Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 62 of 335
Found at i:21721851 original size:16 final size:16
Alignment explanation
Indices: 21721826--21721856 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21721816 TTTTGTAGTT
*
21721826 TTTTATTAATTTAATA
1 TTTTAATAATTTAATA
21721842 TTTTAATAATTTAAT
1 TTTTAATAATTTAAT
21721857 CTTTAAATTT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAATAATTTAATA
Found at i:21725594 original size:33 final size:34
Alignment explanation
Indices: 21725543--21725609 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
21725533 AATTTTGTGC
21725543 CATTGTTTAAAAAATTTCTTGCATTGAGAATATT
1 CATTGTTTAAAAAATTTCTTGCATTGAGAATATT
21725577 CATTGTTT-AAAAATTTCTTGCATTGAGAATATT
1 CATTGTTTAAAAAATTTCTTGCATTGAGAATATT
21725610 AGCTATTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (34 bp):
CATTGTTTAAAAAATTTCTTGCATTGAGAATATT
Found at i:21729487 original size:27 final size:27
Alignment explanation
Indices: 21729457--21729519 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
21729447 GTGAATGAGA
21729457 AATTTGAGTGAGTTTATTAGTTTAGAC
1 AATTTGAGTGAGTTTATTAGTTTAGAC
21729484 AATTTGAGTGAGTTTATTAGTTTAGAC
1 AATTTGAGTGAGTTTATTAGTTTAGAC
21729511 AATTTGAGT
1 AATTTGAGT
21729520 TGAGCTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.44
Consensus pattern (27 bp):
AATTTGAGTGAGTTTATTAGTTTAGAC
Found at i:21729586 original size:65 final size:65
Alignment explanation
Indices: 21729506--21729636 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 65
21729496 TTTATTAGTT
* * * * * *
21729506 TAGACAATTTGAGTTGAGCTAGTTATTAAGTAATTAAATTTAGTGTTTATAATTATTTATTGTAA
1 TAGACAATTTGAGTTGAACTAATTATTAAATAATTAAATTTAGTGCTTATAATGATTGATTGTAA
* * * * *
21729571 TAGATAATTTGAGTTGAATTAATTATTAAATTATTTAATTTAGTGCTTCTAATGATTGATTGTAA
1 TAGACAATTTGAGTTGAACTAATTATTAAATAATTAAATTTAGTGCTTATAATGATTGATTGTAA
21729636 T
1 T
21729637 TAGAACTATT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (65 bp):
TAGACAATTTGAGTTGAACTAATTATTAAATAATTAAATTTAGTGCTTATAATGATTGATTGTAA
Found at i:21731443 original size:35 final size:35
Alignment explanation
Indices: 21731404--21731476 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
21731394 TCACATTCTT
* *
21731404 TAAATTACTTGTGTTAATTTAAAAAATCAAAATTA
1 TAAATTAATTGTGTTAATTTAAAAAATCAAAATCA
21731439 TAAATTAATTGTGTTAATTTAAAAAATCAAAATCA
1 TAAATTAATTGTGTTAATTTAAAAAATCAAAATCA
21731474 TAA
1 TAA
21731477 GACTTACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (35 bp):
TAAATTAATTGTGTTAATTTAAAAAATCAAAATCA
Found at i:21759883 original size:38 final size:39
Alignment explanation
Indices: 21759841--21759950 Score: 109
Period size: 38 Copynumber: 2.8 Consensus size: 39
21759831 TCGGATAGTT
* *
21759841 CGAAGCAAAGTTGACACCCAGTGTCTCATC-AGCCTAGC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
* * *
21759879 CGAAGTAAAG-TGATACCCAGTAG-CTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCCAGT-GTCTCATCGAACCTAGC
* *
21759917 TGAAGTAACAGTATGACACTCAGTGTCTCATCGA
1 CGAAGTAA-AGT-TGACACCCAGTGTCTCATCGA
21759951 CTTGAGGTCG
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
37 16 0.28
38 22 0.38
39 2 0.03
40 1 0.02
41 17 0.29
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (39 bp):
CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:21764042 original size:13 final size:13
Alignment explanation
Indices: 21764024--21764048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21764014 GTGGATTTGA
21764024 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
21764037 TTTCTTTTTTTC
1 TTTCTTTTTTTC
21764049 ACCTTTCGAT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:21764081 original size:6 final size:6
Alignment explanation
