCAATTATAGGATATTGATTTATTGAGTCCCATAACTATCAAAAGTTACA
*
1360866 AAATAGTCACCCAA
1 AAATGGTC-CCCAA
1360880 CTATTCATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 49 0.75
60 16 0.25
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (59 bp):
AAATGGTCCCCAATTATAGGATATTGATTTATTGAGTCCCATAACTATCAAAAGTTACA
Found at i:1363060 original size:28 final size:29
Alignment explanation
Indices: 1363006--1363061 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1362996 TTTTAATTAT
*
1363006 AAATTTAAAATTATAAACCATAGATTCTA
1 AAATTTAAAATTATAAACCATAAATTCTA
*
1363035 AAATTTAAAATCTA-AATCC-TAAATTCT
1 AAATTTAAAAT-TATAAACCATAAATTCT
1363062 CAATCTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
29 15 0.62
30 2 0.08
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATTTAAAATTATAAACCATAAATTCTA
Found at i:1365791 original size:28 final size:28
Alignment explanation
Indices: 1365746--1365799 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1365736 TTGGTTCGCT
* *
1365746 GAAAACGTTTTCCGGAAAATG-AAATCTG
1 GAAAACGTTTTACAG-AAATGTAAATCTG
*
1365774 GAAAATGTTTTACAGAAATGTAAATC
1 GAAAACGTTTTACAGAAATGTAAATC
1365800 ATTTTCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (28 bp):
GAAAACGTTTTACAGAAATGTAAATCTG
Found at i:1370270 original size:18 final size:17
Alignment explanation
Indices: 1370229--1370275 Score: 80
Period size: 16 Copynumber: 2.9 Consensus size: 17
1370219 AATTTTAGAG
1370229 AATAAAAATATATTATC
1 AATAAAAATATATTATC
1370246 AAT-AAAATATATTATC
1 AATAAAAATATATTATC
1370262 AATAAAAA-ATATTA
1 AATAAAAATATATTA
1370276 AAATATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 22 0.76
17 7 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAAAATATATTATC
Found at i:1376270 original size:17 final size:17
Alignment explanation
Indices: 1376248--1376280 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1376238 AACCCGACCC
1376248 AAAATAATATGTTTATA
1 AAAATAATATGTTTATA
*
1376265 AAAATAATATTTTTAT
1 AAAATAATATGTTTAT
1376281 TCAATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AAAATAATATGTTTATA
Found at i:1379265 original size:26 final size:26
Alignment explanation
Indices: 1379236--1379293 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
1379226 AATTCTGGTA
*
1379236 TTCGACAGAAAAATCCAAGGTTAAGT
1 TTCGACAGAAAAATCCAAGATTAAGT
*
1379262 TTCGATAGAAAAATCCAAGATTAAGT
1 TTCGACAGAAAAATCCAAGATTAAGT
*
1379288 TGCGAC
1 TTCGAC
1379294 GGATTTTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (26 bp):
TTCGACAGAAAAATCCAAGATTAAGT
Found at i:1379986 original size:60 final size:60
Alignment explanation
Indices: 1379880--1380044 Score: 161
Period size: 60 Copynumber: 2.8 Consensus size: 60
1379870 TTGAAGATGT
* * * * * * ** * *
1379880 AAAAGTTTAGGGACCAATTTAGAATGATACTCATGGTTTAGAGATGAAGTTAGAA-TGTTC
1 AAAAGTTTAAGGACTAATTTAAAACGAGAGTCATATTTTAGGGATGAAATTAGAACT-TTC
* * * * *
1379940 AAAAGTTTAAGGACTAATTTAGAACGCGAGTCATATTTTTGGGATGAAATTGGAACTTTT
1 AAAAGTTTAAGGACTAATTTAAAACGAGAGTCATATTTTAGGGATGAAATTAGAACTTTC
* *
1380000 AAAAGTTTAAGGACTAATTTAAAATGAGTGTCATATTTTAGGGAT
1 AAAAGTTTAAGGACTAATTTAAAACGAGAGTCATATTTTAGGGAT
1380045 ATATGATGCA
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 85 0.99
61 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (60 bp):
AAAAGTTTAAGGACTAATTTAAAACGAGAGTCATATTTTAGGGATGAAATTAGAACTTTC
Found at i:1387042 original size:20 final size:20
Alignment explanation
Indices: 1387017--1387056 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1387007 TCGTGAAATC
*
1387017 TTAAAACAAAGTGTTTCCTT
1 TTAAAACAAAGTGGTTCCTT
1387037 TTAAAACAAAGTGGTTCCTT
1 TTAAAACAAAGTGGTTCCTT
1387057 AATTATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
TTAAAACAAAGTGGTTCCTT
Found at i:1387270 original size:2 final size:2
Alignment explanation
Indices: 1387263--1387328 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1387253 AAACATGAAG
1387263 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1387305 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
1387329 CATACCCTAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1391757 original size:17 final size:18
Alignment explanation
Indices: 1391735--1391772 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1391725 ATGAGTGTCG
1391735 TGGGA-TATACCGGGTTT
1 TGGGACTATACCGGGTTT
*
1391752 TGGGATCTATATCGGGTTT
1 TGGGA-CTATACCGGGTTT
1391771 TG
1 TG
1391773 AAATACATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
19 13 0.72
ACGTcount: A:0.16, C:0.11, G:0.34, T:0.39
Consensus pattern (18 bp):
TGGGACTATACCGGGTTT
Found at i:1392645 original size:2 final size:2
Alignment explanation
Indices: 1392633--1392677 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1392623 AATAAATGGA
1392633 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1392674 AT AT
1 AT AT
1392678 TATCTCTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1395515 original size:18 final size:16
Alignment explanation
Indices: 1395469--1395515 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
1395459 TATAAAATAT
1395469 AATAATAAATAATCAA
1 AATAATAAATAATCAA
*
1395485 AATAATAACATAATGAA
1 AATAATAA-ATAATCAA
1395502 AATGAATAAGATAA
1 AAT-AATAA-ATAA
1395516 AGAGATTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 9 0.33
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (16 bp):
AATAATAAATAATCAA
Found at i:1401582 original size:13 final size:13
Alignment explanation
Indices: 1401564--1401588 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1401554 AGCCATTAGT
1401564 TTCATAATCAATA
1 TTCATAATCAATA
1401577 TTCATAATCAAT
1 TTCATAATCAAT
1401589 GTGACATGGT
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:1414940 original size:20 final size:20
Alignment explanation
Indices: 1414915--1414954 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1414905 ATTTTTCCCT
1414915 AAAATAAGAAATGGTTTCTA
1 AAAATAAGAAATGGTTTCTA
1414935 AAAATAAGAAATGGTTTCTA
1 AAAATAAGAAATGGTTTCTA
1414955 CTAGAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (20 bp):
AAAATAAGAAATGGTTTCTA
Found at i:1425474 original size:3 final size:3
Alignment explanation
Indices: 1425463--1425493 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1425453 TATAGTAAAA
1425463 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1425494 ACAAAGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1428426 original size:233 final size:233
Alignment explanation
Indices: 1428000--1428465 Score: 783
Period size: 234 Copynumber: 2.0 Consensus size: 233
1427990 TTGAATATTA
1428000 TAATTTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAATCATAGTTTAACCTAAATTTTG
1 TAATTTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAATCATAGTTTAACCTAAATTTTG
1428065 TTTTTCTTCAAAAAAAACATATAATAATACAACTTGGACTAACGATTTCATTAATAAAGAATGTG
66 TTTTTCTTCAAAAAAAACATATAATAATACAACTTGGACTAACGATTTCATTAATAAAGAATGTG
* * * * *
1428130 ATTTGTACATACGTATAGTTTGGGATGAAATTGGAATTCTCAAAAAAGTTTGGGGATCAATTTAG
131 ATTTGTACATACATATAGTTTGAGATGAAATTGAAATTCTCAAAAAAGTTTAGGGACCAATTTAG
*
1428195 AAAGAGAGTCAATAGTTTAAAGAAGAAATTGAAATGTTC
196 AAAGAGAGTC-ATAGTTTAAAGAAGAAATTAAAATGTTC
* *
1428234 TAATTTCAT-CCCAAATTCATCCAAATGTGTAATTAGTTTCAATCATAGTTTAACCTGAATTTTG
1 TAATTTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAATCATAGTTTAACCTAAATTTTG
*
1428298 TTTTTCTTCAAAAAAAAACATATAATAATACAACTTGGACTAATGATTTCATTAATAAAGAATGT
66 TTTTTCTTC-AAAAAAAACATATAATAATACAACTTGGACTAACGATTTCATTAATAAAGAATGT
* *
1428363 GATTTGTATATACATATAGTTTGAGATGAAATTGAAATTCTC-AAAAAGTTTAGGTACCAATTTA
130 GATTTGTACATACATATAGTTTGAGATGAAATTGAAATTCTCAAAAAAGTTTAGGGACCAATTTA
* *
1428427 GAAAGAGAGTCATAGTTTGAAGATGAAATTAAAATGTTC
195 GAAAGAGAGTCATAGTTTAAAGAAGAAATTAAAATGTTC
1428466 AAAAGTTTGA
Statistics
Matches: 218, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
232 25 0.11
233 92 0.42
234 101 0.46
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (233 bp):
TAATTTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAATCATAGTTTAACCTAAATTTTG
TTTTTCTTCAAAAAAAACATATAATAATACAACTTGGACTAACGATTTCATTAATAAAGAATGTG
ATTTGTACATACATATAGTTTGAGATGAAATTGAAATTCTCAAAAAAGTTTAGGGACCAATTTAG
AAAGAGAGTCATAGTTTAAAGAAGAAATTAAAATGTTC
Found at i:1429934 original size:2 final size:2
Alignment explanation
Indices: 1429927--1429957 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1429917 GAGGAAAGGA
1429927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1429958 AAACATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1430602 original size:6 final size:6
Alignment explanation
Indices: 1430585--1430614 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1430575 AGGCGAAACT
*
1430585 GAAGCC GGAGCC GAAGCC GAAGCC GAAGCC
1 GAAGCC GAAGCC GAAGCC GAAGCC GAAGCC
1430615 ACAGGTGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.37, T:0.00
Consensus pattern (6 bp):
GAAGCC
Found at i:1430791 original size:27 final size:27
Alignment explanation
Indices: 1430761--1430822 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
1430751 TAGACAACAA
