Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 63 of 203
Found at i:20233296 original size:20 final size:21
Alignment explanation
Indices: 20233260--20233307 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
20233250 GGAGCAATTC
*
20233260 TGACTTGTTTGAAAATCATTT
1 TGACTTGGTTGAAAATCATTT
20233281 TGACTTGGTT-AAAATCATTT
1 TGACTTGGTTGAAAATCATTT
*
20233301 TCACTTG
1 TGACTTG
20233308 ATTTTAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (21 bp):
TGACTTGGTTGAAAATCATTT
Found at i:20236672 original size:3 final size:3
Alignment explanation
Indices: 20236659--20236758 Score: 191
Period size: 3 Copynumber: 33.0 Consensus size: 3
20236649 AAATATAAGA
20236659 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20236705 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20236753 AAT AAT
1 AAT AAT
20236759 GCACAAGGAC
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 93 0.97
4 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20270406 original size:23 final size:22
Alignment explanation
Indices: 20270363--20270420 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
20270353 AAAGGGTATC
* *
20270363 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
20270384 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
20270407 TGCATATCATATCT
1 TACAAATCATATCT
20270421 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:20270673 original size:19 final size:20
Alignment explanation
Indices: 20270641--20270678 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
20270631 AGGCTTACAT
20270641 ATTCTATCAATTTGATCCTA
1 ATTCTATCAATTTGATCCTA
20270661 ATTCTAT-AATTTGATCCT
1 ATTCTATCAATTTGATCCT
20270679 CAAATTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (20 bp):
ATTCTATCAATTTGATCCTA
Found at i:20276917 original size:12 final size:12
Alignment explanation
Indices: 20276900--20276935 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
20276890 TTACATACGT
20276900 TCGTTTTAAAAC
1 TCGTTTTAAAAC
20276912 TCGTTTTAAAAC
1 TCGTTTTAAAAC
20276924 TCGTTTTAAAAC
1 TCGTTTTAAAAC
20276936 CAGAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (12 bp):
TCGTTTTAAAAC
Found at i:20277486 original size:24 final size:23
Alignment explanation
Indices: 20277424--20277493 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 23
20277414 ACGTTTTCAG
*
20277424 ATGCAATTCAAATACAGATTCAA
1 ATGCAATTCAAATACAGAATCAA
** * * *
20277447 ATAAAATCTTAGATACAGAATCAT
1 ATGCAAT-TCAAATACAGAATCAA
*
20277471 ATGCAATATCAAATACAAAATCA
1 ATGCAAT-TCAAATACAGAATCA
20277494 GATCCTACCC
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (23 bp):
ATGCAATTCAAATACAGAATCAA
Found at i:20287601 original size:28 final size:26
Alignment explanation
Indices: 20287567--20287634 Score: 95
Period size: 25 Copynumber: 2.6 Consensus size: 26
20287557 ATTTTAGATT
*
20287567 AATTATTTCAAAAATAATATTATTTTA
1 AATTATTTCAAAAA-AATATTATATTA
20287594 ATATTATTTC--AAAAATATTATATTA
1 A-ATTATTTCAAAAAAATATTATATTA
20287619 AATTATTTCAAAAAAA
1 AATTATTTCAAAAAAA
20287635 GTTACACTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 8 0.22
25 12 0.32
26 8 0.22
27 1 0.03
28 8 0.22
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTATTTCAAAAAAATATTATATTA
Found at i:20287610 original size:25 final size:24
Alignment explanation
Indices: 20287567--20287632 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 24
20287557 ATTTTAGATT
*
20287567 AATTATTTCAAAAATAATATTATTTTA
1 AATTATTTC--AAA-AATATTATATTA
20287594 ATATTATTTCAAAAATATTATATTA
1 A-ATTATTTCAAAAATATTATATTA
20287619 AATTATTTCAAAAA
1 AATTATTTCAAAAA
20287633 AAGTTACACT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 13 0.35
25 12 0.32
26 3 0.08
27 1 0.03
28 8 0.22
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTATTTCAAAAATATTATATTA
Found at i:20291262 original size:40 final size:40
Alignment explanation
Indices: 20291225--20291408 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
20291215 GCTACTCGTT
*
20291225 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
20291265 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
20291305 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * * * *
20291344 CAAATGCCTTC-GGATTTTAGTCCAGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
*
20291385 CAAA-GCCTTTGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
20291409 ACATCATTCG
Statistics
Matches: 117, Mismatches: 19, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
38 2 0.02
39 30 0.26
40 71 0.61
41 14 0.12
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:20291343 original size:39 final size:40
Alignment explanation
Indices: 20291225--20291356 Score: 189
Period size: 40 Copynumber: 3.3 Consensus size: 40
20291215 GCTACTCGTT
* *
20291225 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTATCTCGCA
*
20291265 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ATCTCGCA
*
20291305 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
20291344 CAAATGCCTTCGG
1 CAAATGCCTTCGG
20291357 ATTTTAGTCC
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.39
40 46 0.55
41 3 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:20294002 original size:20 final size:20
Alignment explanation
Indices: 20293961--20294002 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
20293951 TCATGCTTGA
* *
20293961 AGTAGTGATTTATACTTTTT
1 AGTAGTGATTTATACATCTT
20293981 AGTAGT-ATTTATTACATCTT
1 AGTAGTGATTTA-TACATCTT
20294001 AG
1 AG
20294003 ATATCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
AGTAGTGATTTATACATCTT
Found at i:20299101 original size:40 final size:40
Alignment explanation
Indices: 20299046--20299122 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
20299036 CCCTGAACCG
*
20299046 GTCTGGACTGTGAGGTTAGAAGATAAGTAGTTCTTGCCCA
1 GTCTGGACTGTGAGGTTAAAAGATAAGTAGTTCTTGCCCA
20299086 GTCTGGACTGTGAGGTTAAAAGATAAGTAGTTCTTGC
1 GTCTGGACTGTGAGGTTAAAAGATAAGTAGTTCTTGC
20299123 TGACTCGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31
Consensus pattern (40 bp):
GTCTGGACTGTGAGGTTAAAAGATAAGTAGTTCTTGCCCA
Found at i:20301017 original size:37 final size:37
Alignment explanation
Indices: 20300955--20301089 Score: 198
Period size: 37 Copynumber: 3.6 Consensus size: 37
20300945 TGGTTTATTT
* *
20300955 TCGGTTGGACTAGCTTTTATGAGCATCTGGCGTGTTA
1 TCGGGTGGACTAGCTCTTATGAGCATCTGGCGTGTTA
*
20300992 TCGGGTGGACTAGCTCTTATAAGCATCTGGCGTGTTA
1 TCGGGTGGACTAGCTCTTATGAGCATCTGGCGTGTTA
* * *
20301029 TCAGGTGGATTAGCTCTTATGAGCATCTGGCATGTTA
1 TCGGGTGGACTAGCTCTTATGAGCATCTGGCGTGTTA
* *
20301066 TCGGGTGGATTAGCTCTTACGAGC
1 TCGGGTGGACTAGCTCTTATGAGC
20301090 GTGTTTCGGT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 89 1.00
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.34
Consensus pattern (37 bp):
TCGGGTGGACTAGCTCTTATGAGCATCTGGCGTGTTA
Found at i:20311084 original size:49 final size:49
Alignment explanation
Indices: 20311027--20311128 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
20311017 TCACTCATAT
20311027 TTAATAACTAGTGTACCAAATATAAAATCTCTTCCAAGATATTTAGAAA
1 TTAATAACTAGTGTACCAAATATAAAATCTCTTCCAAGATATTTAGAAA
*
20311076 TTAATAACTAGTGTACCAAATATAAAATTTCTTCCAAGATATTTAGAAA
1 TTAATAACTAGTGTACCAAATATAAAATCTCTTCCAAGATATTTAGAAA
20311125 TTAA
1 TTAA
20311129 ATAATTGAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (49 bp):
TTAATAACTAGTGTACCAAATATAAAATCTCTTCCAAGATATTTAGAAA
Found at i:20312326 original size:45 final size:45
Alignment explanation
Indices: 20312257--20312344 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
20312247 TTTGTAGATT
* * *
20312257 AAAGCTACTAATATGGTGTAGGTAAACTACTAATCGGTGCAAAGA
1 AAAGCTACTAATATGATGTAGGTAAACCACTAAACGGTGCAAAGA
* *
20312302 AAAGTTACTAATATGATGTGGGTAAACCACTAAACGGTGCAAA
1 AAAGCTACTAATATGATGTAGGTAAACCACTAAACGGTGCAAA
20312345 CAAGCTACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (45 bp):
AAAGCTACTAATATGATGTAGGTAAACCACTAAACGGTGCAAAGA
Found at i:20313112 original size:182 final size:181
Alignment explanation
Indices: 20312805--20313166 Score: 697
Period size: 182 Copynumber: 2.0 Consensus size: 181
20312795 TTTGTATATT
20312805 AATTATTTAAGGTTAAATTGGTAAACTAAAAATTTTGATAATATATGTTATAATAAAACATAAAA
1 AATTATTTAAGGTTAAATTGGTAAACTAAAAATTTTGATAATATATGTTATAATAAAACATAAAA
20312870 ATAAAAGAAACATGCAAAAAGGTTCATCATTTTAGCCAAAACTTCAAAAGACAAAGAAAAAAAAA
66 ATAAAAGAAACATGCAAAAAGGTTCATCATTTTAGCCAAAACTTCAAAAGACAAAG-AAAAAAAA
20312935 AGAAAGCTTGGTTCGGCACTTGTAATCCTTAATTTAGGTATGTATTTTGTTA
130 AGAAAGCTTGGTTCGGCACTTGTAATCCTTAATTTAGGTATGTATTTTGTTA
*
20312987 AATTATTTAAGGTTAAATTGGTAAACTAGAAATTTTGATAATATATGTTATAATAAAACATAAAA
1 AATTATTTAAGGTTAAATTGGTAAACTAAAAATTTTGATAATATATGTTATAATAAAACATAAAA
*
20313052 ATAAAAGAAACATGCAAAAAGGTTCATCATTTTAGCCGAAACTTCAAAAGACAAAGAAAAAAAAA
66 ATAAAAGAAACATGCAAAAAGGTTCATCATTTTAGCCAAAACTTCAAAAGACAAAGAAAAAAAAA
20313117 GAAAGCTTGGTTCGGCACTTGTAATCCTTAATTTAGGTATGTATTTTGTT
131 GAAAGCTTGGTTCGGCACTTGTAATCCTTAATTTAGGTATGTATTTTGTT
20313167 GGGTTTTTAA
Statistics
Matches: 178, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
181 59 0.33
182 119 0.67
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.31
Consensus pattern (181 bp):
AATTATTTAAGGTTAAATTGGTAAACTAAAAATTTTGATAATATATGTTATAATAAAACATAAAA
ATAAAAGAAACATGCAAAAAGGTTCATCATTTTAGCCAAAACTTCAAAAGACAAAGAAAAAAAAA
GAAAGCTTGGTTCGGCACTTGTAATCCTTAATTTAGGTATGTATTTTGTTA
Found at i:20314803 original size:41 final size:41
Alignment explanation
Indices: 20314753--20314870 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 41
20314743 GTGAAAATAT
* *
20314753 TCAGACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACAGAA
* *
20314794 TCAGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAACAGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACAGAA
* * * * *
20314835 TTAAACTATAAGCCTATCAGG-TGAAGTGCCAGTGAA
1 TCAGACTATACGCCTAGCAGGCT-AAGTGCCGGTGAA
20314871 TCTGTTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
40 1 0.02
41 65 0.98
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (41 bp):
TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACAGAA
Found at i:20325774 original size:6 final size:6
Alignment explanation
Indices: 20325763--20325814 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 6
20325753 TTGGCCTCTC
*
20325763 CTTTTT CTTTTT CTTTTT TTCTTTT CTTTTTT CATTTTTT CATTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CT-TTTT C-TTTTT C--TTTTT C-TTTTT CTTTT
20325815 CGTTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 17 0.43
7 15 0.38
8 8 0.20
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:20325783 original size:8 final size:7
Alignment explanation
Indices: 20325764--20325814 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
20325754 TGGCCTCTCC
20325764 TTTTTC-
1 TTTTTCT
20325770 TTTTTCT
1 TTTTTCT
20325777 TTTTT-T
1 TTTTTCT
*
20325783 CTTTTCT
1 TTTTTCT
20325790 TTTTTCAT
1 TTTTTC-T
*
20325798 TTTTTCA
1 TTTTTCT
20325805 TTTTTCT
1 TTTTTCT
20325812 TTT
1 TTT
20325815 CGTTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 11 0.29
7 20 0.53
8 7 0.18
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:20325786 original size:20 final size:20
Alignment explanation
Indices: 20325763--20325823 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
20325753 TTGGCCTCTC
20325763 CTTTTTCTTTTTCTTTTTTT
1 CTTTTTCTTTTTCTTTTTTT
*
20325783 C-TTTTCTTTTTTCATTTTTT
1 CTTTTTC-TTTTTCTTTTTTT
20325803 CATTTTTC-TTTTCGTTTTTTT
1 C-TTTTTCTTTTTC-TTTTTTT
20325824 TAAGTGAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 5 0.14
20 19 0.54
21 6 0.17
22 5 0.14
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (20 bp):
CTTTTTCTTTTTCTTTTTTT
Found at i:20326248 original size:11 final size:11
Alignment explanation
Indices: 20326232--20326288 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
20326222 TCCTGGTAGA
20326232 GTTTTTTTTTT
1 GTTTTTTTTTT
*
20326243 GTTTTTGCTTTT
1 GTTTTT-TTTTT
*
20326255 GTTTTTTATTT
1 GTTTTTTTTTT
* *
20326266 GGTTTTTATTT
1 GTTTTTTTTTT
20326277 GTTCTTTTTTTT
1 GTT-TTTTTTTT
20326289 TTTGGCCTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
11 21 0.55
12 17 0.45
ACGTcount: A:0.04, C:0.04, G:0.12, T:0.81
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:20327631 original size:62 final size:62
Alignment explanation
Indices: 20327527--20327710 Score: 323
Period size: 62 Copynumber: 3.0 Consensus size: 62
20327517 CTAAACTCGA
* *
20327527 CGTACTTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTGATGCATGAACG
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTAATGCATGAACG
* *
20327589 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATAAAATGTAATGTTAATGCATGAACG
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTAATGCATGAACG
*
20327651 CGTATTTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTAATGAATGAA
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTAATGCATGAA
20327711 GAGATACGTG
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 115 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (62 bp):
CGTATTTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTAATGCATGAACG
Found at i:20336135 original size:22 final size:22
Alignment explanation
Indices: 20336086--20336127 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
20336076 ATAAAAATAA
20336086 AAATTCTAAAAAATCATTAAATT
1 AAATTCTAAAAAAT-ATTAAATT
20336109 AAATTCTAAAAAAT-TTAAA
1 AAATTCTAAAAAATATTAAA
20336128 ATTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATTCTAAAAAATATTAAATT
Found at i:20336657 original size:18 final size:19
Alignment explanation
Indices: 20336634--20336679 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
20336624 ATTTTAGAAA
20336634 TAATTTTAA-ATAATTTTT
1 TAATTTTAATATAATTTTT
*
20336652 TAA-TTTAATTTAATTTTT
1 TAATTTTAATATAATTTTT
20336670 TAATTATTAA
1 TAATT-TTAA
20336680 CATTGCTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 1 0.04
20 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATTTTAATATAATTTTT
Found at i:20340188 original size:34 final size:35
Alignment explanation
Indices: 20340124--20340198 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 35
20340114 TCTTTTAGTT
**
20340124 TTTAGGGTTTATGTGTTCACGCGAGATTGAAAGCAG
1 TTTAGGGTTTATGTCATCAC-CGAGATTGAAAGCAG
*
20340160 TTTAGGGTTTATGTCATCA-CGAGATTGAAAGTAG
1 TTTAGGGTTTATGTCATCACCGAGATTGAAAGCAG
20340194 TTTAG
1 TTTAG
20340199 CATGGAGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 19 0.53
36 17 0.47
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.36
Consensus pattern (35 bp):
TTTAGGGTTTATGTCATCACCGAGATTGAAAGCAG
Found at i:20344549 original size:16 final size:17
Alignment explanation
Indices: 20344528--20344559 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20344518 AATCAAACCC
20344528 TAAAATTAA-AAAAATG
1 TAAAATTAATAAAAATG
20344544 TAAAATTAATAAAAAT
1 TAAAATTAATAAAAAT
20344560 CCTCAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
TAAAATTAATAAAAATG
Found at i:20356955 original size:21 final size:22
Alignment explanation
Indices: 20356923--20356963 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
20356913 CTAGCCTTAT
20356923 CTTTCTTCTTTC-TTTCTTTCC
1 CTTTCTTCTTTCTTTTCTTTCC
20356944 CTTT-TTCTTTTCTTTTCTTT
1 CTTTCTTC-TTTCTTTTCTTT
20356964 TTGTTTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 8 0.44
22 7 0.39
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (22 bp):
CTTTCTTCTTTCTTTTCTTTCC
Found at i:20356963 original size:16 final size:15
Alignment explanation
Indices: 20356924--20356999 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 15
20356914 TAGCCTTATC
20356924 TTTCTTCTTTCTTTCT
1 TTTCTT-TTTCTTTCT
*
20356940 TTCCCTTTTTCTTTTCT
1 TT-TCTTTTTC-TTTCT
*
20356957 TTTCTTTTTGTTTCGT
1 TTTCTTTTTCTTTC-T
***
20356973 TTTAGCTTT-TTTCT
1 TTTCTTTTTCTTTCT
20356987 TTCTCTTTTTCTT
1 TT-TCTTTTTCTT
20357000 ATTTTGTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
14 3 0.07
15 12 0.26
16 21 0.46
17 10 0.22
ACGTcount: A:0.01, C:0.21, G:0.04, T:0.74
Consensus pattern (15 bp):
TTTCTTTTTCTTTCT
Found at i:20357009 original size:34 final size:35
Alignment explanation
Indices: 20356945--20357010 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
20356935 TTTCTTTCCC
*
20356945 TTTTTCTTTTCTTTTCTTTTTGTTTCGTTTTAGCT
1 TTTTTCTTTTCTTTTCTTTATGTTTCGTTTTAGCT
20356980 TTTTTCTTTCTCTTTT-TCTTAT-TTT-GTTTTA
1 TTTTTCTTT-TCTTTTCT-TTATGTTTCGTTTTA
20357011 TTATAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 6 0.21
35 13 0.46
36 9 0.32
ACGTcount: A:0.05, C:0.14, G:0.06, T:0.76
Consensus pattern (35 bp):
TTTTTCTTTTCTTTTCTTTATGTTTCGTTTTAGCT
Found at i:20359112 original size:12 final size:12
Alignment explanation
Indices: 20359095--20359133 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
20359085 AGATCAATTT
20359095 TGACGGTGCATA
1 TGACGGTGCATA
20359107 TGACGGTGCATA
1 TGACGGTGCATA
20359119 TGACGGTGCATA
1 TGACGGTGCATA
20359131 TGA
1 TGA
20359134 GATAGCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (12 bp):
TGACGGTGCATA
Found at i:20359141 original size:24 final size:24
Alignment explanation
Indices: 20359095--20359141 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
20359085 AGATCAATTT
*
20359095 TGACGGTGCATATGACGGTGCATA
1 TGACGGTGCATATGACGATGCATA
20359119 TGACGGTGCATATGA-GATAGCAT
1 TGACGGTGCATATGACGAT-GCAT
20359142 TATATTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.26
Consensus pattern (24 bp):
TGACGGTGCATATGACGATGCATA
Found at i:20359598 original size:2 final size:2
Alignment explanation
Indices: 20359591--20359621 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20359581 TGAGTAACCA
20359591 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20359622 GTTTGAAACC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:20365022 original size:82 final size:82
Alignment explanation
Indices: 20364877--20365037 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 82
20364867 AAAAAAAAAA
* * *
20364877 TTGTTCATAGAAAATTTAGATGGTGGTGAAACTGAGAGCTGACTGATTTTGATTCTTGATATCTA
1 TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGACTGATTTTAATTCTCGATATCTA
*
20364942 A-AATTATAAAATTTATT
66 AGAA-AATAAAATTTATT
* *
20364959 TTGTTCATACAAAATTTAGATGGTGGTGAAATTGAGAGTTGA-TCGATTTTAATTCTCCG-TATC
1 TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGACT-GATTTTAATTCT-CGATATC
20365022 TAAGAAAATAAAATTT
64 TAAGAAAATAAAATTT
20365038 TGTTATTCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
81 1 0.01
82 66 0.94
83 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (82 bp):
TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGACTGATTTTAATTCTCGATATCTA
AGAAAATAAAATTTATT
Found at i:20365244 original size:82 final size:82
Alignment explanation
Indices: 20365099--20365259 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 82
20365089 AAAAAAAAAA
* * *
20365099 TTGTTCATAGAAAATTTAGATGGTGGTGAAACTGAGAGCTGACTGATTTTGATTCTTGATATCTA
1 TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGACTGATTTTAATTCTCGATATCTA
*
20365164 A-AATTATAAAATTTATT
66 AGAA-AATAAAATTTATT
* *
20365181 TTGTTCATACAAAATTTAGATGGTGGTGAAATTGAGAGTTGA-TCGATTTTAATTCTCCG-TATC
1 TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGACT-GATTTTAATTCT-CGATATC
20365244 TAAGAAAATAAAATTT
64 TAAGAAAATAAAATTT
20365260 TGTTATTCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
81 1 0.01
82 66 0.94
83 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (82 bp):
TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGACTGATTTTAATTCTCGATATCTA
AGAAAATAAAATTTATT
Found at i:20365324 original size:222 final size:222
Alignment explanation
Indices: 20364843--20365287 Score: 881
Period size: 222 Copynumber: 2.0 Consensus size: 222
20364833 CTTCTTGATC
*
20364843 TAAAATACTTTCAAAAAAGATAAAAAAAAAAAAATTGTTCATAGAAAATTTAGATGGTGGTGAAA
1 TAAAATACTTTCAAAAAAGAAAAAAAAAAAAAAATTGTTCATAGAAAATTTAGATGGTGGTGAAA
20364908 CTGAGAGCTGACTGATTTTGATTCTTGATATCTAAAATTATAAAATTTATTTTGTTCATACAAAA
66 CTGAGAGCTGACTGATTTTGATTCTTGATATCTAAAATTATAAAATTTATTTTGTTCATACAAAA