Indices: 21764072--21764099 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21764062 CTGTTCCTTC
21764072 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
21764100 TTTGTGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:21765630 original size:20 final size:20
Alignment explanation
Indices: 21765605--21765648 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
21765595 TTTCATTGCT
*
21765605 TTTAATTATTAATGTTAATA
1 TTTAATTATTAACGTTAATA
* *
21765625 TTTAATTGTTAGCGTTAATA
1 TTTAATTATTAACGTTAATA
21765645 TTTA
1 TTTA
21765649 TACATTGTTT
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:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTAATTATTAACGTTAATA
Found at i:21776286 original size:15 final size:15
Alignment explanation
Indices: 21776266--21776295 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21776256 TAATTGAAAA
21776266 TTAAAAAATATATAT
1 TTAAAAAATATATAT
21776281 TTAAAAAATATATAT
1 TTAAAAAATATATAT
21776296 ATGTAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAAATATATAT
Found at i:21776293 original size:17 final size:16
Alignment explanation
Indices: 21776268--21776302 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
21776258 ATTGAAAATT
*
21776268 AAAAAATATATATTTA
1 AAAAAATATATATGTA
21776284 AAAAATATATATATGTA
1 AAAAA-ATATATATGTA
21776301 AA
1 AA
21776303 TGTTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AAAAAATATATATGTA
Found at i:21781169 original size:99 final size:101
Alignment explanation
Indices: 21780979--21781175 Score: 308
Period size: 102 Copynumber: 2.0 Consensus size: 101
21780969 GGCGTAAGCC
* ** *
21780979 GCATCCTCTTTGCTGCTGGTTGCTGGGATAACTCTCCCAGAGAATCATTGACAATGATGGCCTCC
1 GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTCCAAGAGAATCATTGACAATGA-GGCCTCC
21781044 TTGTTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
65 TTGTTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
* **
21781081 GCATCCTCTTTGCTGCCGGTTGCTCAGATAATTCTGTAAGAGAATCATTGACAAT-A-GCCTCCT
1 GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTCCAAGAGAATCATTGACAATGAGGCCTCCT
21781144 TGTTTTCAGCCACTTCAGAATCTTGATTCAAT
66 TGTTTTCAGCCACTTCAGAATCTTGATTCAAT
21781176 GGTTCAGCCA
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 39 0.44
101 1 0.01
102 48 0.55
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (101 bp):
GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTCCAAGAGAATCATTGACAATGAGGCCTCCT
TGTTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
Found at i:21791353 original size:2 final size:2
Alignment explanation
Indices: 21791340--21791379 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
21791330 GCTATGGATC
*
21791340 AT AT AT AA 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
21791380 TAATTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21793307 original size:35 final size:35
Alignment explanation
Indices: 21793228--21793300 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
21793218 TCATAAATTT
21793228 CTTTACTTCTCAATTTCTATCTTCTTATTTATTCC
1 CTTTACTTCTCAATTTCTATCTTCTTATTTATTCC
21793263 CTTTACTTCTCAATTTCTATCTTCTTATTTATTCC
1 CTTTACTTCTCAATTTCTATCTTCTTATTTATTCC
21793298 CTT
1 CTT
21793301 ACCTTCTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (35 bp):
CTTTACTTCTCAATTTCTATCTTCTTATTTATTCC
Found at i:21793574 original size:46 final size:44
Alignment explanation
Indices: 21793470--21793577 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
21793460 TGTCTTTGAC
** * * *
21793470 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
21793514 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
21793560 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
21793578 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:21800488 original size:46 final size:44