1430761 TCGATGTCGATGAAAAGGCAACAGTCG
1 TCGATGTCGATGAAAAGGCAACAGTCG
*
1430788 TCGATGTCGATGCAAAGGCAACAGTCG
1 TCGATGTCGATGAAAAGGCAACAGTCG
1430815 TCGATGTC
1 TCGATGTC
1430823 AATGTCGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (27 bp):
TCGATGTCGATGAAAAGGCAACAGTCG
Found at i:1430798 original size:33 final size:32
Alignment explanation
Indices: 1430761--1430843 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 32
1430751 TAGACAACAA
1430761 TCGATGTCGATGAAAAGGCAACAGTCGTCGATG
1 TCGATGTCGATG-AAAGGCAACAGTCGTCGATG
1430794 TCGATG-C----AAAGGCAACAGTCGTCGATG
1 TCGATGTCGATGAAAGGCAACAGTCGTCGATG
* *
1430821 TCAATGTCGATGCAAAGACAACA
1 TCGATGTCGATG-AAAGGCAACA
1430844 ATCCAAGGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
27 25 0.60
28 1 0.02
32 1 0.02
33 15 0.36
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (32 bp):
TCGATGTCGATGAAAGGCAACAGTCGTCGATG
Found at i:1438711 original size:10 final size:10
Alignment explanation
Indices: 1438696--1438739 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
1438686 GTTGTTGTGG
1438696 TTTATGTTCA
1 TTTATGTTCA
1438706 TTTATGTT-A
1 TTTATGTTCA
*
1438715 GTTTACGTTCA
1 -TTTATGTTCA
1438726 TTTATGTTCA
1 TTTATGTTCA
1438736 TTTA
1 TTTA
1438740 CATTCGTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 1 0.03
10 28 0.93
11 1 0.03
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.59
Consensus pattern (10 bp):
TTTATGTTCA
Found at i:1439318 original size:31 final size:31
Alignment explanation
Indices: 1439283--1439382 Score: 130
Period size: 31 Copynumber: 3.2 Consensus size: 31
1439273 TTTAAAATTA
*
1439283 TACCTAATATTTACTTTTTATTTCATTTTAG
1 TACCTAATATTAACTTTTTATTTCATTTTAG
* *
1439314 TACCTAATATTAATTTTTTATTTCATTTTAA
1 TACCTAATATTAACTTTTTATTTCATTTTAG
* * *
1439345 TATCC-AAAATTAACTTTTTACTTCAATTTAG
1 TA-CCTAATATTAACTTTTTATTTCATTTTAG
1439376 TACCTAA
1 TACCTAA
1439383 ATTTTTAACG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.03
31 55 0.93
32 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (31 bp):
TACCTAATATTAACTTTTTATTTCATTTTAG
Found at i:1449072 original size:15 final size:14
Alignment explanation
Indices: 1449035--1449072 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1449025 ATGGTAGCGT
1449035 TGGGTAATTACTTA
1 TGGGTAATTACTTA
1449049 TGGTGTAATTACTTA
1 TGG-GTAATTACTTA
1449064 TGGGATAAT
1 TGGG-TAAT
1449073 AAATATATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (14 bp):
TGGGTAATTACTTA
Found at i:1461397 original size:31 final size:31
Alignment explanation
Indices: 1461355--1461416 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1461345 CAGGAAACTT
*
1461355 AGTCTAGATTCTATGTAGTAAA-TGCATTTTC
1 AGTCTAAATTCTATGTAGTAAAGT-CATTTTC
1461386 AGTCTAAATTCTATGTAGTAAAGTCATTTTC
1 AGTCTAAATTCTATGTAGTAAAGTCATTTTC
1461417 TTTTATCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (31 bp):
AGTCTAAATTCTATGTAGTAAAGTCATTTTC
Found at i:1464971 original size:27 final size:28
Alignment explanation
Indices: 1464926--1464980 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1464916 TCAGTGATTA
1464926 AAAAAATTCAAACTATT-AAGTTTAGTG
1 AAAAAATTCAAACTATTAAAGTTTAGTG
* * *
1464953 AAAAAATTGAAATTTTTAAAGTTTAGTG
1 AAAAAATTCAAACTATTAAAGTTTAGTG
1464981 CACAAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (28 bp):
AAAAAATTCAAACTATTAAAGTTTAGTG
Found at i:1472607 original size:60 final size:60
Alignment explanation
Indices: 1472489--1472637 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
1472479 TATCCTATTT
* * * ** *
1472489 TAAATTTGTACTTAAACTTTTAAATATTCTAAATTTATCCTTAAACTATGACTATCATT-
1 TAAATTAGTCCTTAAACTTTTAAACATTCTAAATCCATCCTCAAACTATGACTATCATTC
* *
1472548 TGAAGTTGGTCCTTAAACTTTTAAACATTC-AGAATCCATCCTCAAACTATGAC-ACTCATTC
1 T-AAATTAGTCCTTAAACTTTTAAACATTCTA-AATCCATCCTCAAACTATGACTA-TCATTC
**
1472609 TAAATTAGTCCCCAAACTTTTAAACATTC
1 TAAATTAGTCCTTAAACTTTTAAACATTC
1472638 CAATAACTTC
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
59 3 0.04
60 71 0.95
61 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTAAACATTCTAAATCCATCCTCAAACTATGACTATCATTC
Found at i:1479330 original size:12 final size:12
Alignment explanation
Indices: 1479313--1479353 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1479303 TGGGGTGGAG
1479313 AAGGAAGCGAAA
1 AAGGAAGCGAAA
*
1479325 AAGGAAGCGAAG
1 AAGGAAGCGAAA
*
1479337 AAGGAAGGGAAGA
1 AAGGAAGCGAA-A
1479350 AAGG
1 AAGG
1479354 GTTTAAGACG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.54, C:0.05, G:0.41, T:0.00
Consensus pattern (12 bp):
AAGGAAGCGAAA
Found at i:1479670 original size:22 final size:22
Alignment explanation
Indices: 1479644--1479689 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1479634 TGTTTTCGGC
1479644 TGTGTTATGTTTATTGCAATTG
1 TGTGTTATGTTTATTGCAATTG
*
1479666 TGTGTTGTGTTTATTGCAATTG
1 TGTGTTATGTTTATTGCAATTG
1479688 TG
1 TG
1479690 ACAATAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.04, G:0.26, T:0.54
Consensus pattern (22 bp):
TGTGTTATGTTTATTGCAATTG
Found at i:1485574 original size:60 final size:60
Alignment explanation
Indices: 1485441--1485564 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
1485431 GTTGGGTGAT
* * * ** *
1485441 CATTTTGTAATTTTTAATAGTCGAGGGACTCAACAAAGCAATACTTTATAGTTAGAGGAC
1 CATTCTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAATACCCTATAGTGAGAGGAC
* *
1485501 CATTCTGTAACTTTTAATAGTCGATGAG-CTTAACAAAGCGATACCCTATAGTCGAG-GGAC
1 CATTCTGTAACTTTTAATAGTCGA-GAGACTCAACAAAGCAATACCCTATAGT-GAGAGGAC
1485561 CATT
1 CATT
1485565 TGTGTACTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 50 0.93
61 4 0.07
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (60 bp):
CATTCTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAATACCCTATAGTGAGAGGAC
Found at i:1486436 original size:25 final size:25
Alignment explanation
Indices: 1486398--1486451 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
1486388 ATGATGTGAT
*
1486398 ACATGTCACATCATCATTCTGAGTG
1 ACATGCCACATCATCATTCTGAGTG
* * * *
1486423 ACATGCCACGTCATCTTTTTGTGTG
1 ACATGCCACATCATCATTCTGAGTG
1486448 ACAT
1 ACAT
1486452 TGCACATACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (25 bp):
ACATGCCACATCATCATTCTGAGTG
Found at i:1489546 original size:59 final size:59
Alignment explanation
Indices: 1489448--1489561 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
1489438 GATTTTCTAA
** *
1489448 CTTTTAACAGTCAATGGACTTAACAAAACAACATTCTATAGTCAGAGTACCATTTCAAT
1 CTTTTAACAGTCAATGGACTTAACAAAACAACACCCTATAGTCAGAGGACCATTTCAAT
* * ** *
1489507 CTTTTAATAGTCAAAT-GACTTAATAAAACAGTACCCTATAGTCAGGGGACCATTT
1 CTTTTAACAGTC-AATGGACTTAACAAAACAACACCCTATAGTCAGAGGACCATTT
1489562 ATGTACTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 43 0.93
60 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (59 bp):
CTTTTAACAGTCAATGGACTTAACAAAACAACACCCTATAGTCAGAGGACCATTTCAAT
Found at i:1490560 original size:2 final size:2
Alignment explanation
Indices: 1490555--1490605 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1490545 AAAAAAAAAA
1490555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1490597 AT AT AT AT A
1 AT AT AT AT A
1490606 GAGAGACTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1491875 original size:60 final size:60
Alignment explanation
Indices: 1491796--1491930 Score: 175
Period size: 60 Copynumber: 2.2 Consensus size: 60
1491786 TTAGCCCTTC
* *
1491796 AACTTTTAAACATTCTAATTTCACCCCTAAACCATGA-TCCTCATTCTAAATAAGTATC-CA
1 AACTTTTGAACATTCTAATTTCACCCCTAAACCATGACT-CTCATTCTAAATAAG-ACCTCA
* * * * *
1491856 AACTTTTGAACATTCTAATTTTATCCCTAAACTATGACTCTCATTCTAAATTAGCCCTCA
1 AACTTTTGAACATTCTAATTTCACCCCTAAACCATGACTCTCATTCTAAATAAGACCTCA
1491916 AACTTTTGAACATTC
1 AACTTTTGAACATTC
1491931 CAATAACTTC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 1 0.02
60 64 0.97
61 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.36
Consensus pattern (60 bp):
AACTTTTGAACATTCTAATTTCACCCCTAAACCATGACTCTCATTCTAAATAAGACCTCA
Found at i:1492070 original size:60 final size:60
Alignment explanation
Indices: 1491997--1492139 Score: 187
Period size: 60 Copynumber: 2.4 Consensus size: 60
1491987 AGTTTGCAGG
* ** *
1491997 GAATGAGGGTCATAATTTGAGGATGCATTTACAATGTTTAAAAGTTTAAGGACTAATTTA
1 GAATGAGGGTCATAGTTTGAGGATAAATTCACAATGTTTAAAAGTTTAAGGACTAATTTA
* * *
1492057 GAATGAGGGTCATAGTTTGAGTATAAATTCATAATGTTTAAAAGTTTATGGACTAATTTA
1 GAATGAGGGTCATAGTTTGAGGATAAATTCACAATGTTTAAAAGTTTAAGGACTAATTTA
* * **
1492117 TAATAAAAGTCATAGTTTGAGGA
1 GAATGAGGGTCATAGTTTGAGGA
1492140 CATATAATAC
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.36
Consensus pattern (60 bp):
GAATGAGGGTCATAGTTTGAGGATAAATTCACAATGTTTAAAAGTTTAAGGACTAATTTA
Found at i:1492486 original size:3 final size:3
Alignment explanation
Indices: 1492478--1492528 Score: 57
Period size: 3 Copynumber: 16.0 Consensus size: 3
1492468 TATGTTCTTT
* *
1492478 ATC ATC ATC ATC ACTC ATC ATC ATC ACTT ATC ATC ATC ACTT ATC ATC
1 ATC ATC ATC ATC A-TC ATC ATC ATC A-TC ATC ATC ATC A-TC ATC ATC
1492526 ATC
1 ATC