20364973 TTTAGATGGTGGTGAAATTGAGAGTTGATCGATTTTAATTCTCCGTATCTAAGAAAATAAAATTT
131 TTTAGATGGTGGTGAAATTGAGAGTTGATCGATTTTAATTCTCCGTATCTAAGAAAATAAAATTT
20365038 TGTTATTCTATTATTAAATTAATTTAA
196 TGTTATTCTATTATTAAATTAATTTAA
20365065 TAAAATACTTTCAAAAAAGAAAAAAAAAAAAAAATTGTTCATAGAAAATTTAGATGGTGGTGAAA
1 TAAAATACTTTCAAAAAAGAAAAAAAAAAAAAAATTGTTCATAGAAAATTTAGATGGTGGTGAAA
20365130 CTGAGAGCTGACTGATTTTGATTCTTGATATCTAAAATTATAAAATTTATTTTGTTCATACAAAA
66 CTGAGAGCTGACTGATTTTGATTCTTGATATCTAAAATTATAAAATTTATTTTGTTCATACAAAA
20365195 TTTAGATGGTGGTGAAATTGAGAGTTGATCGATTTTAATTCTCCGTATCTAAGAAAATAAAATTT
131 TTTAGATGGTGGTGAAATTGAGAGTTGATCGATTTTAATTCTCCGTATCTAAGAAAATAAAATTT
20365260 TGTTATTCTATTATTAAATTAATTTAA
196 TGTTATTCTATTATTAAATTAATTTAA
20365287 T
1 T
20365288 CTTTATATTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 222 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (222 bp):
TAAAATACTTTCAAAAAAGAAAAAAAAAAAAAAATTGTTCATAGAAAATTTAGATGGTGGTGAAA
CTGAGAGCTGACTGATTTTGATTCTTGATATCTAAAATTATAAAATTTATTTTGTTCATACAAAA
TTTAGATGGTGGTGAAATTGAGAGTTGATCGATTTTAATTCTCCGTATCTAAGAAAATAAAATTT
TGTTATTCTATTATTAAATTAATTTAA
Found at i:20366142 original size:50 final size:50
Alignment explanation
Indices: 20366079--20366174 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
20366069 ACAAATTTAG
** * * *
20366079 CCCTCAACTTTTACATATTATATCAATTT-AGTCATAATTTTAAAAATTAA
1 CCCTCAAAATTTACAAATGATATCAATTTGA-TCATAATTCTAAAAATTAA
* *
20366129 CCCTCAAAATTTACAAATGATTTCAATTTGATCCTAATTCTAAAAA
1 CCCTCAAAATTTACAAATGATATCAATTTGATCATAATTCTAAAAA
20366175 ATTCAAAGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 37 0.97
51 1 0.03
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.39
Consensus pattern (50 bp):
CCCTCAAAATTTACAAATGATATCAATTTGATCATAATTCTAAAAATTAA
Found at i:20366370 original size:25 final size:24
Alignment explanation
Indices: 20366337--20366384 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
20366327 ATTTAAATTA
20366337 ATATTAATATTAAATAAAGATAAAT
1 ATATTAATATTAAATAAA-ATAAAT
*
20366362 ATATTAATATTAGATAAAATAAA
1 ATATTAATATTAAATAAAATAAA
20366385 AATCCCCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAAAT
Found at i:20366574 original size:25 final size:25
Alignment explanation
Indices: 20366521--20366575 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
20366511 AATTTTAATT
* * *
20366521 TATTATTATATTTTTTGAAAATATT
1 TATTTTTATATATTTTGAAAATATA
* *
20366546 TATTTTTATATATTTTTAAATTATA
1 TATTTTTATATATTTTGAAAATATA
20366571 TATTT
1 TATTT
20366576 GAAAATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTTTTATATATTTTGAAAATATA
Found at i:20369430 original size:41 final size:41
Alignment explanation
Indices: 20369373--20369516 Score: 168
Period size: 41 Copynumber: 3.5 Consensus size: 41
20369363 TTAACATATC
20369373 CACCGGCACTTAGCCTGCTAGGCTTATATCCTGATTCAGAT
1 CACCGGCACTTAGCCTGCTAGGCTTATATCCTGATTCAGAT
* *
20369414 CACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGAT
1 CACCGGCACTTAGCCTGCTAGGCTTATATCCTGATTCAGAT
* * * * **
20369455 TACCGGCAGTTAGCCTGCT-GGACTTAAAGT-CTGAATCATTT
1 CACCGGCACTTAGCCTGCTAGG-CTTATA-TCCTGATTCAGAT
20369496 CACCGGC-CTTAAGCCTGCTAG
1 CACCGGCACTT-AGCCTGCTAG
20369517 ACATAAAGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
40 4 0.05
41 82 0.94
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (41 bp):
CACCGGCACTTAGCCTGCTAGGCTTATATCCTGATTCAGAT
Found at i:20369612 original size:41 final size:41
Alignment explanation
Indices: 20369456--20369598 Score: 200
Period size: 41 Copynumber: 3.5 Consensus size: 41
20369446 GATTCAGATT
* * *
20369456 ACCGGCAGTT-AGCCTGCTGGACTTAAAGTCTG-AATCATTTC
1 ACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAAT-AATTC
*
20369497 ACCGGCCTTAAGCCTGCTAGACATAAAGTCTGAAATAATTC
1 ACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATTC
20369538 ACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATTC
1 ACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATTC
* *
20369579 ACCGGTATTAAACCTGCTAG
1 ACCGGCATTAAGCCTGCTAG
20369599 GCATCGAGCC
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 2 0.02
41 88 0.95
42 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (41 bp):
ACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATTC
Found at i:20370397 original size:196 final size:198
Alignment explanation
Indices: 20369933--20370363 Score: 636
Period size: 203 Copynumber: 2.2 Consensus size: 198
20369923 AATTCAATAC
* ** *
20369933 ATACATTCGGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACTCAGCATATAT
1 ATACATTCAGCTAACATATATACAATTCATTAAATTTCATTCAACTTACAAAAC-CAACATATAT
*
20369998 ATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTATCTTATAAACTCAAATATACATT
65 ATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAACTCAAATATACATT
*
20370063 GACTAACACACGCACATATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAA
130 GACT-A-ACAC-CACA-ATATATATATACAATTCATACATTTTATTTGAACTTATAAAATTCAAA
20370128 ACATATAT
191 ACATATAT
**
20370136 ATACATTCAGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACCCAACATATAT
1 ATACATTCAGCTAACATATATACAATTCATTAAATTTCATTCAACTTACAAAA-CCAACATATAT
* *
20370201 ATATTCGGCTAAATATATATAGAATTTCTGTAATTTATTTTAACTTATAAAACTCAAATATACAT
65 ATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTAT-AAACTCAAATATACAT
20370266 TGACT-A-A-CAC-ATATATATATACAATTCATACATTTTATTTGAACTTATAAAATTCAAAACA
129 TGACTAACACCACAATATATATATACAATTCATACATTTTATTTGAACTTATAAAATTCAAAACA
*
20370327 TTTAT
194 TATAT
* *
20370332 ATACATTCGGCTAACATTTTTATACAATTCAT
1 ATACATTCAGCTAACA--TATATACAATTCAT
20370364 ACCATTATAT
Statistics
Matches: 213, Mismatches: 11, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
196 69 0.32
198 14 0.07
200 1 0.00
201 1 0.00
203 106 0.50
204 22 0.10
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (198 bp):
ATACATTCAGCTAACATATATACAATTCATTAAATTTCATTCAACTTACAAAACCAACATATATA
TATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAACTCAAATATACATTG
ACTAACACCACAATATATATATACAATTCATACATTTTATTTGAACTTATAAAATTCAAAACATA
TAT
Found at i:20371341 original size:13 final size:13
Alignment explanation
Indices: 20371323--20371347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20371313 ACAAACGATA
20371323 AAATTTTCACACG
1 AAATTTTCACACG
20371336 AAATTTTCACAC
1 AAATTTTCACAC
20371348 AAGTAAATTC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:20398180 original size:51 final size:51
Alignment explanation
Indices: 20398063--20398249 Score: 200
Period size: 51 Copynumber: 3.7 Consensus size: 51
20398053 GATGGTCATG
* *
20398063 TGTGTAGTACTATGTGAAGGCTACTACT-TGTACCGGA-A-TGATAGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTA-TGTGTACCGGATAGT-ATCGGTCACA
* * * *
20398113 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTATCGGTCACA
* * * * * *
20398164 TGTGTAGTACTATGTGCAGACTACTACGTGTATCGAATGGTAACGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTATCGGTCACA
* * *
20398215 TGTGTAATACTATGTGTAGGCTACTATGTGAACCG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
20398250 AACATCATTG
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
49 1 0.01
50 33 0.29
51 77 0.69
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTATCGGTCACA
Found at i:20398316 original size:45 final size:45
Alignment explanation
Indices: 20398246--20398340 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
20398236 TACTATGTGA
* * * *
20398246 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGCTTGCTATGTGCTGAATCC
* *
20398291 ACCGGACATCATTGATTAATGAGGTGCTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGCTTGCTATGTGCTGAATCC
20398336 ACCGA
1 ACCGA
20398341 GTATCTGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGCTTGCTATGTGCTGAATCC
Found at i:20399575 original size:41 final size:41
Alignment explanation
Indices: 20399530--20399614 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
20399520 TAAAAGTATG
20399530 CATTGAGATGGTAAATGTCTAAATGAAAATATGCTTGTGAT
1 CATTGAGATGGTAAATGTCTAAATGAAAATATGCTTGTGAT
*
20399571 CATTGAGATGGTAAATGTCTAGATGAAAATATGCTTGTGAT
1 CATTGAGATGGTAAATGTCTAAATGAAAATATGCTTGTGAT
20399612 CAT
1 CAT
20399615 AAAAGGGTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.34
Consensus pattern (41 bp):
CATTGAGATGGTAAATGTCTAAATGAAAATATGCTTGTGAT
Found at i:20401416 original size:21 final size:21
Alignment explanation
Indices: 20401399--20401438 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20401389 ATGCACACGA
*
20401399 GCGTGTGGAGTAGTCACACAG
1 GCGTGTGGAGTAGCCACACAG
20401420 GCGTGTGGAGTAGCCACAC
1 GCGTGTGGAGTAGCCACAC
20401439 TGCCATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.17
Consensus pattern (21 bp):
GCGTGTGGAGTAGCCACACAG
Found at i:20402723 original size:60 final size:60
Alignment explanation
Indices: 20402593--20402732 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
20402583 AGGGTGTTGG
** *
20402593 CCATCAGTGTCCCAACACCCCCAAAAAATATTTTTTAAAAAATTTGGTATTGAGGTGCCAG
1 CCATCAGTGTCCCAACA-CCCCAAAAAATATTTTTTAAAAAATTTGGTATAAAGGTGCCAA
* * * * ***
20402654 TCATTAGTGTCCCAGCACCCTAAAAAA-ATTGTTTTTTTAAATTTGGTATAAAGGTGCCAA
1 CCATCAGTGTCCCAACACCCCAAAAAATATT-TTTTAAAAAATTTGGTATAAAGGTGCCAA
*
20402714 CCATCAGTGTTCCAACACC
1 CCATCAGTGTCCCAACACC
20402733 TAATTTTTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 3 0.05
60 47 0.73
61 14 0.22
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (60 bp):
CCATCAGTGTCCCAACACCCCAAAAAATATTTTTTAAAAAATTTGGTATAAAGGTGCCAA
Found at i:20402761 original size:51 final size:53
Alignment explanation
Indices: 20402680--20402940 Score: 198
Period size: 52 Copynumber: 5.0 Consensus size: 53
20402670 ACCCTAAAAA
* ** *
20402680 AATTGTTTTTTTAAATTTGGTA-TAAAGGTGCCAACCATCAGTGTTCCAACACCT
1 AATT-TTTTTTTAAATCTGGTACT-GGGGTGCCAACCATCAGTGTCCCAACACCT
* *
20402734 AA-TTTTTTTT-AATCTGGTACTGGGGTGCCAGCCATCAGTGTCCCAGCATCC-
1 AATTTTTTTTTAAATCTGGTACTGGGGTGCCAACCATCAGTGTCCCAACA-CCT
* ** * * ** * * *
20402785 AATTTATTTTTAAATCTGGTACAAGAGTGTCGGCCATCAATGTCCTAGCA-CT