Alignment explanation
Indices: 21800384--21800491 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
21800374 TGTCTTTGAC
** * * *
21800384 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
21800428 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
21800474 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
21800492 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:21805988 original size:16 final size:16
Alignment explanation
Indices: 21805969--21806000 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21805959 AACGATTAAA
*
21805969 TTAATTTTTTTAATTT
1 TTAATTTTTATAATTT
21805985 TTAATTTTTATAATTT
1 TTAATTTTTATAATTT
21806001 ATTCAATCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTAATTTTTATAATTT
Found at i:21808501 original size:25 final size:25
Alignment explanation
Indices: 21808467--21808516 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
21808457 TCTACGATAT
21808467 GTTAGTATAGCTTTATTGCAATAAA
1 GTTAGTATAGCTTTATTGCAATAAA
21808492 GTTAGTATAGCTTTATTGCAATAAA
1 GTTAGTATAGCTTTATTGCAATAAA
21808517 TACCTTGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (25 bp):
GTTAGTATAGCTTTATTGCAATAAA
Found at i:21812129 original size:19 final size:19
Alignment explanation
Indices: 21812101--21812139 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21812091 GGAAGATAAG
* *
21812101 TTCAGTCAAGCTCCTTCTT
1 TTCAGCCAAGCTACTTCTT
21812120 TTCAGCCAAGCTACTTCTT
1 TTCAGCCAAGCTACTTCTT
21812139 T
1 T
21812140 GCATTTCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41
Consensus pattern (19 bp):
TTCAGCCAAGCTACTTCTT
Found at i:21822637 original size:46 final size:46
Alignment explanation
Indices: 21822587--21822894 Score: 402
Period size: 46 Copynumber: 6.7 Consensus size: 46
21822577 GAAATGTGTG
* * * **
21822587 AGACCATGGTTGAAAGATACCATGACAACCTGATATGAAATGTGTA
1 AGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATA
* ** *
21822633 AGACCATAGTTGAAAGATACCATGGCAATGTGATATGAAATGAATA
1 AGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATA
* **
21822679 AGACCGTGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATA
1 AGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATA
* *
21822725 AGACCATGGTTGAAAGATACCATGGCAGCATGACATGAAATGACTA
1 AGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATA
** *
21822771 AGACCATGGTTGAAAGATACCATGATAGCATGACATGAAATGAATA
1 AGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATA
*
21822817 AGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTA
1 AGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAATA
* * * *
21822863 AGACCATAGTTGAAAGACACTATGGCATCATG
1 AGACCATGGTTGAAAGATACCATGGCAACATG
21822895 TTAAAGATAA
Statistics
Matches: 232, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.00
46 231 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
AGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATA
Found at i:21824849 original size:17 final size:18
Alignment explanation
Indices: 21824817--21824854 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
21824807 TTAAGGTTAA
21824817 AAAGGTAAATTAATAATT
1 AAAGGTAAATTAATAATT
*
21824835 AAAGGTTAA-TAATAATT
1 AAAGGTAAATTAATAATT
21824852 AAA
1 AAA
21824855 ACAGAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (18 bp):
AAAGGTAAATTAATAATT
Found at i:21825213 original size:29 final size:29
Alignment explanation
Indices: 21825181--21825237 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
21825171 AAATAGGGAT
* *
21825181 TAAATTGAGAAAT-ATTGAAAATTTATGGA
1 TAAAATGAGAAATAAATGAAAA-TTATGGA
*
21825210 TAAAATGTGAAATAAATGAAAATTATGG
1 TAAAATGAGAAATAAATGAAAATTATGG
21825238 GCTTCTAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.32
Consensus pattern (29 bp):
TAAAATGAGAAATAAATGAAAATTATGGA