1492529 TTGGCTGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 34 0.83
4 7 0.17
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1492497 original size:13 final size:13
Alignment explanation
Indices: 1492479--1492528 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
1492469 ATGTTCTTTA
1492479 TCATCATCATCAC
1 TCATCATCATCAC
1492492 TCATCATCATCAC
1 TCATCATCATCAC
*
1492505 TTATCATCATCAC
1 TCATCATCATCAC
*
1492518 TTATCATCATC
1 TCATCATCATC
1492529 TTGGCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.30, C:0.34, G:0.00, T:0.36
Consensus pattern (13 bp):
TCATCATCATCAC
Found at i:1493825 original size:29 final size:30
Alignment explanation
Indices: 1493793--1493851 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1493783 CGTTATAAAA
*
1493793 TCGAGAATTT-TTA-AATTATATGTATGAAT
1 TCGAGAATTTAATATAATT-TATGTATGAAT
1493822 TCGAGAATTTAATATAATTTATGTATGAAT
1 TCGAGAATTTAATATAATTTATGTATGAAT
1493852 GAGGTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.44
Consensus pattern (30 bp):
TCGAGAATTTAATATAATTTATGTATGAAT
Found at i:1500216 original size:2 final size:2
Alignment explanation
Indices: 1500209--1500252 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1500199 CCAATAAAAG
1500209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1500251 AT
1 AT
1500253 TTTTCCAGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1500561 original size:2 final size:2
Alignment explanation
Indices: 1500554--1500589 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1500544 TGGTTAACTA
1500554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1500590 CCATGCGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1510056 original size:2 final size:2
Alignment explanation
Indices: 1510049--1510074 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1510039 TTCGAAATAT
1510049 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1510075 AGGAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1513624 original size:13 final size:13
Alignment explanation
Indices: 1513606--1513630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1513596 AGTAATATAT
1513606 TATATATATTAAA
1 TATATATATTAAA
1513619 TATATATATTAA
1 TATATATATTAA
1513631 GCTCAAACTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATTAAA
Found at i:1513997 original size:21 final size:21
Alignment explanation
Indices: 1513971--1514014 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1513961 TATCGTCCAT
*
1513971 TTTTAACGAAAAATGACGAGC
1 TTTTAACGAAAAAGGACGAGC
1513992 TTTTAACGAAAAAGGACGAGC
1 TTTTAACGAAAAAGGACGAGC
1514013 TT
1 TT
1514015 AGAACATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (21 bp):
TTTTAACGAAAAAGGACGAGC
Found at i:1516662 original size:18 final size:17
Alignment explanation
Indices: 1516639--1516683 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
1516629 TTTATGAGAT
1516639 AAAAATATTATTATTATA
1 AAAAATATTATTATT-TA
*
1516657 AAAAATATAATTATTTA
1 AAAAATATTATTATTTA
1516674 AAACAATATT
1 AAA-AATATT
1516684 TAATTTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAAATATTATTATTTA
Found at i:1518098 original size:14 final size:14
Alignment explanation
Indices: 1518079--1518106 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1518069 TACTCCTCAA
1518079 CCGTAGTCCAATGT
1 CCGTAGTCCAATGT
1518093 CCGTAGTCCAATGT
1 CCGTAGTCCAATGT
1518107 ATAACATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
CCGTAGTCCAATGT
Found at i:1518266 original size:3 final size:3
Alignment explanation
Indices: 1518258--1518315 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
1518248 GCGGGTTATG
1518258 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1518306 GAA GAA GAA G
1 GAA GAA GAA G
1518316 TGTCCTTTGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1519162 original size:37 final size:37
Alignment explanation
Indices: 1519091--1519162 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 37
1519081 ATATTTTTTT
*
1519091 ATTTTGTAAAAAAATTATATAAATATTATGAATTTAA
1 ATTTTGTAAAAAAATTATATAAATATTATCAATTTAA
*
1519128 ATTTT-TAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
1519163 GTAATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 17 0.55
37 14 0.45
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (37 bp):
ATTTTGTAAAAAAATTATATAAATATTATCAATTTAA
Found at i:1519184 original size:17 final size:17
Alignment explanation
Indices: 1519140--1519185 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1519130 TTTTAAAGAA
*
1519140 AATATATAAATATTTTAC
1 AATATAT-AATATTATAC
* *
1519158 AATTTGTAATATTATAC
1 AATATATAATATTATAC
1519175 AATATATAATA
1 AATATATAATA
1519186 AGGACAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATATAATATTATAC
Found at i:1519344 original size:19 final size:18
Alignment explanation
Indices: 1519302--1519344 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1519292 CAGTAATCAT
**
1519302 ATTCCCTGGTAATCTTTT
1 ATTCCCTGGTAATCTTAC
1519320 ATTTCCACTGGTAATCTTAC
1 A-TTCC-CTGGTAATCTTAC
1519340 ATTCC
1 ATTCC
1519345 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTCCCTGGTAATCTTAC
Found at i:1519598 original size:24 final size:24
Alignment explanation
Indices: 1519571--1519616 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1519561 GTGATATGAT
* *
1519571 TTTTCTCTGTTCTTGTGGCACACA
1 TTTTCTCTGCTCTTGTGACACACA
*
1519595 TTTTTTCTGCTCTTGTGACACA
1 TTTTCTCTGCTCTTGTGACACA
1519617 ATTCTCATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.24, G:0.15, T:0.48
Consensus pattern (24 bp):
TTTTCTCTGCTCTTGTGACACACA
Found at i:1526830 original size:19 final size:19
Alignment explanation
Indices: 1526785--1526848 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 19
1526775 ACCCTCATGA
1526785 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--T--AG
1526808 GGGAACCGATTCCCCCTAG
1 GGGAACCGATTCCCCCTAG
* *
1526827 GGGAATCGATACCCCCCTAG
1 GGGAACCGAT-TCCCCCTAG
1526847 GG
1 GG
1526849 TTTTGGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 11 0.29
20 10 0.26
21 1 0.03
23 16 0.42
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (19 bp):
GGGAACCGATTCCCCCTAG
Found at i:1526844 original size:20 final size:19
Alignment explanation
Indices: 1526806--1526848 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1526796 CCCCCTTTGA
*
1526806 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATCCCCCCT
*
1526825 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
1526845 AGGG
1 AGGG
1526849 TTTTGGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:1538364 original size:47 final size:47
Alignment explanation
Indices: 1538290--1538384 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
1538280 TCCAAATACA
*
1538290 TATAAAGAAGTCTTAAGGGTGGGGATTGTTTTCCAACCTTGATACTC
1 TATAAAGAAGTCTTAAGGGTGGAGATTGTTTTCCAACCTTGATACTC
1538337 TATAAAGAAGTCTTAAGGGTGGAGATTGTTTTCCAACCTTGATACTC
1 TATAAAGAAGTCTTAAGGGTGGAGATTGTTTTCCAACCTTGATACTC
1538384 T
1 T
1538385 CTGGGCTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (47 bp):
TATAAAGAAGTCTTAAGGGTGGAGATTGTTTTCCAACCTTGATACTC
Found at i:1545166 original size:145 final size:145
Alignment explanation
Indices: 1544903--1545191 Score: 569
Period size: 145 Copynumber: 2.0 Consensus size: 145
1544893 GCCTGGAACT
*
1544903 TTGCCCGGTTCACCTTCTTGATTTGATTACAGAAATTTAGAAGACAGTTGTGCATTCTAATGTTA
1 TTGCCCGATTCACCTTCTTGATTTGATTACAGAAATTTAGAAGACAGTTGTGCATTCTAATGTTA
1544968 TTATTAGGCATATCAGCAGATGTATTAATGAGGAAGCTGATTGTCTAGCTAAGTCAGGAATTGGT
66 TTATTAGGCATATCAGCAGATGTATTAATGAGGAAGCTGATTGTCTAGCTAAGTCAGGAATTGGT
1545033 TAGTGAGTGAGGTTC
131 TAGTGAGTGAGGTTC
1545048 TTGCCCGATTCACCTTCTTGATTTGATTACAGAAATTTAGAAGACAGTTGTGCATTCTAATGTTA
1 TTGCCCGATTCACCTTCTTGATTTGATTACAGAAATTTAGAAGACAGTTGTGCATTCTAATGTTA
1545113 TTATTAGGCATATCAGCAGATGTATTAATGAGGAAGCTGATTGTCTAGCTAAGTCAGGAATTGGT
66 TTATTAGGCATATCAGCAGATGTATTAATGAGGAAGCTGATTGTCTAGCTAAGTCAGGAATTGGT
1545178 TAGTGAGTGAGGTT
131 TAGTGAGTGAGGTT
1545192 GTTGTTGTTA
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (145 bp):
TTGCCCGATTCACCTTCTTGATTTGATTACAGAAATTTAGAAGACAGTTGTGCATTCTAATGTTA
TTATTAGGCATATCAGCAGATGTATTAATGAGGAAGCTGATTGTCTAGCTAAGTCAGGAATTGGT
TAGTGAGTGAGGTTC
Found at i:1546024 original size:23 final size:23
Alignment explanation
Indices: 1545990--1546081 Score: 130
Period size: 23 Copynumber: 4.0 Consensus size: 23
1545980 CACCACAGCT
*
1545990 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1546013 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1546036 CGTAGAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1546059 CGTAGAAAAGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1546082 TATAATAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.32, C:0.26, G:0.27, T:0.15
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1547504 original size:21 final size:21
Alignment explanation
Indices: 1547480--1547522 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1547470 TTTTGTTCGT
* *
1547480 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1547501 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1547522 T