1 AATTTTTTTTTAAATCTGGTACTGGGGTGCCAACCATCAGTGTCCCAACACCT
* * * *
20402837 AATTTTTTTTTAAACCTGGTACTGGGGTGTCGA-CATCAGTGTCCCAACACCC
1 AATTTTTTTTTAAATCTGGTACTGGGGTGCCAACCATCAGTGTCCCAACACCT
* * *
20402889 AATTTTTCTTTT-AATCTGGTA-TAAGGGTG-CAGACCATCAATGTCCTAACACC
1 AATTTTT-TTTTAAATCTGGTACT-GGGGTGCCA-ACCATCAGTGTCCCAACACC
20402941 CAAAAAAGAT
Statistics
Matches: 168, Mismatches: 29, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
51 48 0.29
52 66 0.39
53 52 0.31
54 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (53 bp):
AATTTTTTTTTAAATCTGGTACTGGGGTGCCAACCATCAGTGTCCCAACACCT
Found at i:20402844 original size:104 final size:103
Alignment explanation
Indices: 20402732--20402935 Score: 270
Period size: 104 Copynumber: 2.0 Consensus size: 103
20402722 GTTCCAACAC
* * * *
20402732 CTAATTTTTTTT-AATCTGGTACTGGGGTGCCAGCCATCAGTGTCCCAGCATCCAATTTATT-TT
1 CTAATTTTTTTTAAACCTGGTACTGGGGTGCC-GACATCAGTGTCCCAACACCCAATTT-TTCTT
*
20402795 TAAATCTGGTACAAGAGTGTC-GGCCATCAATGTCCTAGCA
64 TAAATCTGGTACAAGAGTG-CAGACCATCAATGTCCTAGCA
*
20402835 CTAATTTTTTTTTAAACCTGGTACTGGGGTGTCGACATCAGTGTCCCAACACCCAATTTTTCTTT
1 CTAA-TTTTTTTTAAACCTGGTACTGGGGTGCCGACATCAGTGTCCCAACACCCAATTTTTCTTT
* * *
20402900 TAATCTGGTATAAGGGTGCAGACCATCAATGTCCTA
65 AAATCTGGTACAAGAGTGCAGACCATCAATGTCCTA
20402936 ACACCCAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
103 7 0.08
104 64 0.73
105 17 0.19
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (103 bp):
CTAATTTTTTTTAAACCTGGTACTGGGGTGCCGACATCAGTGTCCCAACACCCAATTTTTCTTTA
AATCTGGTACAAGAGTGCAGACCATCAATGTCCTAGCA
Found at i:20402933 original size:53 final size:53
Alignment explanation
Indices: 20402680--20402943 Score: 206
Period size: 53 Copynumber: 5.0 Consensus size: 53
20402670 ACCCTAAAAA
* * * *
20402680 AATTGTTTTTTTAAATTTGGTATAAAGGTGCCA-ACCATCAGTGTTCCAACACCT
1 AATT-TTTTTTT-AATCTGGTATAAGGGTGCCAGACCATCAGTGTCCCAACACCC
* * *
20402734 AA-TTTTTTTTAATCTGGTACT-GGGGTGCCAG-CCATCAGTGTCCCAGCATCC
1 AATTTTTTTTTAATCTGGTA-TAAGGGTGCCAGACCATCAGTGTCCCAACACCC
* * * * * * * * *
20402785 AATTTATTTTTAAATCTGGTACAAGAGTGTC-GGCCATCAATGTCCTAGCA-CT
1 AATTT-TTTTTTAATCTGGTATAAGGGTGCCAGACCATCAGTGTCCCAACACCC
* * *
20402837 AATTTTTTTTTAAACCTGGTACT-GGGGTGTC-GA-CATCAGTGTCCCAACACCC
1 AATTTTTTTTT-AATCTGGTA-TAAGGGTGCCAGACCATCAGTGTCCCAACACCC
* *
20402889 AATTTTTCTTTTAATCTGGTATAAGGGTG-CAGACCATCAATGTCCTAACACCC
1 AATTTTT-TTTTAATCTGGTATAAGGGTGCCAGACCATCAGTGTCCCAACACCC
20402942 AA
1 AA
20402944 AAAAGATATT
Statistics
Matches: 168, Mismatches: 29, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
51 53 0.32
52 55 0.33
53 58 0.35
54 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (53 bp):
AATTTTTTTTTAATCTGGTATAAGGGTGCCAGACCATCAGTGTCCCAACACCC
Found at i:20404769 original size:19 final size:19
Alignment explanation
Indices: 20404745--20404783 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20404735 AGGAATTGTG
20404745 ACTTTGAAAAAGAAATATT
1 ACTTTGAAAAAGAAATATT
20404764 ACTTTGAAAAAGAAATATT
1 ACTTTGAAAAAGAAATATT
20404783 A
1 A
20404784 ACACCATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (19 bp):
ACTTTGAAAAAGAAATATT
Found at i:20405397 original size:3 final size:3
Alignment explanation
Indices: 20405389--20405424 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
20405379 GATCTAAAAC
20405389 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20405425 CAGCAACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20412780 original size:18 final size:16
Alignment explanation
Indices: 20412757--20412791 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
20412747 AATTTAACTT
20412757 TAATTAAATTATTTAAAA
1 TAATT-AATT-TTTAAAA
20412775 TAATTAATTTTTAAAA
1 TAATTAATTTTTAAAA
20412791 T
1 T
20412792 TATAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTAATTTTTAAAA
Found at i:20413078 original size:15 final size:15
Alignment explanation
Indices: 20413058--20413094 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20413048 TTAAGTTCAG
20413058 TGTTTAAGGATTTGA
1 TGTTTAAGGATTTGA
*
20413073 TGTTT-AGGGTTTGA
1 TGTTTAAGGATTTGA
20413087 -GTTTAAGG
1 TGTTTAAGG
20413095 TTTAAAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (15 bp):
TGTTTAAGGATTTGA
Found at i:20413559 original size:7 final size:7
Alignment explanation
Indices: 20413549--20413575 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
20413539 GATTTTGATT
20413549 TTTGTTG
1 TTTGTTG
20413556 TTTGTTG
1 TTTGTTG
20413563 TTTGTTG
1 TTTGTTG
20413570 TTTGTT
1 TTTGTT
20413576 TAGAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (7 bp):
TTTGTTG
Found at i:20416343 original size:24 final size:24
Alignment explanation
Indices: 20416316--20416367 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20416306 TTAGTAAGTC
*
20416316 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
***
20416340 AAATATGTTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
20416364 AAAT
1 AAAT
20416368 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:20418971 original size:23 final size:23
Alignment explanation
Indices: 20418945--20419020 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
20418935 ATAAGTGCAA
20418945 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20418968 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
20418991 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20419014 TACTGAT
1 CACTGAT
20419021 CAATAACACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:20420930 original size:24 final size:24
Alignment explanation
Indices: 20420903--20420954 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
20420893 TTAGTAAGTC
*
20420903 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
20420927 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
20420951 AAAT
1 AAAT
20420955 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:20421076 original size:22 final size:21
Alignment explanation
Indices: 20421045--20421109 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
20421035 GATAAAAAAA
* *
20421045 TTGTTATTTTCTTGCTATTTTT
1 TTGTTGTTTTCTT-CTATTTTC
20421067 TTGTTGTTTTACTAT-TATTTTC
1 TTGTTGTTTT-CT-TCTATTTTC
*
20421089 TTGTTGTTTTCTCACTATTTT
1 TTGTTGTTTTCT-TCTATTTT
20421110 GCTACCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.06
22 31 0.86
23 2 0.06
24 1 0.03
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (21 bp):
TTGTTGTTTTCTTCTATTTTC
Found at i:20421098 original size:11 final size:11
Alignment explanation
Indices: 20421045--20421100 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
20421035 GATAAAAAAA
20421045 TTGTTATTTTC
1 TTGTTATTTTC
* *
20421056 TTGCTATTTTT
1 TTGTTATTTTC
*
20421067 TTGTTGTTTTAC
1 TTGTTATTTT-C
*
20421079 -TATTATTTTC
1 TTGTTATTTTC
*
20421089 TTGTTGTTTTC
1 TTGTTATTTTC
20421100 T
1 T
20421101 CACTATTTTG
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
10 1 0.03
11 33 0.97
ACGTcount: A:0.09, C:0.09, G:0.11, T:0.71
Consensus pattern (11 bp):
TTGTTATTTTC
Found at i:20421331 original size:17 final size:17
Alignment explanation
Indices: 20421281--20421334 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
20421271 AGAAAATATT
20421281 TATTTTAATATTTTTAGTA
1 TATTTTAA-ATTTTTA-TA
* *
20421300 -ATTTTAAAGTATTATA
1 TATTTTAAATTTTTATA
*
20421316 TTTTTTAAATTTTTATA
1 TATTTTAAATTTTTATA
20421333 TA
1 TA
20421335 AAAAATAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 2 0.07
17 19 0.68
18 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTTTAAATTTTTATA
Found at i:20421741 original size:18 final size:19
Alignment explanation
Indices: 20421708--20421744 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20421698 TCCTCTTCCT
*
20421708 TCTTCCATATAAAAATAAA
1 TCTTCCATACAAAAATAAA
20421727 TCTTCCA-ACAAAAATAAA
1 TCTTCCATACAAAAATAAA
20421745 AATAATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (19 bp):
TCTTCCATACAAAAATAAA
Found at i:20422847 original size:25 final size:24
Alignment explanation
Indices: 20422794--20422847 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
20422784 ACAATCATCT
* * *
20422794 TAAATTTTTATAATAATATTTAAG
1 TAAAATTTTATAATAATAATTAAA
*
20422818 GAAAATTTTATAATAATTAATTAAA
1 TAAAATTTTATAATAA-TAATTAAA
20422843 TAAAA
1 TAAAA
20422848 AATAACCTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TAAAATTTTATAATAATAATTAAA
Found at i:20422922 original size:20 final size:21
Alignment explanation
Indices: 20422899--20422945 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
20422889 ACAAGAGTAA
*
20422899 AGATTTTAAGGTTTA-AGGTT
1 AGATTTTAAGATTTAGAGGTT
20422919 AGA-TTTAAGATTTAGAGGTT
1 AGATTTTAAGATTTAGAGGTT
20422939 AGGATTT
1 A-GATTT
20422946 GGATTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 10 0.43
20 9 0.39
21 2 0.09
22 2 0.09
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.43
Consensus pattern (21 bp):
AGATTTTAAGATTTAGAGGTT
Found at i:20422950 original size:20 final size:21
Alignment explanation
Indices: 20422910--20422965 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
20422900 GATTTTAAGG
20422910 TTTAAGGTTA-GATTTAAGA-
1 TTTAAGGTTAGGATTTAAGAT
*
20422929 TTTAGAGGTTAGGATTT-GGAT
1 TTTA-AGGTTAGGATTTAAGAT
20422950 TTTAAGGTTTAGGATT
1 TTTAAGG-TTAGGATT
20422966 AAGTTCTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.12
20 11 0.34
21 17 0.53
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.45
Consensus pattern (21 bp):
TTTAAGGTTAGGATTTAAGAT
Found at i:20422982 original size:18 final size:19
Alignment explanation
Indices: 20422959--20422996 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20422949 TTTTAAGGTT
20422959 TAGGA-TTAA-GTTCTAAAA
1 TAGGATTTAAGGTT-TAAAA
20422977 TAGGATTTAAGGTTTAAAA
1 TAGGATTTAAGGTTTAAAA
20422996 T
1 T
20422997 TGGCTTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 10 0.56
20 3 0.17
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (19 bp):
TAGGATTTAAGGTTTAAAA
Found at i:20424826 original size:29 final size:29
Alignment explanation