Found at i:21830215 original size:25 final size:24
Alignment explanation
Indices: 21830138--21830221 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 24
21830128 TGTTAACTAG
21830138 TTTATAACATCTTTACTTCAATTCA
1 TTTA-AACATCTTTACTTCAATTCA
* * * *
21830163 TTTAAAC-TCTATACATGCCATATAA
1 TTTAAACATCTTTAC-TTCAAT-TCA
21830188 TTTATAACATCTTTACTTCAATTCA
1 TTTA-AACATCTTTACTTCAATTCA
21830213 TTTAAACAT
1 TTTAAACAT
21830222 AAAACAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
23 6 0.13
24 12 0.26
25 16 0.34
26 7 0.15
27 6 0.13
ACGTcount: A:0.36, C:0.19, G:0.01, T:0.44
Consensus pattern (24 bp):
TTTAAACATCTTTACTTCAATTCA
Found at i:21830712 original size:40 final size:37
Alignment explanation
Indices: 21830609--21830743 Score: 161
Period size: 35 Copynumber: 3.7 Consensus size: 37
21830599 TTTTCCTCAT
* *
21830609 TGAAATACCATACCTACATTTTACAACTCGGTATGG-
1 TGAAATACCATACCTACATTTCACAACTCAGTATGGA
* * **
21830645 -GAAATGCAATACCTACATTTCTTAACTCAGTATGGA
1 TGAAATACCATACCTACATTTCACAACTCAGTATGGA
21830681 TTTGATAATACCATACCTACATTTCACAACTCAGTATGGA
1 --TGA-AATACCATACCTACATTTCACAACTCAGTATGGA
21830721 TG--ATACCATACCTACATTTCACA
1 TGAAATACCATACCTACATTTCACA
21830744 CTTTTTCATG
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
35 50 0.60
38 2 0.02
39 2 0.02
40 30 0.36
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (37 bp):
TGAAATACCATACCTACATTTCACAACTCAGTATGGA
Found at i:21834219 original size:38 final size:40
Alignment explanation
Indices: 21834176--21834251 Score: 102
Period size: 38 Copynumber: 1.9 Consensus size: 40
21834166 ATGTTTAAGG
*
21834176 ATGAATTATATTATGATTA-TC-ATAATGTTTCAAAACCA
1 ATGAATTAGATTATGATTATTCGATAATGTTTCAAAACCA
* * *
21834214 ATGAATTAGATTATGTTTATTCGGTAATGTTTCGAAAC
1 ATGAATTAGATTATGATTATTCGATAATGTTTCAAAAC
21834252 TCTATTCCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 17 0.53
39 2 0.06
40 13 0.41
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (40 bp):
ATGAATTAGATTATGATTATTCGATAATGTTTCAAAACCA
Found at i:21840651 original size:2 final size:2
Alignment explanation
Indices: 21840644--21840682 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21840634 CTACCTCCTT
21840644 TA TA TA TA TA 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 TA TA TA TA TA T
21840683 TTACTTTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21851464 original size:16 final size:17
Alignment explanation
Indices: 21851443--21851476 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21851433 CTATTACAAG
21851443 TATTGAA-ATAACTTAA
1 TATTGAATATAACTTAA
*
21851459 TATTGAATTTAACTTAA
1 TATTGAATATAACTTAA
21851476 T
1 T
21851477 TAATTAATGT
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:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (17 bp):
TATTGAATATAACTTAA
Found at i:21862987 original size:18 final size:19
Alignment explanation
Indices: 21862966--21863006 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
21862956 TAGAATTACT
21862966 AAAATTTAT-ATTTTTAAA
1 AAAATTTATAATTTTTAAA
*
21862984 AAAA-TTATAATTTTTTAA
1 AAAATTTATAATTTTTAAA
21863002 AAAAT
1 AAAAT
21863007 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATTTATAATTTTTAAA
Found at i:21876237 original size:65 final size:65
Alignment explanation
Indices: 21876161--21876310 Score: 228
Period size: 65 Copynumber: 2.3 Consensus size: 65
21876151 TGTGGACTAC
* * *
21876161 CGCAGATCTTTGTGAGCGTCTTGTTATATGATTGATTGTGATCCTGCACATATTGCAGACATAAA
1 CGCAGCTCTTTGTGAGCGTCTTGTTATATGATCGATTGTGATCCTGCACATATTGCAGACACAAA
* * * * *
21876226 CGCAGCTCTTTGTGAGCGTCTTGTTTTATGATCGGTTGTGATCTTGCATATGTTGCAGACACAAA
1 CGCAGCTCTTTGTGAGCGTCTTGTTATATGATCGATTGTGATCCTGCACATATTGCAGACACAAA
21876291 CGCAGCTCTTTGTGAGCGTC
1 CGCAGCTCTTTGTGAGCGTC