1 T
1547523 AGCCCAGAAA
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:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1553950 original size:202 final size:197
Alignment explanation
Indices: 1553569--1553969 Score: 687
Period size: 202 Copynumber: 2.0 Consensus size: 197
1553559 ATCTATTTAA
1553569 GAGGCCAACTTGGAGGAAATAAACAAACTTTTACAGGATTTAAAATTCTCTTTAGCACGCCTAAG
1 GAGGCCAACTTGGAGGAAATAAACAAACTTTTACAGGATTTAAAATTCTCTTTAGCACGCCTAAG
*
1553634 GTCTAAAAGTCGTTCGACAGGTTCCACTATCAATCTCCAAATACACAATCATTACAATTTAGTAC
66 GTCTAAAAGTCGTTCGACAGGTTCCACTACCAATCTCCAAATACACAATCATTACAATTTAGTAC
*
1553699 AATTACATGGTTGAAGGTTTATTGTCATAAAGTTGTTTGGAATTTTCAATTTTGCTTCATGTATG
131 AATTACATGGTTGAAGGTTTATTGTCATAAAGTTGTTTGGAATTTTCAATTTTGCCTCATGTATG
1553764 AG
196 AG
*
1553766 GAGGCCAACTTGGAGGAAATAAACAAACTTTTACAGGATTTAAAAATTCTCTTTAGCACGTCTAA
1 GAGGCCAACTTGGAGGAAATAAACAAACTTTTACAGGATTT-AAAATTCTCTTTAGCACGCCTAA
* * *
1553831 GGTCTGAAAGTCCGTTCGACAGGTTCCACTACCAATCTCCAAATAGACAATCGTTACAATTT-GA
65 GGTCTAAAAGT-CGTTCGACAGGTTCCACTACCAATCTCCAAATACACAATCATTACAATTTAG-
1553895 TACAATTGTTACATGGTTGAAGGTTTATTGTCATAAAGTTGTTTGGAATTTTCAATTTTGCCTCA
128 TACAA---TTACATGGTTGAAGGTTTATTGTCATAAAGTTGTTTGGAATTTTCAATTTTGCCTCA
1553960 TGTATGAG
190 TGTATGAG
1553968 GA
1 GA
1553970 TCTTCTGTTT
Statistics
Matches: 192, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
197 41 0.21
198 33 0.17
199 52 0.27
202 66 0.34
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (197 bp):
GAGGCCAACTTGGAGGAAATAAACAAACTTTTACAGGATTTAAAATTCTCTTTAGCACGCCTAAG
GTCTAAAAGTCGTTCGACAGGTTCCACTACCAATCTCCAAATACACAATCATTACAATTTAGTAC
AATTACATGGTTGAAGGTTTATTGTCATAAAGTTGTTTGGAATTTTCAATTTTGCCTCATGTATG
AG
Found at i:1558865 original size:21 final size:21
Alignment explanation
Indices: 1558841--1558986 Score: 118
Period size: 21 Copynumber: 7.1 Consensus size: 21
1558831 GCAAATTCGC
1558841 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
1558862 GTTGGAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1558882 TTTTCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
1558903 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * *
1558923 TTTCCATTTCGCGTTGCTATA
1 GTTGCATTTCGCGTTGCGATA
**
1558944 GTTGCAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* ** *
1558964 TTTTTATTTCGCATTGCGATA
1 GTTGCATTTCGCGTTGCGATA
1558985 GT
1 GT
1558987 CTACAATGTC
Statistics
Matches: 91, Mismatches: 31, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
20 43 0.47
21 48 0.53
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:1558890 original size:41 final size:41
Alignment explanation
Indices: 1558845--1559007 Score: 231
Period size: 41 Copynumber: 4.0 Consensus size: 41
1558835 ATTCGCGTTG
*
1558845 CATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
*
1558886 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
* *
1558927 CATTTCGCGTTGCTATAGTTGCAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
* * *
1558968 TATTTCGCATTGCGATAGTCT-ACAAT-GTCGTTGCGATTTT
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTT
1559008 CCAAATTCGT
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 1 0.01
41 108 0.98
42 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
Found at i:1558934 original size:82 final size:82
Alignment explanation
Indices: 1558845--1559026 Score: 255
Period size: 82 Copynumber: 2.2 Consensus size: 82
1558835 ATTCGCGTTG
* *
1558845 CATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGT-TGAA
1 CATTTCGCGTTGCGATAGTTGCAAATCGCGTTGCGATTTTTCATTTCGCATTGCGATAGTCT-AA
1558909 AATCG-CGTTGCGATTTTC
65 AAT-GTCGTTGCGATTTTC
* * *
1558927 CATTTCGCGTTGCTATAGTTGCAAATCGCGTTGCGATTTTTTATTTCGCATTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGCAAATCGCGTTGCGATTTTTCATTTCGCATTGCGATAGTCTAAA
1558992 ATGTCGTTGCGATTTTC
66 ATGTCGTTGCGATTTTC
*
1559009 CAAATT--CGTTGCGATAGT
1 C-ATTTCGCGTTGCGATAGT
1559027 CTACAGTTGT
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
81 12 0.13
82 74 0.82
83 4 0.04
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (82 bp):
CATTTCGCGTTGCGATAGTTGCAAATCGCGTTGCGATTTTTCATTTCGCATTGCGATAGTCTAAA
ATGTCGTTGCGATTTTC
Found at i:1559043 original size:22 final size:22
Alignment explanation
Indices: 1559013--1559067 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1559003 ATTTTCCAAA
1559013 TTCGTTGCGATAGTCTACAGTT
1 TTCGTTGCGATAGTCTACAGTT
*
1559035 GTT-GTTGCGAAAGTCTACAGTT
1 -TTCGTTGCGATAGTCTACAGTT
1559057 TTCGTTGCGAT
1 TTCGTTGCGAT
1559068 TTTTCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 25 0.86
23 2 0.07
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.40
Consensus pattern (22 bp):
TTCGTTGCGATAGTCTACAGTT
Found at i:1559206 original size:5 final size:6
Alignment explanation
Indices: 1559167--1559203 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1559157 GACACGTATT
1559167 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1559204 CGAGACGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1559843 original size:26 final size:26
Alignment explanation
Indices: 1559813--1559862 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1559803 GGAAAATCGC
* *
1559813 AACGATAACTATAGACTATTGCAATG
1 AACGACAACTATAGACTATCGCAATG
*
1559839 AACGACAACTGTAGACTATCGCAA
1 AACGACAACTATAGACTATCGCAA
1559863 CGCGATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (26 bp):
AACGACAACTATAGACTATCGCAATG
Found at i:1559902 original size:20 final size:20
Alignment explanation
Indices: 1559877--1559989 Score: 133
Period size: 20 Copynumber: 5.6 Consensus size: 20
1559867 ATTTTCAACT
1559877 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
1559897 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
1559916 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
1559938 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
1559958 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
1559978 ATCGCAACGCGA
1 ATCGCAACGCGA
1559990 TTTTCAACTA
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.05
19 13 0.16
20 42 0.53
21 3 0.04
22 17 0.22
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:1560005 original size:61 final size:60
Alignment explanation
Indices: 1559856--1560010 Score: 215
Period size: 61 Copynumber: 2.5 Consensus size: 60
1559846 ACTGTAGACT
*
1559856 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGAATTTGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGAATATGGAAA
* * *
1559916 ATCGCAACGACAACTGT-AGACTATCGCAACGCGAACTGGAAAATCGCAACGCGAA-ATGGAAA
1 ATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAACTGGAAAATCGCAA--CGAATATGGAAA
*
1559978 ATCGCAACGCGATTTTCAACTACCGCAACGCGA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGA
1560011 TTTTCAATTA
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
60 10 0.12
61 52 0.63
62 16 0.20
63 4 0.05
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.17
Consensus pattern (60 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGAATATGGAAA
Found at i:1560006 original size:21 final size:21
Alignment explanation
Indices: 1559980--1560031 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1559970 AATGGAAAAT
1559980 CGCAACGCGATTTTCAACTAC
1 CGCAACGCGATTTTCAACTAC
* *
1560001 CGCAACGCGATTTTCAATTAT
1 CGCAACGCGATTTTCAACTAC
1560022 CGCAACGCGA
1 CGCAACGCGA
1560032 AATGCAACGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAC
Found at i:1567975 original size:26 final size:25
Alignment explanation
Indices: 1567946--1568004 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
1567936 GGCATTTAAC
*
1567946 TTTTTGATGCAATTAAATA-CTAAATA
1 TTTTT-ATACAATTAAATATCT-AATA
* *
1567972 TTTTTATATAATTAGATATCTAATA
1 TTTTTATACAATTAAATATCTAATA
1567997 TTTTTATA
1 TTTTTATA
1568005 TAAATATAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (25 bp):
TTTTTATACAATTAAATATCTAATA
Found at i:1567984 original size:25 final size:25
Alignment explanation
Indices: 1567956--1568007 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1567946 TTTTTGATGC
1567956 AATTAAATA-CTAAATATTTTTATAT
1 AATTAAATATCT-AATATTTTTATAT
*
1567981 AATTAGATATCTAATATTTTTATAT
1 AATTAAATATCTAATATTTTTATAT
1568006 AA
1 AA
1568008 ATATAGAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTAAATATCTAATATTTTTATAT
Found at i:1572110 original size:31 final size:30
Alignment explanation
Indices: 1572061--1572118 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
1572051 GTAAATTATA
* * *
1572061 ATTTTAGTTATTAAACTTTATTATCTTTCTT
1 ATTTTACTCATTAAACTTT-TAATCTTTCTT
*
1572092 ATTTTACTCATTATACTTTTAATCTTT
1 ATTTTACTCATTAAACTTTTAATCTTT
1572119 TCAATTTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 7 0.30
31 16 0.70
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (30 bp):
ATTTTACTCATTAAACTTTTAATCTTTCTT
Found at i:1573503 original size:18 final size:18
Alignment explanation
Indices: 1573444--1573511 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 18
1573434 AAACTGAAAC
1573444 CGGTTTTATCGGTTCGGTT