Indices: 20424794--20424863 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
20424784 GCCCAGTAAC
*
20424794 AAATTTTAAAAATA-AAAGAAAACTCTTTA
1 AAATTTTAAAAATATAAA-AAAACTCATTA
* * *
20424823 AAATTTAAAAAATATTTAAAAAAGTCATTA
1 AAATTTTAAAAATA-TAAAAAAACTCATTA
20424853 AAATTTTAAAA
1 AAATTTTAAAA
20424864 TTTCTATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 13 0.38
30 19 0.56
31 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (29 bp):
AAATTTTAAAAATATAAAAAAACTCATTA
Found at i:20425286 original size:16 final size:17
Alignment explanation
Indices: 20425265--20425298 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20425255 ATTGAATTGA
*
20425265 ATTTTTA-ATAATTTTT
1 ATTTTTATAAAATTTTT
20425281 ATTTTTATAAAATTTTT
1 ATTTTTATAAAATTTTT
20425298 A
1 A
20425299 ATAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTATAAAATTTTT
Found at i:20427473 original size:28 final size:27
Alignment explanation
Indices: 20427437--20427492 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
20427427 TTAAAATATT
*
20427437 AATAATTTA-ATGATTTTTAGTTTTTAAA
1 AATAATTTATAT-A-TTTTAATTTTTAAA
*
20427465 AATAGTTTATATATTTTAATTTTTAAA
1 AATAATTTATATATTTTAATTTTTAAA
20427492 A
1 A
20427493 TTAAAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 14 0.56
28 9 0.36
29 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (27 bp):
AATAATTTATATATTTTAATTTTTAAA
Found at i:20427535 original size:79 final size:79
Alignment explanation
Indices: 20427449--20427594 Score: 292
Period size: 79 Copynumber: 1.8 Consensus size: 79
20427439 TAATTTAATG
20427449 ATTTTTAGTTTTTAAAAATAGTTTATATATTTTAATTTTTAAAATTAAAAAAACTAATTAAACAA
1 ATTTTTAGTTTTTAAAAATAGTTTATATATTTTAATTTTTAAAATTAAAAAAACTAATTAAACAA
20427514 ATATCTCGTCCGGA
66 ATATCTCGTCCGGA
20427528 ATTTTTAGTTTTTAAAAATAGTTTATATATTTTAATTTTTAAAATTAAAAAAACTAATTAAACAA
1 ATTTTTAGTTTTTAAAAATAGTTTATATATTTTAATTTTTAAAATTAAAAAAACTAATTAAACAA
20427593 AT
66 AT
20427595 CATCCACGTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (79 bp):
ATTTTTAGTTTTTAAAAATAGTTTATATATTTTAATTTTTAAAATTAAAAAAACTAATTAAACAA
ATATCTCGTCCGGA
Found at i:20431083 original size:41 final size:41
Alignment explanation
Indices: 20431026--20431242 Score: 344
Period size: 41 Copynumber: 5.3 Consensus size: 41
20431016 GTTTGGAATT
20431026 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* *
20431067 GGTGATCTGAATCAGGCTATAAGCCTAGTAGGCTAAATGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* * *
20431108 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* *
20431149 GGTGATCTGAATCAGGCTATAAGCCTAGTAGGCTAAATGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* * *
20431190 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
20431231 GGTGATCTGAAT
1 GGTGATCTGAAT
20431243 ATGTTAAATT
Statistics
Matches: 158, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 158 1.00
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
Found at i:20431120 original size:82 final size:82
Alignment explanation
Indices: 20431026--20431242 Score: 407
Period size: 82 Copynumber: 2.6 Consensus size: 82
20431016 GTTTGGAATT
* * *
20431026 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
20431091 CTAGTAGGCTAAATGCC
66 CTAGTAGGCTAAATGCC
20431108 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
20431173 CTAGTAGGCTAAATGCC
66 CTAGTAGGCTAAATGCC
20431190 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAAT
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAAT
20431243 ATGTTAAATT
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 132 1.00
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
CTAGTAGGCTAAATGCC
Found at i:20437851 original size:100 final size:99
Alignment explanation
Indices: 20437678--20437875 Score: 378
Period size: 100 Copynumber: 2.0 Consensus size: 99
20437668 GAGAGACTAA
20437678 AATGTGAAATAAATGCAATGTTTGGACTCGTATGAGAACCATGAATATTCGGCCCTTGTGTGGTA
1 AATGTGAAATAAATGCAATGTTTGGACTCGTATGAGAACCATGAATATTCGGCCCTTGTGTGGTA
*
20437743 TGGGCAAATTTTGTGTAAATTGTGTTTTATGCAAC
66 TGGGCAAATTTTGTGTAAATTGTGCTTT-TGCAAC
20437778 AATGTGAAATAAATGCAATGTTTGGACTCGTATGAGAACCATGAATATTCGGCCCTTGTGTGGTA
1 AATGTGAAATAAATGCAATGTTTGGACTCGTATGAGAACCATGAATATTCGGCCCTTGTGTGGTA
20437843 TGGGCAAATTTTGTGTAAATTGTGCTTTTGCAA
66 TGGGCAAATTTTGTGTAAATTGTGCTTTTGCAA
20437876 TAGTTCTTCA
Statistics
Matches: 97, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
99 5 0.05
100 92 0.95
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (99 bp):
AATGTGAAATAAATGCAATGTTTGGACTCGTATGAGAACCATGAATATTCGGCCCTTGTGTGGTA
TGGGCAAATTTTGTGTAAATTGTGCTTTTGCAAC
Found at i:20441123 original size:71 final size:71
Alignment explanation
Indices: 20441047--20441200 Score: 184
Period size: 71 Copynumber: 2.2 Consensus size: 71
20441037 TGACTAACAT
* * * *
20441047 TGGGTGCAAAACATCGTCGGTTTATCCTACCAGTACAGGGCACAACTATTGTTGGTTTA-TCCAA
1 TGGGTGCAAAACATCGTCGGTTTAACCAACCAGTACAGGGCACAACTATTGTCGGTATACT-CAA
20441111 CCAGCGC
65 CCAGCGC
* ** * * **
20441118 TGGGTGCAAAACATTGTCTTTTTAACCAACCAGTGCAGGGCACAATTATTGTCGGTATACTTGAC
1 TGGGTGCAAAACATCGTCGGTTTAACCAACCAGTACAGGGCACAACTATTGTCGGTATACTCAAC
*
20441183 TAGCGC
66 CAGCGC
20441189 TGGGTGCAAAAC
1 TGGGTGCAAAAC
20441201 TTTAGTACGG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
71 69 0.99
72 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (71 bp):
TGGGTGCAAAACATCGTCGGTTTAACCAACCAGTACAGGGCACAACTATTGTCGGTATACTCAAC
CAGCGC
Found at i:20445609 original size:20 final size:20
Alignment explanation
Indices: 20445571--20445609 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20445561 CTGCCTACTC
*
20445571 TAAAATGCATGGATTTCAAA
1 TAAAATGCATGGATCTCAAA
* *
20445591 TAAAATGCCTTGATCTCAA
1 TAAAATGCATGGATCTCAA
20445610 TAATGGGCTT
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:0.15, G:0.13, T:0.31
Consensus pattern (20 bp):
TAAAATGCATGGATCTCAAA
Found at i:20456975 original size:43 final size:43
Alignment explanation
Indices: 20456924--20457006 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
20456914 ATTGAGATCA
*
20456924 GAAGATAAAATGGAG-CAATTTGGTAATTTACGCAATTTATGCG
1 GAAGATAAAATGGAGTC-ACTTGGTAATTTACGCAATTTATGCG
*
20456967 GAAGATAAAATGGAGTCACTTGGTAATTTACGCTATTTAT
1 GAAGATAAAATGGAGTCACTTGGTAATTTACGCAATTTAT
20457007 ATCCCTAGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.33
Consensus pattern (43 bp):
GAAGATAAAATGGAGTCACTTGGTAATTTACGCAATTTATGCG
Found at i:20461446 original size:24 final size:25
Alignment explanation
Indices: 20461419--20461469 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
20461409 AAGCTCATAC
*
20461419 GAGCCA-TAAACGGGAAGCTCAAGA
1 GAGCCATTAAACGAGAAGCTCAAGA
* * *
20461443 GAGCTATTAATCGAGAAGCTCATGA
1 GAGCCATTAAACGAGAAGCTCAAGA
20461468 GA
1 GA
20461470 TCTAAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (25 bp):
GAGCCATTAAACGAGAAGCTCAAGA
Found at i:20463397 original size:46 final size:46
Alignment explanation
Indices: 20463329--20463458 Score: 224
Period size: 46 Copynumber: 2.8 Consensus size: 46
20463319 GTATCTATAA
*
20463329 ACTTAACTTTTTTTTCTAATTATCTTCATAATAATCATGCATTAATT
1 ACTTAAC-TTTTTTTCTAATTATCTTCCTAATAATCATGCATTAATT
20463376 ACTTAACTTTTTTTCTAATTATCTTCCTAATAATCATGCATTAATT
1 ACTTAACTTTTTTTCTAATTATCTTCCTAATAATCATGCATTAATT
* *
20463422 GCTTAACTTTTTTTCTAATTATCTTCCCAATAATCAT
1 ACTTAACTTTTTTTCTAATTATCTTCCTAATAATCAT
20463459 TCAATCATAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 73 0.91
47 7 0.09
ACGTcount: A:0.30, C:0.18, G:0.02, T:0.50
Consensus pattern (46 bp):
ACTTAACTTTTTTTCTAATTATCTTCCTAATAATCATGCATTAATT
Found at i:20465845 original size:14 final size:15
Alignment explanation
Indices: 20465817--20465845 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20465807 ATTACTTTAA
20465817 TAAAATAATATTATT
1 TAAAATAATATTATT
20465832 TAAAATAA-ATTATT
1 TAAAATAATATTATT
20465846 AATTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATAATATTATT
Found at i:20480552 original size:15 final size:13
Alignment explanation
Indices: 20480527--20480575 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
20480517 AGGCACGCCC
20480527 AGAAAAAAAGAAAA
1 AGAAAAAAAG-AAA
20480541 AGAAAAATAAGAAA
1 AGAAAAA-AAGAAA
*
20480555 AGAAAAGAA-AAA
1 AGAAAAAAAGAAA
*
20480567 TGAAAAAAA
1 AGAAAAAAA
20480576 TTAAGAGGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 10 0.32
13 2 0.06
14 16 0.52
15 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:20480574 original size:19 final size:19
Alignment explanation
Indices: 20480530--20480574 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
20480520 CACGCCCAGA
20480530 AAAAAAGAAAAAGAAAAAT
1 AAAAAAGAAAAAGAAAAAT
20480549 AAGAAAAG-AAAAGAAAAAT
1 AA-AAAAGAAAAAGAAAAAT
20480568 GAAAAAA
1 -AAAAAA
20480575 ATTAAGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAAGAAAAAGAAAAAT
Found at i:20480575 original size:20 final size:21
Alignment explanation
Indices: 20480528--20480575 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
20480518 GGCACGCCCA
20480528 GAAAAAAAGAAAAAGAAAAAT
1 GAAAAAAAGAAAAAGAAAAAT
*
20480549 -AAGAAAAG-AAAAGAAAAAT
1 GAAAAAAAGAAAAAGAAAAAT
20480568 GAAAAAAA
1 GAAAAAAA
20480576 TTAAGAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (21 bp):
GAAAAAAAGAAAAAGAAAAAT
Found at i:20481660 original size:25 final size:23
Alignment explanation
Indices: 20481614--20481661 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
20481604 TGACCCCATA
20481614 ATCCTAATATATCTCTTTTATAT
1 ATCCTAATATATCTCTTTTATAT
* * *
20481637 ATCCTAATATCTATCTTTTGTAT
1 ATCCTAATATATCTCTTTTATAT
20481660 AT
1 AT
20481662 GCACGATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (23 bp):
ATCCTAATATATCTCTTTTATAT
Found at i:20486565 original size:17 final size:16
Alignment explanation
Indices: 20486543--20486579 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
20486533 AAATACGCTC
20486543 TCTCTTTGCTCTTCTAT
1 TCTCTTTGCTCTT-TAT
*
20486560 TCTCTTTGTTCTTTAT
1 TCTCTTTGCTCTTTAT
20486576 TCTC
1 TCTC
20486580 CGTCTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.05, C:0.27, G:0.05, T:0.62