21876311 CTAATATAGT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 77 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (65 bp):
CGCAGCTCTTTGTGAGCGTCTTGTTATATGATCGATTGTGATCCTGCACATATTGCAGACACAAA
Found at i:21876417 original size:26 final size:26
Alignment explanation
Indices: 21876360--21876442 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 26
21876350 CGGAGCTCCC
* * *
21876360 GATTAATGGCTCTTCGTGAGCTTCTC
1 GATTAAAGGCTCTTTGTGAGCTTCTT
*
21876386 GTTTAAAGGCTCTTTGTGAGCTTCTT
1 GATTAAAGGCTCTTTGTGAGCTTCTT
* * * * *
21876412 GATTAAAAGTTATTTGTGAACTTCCT
1 GATTAAAGGCTCTTTGTGAGCTTCTT
21876438 GATTA
1 GATTA
21876443 TGACTCTTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (26 bp):
GATTAAAGGCTCTTTGTGAGCTTCTT
Found at i:21878660 original size:26 final size:26
Alignment explanation
Indices: 21878624--21878675 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
21878614 AGTTACATAG
21878624 TGCATAATTATACATCAAGAACTATC
1 TGCATAATTATACATCAAGAACTATC
*
21878650 TGCATAATTATACATCAAGAATTATC
1 TGCATAATTATACATCAAGAACTATC
21878676 CTATATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (26 bp):
TGCATAATTATACATCAAGAACTATC
Found at i:21881932 original size:19 final size:19
Alignment explanation
Indices: 21881895--21881934 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21881885 ATTTCTAAAG
* *
21881895 TTTAAACTTATATTCTATT
1 TTTAAACTTATAATATATT
*
21881914 TTTAAATTTATAATATATT
1 TTTAAACTTATAATATATT
21881933 TT
1 TT
21881935 ACTATTATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAAACTTATAATATATT
Found at i:21882429 original size:2 final size:2
Alignment explanation
Indices: 21882422--21882476 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
21882412 AATTTGAAAG
21882422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21882464 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
21882477 GTGTGTGTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21884644 original size:21 final size:19
Alignment explanation
Indices: 21884619--21884668 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
21884609 TAAAATGATG
21884619 AAAAATAAAATTTAACTAAAA
1 AAAAATAAAA-TTAAC-AAAA
* *
21884640 AAAAATCAAATTGACAAAA
1 AAAAATAAAATTAACAAAA
*
21884659 AAATATAAAA
1 AAAAATAAAA
21884669 CTAAATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 12 0.48
20 4 0.16
21 9 0.36
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAAATAAAATTAACAAAA
Found at i:21886434 original size:27 final size:27
Alignment explanation
Indices: 21886404--21886457 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21886394 GGGCGATGAA
21886404 GATTTGTTTGTGAAATTTGGTGATTTT
1 GATTTGTTTGTGAAATTTGGTGATTTT
21886431 GATTTGTTTGTGAAATTTGGTGATTTT
1 GATTTGTTTGTGAAATTTGGTGATTTT
21886458 CCTTAGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.56
Consensus pattern (27 bp):
GATTTGTTTGTGAAATTTGGTGATTTT
Found at i:21895524 original size:28 final size:28
Alignment explanation
Indices: 21895492--21895547 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
21895482 TATATTTTTA
21895492 TTAGTATTTGAGTTTCTTAAGGTCCAAG
1 TTAGTATTTGAGTTTCTTAAGGTCCAAG
21895520 TTAGTATTTGAGTTTCTTAAGGTCCAAG
1 TTAGTATTTGAGTTTCTTAAGGTCCAAG
21895548 CAATTTGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (28 bp):
TTAGTATTTGAGTTTCTTAAGGTCCAAG
Found at i:21896284 original size:3 final size:3
Alignment explanation
Indices: 21896276--21896312 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
21896266 TAAATCTCAC
* *
21896276 TTA TTA TTA TTA TTA TTA CTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21896313 ACTTTTCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:21903445 original size:36 final size:35
Alignment explanation
Indices: 21903362--21903459 Score: 121