1 CGGTTTT-TCGGTTCGGTT
*
1573463 TGGTTTTT---TTAACGGTT
1 CGGTTTTTCGGTT--CGGTT
1573480 CGGGTTTTTCGGTTCGGTT
1 C-GGTTTTTCGGTTCGGTT
1573499 CGGTTTTTCGGTT
1 CGGTTTTTCGGTT
1573512 TTTCAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 5 0.12
18 20 0.49
19 12 0.29
21 2 0.05
ACGTcount: A:0.04, C:0.13, G:0.31, T:0.51
Consensus pattern (18 bp):
CGGTTTTTCGGTTCGGTT
Found at i:1582560 original size:3 final size:3
Alignment explanation
Indices: 1582552--1582614 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
1582542 TATACGTCAA
1582552 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1582600 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
1582615 TTACGAAGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1594534 original size:12 final size:12
Alignment explanation
Indices: 1594517--1594542 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1594507 AGCAGAGATA
1594517 TGAACTCGGGCG
1 TGAACTCGGGCG
1594529 TGAACTCGGGCG
1 TGAACTCGGGCG
1594541 TG
1 TG
1594543 GTGAATTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.42, T:0.19
Consensus pattern (12 bp):
TGAACTCGGGCG
Found at i:1608043 original size:2 final size:2
Alignment explanation
Indices: 1608036--1608069 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1608026 ACAGAATGAT
1608036 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1608070 CAGTGTTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1610315 original size:175 final size:175
Alignment explanation
Indices: 1610024--1610357 Score: 632
Period size: 175 Copynumber: 1.9 Consensus size: 175
1610014 GTAATCTTAC
* *
1610024 ATTCCTGCTAAACCAACCAAACACAAAATGCAACATTCTCAGTAATCTTATTCCCTAGTAATCTT
1 ATTCCTGCTAAACCAACCAAACACAAAATGCAACATTCCCAGTAATCCTATTCCCTAGTAATCTT
*
1610089 TTATTCCCACTGGTAATCTTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
66 TTATTCACACTGGTAATCTTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
1610154 AAATTATCTCATATAAGACGTTGTTACAAAATGCAATAAGATTAT
131 AAATTATCTCATATAAGACGTTGTTACAAAATGCAATAAGATTAT
*
1610199 ATTCCTGCTAAACCAACCAAACACAAAATGCAACATTCCCAGTAATCCTATTCCCTGGTAATCTT
1 ATTCCTGCTAAACCAACCAAACACAAAATGCAACATTCCCAGTAATCCTATTCCCTAGTAATCTT
1610264 TTATTCACACTGGTAATCTTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
66 TTATTCACACTGGTAATCTTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
1610329 AAATTATCTCATATAAGACGTTGTTACAA
131 AAATTATCTCATATAAGACGTTGTTACAA
1610358 TTATTATTGT
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 155 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.31
Consensus pattern (175 bp):
ATTCCTGCTAAACCAACCAAACACAAAATGCAACATTCCCAGTAATCCTATTCCCTAGTAATCTT
TTATTCACACTGGTAATCTTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
AAATTATCTCATATAAGACGTTGTTACAAAATGCAATAAGATTAT
Found at i:1612405 original size:42 final size:41
Alignment explanation
Indices: 1612311--1612405 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 41
1612301 AAAAAATAAT
1612311 AATTATATATATATATATATAATATTAATAAATTTAATTTA
1 AATTATATATATATATATATAATATTAATAAATTTAATTTA
* * * *
1612352 AATTAAAATATATATATATATAATATTTATATATTTCATTTA
1 AATT-ATATATATATATATATAATATTAATAAATTTAATTTA
1612394 AA-TATATATATA
1 AATTATATATATA
1612406 CCCGGCCCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 8 0.17
41 5 0.10
42 35 0.73
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (41 bp):
AATTATATATATATATATATAATATTAATAAATTTAATTTA
Found at i:1615565 original size:18 final size:20
Alignment explanation
Indices: 1615542--1615581 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1615532 GAATAAAAAA
1615542 ATGTCT-AATAT-AATACAT
1 ATGTCTAAATATAAATACAT
1615560 ATGTCTAGAATATAAATACAT
1 ATGTCTA-AATATAAATACAT
1615581 A
1 A
1615582 AACCTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 5 0.26
21 8 0.42
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (20 bp):
ATGTCTAAATATAAATACAT
Found at i:1617602 original size:114 final size:114
Alignment explanation
Indices: 1617395--1617627 Score: 421
Period size: 114 Copynumber: 2.0 Consensus size: 114
1617385 TGTTTGGATC
* *
1617395 AATTACTCATTCAAATCTCTAAAATTATCAATTTTTTCTAACAAACTCTTATACGAGATAAGAGA
1 AATTTCTCATTCAAATCTCTAAAATTATCAATTTTTTCTAACAAACTCCTATACGAGATAAGAGA
1617460 AAATACGATATGATATATTTCTTGGAGACCATAACCCCTTTATATAACT
66 AAATACGATATGATATATTTCTTGGAGACCATAACCCCTTTATATAACT
*
1617509 AATTTCTCATTCAAATCTCTAAAATTATCAATTTTTTCTAACAAACTCCTCTACGAGATAAGAGA
1 AATTTCTCATTCAAATCTCTAAAATTATCAATTTTTTCTAACAAACTCCTATACGAGATAAGAGA
* *
1617574 AAATACGATATGATATATTTCTTTGAGACCATACCCCCTTTATATAACT
66 AAATACGATATGATATATTTCTTGGAGACCATAACCCCTTTATATAACT
1617623 AATTT
1 AATTT
1617628 AAGAATCAAT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.36
Consensus pattern (114 bp):
AATTTCTCATTCAAATCTCTAAAATTATCAATTTTTTCTAACAAACTCCTATACGAGATAAGAGA
AAATACGATATGATATATTTCTTGGAGACCATAACCCCTTTATATAACT
Found at i:1621469 original size:51 final size:50
Alignment explanation
Indices: 1621357--1621470 Score: 113
Period size: 51 Copynumber: 2.2 Consensus size: 50
1621347 TCGAAGTGAC
* ** * *
1621357 AAGTTTCAATAAAAAATATTTTTTATTCAAAATTTTCATCTCGATGTAGTA
1 AAGTTT-AATAAAAAATATATTTTATTCAAAATCGTCACCTCGACGTAGTA
* * * *
1621408 AAATTTAATAAAAAATTATATTTTATTGAAACTCGTCACCTCGACGTTGT-
1 AAGTTTAATAAAAAA-TATATTTTATTCAAAATCGTCACCTCGACGTAGTA
1621458 AAGTTTGAATAAA
1 AAGTTT-AATAAA
1621471 TTATTTTAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
50 14 0.27
51 37 0.73
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (50 bp):
AAGTTTAATAAAAAATATATTTTATTCAAAATCGTCACCTCGACGTAGTA
Found at i:1627276 original size:2 final size:2
Alignment explanation
Indices: 1627271--1627302 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1627261 CTTATGTGTG
1627271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1627303 AAGAGGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1632470 original size:161 final size:162
Alignment explanation
Indices: 1632232--1632569 Score: 525
Period size: 161 Copynumber: 2.1 Consensus size: 162
1632222 CGGTATTGAA
* * *
1632232 ATGATAAAACCGGTAAAGCGCTACCAGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGA
1 ATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGA
* * *
1632297 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAAATG
66 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAATA
* *
1632362 TATCGATCCAAAACGATATACCAGGTAAAAAT
131 TATCGATCCAAAACGATATAACAGGAAAAAAT
* * *
1632394 ATGATAAAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGA
1 ATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGA
* ** *
1632458 CACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAAAATA
66 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAATA
*
1632523 TATCGATCCACAACGATATAACAGGAAAAAAT
131 TATCGATCCAAAACGATATAACAGGAAAAAAT
1632555 ATGATAAAACCGGTA
1 ATGATAAAACCGGTA
1632570 TCAAAATGAT
Statistics
Matches: 160, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
161 115 0.72
162 45 0.28
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (162 bp):
ATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGA
CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAATA
TATCGATCCAAAACGATATAACAGGAAAAAAT
Found at i:1634823 original size:21 final size:21
Alignment explanation
Indices: 1634797--1634861 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1634787 AAGACAATCA
*
1634797 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1634818 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1634839 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1634860 AG
1 AG
1634862 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1634951 original size:33 final size:33
Alignment explanation
Indices: 1634895--1634958 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1634885 AAATAGATGG
* *
1634895 AGTGGTGAAAGAAGTAGATGTGTTGAGGGGTTA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTTA
* *
1634928 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGT
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGT
1634959 GATATTAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.27
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTTA
Found at i:1637236 original size:200 final size:200
Alignment explanation
Indices: 1636893--1637640 Score: 1254
Period size: 200 Copynumber: 3.8 Consensus size: 200
1636883 AATTTACAAT
*
1636893 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * * *
1636958 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTGCAAGTATACCGATTTT
66 CGAAAACCAAAAGAATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
1637023 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAT
131 ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
1637088 AATGA
196 AATGA
*
1637093 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
1637158 CGAAAACCAAAAGAATATTGTAATATGTAATTTTTCAATATAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGAATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1637223 ATGAGAGAATAGGTCTTAATAATGTGTTGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