Consensus pattern (16 bp):
TCTCTTTGCTCTTTAT
Found at i:20488930 original size:30 final size:30
Alignment explanation
Indices: 20488893--20488973 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
20488883 AAATTTTTAA
* * *
20488893 AAATTACATTTTGACCCCTAATTTTTTC-T
1 AAATTACATTTCGGCCCCTAATATTTTCAT
*
20488922 AAATTTACATCTCGGCCCCTAATATTTTCAT
1 AAA-TTACATTTCGGCCCCTAATATTTTCAT
*
20488953 AAATTACATTTGGGCCCCTAA
1 AAATTACATTTCGGCCCCTAA
20488974 ACTTTCTCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.07
30 37 0.84
31 4 0.09
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (30 bp):
AAATTACATTTCGGCCCCTAATATTTTCAT
Found at i:20489566 original size:14 final size:13
Alignment explanation
Indices: 20489541--20489603 Score: 65
Period size: 14 Copynumber: 4.7 Consensus size: 13
20489531 CCCGAAGAAG
*
20489541 AAGAAGAAAAAGA
1 AAGAAAAAAAAGA
20489554 AAGGAAAAAAAAGA
1 AA-GAAAAAAAAGA
*
20489568 ACAGAAAAAAGAGA
1 A-AGAAAAAAAAGA
*
20489582 GAAG-AAAAAGAGA
1 -AAGAAAAAAAAGA
20489595 AAGAAAAAA
1 AAGAAAAAA
20489604 TATCTTACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 3 0.07
13 16 0.36
14 23 0.52
15 2 0.05
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAGA
Found at i:20489576 original size:26 final size:26
Alignment explanation
Indices: 20489547--20489603 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
20489537 GAAGAAGAAG
20489547 AAAAAGAAAGGAA-AAAAA-AGAACAGA
1 AAAAAGAAA-GAAGAAAAAGAGAA-AGA
*
20489573 AAAAAGAGAGAAGAAAAAGAGAAAGA
1 AAAAAGAAAGAAGAAAAAGAGAAAGA
20489599 AAAAA
1 AAAAA
20489604 TATCTTACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 3 0.11
26 21 0.75
27 4 0.14
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAGAAGAAAAAGAGAAAGA
Found at i:20489601 original size:11 final size:13
Alignment explanation
Indices: 20489538--20489602 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 13
20489528 GGCCCCGAAG
20489538 AAGA-AGAAGAAA
1 AAGAGAGAAGAAA
*
20489550 AAGAAAGGAA-AAA
1 AAGAGA-GAAGAAA
20489563 AA-AGA-ACAGAAAA
1 AAGAGAGA-AG-AAA
20489576 AAGAGAGAAGAAA
1 AAGAGAGAAGAAA
20489589 AAGAGA-AAGAAA
1 AAGAGAGAAGAAA
20489601 AA
1 AA
20489603 ATATCTTACA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
10 1 0.02
11 1 0.02
12 14 0.31
13 20 0.44
14 8 0.18
15 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (13 bp):
AAGAGAGAAGAAA
Found at i:20490298 original size:20 final size:20
Alignment explanation
Indices: 20490256--20490299 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
20490246 GAAAATGTTC
* *
20490256 AAAATTTCTCGTGTTTTAAT
1 AAAAATTCTCGTGTTTGAAT
*
20490276 AAAAATTCTCGTGTTTGATT
1 AAAAATTCTCGTGTTTGAAT
20490296 AAAA
1 AAAA
20490300 TCCCGATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (20 bp):
AAAAATTCTCGTGTTTGAAT
Found at i:20490610 original size:18 final size:18
Alignment explanation
Indices: 20490599--20490905 Score: 120
Period size: 18 Copynumber: 16.5 Consensus size: 18
20490589 ATTTTCGTAT
20490599 TTTCAAAAATTTCTCGTG
1 TTTCAAAAATTTCTCGTG
*
20490617 TTTCAAAAAAATTTTGACTTTTCGCG
1 TTTC--AAAAA-TTT--C---TCGTG
* *
20490643 TTTTAAAAAATT-TCGTG
1 TTTCAAAAATTTCTCGTG
* *
20490660 TTTTCAAAAAATTCTCATG
1 -TTTCAAAAATTTCTCGTG
* *
20490679 CTTCAAAAATCT-TCGTG
1 TTTCAAAAATTTCTCGTG
*
20490696 TTTTC-AAAA-TTCTAGTG
1 -TTTCAAAAATTTCTCGTG
20490713 TTTCAAAAAATTT-TCGTG
1 TTTC-AAAAATTTCTCGTG
20490731 TTTTC-AAAATTTCTCGTG
1 -TTTCAAAAATTTCTCGTG
* * *
20490749 TTTTCGAAAA-TTCCCGTT
1 -TTTCAAAAATTTCTCGTG
* * *
20490767 TTTCGAAAATTT-TCTTAT
1 TTTCAAAAATTTCTCGT-G
20490785 TTTCAAAAAATATT-TCCGTG
1 TTTC-AAAAAT-TTCT-CGTG
*
20490805 TTTCATAAATTTC-CGTG
1 TTTCAAAAATTTCTCGTG
* * *
20490822 TTTGAAAAAAAAATTCTCGTC
1 TTT---CAAAAATTTCTCGTG
20490843 TTTCAAAAAAATTTC-CGTG
1 TTTC--AAAAATTTCTCGTG
*
20490862 TTTTCAAAAATTGAC-CGTG
1 -TTTCAAAAATT-TCTCGTG
*
20490881 TTTCATAAATTT-TCGTG
1 TTTCAAAAATTTCTCGTG
20490898 TTT-AAAAA
1 TTTCAAAAA
20490906 AAAATCTTCG
Statistics
Matches: 223, Mismatches: 33, Indels: 68
0.69 0.10 0.21
Matches are distributed among these distances:
16 9 0.04
17 48 0.22
18 77 0.35
19 32 0.14
20 31 0.14
21 11 0.05
23 3 0.01
24 5 0.02
26 7 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (18 bp):
TTTCAAAAATTTCTCGTG
Found at i:20490759 original size:36 final size:37
Alignment explanation
Indices: 20490642--20490920 Score: 158
Period size: 36 Copynumber: 7.6 Consensus size: 37
20490632 GACTTTTCGC
* *
20490642 GTTTT-AAAAAA-TTTCGTGTTTTCAAAAAATTCTCAT
1 GTTTTCAAAAAATTTTCGTGTTTTC-AAAATTTCTCGT
* * *
20490678 G-CTTC-AAAAATCTTCGTGTTTTCAAAA-TTCTAGT
1 GTTTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGT
20490712 G-TTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGT
1 GTTTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGT
* ** *
20490748 GTTTTC-GAAAATTCCCGT-TTTTCGAAAATTT-TCTT
1 GTTTTCAAAAAATTTTCGTGTTTTC-AAAATTTCTCGT
*
20490783 ATTTTCAAAAAATATTTCCGTG-TTTCATAAATTTC-CGT
1 GTTTTCAAAAAAT-TTT-CGTGTTTTCA-AAATTTCTCGT
** * *
20490821 GTTTGAAAAAAAAATTCTCGT-CTTTCAAAAAAATTTC-CGT
1 GTTT--TCAAAAAATTTTCGTGTTTTC---AAAATTTCTCGT
**
20490861 GTTTTC-AAAAATTGACCGTG-TTTCATAAATTT-TCGT
1 GTTTTCAAAAAATT-TTCGTGTTTTCA-AAATTTCTCGT
** *
20490897 GTTTAAAAAAAAATCTTCGTGTTT
1 GTTT-TCAAAAAATTTTCGTGTTT
20490921 CGTTTTTTAT
Statistics
Matches: 189, Mismatches: 29, Indels: 48
0.71 0.11 0.18
Matches are distributed among these distances:
34 9 0.05
35 46 0.24
36 53 0.28
37 17 0.09
38 40 0.21
39 2 0.01
40 21 0.11
41 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (37 bp):
GTTTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGT
Found at i:20490776 original size:53 final size:53
Alignment explanation
Indices: 20490691--20490792 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
20490681 TCAAAAATCT
* *
20490691 TCGTGTTTTCAAAATTCTAGTGTTTCAAAAAATTTTCGTGTTTTCAAAATTTC
1 TCGTGTTTTCAAAATTCCAGTGTTTCAAAAAATTTTCGTATTTTCAAAATTTC
* * * *
20490744 TCGTGTTTTCGAAAATTCCCGTTTTTC-GAAAATTTTCTTATTTTCAAAA
1 TCGTGTTTTC-AAAATTCCAGTGTTTCAAAAAATTTTCGTATTTTCAAAA
20490793 AATATTTCCG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 29 0.69
54 13 0.31
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (53 bp):
TCGTGTTTTCAAAATTCCAGTGTTTCAAAAAATTTTCGTATTTTCAAAATTTC
Found at i:20490792 original size:17 final size:18
Alignment explanation
Indices: 20490635--20490824 Score: 99
Period size: 17 Copynumber: 10.6 Consensus size: 18
20490625 AAATTTTGAC
* *
20490635 TTTTCGCGTTTT-AAAAA
1 TTTTCGTGTTTTCGAAAA
* *
20490652 ATTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-GAAAA
* * * *
20490671 TTCTCATG-CTTCAAAAA
1 TTTTCGTGTTTTCGAAAA
*
20490688 TCTTCGTGTTTTC-AAAA
1 TTTTCGTGTTTTCGAAAA
* * *
20490705 TTCTAGTG-TTTCAAAAAA
1 TTTTCGTGTTTTC-GAAAA
20490723 TTTTCGTGTTTTC-AAAA
1 TTTTCGTGTTTTCGAAAA
20490740 TTTCTCGTGTTTTCGAAAA
1 TTT-TCGTGTTTTCGAAAA
**
20490759 TTCCCGT-TTTTCGAAAA
1 TTTTCGTGTTTTCGAAAA
* * *
20490776 TTTTCTTATTTTCAAAAAA
1 TTTTCGTGTTTTC-GAAAA
20490795 TATTTCCGTG-TTTC-ATAAA
1 T-TTT-CGTGTTTTCGA-AAA
*
20490814 TTTCCGTGTTT
1 TTTTCGTGTTT
20490825 GAAAAAAAAA
Statistics
Matches: 135, Mismatches: 24, Indels: 27
0.73 0.13 0.15
Matches are distributed among these distances:
16 4 0.03
17 54 0.40
18 39 0.29
19 29 0.21
20 7 0.05
21 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (18 bp):
TTTTCGTGTTTTCGAAAA
Found at i:20490831 original size:38 final size:37
Alignment explanation
Indices: 20490789--20490921 Score: 119
Period size: 38 Copynumber: 3.5 Consensus size: 37
20490779 TCTTATTTTC
20490789 AAAAAATATTTCCGTGTTTCATAAATTTCCGTGTTTGA
1 AAAAAATATTTCCGTGTTTCATAAATTTCCGTGTTT-A
* * * *
20490827 AAAAAA-AATTCTCGTCTTTCAAAAAAATTTCCGTGTTTT
1 AAAAAATATTTC-CGTGTTTC--ATAAATTTCCGTGTTTA
* ** *
20490866 CAAAAAT-TGACCGTGTTTCATAAATTTTCGTGTTTA
1 AAAAAATATTTCCGTGTTTCATAAATTTCCGTGTTTA
*
20490902 AAAAAAAATCTT-CGTGTTTC
1 AAAAAATAT-TTCCGTGTTTC
20490922 GTTTTTTATC
Statistics
Matches: 73, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
36 19 0.26
37 13 0.18
38 20 0.27
39 6 0.08
40 15 0.21
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (37 bp):
AAAAAATATTTCCGTGTTTCATAAATTTCCGTGTTTA
Found at i:20490870 original size:17 final size:18
Alignment explanation
Indices: 20490642--20490900 Score: 135
Period size: 18 Copynumber: 14.2 Consensus size: 18
20490632 GACTTTTCGC
*
20490642 GTTTTAAAAAATTT-CGT
1 GTTTTCAAAAATTTCCGT
* *
20490659 GTTTTCAAAAAATTCTCAT
1 GTTTTCAAAAATTTC-CGT
*
20490678 G-CTTCAAAAATCTT-CGT
1 GTTTTCAAAAAT-TTCCGT
*
20490695 GTTTTC-AAAA-TTCTAGT
1 GTTTTCAAAAATTTC-CGT
*
20490712 G-TTTCAAAAAATTTTCGT
1 GTTTTC-AAAAATTTCCGT
20490730 GTTTTC-AAAATTTCTCGT
1 GTTTTCAAAAATTTC-CGT
* *
20490748 GTTTTCGAAAATTCCCGT
1 GTTTTCAAAAATTTCCGT
* * *
20490766 -TTTTCGAAAATTTTCTT
1 GTTTTCAAAAATTTCCGT
*
20490783 ATTTTCAAAAAATATTTCCGT
1 GTTTTC--AAAA-ATTTCCGT
*
20490804 G-TTTCATAAATTTCCGT
1 GTTTTCAAAAATTTCCGT
** *
20490821 GTTTGAAAAAAAAATTCTCGT
1 GTTT--TCAAAAATTTC-CGT
*
20490842 -CTTTCAAAAAAATTTCCGT
1 GTTTTC--AAAAATTTCCGT
*
20490861 GTTTTCAAAAATTGACCGT
1 GTTTTCAAAAATT-TCCGT
* *
20490880 G-TTTCATAAATTTTCGT
1 GTTTTCAAAAATTTCCGT
20490897 GTTT
1 GTTT
20490901 AAAAAAAAAT
Statistics
Matches: 184, Mismatches: 33, Indels: 49
0.69 0.12 0.18
Matches are distributed among these distances:
15 2 0.01
16 4 0.02
17 56 0.30
18 59 0.32
19 26 0.14
20 28 0.15
21 9 0.05
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (18 bp):
GTTTTCAAAAATTTCCGT
Found at i:20490996 original size:20 final size:19
Alignment explanation
Indices: 20490945--20491022 Score: 83
Period size: 20 Copynumber: 4.2 Consensus size: 19
20490935 ATGTTTATGT
*
20490945 TTTCAAAAACAAATT--T-
1 TTTCAAAAAAAAATTCGTG
*
20490961 TTT-AAAAAAAATTTCGTG
1 TTTCAAAAAAAAATTCGTG
20490979 TTTCAAAAAGAAAATTCGTG
1 TTTCAAAAA-AAAATTCGTG
20490999 TTTTCAAAAAAAAATCTCGTG
1 -TTTCAAAAAAAAAT-TCGTG
20491020 TTT
1 TTT
20491023 TAGAATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
15 9 0.17
16 3 0.06
17 1 0.02
18 3 0.06
19 5 0.10