Period size: 36 Copynumber: 2.9 Consensus size: 35
21903352 TACCTCTAAA
* *
21903362 ATAATAGCAAA-AATAACAATAAAATAAGAGTTAT
1 ATAATAGCAAATAATAACAATAAAATAATAGTAAT
* *
21903396 ATAACATCTAAATAATAACAATAAAATAATAGTAAT
1 ATAATAGC-AAATAATAACAATAAAATAATAGTAAT
*
21903432 ATAATAGC-AA-AATAAAAATAAAATAATA
1 ATAATAGCAAATAATAACAATAAAATAATA
21903460 ACGAAATGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
33 17 0.31
34 8 0.15
35 3 0.05
36 27 0.49
ACGTcount: A:0.64, C:0.06, G:0.05, T:0.24
Consensus pattern (35 bp):
ATAATAGCAAATAATAACAATAAAATAATAGTAAT
Found at i:21903457 original size:22 final size:22
Alignment explanation
Indices: 21903418--21903459 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21903408 TAATAACAAT
* * *
21903418 AAAATAATAGTAATATAATAGC
1 AAAATAAAAATAAAATAATAGC
21903440 AAAATAAAAATAAAATAATA
1 AAAATAAAAATAAAATAATA
21903460 ACGAAATGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAATAAAAATAAAATAATAGC
Found at i:21907689 original size:87 final size:87
Alignment explanation
Indices: 21907342--21907689 Score: 491
Period size: 87 Copynumber: 4.0 Consensus size: 87
21907332 TTGAGGTGAA
* ** *
21907342 TGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGGTTCTACTTTGTCCACATTCGT
1 TGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCGCTTTGTCCACATTCAT
* *
21907407 TTCCTGCTGAAGCAGATTCTTT
66 TTCCTGCTGAACCAGATTCTTG
* * * *
21907429 TGTTTATTTTCCGT-GAATGATTCTTGCTTCTTCCCTTTCTCGGATTCAGCTTTGTCCACATTCG
1 TGTTTATTTGCCGTAG-ATGATTCTTGCTTCTTCCCTTTCTCAGATTCCGCTTTGTCCACATTCA
* *
21907493 TTTCCTGCTGAACCGGATTCTTA
65 TTTCCTGCTGAACCAGATTCTTG
* *
21907516 TGTTTATTTGCTGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCGCTTTGTCCACATCCAT
1 TGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCGCTTTGTCCACATTCAT
21907581 TTCCTGCTGAACCAGATTCTTG
66 TTCCTGCTGAACCAGATTCTTG
* ** *
21907603 TGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCACCTTCCGCTTTGTCCACTTTCAT
1 TGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCGCTTTGTCCACATTCAT
* * *
21907668 TTCCTTCTGCAGCAGATTCTTG
66 TTCCTGCTGAACCAGATTCTTG
21907690 GTTCAGAGAA
Statistics
Matches: 234, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
86 1 0.00
87 232 0.99
88 1 0.00
ACGTcount: A:0.14, C:0.26, G:0.15, T:0.45
Consensus pattern (87 bp):
TGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCGCTTTGTCCACATTCAT
TTCCTGCTGAACCAGATTCTTG
Found at i:21911096 original size:9 final size:9
Alignment explanation
Indices: 21911084--21911117 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
21911074 CGTCATCACA
*
21911084 TTCATCGTC
1 TTCATCATC
*
21911093 TTCATAATC
1 TTCATCATC
21911102 TTCATCATC
1 TTCATCATC
21911111 TTCATCA
1 TTCATCA
21911118 GACTCATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.44
Consensus pattern (9 bp):
TTCATCATC
Found at i:21913118 original size:1 final size:1
Alignment explanation
Indices: 21913082--21913106 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21913072 ATTACAAGAC
21913082 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
21913107 GAAACCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21917927 original size:11 final size:11
Alignment explanation
Indices: 21917886--21917929 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
21917876 AATATTTCAA
*
21917886 AAAAAAAAACT
1 AAAAGAAAACT
21917897 AAAAGAAAACT
1 AAAAGAAAACT
21917908 AAAGAAGAAAACT
1 -AA-AAGAAAACT
*
21917921 AATAGAAAA
1 AAAAGAAAA
21917930 GAAAGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 16 0.55
12 4 0.14
13 9 0.31
ACGTcount: A:0.75, C:0.07, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAAGAAAACT
Found at i:21921789 original size:30 final size:31
Alignment explanation