131 ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
1637288 AATGA
196 AATGA
1637293 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1637358 -------C----G-A-AAT-TAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGAATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1637409 ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
131 ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
1637474 AATGA
196 AATGA
*
1637479 ATGGCAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1637544 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGAATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1637609 ATGAGAGAATAGGTCTTAATAATGTGTCGACA
131 ATGAGAGAATAGGTCTTAATAATGTGTCGACA
1637641 TTGTTTAATG
Statistics
Matches: 514, Mismatches: 20, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
186 176 0.34
187 2 0.00
188 1 0.00
189 1 0.00
193 2 0.00
197 1 0.00
198 1 0.00
199 3 0.01
200 327 0.64
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAAACCAAAAGAATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
AATGA
Found at i:1639149 original size:6 final size:6
Alignment explanation
Indices: 1639138--1639213 Score: 71
Period size: 6 Copynumber: 12.7 Consensus size: 6
1639128 CGAGCGGTCA
* * * *
1639138 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * *
1639186 ATGACG ACGATG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGA
1639214 TGATCCAAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:1639200 original size:3 final size:3
Alignment explanation
Indices: 1639155--1639217 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
1639145 TGAAGCTGAC
* * * * * * *
1639155 GAT GAA GAT GAC GAT GAA GAT GAC GAT GAA GAT GAC GAC GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1639203 GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT
1639218 CCAAACAAGT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.22
Consensus pattern (3 bp):
GAT
Found at i:1639217 original size:12 final size:12
Alignment explanation
Indices: 1639138--1639213 Score: 98
Period size: 12 Copynumber: 6.3 Consensus size: 12
1639128 CGAGCGGTCA
*
1639138 ATGAAGATGAAG
1 ATGACGATGAAG
*
1639150 CTGACGATGAAG
1 ATGACGATGAAG
1639162 ATGACGATGAAG
1 ATGACGATGAAG
1639174 ATGACGATGAAG
1 ATGACGATGAAG
* *
1639186 ATGACGACGATG
1 ATGACGATGAAG
* *
1639198 ATGATGATGATG
1 ATGACGATGAAG
1639210 ATGA
1 ATGA
1639214 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 57 1.00
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1640735 original size:183 final size:183
Alignment explanation
Indices: 1640427--1641182 Score: 1413
Period size: 183 Copynumber: 4.1 Consensus size: 183
1640417 CAAAGTTTTC
* *
1640427 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1640492 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1640557 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1640610 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
* *
1640675 CAAAAAGTGTCGACATTTATACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1640740 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1640793 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1640858 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
1640923 AACCGGTATAAATATACCAGTTTTATGAGCGAACAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
1640976 ACACTTTTTAATATTATGTTGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
* * *
1641041 CAAAAAGTGTCGATATTTATACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1641106 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1641159 ACACTTTTTAATATTGTGTCGGTA
1 ACACTTTTTAATATTGTGTCGGTA
1641183 ATTTTAAGTA
Statistics
Matches: 556, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 556 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1643998 original size:23 final size:23
Alignment explanation
Indices: 1643968--1644035 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
1643958 TAAAAAAATG
1643968 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1643991 ATGTAATAGGTAACGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1644014 ATGTAATAGGTAGTGCTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1644036 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1644487 original size:23 final size:23
Alignment explanation
Indices: 1644457--1644524 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
1644447 TAAAAAAATG
1644457 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1644480 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1644503 ATGTAATAGGTAGTGCTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1644525 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1644652 original size:489 final size:489
Alignment explanation
Indices: 1643734--1647327 Score: 6440
Period size: 489 Copynumber: 7.4 Consensus size: 489
1643724 GCGTCTAATG
1643734 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1643799 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
66 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
1643864 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATA
131 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATA
*
1643929 AAAAGTATGGACACTTTCGATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
196 AAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
*
1643994 TAATAGGTAACGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
261 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
1644059 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
326 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
1644124 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
391 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
1644189 ATTAAATTAAAAACAATAAACATATATATTACAT
456 ATTAAATTAAAAACAATAAACATATATATTACAT
*
1644223 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAACTAATATTTTATAAAATATCA
1 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1644288 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
66 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
*
1644353 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCATTTTTATA
131 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATA
1644418 AAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
196 AAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
1644483 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
261 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
*
1644548 AAAAGTGTCCATATTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
326 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
1644613 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
391 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
*
1644678 TTTAAATTAAAAACAATAAACATATATATTACAT
456 ATTAAATTAAAAACAATAAACATATATATTACAT
1644712 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1644777 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
66 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
* *
1644842 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAATGTATCGATCATTTTTATA
131 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATA
*
1644907 AAAAGTATGGACACTTTCGATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
196 AAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
1644972 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
261 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
*
1645037 AAAAGTGTCCATACTTTTTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
326 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
1645102 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
391 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
1645167 ATTAAATTAAAAACAATAAACATATATATTACAT
456 ATTAAATTAAAAACAATAAACATATATATTACAT
*
1645201 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAACTAATATTTTATAAAATATCA
1 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1645266 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
66 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
1645331 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATA
131 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATA
1645396 AAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
196 AAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
*
1645461 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAATATCTATCCTTTTTAT
261 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
1645526 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
326 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
1645591 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
391 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
*
1645656 TTTAAATTAAAAACAATAAACATATATATTACAT
456 ATTAAATTAAAAACAATAAACATATATATTACAT
1645690 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1645755 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
66 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
* *