20 17 0.33
21 14 0.27
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (19 bp):
TTTCAAAAAAAAATTCGTG
Found at i:20491038 original size:38 final size:35
Alignment explanation
Indices: 20490989--20491102 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 35
20490979 TTTCAAAAAG
20490989 AAAATTC--GTGTTTTCAAAAAAAAATCTCGTGTTTT
1 AAAATTCTTGTGTTTT-AAAAAAAAAT-TCGTGTTTT
* *
20491024 AGAATTTTTTGTGTTTTTTAAAAAAAAATTCGTGTTTCT
1 A-AAATTCTTGTG--TTTTAAAAAAAAATTCGTGTTT-T
* *
20491063 AAAATTCTTGTATTTTTAAAAAAAATTCGTGTTTT
1 AAAATTCTTGTGTTTTAAAAAAAAATTCGTGTTTT
20491098 CAAAA
1 -AAAA
20491103 AAAGGAAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
35 2 0.03
36 29 0.44
38 19 0.29
39 12 0.18
40 4 0.06
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (35 bp):
AAAATTCTTGTGTTTTAAAAAAAAATTCGTGTTTT
Found at i:20491059 original size:21 final size:20
Alignment explanation
Indices: 20490959--20491105 Score: 87
Period size: 21 Copynumber: 7.6 Consensus size: 20
20490949 AAAAACAAAT
*
20490959 TTTTTAAAAAAAATTTCGTG
1 TTTTTAAAAAAAAATTCGTG
*
20490979 -TTTCAAAAAGAAAATTCGTG
1 TTTTTAAAAA-AAAATTCGTG
*
20490999 TTTTCAAAAAAAAATCTCGTG
1 TTTTTAAAAAAAAAT-TCGTG
* *** *
20491020 -TTTT--AGAATTTTTTGTG
1 TTTTTAAAAAAAAATTCGTG
20491037 TTTTTTAAAAAAAAATTCGTG
1 -TTTTTAAAAAAAAATTCGTG
* *
20491058 TTTCT-----AAAATTCTTG
1 TTTTTAAAAAAAAATTCGTG
*
20491073 TATTTTTAAAAAAAATTCGTG
1 T-TTTTAAAAAAAAATTCGTG
*
20491094 TTTTCAAAAAAA
1 TTTTTAAAAAAA
20491106 GGAAAAGTTG
Statistics
Matches: 95, Mismatches: 19, Indels: 26
0.68 0.14 0.19
Matches are distributed among these distances:
15 10 0.11
16 3 0.03
17 4 0.04
18 4 0.04
19 12 0.13
20 30 0.32
21 32 0.34
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (20 bp):
TTTTTAAAAAAAAATTCGTG
Found at i:20491091 original size:36 final size:38
Alignment explanation
Indices: 20490999--20491097 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 38
20490989 AAAATTCGTG
* * * *
20490999 TTTTCAAAAAAAAATCTCGTGTTTTAGAATTTTTTGTGT
1 TTTTTAAAAAAAAAT-TCGTGTTTTAGAAATTCTTGTGA
20491038 TTTTTAAAAAAAAATTCGTGTTTCTA-AAATTCTTGT-A
1 TTTTTAAAAAAAAATTCGTGTTT-TAGAAATTCTTGTGA
20491075 TTTTT-AAAAAAAATTCGTGTTTT
1 TTTTTAAAAAAAAATTCGTGTTTT
20491098 CAAAAAAAGG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
35 1 0.02
36 17 0.31
37 5 0.09
38 16 0.29
39 16 0.29
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (38 bp):
TTTTTAAAAAAAAATTCGTGTTTTAGAAATTCTTGTGA
Found at i:20499239 original size:9 final size:9
Alignment explanation
Indices: 20499225--20499302 Score: 70
Period size: 9 Copynumber: 8.4 Consensus size: 9
20499215 TATTATGCCT
20499225 AAAAAAACA
1 AAAAAAACA
*
20499234 AAAAAATA-G
1 AAAAAA-ACA
*
20499243 AAAAAAATA
1 AAAAAAACA
*
20499252 GAAAAAACA
1 AAAAAAACA
*
20499261 GAAAGAAACA
1 -AAAAAAACA
20499271 AAAAAAACA
1 AAAAAAACA
20499280 AAAAACAA-A
1 AAAAA-AACA
20499289 CAAAAAAACA
1 -AAAAAAACA
20499299 AAAA
1 AAAA
20499303 TGGAAAAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
8 1 0.02
9 39 0.70
10 16 0.29
ACGTcount: A:0.83, C:0.09, G:0.05, T:0.03
Consensus pattern (9 bp):
AAAAAAACA
Found at i:20499269 original size:10 final size:9
Alignment explanation
Indices: 20499226--20499302 Score: 61
Period size: 10 Copynumber: 8.4 Consensus size: 9
20499216 ATTATGCCTA
20499226 AAAAAACA-
1 AAAAAACAG
*
20499234 AAAAAATAG
1 AAAAAACAG
*
20499243 AAAAAAATAG
1 -AAAAAACAG
20499253 AAAAAACAG
1 AAAAAACAG
*
20499262 AAAGAAACAA
1 AAA-AAACAG
*
20499272 AAAAAACAAA
1 AAAAAAC-AG
20499282 AAACAAACA-
1 AAA-AAACAG
20499291 AAAAAACA-
1 AAAAAACAG
20499299 AAAA
1 AAAA
20499303 TGGAAAAATC
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
8 16 0.26
9 18 0.30
10 23 0.38
11 4 0.07
ACGTcount: A:0.83, C:0.09, G:0.05, T:0.03
Consensus pattern (9 bp):
AAAAAACAG
Found at i:20499297 original size:19 final size:18
Alignment explanation
Indices: 20499225--20499302 Score: 84
Period size: 19 Copynumber: 4.2 Consensus size: 18
20499215 TATTATGCCT
* *
20499225 AAAAAAACAAAAAAATAG
1 AAAAAAACAAAAAAACAA
* *
20499243 AAAAAAATAGAAAAAACAG
1 AAAAAAACA-AAAAAACAA
*
20499262 AAAGAAACAAAAAAAACAA
1 AAAAAAAC-AAAAAAACAA
20499281 AAAACAAACAAAAAAACAA
1 AAAA-AAACAAAAAAACAA
20499300 AAA
1 AAA
20499303 TGGAAAAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
18 8 0.16
19 38 0.75
20 5 0.10
ACGTcount: A:0.83, C:0.09, G:0.05, T:0.03
Consensus pattern (18 bp):
AAAAAAACAAAAAAACAA
Found at i:20500307 original size:79 final size:78
Alignment explanation
Indices: 20500172--20500793 Score: 714
Period size: 79 Copynumber: 7.9 Consensus size: 78
20500162 ATATTTTTTT
*
20500172 ATTTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAG
1 ATTTCTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAG
20500237 GTATTTCTTTTAA
66 GTATTTCTTTTAA
20500250 ATTTCTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGA
1 ATTTCTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGA
20500315 GGTATTTCTTTTAA
65 GGTATTTCTTTTAA
20500329 ATTTCTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGA
1 ATTTCTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGA
20500394 GGTATTTCTTTTAA
65 GGTATTTCTTTTAA
* *
20500408 ATTTCTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTCAC--GCTG
1 ATTTCTTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCG
*
20500471 AGGTA----TTTTCA
64 AGGTATTTCTTTTAA
* * * *
20500482 ATTTCTATTTTTTCAAAAAAATCAAATCAACTCATAATACGAGAGGTGAGTTGACCCTCCGGTAA
1 ATTTC--TTTTTTC-----AA--AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
20500547 CATGCCGAGGTATTTCTTTTAA
57 CATGCCGAGGTATTTCTTTTAA
* * * * * **
20500569 ATTTCTACTTTTCAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACACACCGA
1 ATTTCT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGA
20500634 GGTA--TC-TTT-A
65 GGTATTTCTTTTAA
* * * * * * *
20500644 ATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCACAT--T
1 ATTTCT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG--TCACATGCC
*
20500707 GAGGTA-TT-TTTCAA
63 GAGGTATTTCTTTTAA
* * * * *
20500721 ATTTTGTTTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGCCACATGCCG
1 A-TTT-CTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCG
*
20500786 AGCTATTT
64 AGGTATTT
20500794 TTTATTTTTG
Statistics
Matches: 473, Mismatches: 45, Indels: 51
0.83 0.08 0.09
Matches are distributed among these distances:
74 10 0.02
75 52 0.11
76 18 0.04
77 8 0.02
78 67 0.14
79 209 0.44
80 45 0.10
81 40 0.08
83 8 0.02
85 1 0.00
86 5 0.01
87 10 0.02
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (78 bp):
ATTTCTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAG
GTATTTCTTTTAA
Found at i:20500612 original size:240 final size:228
Alignment explanation
Indices: 20500172--20500793 Score: 714
Period size: 240 Copynumber: 2.6 Consensus size: 228
20500162 ATATTTTTTT
20500172 ATTTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAG
1 ATTTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA-GCCGAG
* * *
20500237 GTATTTCTTTTAAATTTCTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
65 GTA--T-TTTTAAATTTCTTTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGACCCTCC
* * * *
20500302 GGTCACATGCCGAGGTATTTCTTTTAAATTTCTTTTTTCAAAAAATCAACTCATAATGCGAGAGG
127 GGTAACATGCCGAGGTATTTCTTTTAAATTTCTCTTTTCAAAAAATCAACTCATAATGCGAAAAG
* **
20500367 TGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAA
192 TGAGTTGAGCCTCAGGTCACACACCGAGGTA--TC-TTT-A
* * *
20500408 ATTTCTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTCAC-GCTGA
1 ATTTATTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAGCCGA
*
20500472 GGTA-TTTTCAATTTCTATTTTTTCAAAAAAATCAAATCAACTCATAATACGAGAGGTGAGTTGA
64 GGTATTTTTAAATTTC--TTTTTTC----AAA--AAATCAACTCATAATACGAGAGGTGAGTTGA
*
20500536 CCCTCCGGTAACATGCCGAGGTATTTCTTTTAAATTTCTACTTTTC-AAAAATCAACTCATATTG
121 CCCTCCGGTAACATGCCGAGGTATTTCTTTTAAATTTCT-CTTTTCAAAAAATCAACTCATAATG
20500600 CGAAAAGTGAGTTGAGCCTCAGGTCACACACCGAGGTATCTTTA
185 CGAAAAGTGAGTTGAGCCTCAGGTCACACACCGAGGTATCTTTA
* * * * * **
20500644 ATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCACA-TTG
1 ATTTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG--TCACAGCCG
* * * *
20500708 AGGTATTTTTCAAATTTTGTTTTTTTC-AAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCT
63 AGGTATTTTT-AAA-TTT-CTTTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGACCCT
* ** *
20500772 CAGGCCACATGCCGAGCTATTT
125 CCGGTAACATGCCGAGGTATTT
20500794 TTTATTTTTG
Statistics
Matches: 336, Mismatches: 31, Indels: 42
0.82 0.08 0.10
Matches are distributed among these distances:
232 60 0.18
234 9 0.03
235 37 0.11
236 25 0.07
237 19 0.06
238 53 0.16
239 9 0.03
240 119 0.35
241 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (228 bp):
ATTTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAGCCGAGG
TATTTTTAAATTTCTTTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGACCCTCCGGTA
ACATGCCGAGGTATTTCTTTTAAATTTCTCTTTTCAAAAAATCAACTCATAATGCGAAAAGTGAG
TTGAGCCTCAGGTCACACACCGAGGTATCTTTA
Found at i:20501028 original size:30 final size:30
Alignment explanation
Indices: 20500969--20501073 Score: 79
Period size: 30 Copynumber: 3.4 Consensus size: 30
20500959 ACAAAAAATA
*
20500969 AAAAATTACATTTT-AGTCCCTAA-ACTTTTT
1 AAAAATTACATTTTGA-CCCCTAATA-TTTTT
*
20500999 AAAAATTACATTTTGACCCCTAATTTTTTTT
1 AAAAATTACATTTTGACCCCTAA-TATTTTT
* * * * * *
20501030 CTAAATTTACATCTTGGCCCATAATATTTTC
1 -AAAAATTACATTTTGACCCCTAATATTTTT
*
20501061 ATAAATTACATTT
1 AAAAATTACATTT
20501074 GGGCCCCTGA
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
30 29 0.50
31 11 0.19
32 18 0.31
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCTAATATTTTT
Found at i:20501670 original size:13 final size:13
Alignment explanation
Indices: 20501654--20501708 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 13
20501644 AAAAAAAGGA
20501654 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
*
20501667 AAAAAAGAGAGAAG
1 AAAAAA-AGAAAAG
*
20501681 AAAAAGAG-AAAG
1 AAAAAAAGAAAAG
20501693 -AAAAAAGAAAA-