Indices: 21921755--21921814 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
21921745 ATTTTAGGTT
21921755 AAAATATGAT-GTTAATCTT-TATACTTTAAC
1 AAAATATGATAGTTAAT-TTCTATACTTTAAC
* *
21921785 AAAATTTGATATTTAATTTCTATACTTTAA
1 AAAATATGATAGTTAATTTCTATACTTTAA
21921815 AAGTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (31 bp):
AAAATATGATAGTTAATTTCTATACTTTAAC
Found at i:21923891 original size:25 final size:24
Alignment explanation
Indices: 21923863--21923919 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
21923853 CACAGCTCTT
* *
21923863 ATGAGCTTCCTGATATTTAGCTCAC
1 ATGAGCTTCCCGAT-TTCAGCTCAC
**
21923888 ATGAGCTTCCCGATTTCAGCTCTT
1 ATGAGCTTCCCGATTTCAGCTCAC
21923912 ATGAGCTT
1 ATGAGCTT
21923920 TTCGTTTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (24 bp):
ATGAGCTTCCCGATTTCAGCTCAC
Found at i:21923915 original size:24 final size:25
Alignment explanation
Indices: 21923855--21923919 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
21923845 GGACACATCA
*
21923855 CAGCTCTTATGAGCTTCCTGATATT
1 CAGCTCTTATGAGCTTCCCGATATT
* **
21923880 TAGCTCACATGAGCTTCCCGAT-TT
1 CAGCTCTTATGAGCTTCCCGATATT
21923904 CAGCTCTTATGAGCTT
1 CAGCTCTTATGAGCTT
21923920 TTCGTTTACT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 15 0.45
25 18 0.55
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (25 bp):
CAGCTCTTATGAGCTTCCCGATATT
Found at i:21938147 original size:110 final size:109
Alignment explanation
Indices: 21937954--21938173 Score: 422
Period size: 110 Copynumber: 2.0 Consensus size: 109
21937944 GTATGCATGC
21937954 TGAAACATGCATGGTATATGACCTGATATGATGTTCTCAAAAGTGAATAGACATATTGTATCAAC
1 TGAAACATGCATGGTATATGACCTGATATGATGTTCTCAAAAGTGAATAGACATATTGTATCAAC
21938019 AATTTCATTCAAAATGGTAATAAAAAAAAAATTTGCTTAAGCATA
66 AATTTCATTCAAAATGGTAAT-AAAAAAAAATTTGCTTAAGCATA
21938064 TGAAACATGCATGGTATATGACCTGATATGATGTTCTCAAAAGTGAATAGACATATTGTATCAAC
1 TGAAACATGCATGGTATATGACCTGATATGATGTTCTCAAAAGTGAATAGACATATTGTATCAAC
*
21938129 AATTTCATTCAAAATGGTAATAAAAAAAATTTTGCTTAAGCATA
66 AATTTCATTCAAAATGGTAATAAAAAAAAATTTGCTTAAGCATA
21938173 T
1 T
21938174 TAAGCTATAA
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
109 23 0.21
110 86 0.79
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (109 bp):
TGAAACATGCATGGTATATGACCTGATATGATGTTCTCAAAAGTGAATAGACATATTGTATCAAC
AATTTCATTCAAAATGGTAATAAAAAAAAATTTGCTTAAGCATA
Found at i:21943997 original size:13 final size:14
Alignment explanation
Indices: 21943953--21943999 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
21943943 TTTAGCGTTT
21943953 TATATTTTAATTTAA
1 TATATTTT-ATTTAA
* *
21943968 TAAATTTTATTT-T
1 TATATTTTATTTAA
21943981 TATATTTT-TTTAA
1 TATATTTTATTTAA
21943994 TATATT
1 TATATT
21944000 ACTTTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 3 0.11
13 13 0.48
14 4 0.15
15 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATATTTTATTTAA
Found at i:21956162 original size:20 final size:19
Alignment explanation
Indices: 21956132--21956174 Score: 77
Period size: 20 Copynumber: 2.2 Consensus size: 19
21956122 ATCAAAGGTG
21956132 ATCTGCAATTATTAAGTTT
1 ATCTGCAATTATTAAGTTT
21956151 ATCTGTCAATTATTAAGTTT
1 ATCTG-CAATTATTAAGTTT
21956171 ATCT
1 ATCT
21956175 CATTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (19 bp):
ATCTGCAATTATTAAGTTT
Found at i:21970447 original size:72 final size:72
Alignment explanation
Indices: 21970288--21970586 Score: 224
Period size: 72 Copynumber: 4.1 Consensus size: 72
21970278 CTAAAACAAT
* * ** * * * * *
21970288 GGTTTTATTTAATACCAAATTTCAATAAATAAAAACCTAAACTAACCTTCT-AAAAACATATTAC
1 GGTTTTACTTAATATCAAAACTCAATAAAT-CAAA-CTAAAATAACCTTCTCAAAAACACATAAT
*
21970352 CGAATAAAC
64 TGAATAAAC
* * * ** * **
21970361 GATTTTATTTAATATCAAAACTCAATAAATCAAATTAATTTAATCTTCTC-AAAACGTATAACTT