1645820 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAATGTATCGATCATTTTTATA
131 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATA
* * *
1645885 AAAAGTAAGAACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATG
196 AAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
*
1645950 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTAT
261 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
* * *
1646015 AAAAGTGTTCATACTTTTTTTACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGACTTTT
326 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
*
1646080 AAGATATTAATTTAGTAATTATAGGCGTTTAATGATTTATTTTTTACGTTACGGTATATATTATT
391 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
1646145 ATTAAATTAAAAACAATAAACATATATATTACAT
456 ATTAAATTAAAAACAATAAACATATATATTACAT
1646179 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
1 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
* *
1646244 AAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAA
66 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
1646309 AACACTATTTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTAT
131 AACACTA-TTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTAT
* *
1646374 AAAAAGTATGTACACTTTCAATATAATAGGTAAAAACATGATGTAATAGGTAGCGCTTATATAAT
195 AAAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAAT
* * *
1646439 GTAATAGGTAGCGTTTATATAATGTAATAGATAGTGCTTATATTGTAAAGTATTTATCATTTTTA
260 GTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTA
*
1646504 TAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGACTTT
325 TAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
* *
1646569 TAAGATATTAATTTAGTAATTATAGGCGTCTAATAATTTATTTTTTACGTTACGATATATATTAT
390 TAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTAT
*
1646634 TATTAAATTAAAAGCAATAAACATATATATTACAT
455 TATTAAATTAAAAACAATAAACATATATATTACAT
* *
1646669 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCA
1 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
* *
1646734 AAACAATCAAATAATTTTTTGTGTAAATGAAATTATTTAATTAATATTGTAGGTGGAAAACATGA
66 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
*
1646799 AACACTATTAAAAAAAATTAAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTAT
131 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAGTATCGATCCTTTTTAT
1646864 -AAAAGTATGGACACTTTCAATATAATAGGT-----AA--A---AATA--T---G--------AT
195 AAAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAAT
*
1646905 GTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTA
260 GTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTA
* * *
1646970 TAAAAGTGTCCATACTTATTTCACTGTGAAAAACATTAATTTAAGATTATCTTTTGAGTGAGTTT
325 TAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
* * ** *
1647035 TAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTTACGGTATATATTAT
390 TAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTAT
*
1647100 CATTAAATTAAAAACAATAAAC--ATATATTACAT
455 TATTAAATTAAAAACAATAAACATATATATTACAT
* *
1647133 A--T-TTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCA
1 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
* **
1647195 AAACAATCAAATAATTTTTTGTGCGAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
66 AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
* *
1647260 AACACTATT--AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAATATCGATCTTTTTTAT
131 AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAGTATCGATCCTTTTTAT
1647323 AAAAA
195 AAAAA
1647328 AAATATATAC
Statistics
Matches: 3027, Mismatches: 75, Indels: 35
0.96 0.02 0.01
Matches are distributed among these distances:
459 51 0.02
460 4 0.00
461 131 0.04
462 1 0.00
464 12 0.00
466 204 0.07
474 1 0.00
477 1 0.00
479 4 0.00
482 1 0.00
484 1 0.00
489 2121 0.70
490 495 0.16
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (489 bp):
ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
AAACAATCAAATAAGTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
AACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAAAAAATGATGTAATAGGTAGCGCTTATATAATG
TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTAAAAACAATAAACATATATATTACAT
Found at i:1644976 original size:23 final size:23
Alignment explanation
Indices: 1644946--1645013 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
1644936 TAAAAAAATG
1644946 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1644969 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1644992 ATGTAATAGGTAGTGCTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1645014 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1645465 original size:23 final size:23
Alignment explanation
Indices: 1645435--1645502 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
1645425 TAAAAAAATG
1645435 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1645458 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1645481 ATGTAATAGGTAGTGCTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1645503 TGTAAAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1645950 original size:23 final size:23
Alignment explanation
Indices: 1645919--1645991 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1645909 ATAGGTAAAA
*
1645919 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1645942 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1645965 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1645988 ATAT
1 ATAT
1645992 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1646444 original size:23 final size:23
Alignment explanation
Indices: 1646414--1646481 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
1646404 TAAAAACATG
1646414 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1646437 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1646460 ATGTAATAGATAGTGCTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1646482 TGTAAAGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1646929 original size:23 final size:23
Alignment explanation
Indices: 1646898--1646947 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1646888 ATAGGTAAAA
* *
1646898 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1646921 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1646944 ATAT
1 ATAT
1646948 TGTAAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1647991 original size:16 final size:16
Alignment explanation
Indices: 1647961--1647991 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1647951 TAATATTGAA
*
1647961 ACTTGAACTCAAAAAG
1 ACTTGAACTAAAAAAG
1647977 ACTTGAACTAAAAAA
1 ACTTGAACTAAAAAA
1647992 AAATTAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTAAAAAAG
Found at i:1662291 original size:18 final size:18
Alignment explanation
Indices: 1662268--1662302 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1662258 TCTCTCTGTA
1662268 TATATACCTACATATATG
1 TATATACCTACATATATG
**
1662286 TATATATGTACATATAT
1 TATATACCTACATATAT
1662303 TTAGTTTTGA
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:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (18 bp):
TATATACCTACATATATG
Found at i:1667478 original size:42 final size:42
Alignment explanation
Indices: 1667419--1667707 Score: 422
Period size: 42 Copynumber: 7.2 Consensus size: 42
1667409 AATATTTGGA
*
1667419 CTATCGCAATGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
1667461 CTATCACAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1667503 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1667545 CTATCGCAACGAA-TTGGAATGAATCGCAACGCG-A------
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
1667579 --ATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* *
1667618 CTATCGCAACG-GTTTGGAATGAATCGCAACGTGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
1667659 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1667701 CTATCGC
1 CTATCGC
1667708 GTTGCGAATT
Statistics
Matches: 225, Mismatches: 11, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
31 1 0.00
32 29 0.13
33 1 0.00
40 1 0.00
41 67 0.30
42 126 0.56
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:1667491 original size:21 final size:21
Alignment explanation
Indices: 1667421--1667575 Score: 81
Period size: 21 Copynumber: 7.4 Consensus size: 21
1667411 TATTTGGACT
* *
1667421 ATCGCAATGAATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
1667442 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAACTTGGAATGA
* *
1667463 ATCACAACGAATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
1667484 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAACTTGGAATGA
*
1667505 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
1667526 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAACTTGGAATGA
1667547 ATCGCAACGAA-TTGGAATGA
1 ATCGCAACGAACTTGGAATGA
1667567 ATCGCAACG
1 ATCGCAACG
1667576 CGAATCGCAA
Statistics
Matches: 96, Mismatches: 26, Indels: 25
0.65 0.18 0.17
Matches are distributed among these distances:
18 4 0.04
19 20 0.21
20 9 0.09
21 40 0.42
23 23 0.24
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATGA
Found at i:1667588 original size:32 final size:32
Alignment explanation
Indices: 1667547--1667611 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1667537 AACTTCGCCT
1667547 ATCGCAACGAATTGGAATGAATCGCAACGCGA
1 ATCGCAACGAATTGGAATGAATCGCAACGCGA
*
1667579 ATCGCAACGATTTGGAATGAATCGCAACGCGA
1 ATCGCAACGAATTGGAATGAATCGCAACGCGA
1667611 A
1 A
1667612 CTTCGACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.17
Consensus pattern (32 bp):
ATCGCAACGAATTGGAATGAATCGCAACGCGA
Found at i:1667602 original size:20 final size:20
Alignment explanation
Indices: 1667577--1667648 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
1667567 ATCGCAACGC
1667577 GAATCGCAACGATTTGGAAT
1 GAATCGCAACGATTTGGAAT
* * *
1667597 GAATCGCAACGCGAACTTCGACT
1 GAATCGCAA--CG-ATTTGGAAT
*
1667620 --ATCGCAACGGTTTGGAAT
1 GAATCGCAACGATTTGGAAT
1667638 GAATCGCAACG
1 GAATCGCAACG
1667649 TGAACTTCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
18 5 0.12
19 2 0.05
20 18 0.45
21 7 0.17
22 2 0.05
23 6 0.15
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (20 bp):
GAATCGCAACGATTTGGAAT
Found at i:1672472 original size:14 final size:14
Alignment explanation
Indices: 1672453--1672480 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1672443 TTTTGATTGA
1672453 TTCCATGGTACTTT
1 TTCCATGGTACTTT
1672467 TTCCATGGTACTTT
1 TTCCATGGTACTTT
1672481 GTTAGCTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
TTCCATGGTACTTT
Found at i:1680498 original size:17 final size:18
Alignment explanation
Indices: 1680466--1680504 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1680456 GACTTAAAAA
1680466 TTTTATAAAATGATAT-T
1 TTTTATAAAATGATATAT
* *
1680483 TTTTATAAACTTATATAT
1 TTTTATAAAATGATATAT
1680501 TTTT
1 TTTT
1680505 TTCTTGCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTATAAAATGATATAT
Found at i:1683328 original size:22 final size:22
Alignment explanation
Indices: 1683286--1683328 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1683276 GCTTTTATAC
*
1683286 TTTTTGAAAAATAATATTATTT
1 TTTTTGAAAAATAATAATATTT
*
1683308 TTTTTTAAAAA-AAGTAATATT
1 TTTTTGAAAAATAA-TAATATT
1683329 ATTATCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTTGAAAAATAATAATATTT
Found at i:1687591 original size:29 final size:30
Alignment explanation
Indices: 1687519--1687601 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
1687509 CGATTTAACG
1687519 GTTCAGTGGTATAATTGAAACGAAAATAAAA
1 GTTCAGTGGTATAATTGAAAC-AAAATAAAA
* ** *
1687550 GTTCAGTGCTATAATTGGTA-AAATTAAAA
1 GTTCAGTGGTATAATTGAAACAAAATAAAA
* *
1687579 GTTCAGTGGTATAAATGATACAA
1 GTTCAGTGGTATAATTGAAACAA
1687602 CGCCTGAAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 25 0.57
30 2 0.05
31 17 0.39
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.30
Consensus pattern (30 bp):
GTTCAGTGGTATAATTGAAACAAAATAAAA
Found at i:1688034 original size:39 final size:38
Alignment explanation
Indices: 1687972--1688052 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 38
1687962 GGGGGGACTC
* *
1687972 ACTTTTTGGTGGATGAAATAGTCATTACCACATTGCAT
1 ACTTCTTGGTGGATGAAATAGTCATTACCACATTACAT
1688010 ACTTCTTGGTGGATGGAAATAGTCATTACCACATTACAT
1 ACTTCTTGGTGGAT-GAAATAGTCATTACCACATTACAT
1688049 ACTT
1 ACTT
1688053 ATACCCCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 13 0.32
39 27 0.68
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (38 bp):
ACTTCTTGGTGGATGAAATAGTCATTACCACATTACAT
Found at i:1690515 original size:13 final size:13
Alignment explanation
Indices: 1690493--1690529 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1690483 TATTTAATTT
*
1690493 TTTTTTAAAAATA
1 TTTTTAAAAAATA
1690506 TTTTTAAAAAATA
1 TTTTTAAAAAATA
1690519 TTTTTAAAAAA
1 TTTTTAAAAAA
1690530 AATATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:1696254 original size:118 final size:119
Alignment explanation
Indices: 1696040--1696308 Score: 330
Period size: 118 Copynumber: 2.2 Consensus size: 119
1696030 TACTAATATT
* *
1696040 GACCAAAACTGATAGTTTTAGGTACTAAACATTTTAAGTTTTTAACGGTAGGGTACTAAAATGAA
1 GACCAAAACTGATAG-TTTAGGTACTAAACATGTTAAGTTTTT-A--GTAGGCTACTAAAATGAA
*
1696105 ATAAAAACTAAATGTTACGAATGATTTTGAAAA-A-AAAAGAGTTTAGTTATTAAAATA
62 ATAAAAACTAAATGTTACGAATGATTTTGAAAAGATAAAA-AGTTTAGTTATTAAAACA
*
1696162 GACTAAAACTGATAGTTATAGGTACTAAA-AGTGTTAAGTTTTT-GTAGGCTACTAAAATGAAAT
1 GACCAAAACTGATAGTT-TAGGTACTAAACA-TGTTAAGTTTTTAGTAGGCTACTAAAATGAAAT
* * * * * *
1696225 AAAAATTAAATGTTATGTATGCTTTTGAAAAGATTAAAAGTTTAGTTGTTAAAACA
64 AAAAACTAAATGTTACGAATGATTTTGAAAAGATAAAAAGTTTAGTTATTAAAACA
* * *
1696281 TACCAAAATTGATGGTTTAGGTACTAAA
1 GACCAAAACTGATAGTTTAGGTACTAAA
1696309 TGCGTAGTTT
Statistics
Matches: 129, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
118 57 0.44
119 30 0.23
120 3 0.02
121 3 0.02
122 36 0.28
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.33
Consensus pattern (119 bp):
GACCAAAACTGATAGTTTAGGTACTAAACATGTTAAGTTTTTAGTAGGCTACTAAAATGAAATAA
AAACTAAATGTTACGAATGATTTTGAAAAGATAAAAAGTTTAGTTATTAAAACA
Found at i:1697122 original size:27 final size:27
Alignment explanation
Indices: 1697092--1697155 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
1697082 CATAAAATAT
1697092 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
* ** *
1697119 ATATTTTTAAATTAATTTAATAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
*
1697146 ATATATTTAA
1 ATATTTTTAA
1697156 TAAGTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATTTTTAAATGAAAATAAAAATAAA
Found at i:1697168 original size:27 final size:26
Alignment explanation
Indices: 1697113--1697201 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 26
1697103 TGAAAATAAA
*
1697113 AATAAAATATTTT--TAAATTAATTTAAT
1 AATAAAATATTTTAATAAGTTAA--T-AT
1697140 AATAAAATATATTTAATAAGTTAATAT
1 AATAAAATAT-TTTAATAAGTTAATAT
1697167 AA-AAAATATTTT--TAAGTTAATAT
1 AATAAAATATTTTAATAAGTTAATAT
1697190 ATATAAAATATT
1 A-ATAAAATATT
1697202 ATGAATTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
23 12 0.21
24 1 0.02
25 11 0.20
26 7 0.12
27 14 0.25
28 4 0.07
30 7 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AATAAAATATTTTAATAAGTTAATAT
Found at i:1697191 original size:25 final size:25
Alignment explanation
Indices: 1697116--1697201 Score: 86
Period size: 25 Copynumber: 3.3 Consensus size: 25
1697106 AAATAAAAAT
* *
1697116 AAAATATTTTTAAATTAATTTAATAA
1 AAAATATTTTTAAGTTAATAT-ATAA
1697142 TAAAATATATTTAATAAGTT-A-ATATAA
1 -AAAATAT-TTT--TAAGTTAATATATAA
*
1697169 AAAATATTTTTAAGTTAATATATAT
1 AAAATATTTTTAAGTTAATATATAA
1697194 AAAATATT
1 AAAATATT
1697202 ATGAATTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
23 6 0.12
24 1 0.02
25 16 0.31
26 7 0.14
27 11 0.22
28 4 0.08
29 1 0.02
30 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAATATTTTTAAGTTAATATATAA
Found at i:1697211 original size:25 final size:23
Alignment explanation
Indices: 1697135--1697211 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 23
1697125 TTAAATTAAT
*
1697135 TTAATAATAAAATATATTTAAT-AAG
1 TTAAT-ATAAAAAATA-TT-ATGAAG
* *
1697160 TTAATATAAAAAATATTTTTAAG
1 TTAATATAAAAAATATTATGAAG
*
1697183 TTAATATATATAAAATATTATGAAT
1 TTAATATA-A-AAAATATTATGAAG
1697208 TTAA
1 TTAA
1697212 GTATTTGTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.02
23 13 0.30
24 10 0.23
25 20 0.45
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAATATAAAAAATATTATGAAG
Found at i:1698293 original size:2 final size:2
Alignment explanation
Indices: 1698286--1698314 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1698276 ATACTTAAAT
1698286 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
1698315 TATCAATTTA
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:1698343 original size:20 final size:20
Alignment explanation
Indices: 1698320--1698358 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1698310 TATATTATCA
*
1698320 ATTTAATATTTAAAATATTT
1 ATTTAATATCTAAAATATTT
* *
1698340 ATTTCATATCTAAAGTATT
1 ATTTAATATCTAAAATATT
1698359 CATACATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTAATATCTAAAATATTT
Found at i:1698886 original size:20 final size:20
Alignment explanation
Indices: 1698857--1698899 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1698847 TTAGGAGAGC
* **
1698857 GAACTTAAATTTGGGGGGAT
1 GAACTAAAATTTCAGGGGAT
1698877 GAACTAAAATTTCAGGGGAT
1 GAACTAAAATTTCAGGGGAT
1698897 GAA
1 GAA
1698900 AACATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (20 bp):
GAACTAAAATTTCAGGGGAT
Found at i:1700029 original size:31 final size:32
Alignment explanation
Indices: 1699994--1700065 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
1699984 TGGAGTGACC
1699994 ATTTTGTTACAAATCGATAATGTTAGTGA-TA
1 ATTTTGTTACAAATCGATAATGTTAGTGACTA
*
1700025 ATTTTATTACAAATCGATAATGTTAGTGACTA
1 ATTTTGTTACAAATCGATAATGTTAGTGACTA
1700057 A-TTTGTTAC
1 ATTTTGTTAC
1700066 TTTTTGAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 35 0.92
32 3 0.08
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (32 bp):
ATTTTGTTACAAATCGATAATGTTAGTGACTA
Done.