1 AAAAAAAGAAAAG
20501704 AAAAA
1 AAAAA
20501709 TATCTTACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 6 0.17
12 10 0.29
13 8 0.23
14 11 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:20501671 original size:14 final size:14
Alignment explanation
Indices: 20501647--20501708 Score: 69
Period size: 13 Copynumber: 4.6 Consensus size: 14
20501637 GAAGAAGAAA
*
20501647 AAAAGGAAAAAAAAG
1 AAAA-GAAAAAAGAG
20501662 AAAAGAAAAAAGAG
1 AAAAGAAAAAAGAG
*
20501676 AGAAG-AAAAAGAG
1 AAAAGAAAAAAGAG
20501689 -AAAGAAAAAAGA-
1 AAAAGAAAAAAGAG
20501701 AAAA-AAAA
1 AAAAGAAAA
20501709 TATCTTACAC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.17
13 18 0.43
14 13 0.31
15 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAGAG
Found at i:20501684 original size:26 final size:23
Alignment explanation
Indices: 20501635--20501708 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 23
20501625 TTCGGCCCCG
20501635 AAGAAGAAGAAAAAA-AGGAAAAAA
1 AAGAA-AAGAAAAAAGAGG-AAAAA
20501659 AAGAAAAGAAAAAAGAGAGAAGAAA
1 AAGAAAAGAAAAAAGAG-GAA-AAA
*
20501684 AAGAGAAAGAAAAAAGA-AAAAAA
1 AAGA-AAAGAAAAAAGAGGAAAAA
20501707 AA
1 AA
20501709 TATCTTACAC
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
23 14 0.31
24 11 0.24
25 8 0.18
26 12 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
AAGAAAAGAAAAAAGAGGAAAAA
Found at i:20502391 original size:20 final size:21
Alignment explanation
Indices: 20502361--20502404 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
20502351 GAAAATGTTC
20502361 AAAATTCCTCGTGTTTTAATA
1 AAAATTCCTCGTGTTTTAATA
*
20502382 AAAATT-CTCGTGTTTTATTA
1 AAAATTCCTCGTGTTTTAATA
20502402 AAA
1 AAA
20502405 TCCCGGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (21 bp):
AAAATTCCTCGTGTTTTAATA
Found at i:20502696 original size:15 final size:15
Alignment explanation
Indices: 20502678--20502728 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 15
20502668 AAAAAATAAT
20502678 AATTTTCGTGTTTCA
1 AATTTTCGTGTTTCA
20502693 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTC--A
20502711 AATTTCTCGTGTTTCA
1 AATTT-TCGTGTTTCA
20502727 AA
1 AA
20502729 AAAATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.31
16 7 0.22
18 10 0.31
19 5 0.16
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (15 bp):
AATTTTCGTGTTTCA
Found at i:20502729 original size:17 final size:16
Alignment explanation
Indices: 20502678--20502861 Score: 76
Period size: 18 Copynumber: 11.1 Consensus size: 16
20502668 AAAAAATAAT
20502678 AATTTTCGTGTTTC-A
1 AATTTTCGTGTTTCAA
20502693 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTC-AA
20502711 AATTTCTCGTGTTTCAA
1 AATTT-TCGTGTTTCAA
*** * *
20502728 AAAAAT-AT-TTTC-G
1 AATTTTCGTGTTTCAA
*
20502741 AATTTTCGCGTTTTCAAA
1 AATTTTCGTG-TTTC-AA
*
20502759 AAATTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTC-AA
20502777 AATTTCTCGTGTTTCAA
1 AATTT-TCGTGTTTCAA
*** * *
20502794 AAAAAT-AT-TTTC-G
1 AATTTTCGTGTTTCAA
*
20502807 AATTTTCGCGTTTTCAAA
1 AATTTTCGTG-TTTC-AA
*
20502825 AAATTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTC-AA
20502843 AATTTCTCGTGTTTCAA
1 AATTT-TCGTGTTTCAA
20502860 AA
1 AA
20502862 AAATTTTGAC
Statistics
Matches: 125, Mismatches: 28, Indels: 30
0.68 0.15 0.16
Matches are distributed among these distances:
13 6 0.05
14 8 0.06
15 12 0.10
16 14 0.11
17 12 0.10
18 58 0.46
19 15 0.12
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (16 bp):
AATTTTCGTGTTTCAA
Found at i:20502770 original size:66 final size:66
Alignment explanation
Indices: 20502696--20502923 Score: 351
Period size: 66 Copynumber: 3.5 Consensus size: 66
20502686 TGTTTCAAAT
20502696 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATATTTTCGAATTTTCGCGTTTTCAAAAA
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATATTTTCGAATTTTCGCGTTTTCAAAAA
20502761 A
66 A
20502762 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATATTTTCGAATTTTCGCGTTTTCAAAAA
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATATTTTCGAATTTTCGCGTTTTCAAAAA
20502827 A
66 A
* *
20502828 TTTCGTGTTTTCAAAAATTTCTCGTGTTTC-AAAAAA-ATTTT-GACTTTTCGTGTTTTC-AAAA
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATATTTTCGAATTTTCGCGTTTTCAAAAA
20502889 A
66 A
* * *
20502890 TTCTCATG-CTTCAAAAATCT-TCGTGTTTTCAAAA
1 TT-TCGTGTTTTCAAAAATTTCTCGTG-TTTCAAAA
20502924 TTCTAGTATT
Statistics
Matches: 154, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
61 5 0.03
62 21 0.14
63 21 0.14
64 5 0.03
65 6 0.04
66 96 0.62
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (66 bp):
TTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATATTTTCGAATTTTCGCGTTTTCAAAAA
A
Found at i:20502977 original size:35 final size:36
Alignment explanation
Indices: 20502872--20503107 Score: 142
Period size: 35 Copynumber: 6.5 Consensus size: 36
20502862 AAATTTTGAC
* **
20502872 TTTTCGTGTTTTCAAAAATTCTCATGCTT-CAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTATTTCCAAAAA
* * *
20502907 TCTTCGTGTTTTC-AAAATTCTAGTATTTCAAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTATTTCCAAAAA
* * *
20502942 TTTTCGTGTTTTCGAAAATTCCCGT-TTTCCGAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTATTTCCAAAAA
* * * *
20502977 TTTTCTTGTTTTCAAAAAATATTTCCGTGTTT-CATAAA
1 TTTTCGTGTTTTC-AAAAAT-TCT-CGTATTTCCAAAAA
* ** * *
20503015 TTTCCGTGTTTGAAAAAAAAATTCTCGTCTTTCAAAAAAA
1 TTTTCGTGTTT---TCAAAAATTCTCGTATTTC-CAAAAA
* * ** * *
20503055 ATTTCGTGTTTTTAAAAATTGACAGTGTTT-CATAAA
1 TTTTCGTGTTTTCAAAAATTCTC-GTATTTCCAAAAA
20503091 TTTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
20503108 AAAATCTTCG
Statistics
Matches: 153, Mismatches: 36, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
34 11 0.07
35 57 0.37
36 25 0.16
37 9 0.06
38 27 0.18
39 5 0.03
40 19 0.12
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTTCGTGTTTTCAAAAATTCTCGTATTTCCAAAAA
Found at i:20503007 original size:21 final size:20
Alignment explanation
Indices: 20502986--20503065 Score: 78
Period size: 21 Copynumber: 4.2 Consensus size: 20
20502976 ATTTTCTTGT
*
20502986 TTTCAAAAAATATTTCCGTG
1 TTTCAAAAAAAATTTCCGTG
*
20503006 TTTC---ATAAATTTCCGTG
1 TTTCAAAAAAAATTTCCGTG
* * *
20503023 TTTGAAAAAAAAATTCTCGTC
1 TTTCAAAAAAAATTTC-CGTG
20503044 TTTCAAAAAAAATTT-CGTG
1 TTTCAAAAAAAATTTCCGTG
20503063 TTT
1 TTT
20503066 TTAAAAATTG
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
17 14 0.30
19 6 0.13
20 11 0.23
21 16 0.34
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTCAAAAAAAATTTCCGTG
Found at i:20503025 original size:38 final size:37
Alignment explanation
Indices: 20502974--20503108 Score: 110
Period size: 38 Copynumber: 3.6 Consensus size: 37
20502964 CGTTTTCCGA
*
20502974 AAATTTTCTTGTTTTCAAAAAATATTTCCGTGTTTCAT
1 AAATTTTCGTG-TTTCAAAAAATATTTCCGTGTTTCAT
* * * * * *
20503012 AAATTTCCGTGTTTGAAAAAAAAATTCTCGTCTTTCAAAA
1 AAATTTTCGTGTTTCAAAAAATATTTC-CGTGTTTC--AT
* ** ** *
20503052 AAAATTTCGTGTTTTTAAAAAT-TGACAGTGTTTCAT
1 AAATTTTCGTGTTTCAAAAAATATTTCCGTGTTTCAT
20503088 AAATTTTCGTGTTTCAAAAAA
1 AAATTTTCGTGTTTCAAAAAA
20503109 AAATCTTCGT
Statistics
Matches: 73, Mismatches: 21, Indels: 8
0.72 0.21 0.08
Matches are distributed among these distances:
36 19 0.26
37 13 0.18
38 22 0.30
39 1 0.01
40 18 0.25
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (37 bp):
AAATTTTCGTGTTTCAAAAAATATTTCCGTGTTTCAT
Found at i:20503072 original size:21 final size:21
Alignment explanation
Indices: 20503012--20503072 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
20503002 CGTGTTTCAT
*
20503012 AAATTTCCGTG-TTTGAAAAAA
1 AAATTT-CGTGTTTTTAAAAAA
* *
20503033 AAA-TTC-TCGTCTTTCAAAAA
1 AAATTTCGT-GTTTTTAAAAAA
20503053 AAATTTCGTGTTTTTAAAAA
1 AAATTTCGTGTTTTTAAAAA
20503073 TTGACAGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 12 0.39
21 15 0.48
22 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (21 bp):
AAATTTCGTGTTTTTAAAAAA
Found at i:20503195 original size:21 final size:21
Alignment explanation
Indices: 20503170--20503210 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20503160 TTTTTTTAAA
20503170 AAAATTTCATG-TTTCAAAAAG
1 AAAA-TTCATGTTTTCAAAAAG
*
20503191 AAAATTCGTGTTTTCAAAAA
1 AAAATTCATGTTTTCAAAAA
20503211 AAATCTCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (21 bp):
AAAATTCATGTTTTCAAAAAG
Found at i:20503209 original size:20 final size:21
Alignment explanation
Indices: 20503167--20503223 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
20503157 AAATTTTTTT
* *
20503167 AAAAAAATTTCATG-TTTCAA
1 AAAAAAATCTCGTGTTTTCAA
20503187 AAAGAAAAT-TCGTGTTTTC-A
1 AAA-AAAATCTCGTGTTTTCAA
20503207 AAAAAAATCTCGTGTTT
1 AAAAAAATCTCGTGTTT
20503224 CAGAATTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.15
20 19 0.58
21 9 0.27
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (21 bp):
AAAAAAATCTCGTGTTTTCAA
Found at i:20503285 original size:35 final size:36
Alignment explanation
Indices: 20503162--20503295 Score: 103
Period size: 36 Copynumber: 3.6 Consensus size: 36
20503152 AAAACAAATT
* *
20503162 TTTTTAAAAAAATTTCATGTTTCAAAAAGAAAATTCGTGT-
1 TTTTTAAAAAAA-TTCGTGTTTC----AGAATATTCGTGTA
** * *
20503202 TTTCAAAAAAAATCTCGTGTTTCAGAATTTTCGTGTT
1 TTTTTAAAAAAAT-TCGTGTTTCAGAATATTCGTGTA
* *
20503239 TTTTTTAAAAAATTCGTGTTTCTA-AA-ATTCTTGTA
1 TTTTTAAAAAAATTCGTGTTTC-AGAATATTCGTGTA
20503274 TTTTTAAAAAAATTTCGTGTTT
1 TTTTTAAAAAAA-TTCGTGTTT
20503296 TCAAAAAAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
35 17 0.22
36 31 0.40
37 11 0.14
39 1 0.01
40 18 0.23
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (36 bp):
TTTTTAAAAAAATTCGTGTTTCAGAATATTCGTGTA
Found at i:20507940 original size:23 final size:23
Alignment explanation
Indices: 20507909--20507959 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
20507899 ACCTACTTTC
* *
20507909 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
*
20507932 TTACAGTAGTGATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
20507955 TTACA
1 TTACA
20507960 TGAACATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Done.