1 GGTTTTACTTAATATCAAAACTCAATAAATCAAACTAAAATAACCTTCTCAAAAACACATAA-TT
*
21970425 GAATAAAT
65 GAATAAAC
* * ** * *
21970433 GGTTTTACTTAATATCGAAACTCAATGAATTGAACTAAAATAGCCTTTTCAAAAACACATAATTG
1 GGTTTTACTTAATATCAAAACTCAATAAATCAAACTAAAATAACCTTCTCAAAAACACATAATTG
21970498 AATAAAC
66 AATAAAC
* * * ** * * * *
21970505 AGTTCTACTTAATATCAAAATTCAATAAATTGAACTAAATTAACGTTTTAAAAAACACATAATTG
1 GGTTTTACTTAATATCAAAACTCAATAAATCAAACTAAAATAACCTTCTCAAAAACACATAATTG
* **
21970570 AACAAGT
66 AATAAAC
21970577 GGTTTTACTT
1 GGTTTTACTT
21970587 TGTATAATAA
Statistics
Matches: 180, Mismatches: 43, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
71 20 0.11
72 125 0.69
73 35 0.19
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (72 bp):
GGTTTTACTTAATATCAAAACTCAATAAATCAAACTAAAATAACCTTCTCAAAAACACATAATTG
AATAAAC
Found at i:21970659 original size:59 final size:59
Alignment explanation
Indices: 21970595--21970711 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
21970585 TTTGTATAAT
* * * *
21970595 AAAATAAATGGTTTCACTTAATATCAAAACTCAATAAATCGAACTAAATTAAGCTTTTG
1 AAAATAAACGGTTTCACTTAAAATCAAAACTCAATAAATCGAACTAAAATAACCTTTTG
* * *
21970654 AAAATAAACGGTTTCGCTTAAAATCAAAACTTAATAAATTGAACTAAAATAACCTTTT
1 AAAATAAACGGTTTCACTTAAAATCAAAACTCAATAAATCGAACTAAAATAACCTTTT
21970712 TTAAAACACA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (59 bp):
AAAATAAACGGTTTCACTTAAAATCAAAACTCAATAAATCGAACTAAAATAACCTTTTG
Found at i:21973626 original size:43 final size:43
Alignment explanation
Indices: 21973560--21973642 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
21973550 TGGTCCATAC
21973560 ATGATCGATTTAACTTTGATTACTTGCTAATATAGTTTGAATT
1 ATGATCGATTTAACTTTGATTACTTGCTAATATAGTTTGAATT
* *
21973603 ATGATCGATTTAACTTTGGTTACTTGCTAATATGGTTTGA
1 ATGATCGATTTAACTTTGATTACTTGCTAATATAGTTTGA
21973643 TTTTAATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.46
Consensus pattern (43 bp):
ATGATCGATTTAACTTTGATTACTTGCTAATATAGTTTGAATT
Found at i:21977674 original size:3 final size:3
Alignment explanation
Indices: 21977668--21977712 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
21977658 GAGGAGGAGG
*
21977668 AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
21977713 GAAAAATGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:21978780 original size:21 final size:21
Alignment explanation
Indices: 21978756--21978826 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
21978746 AGCTTTTCTC
*
21978756 TTAGGGCAGCTTATTGATAAG
1 TTAGGGCAGCTTATTGATGAG
*
21978777 TTAGGGCA--TTAGTTAACTGAG
1 TTAGGGCAGCTTA-TTGA-TGAG
* *
21978798 TTAGGGCAGCTTGTGGATGAG
1 TTAGGGCAGCTTATTGATGAG
21978819 TTAGGGCA
1 TTAGGGCA
21978827 CTAGGTAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
21 31 0.76
22 2 0.05
23 2 0.05
ACGTcount: A:0.25, C:0.10, G:0.34, T:0.31
Consensus pattern (21 bp):
TTAGGGCAGCTTATTGATGAG
Found at i:21978821 original size:42 final size:42
Alignment explanation
Indices: 21978756--21978853 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
21978746 AGCTTTTCTC
* * * *
21978756 TTAGGGCAGCTTATTGATAAGTTAGGGCATTAGTTAACTGAG
1 TTAGGGCAGCTTGTGGATAAGTTAGGGCACTAGGTAACTGAG
*
21978798 TTAGGGCAGCTTGTGGATGAGTTAGGGCACTAGGTAACTGAG
1 TTAGGGCAGCTTGTGGATAAGTTAGGGCACTAGGTAACTGAG
*
21978840 TTGGGGCAGCTTGT
1 TTAGGGCAGCTTGT
21978854 TGAGTTGGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.23, C:0.11, G:0.35, T:0.31
Consensus pattern (42 bp):
TTAGGGCAGCTTGTGGATAAGTTAGGGCACTAGGTAACTGAG
Found at i:21978839 original size:21 final size:21
Alignment explanation
Indices: 21978775--21978847 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
21978765 CTTATTGATA
* *
21978775 AGTTAGGGCATTAGTTAACTG
1 AGTTAGGGCACTAGGTAACTG
* *
21978796 AGTTAGGGCAGCT-TGTGGA-TG
1 AGTTAGGGCA-CTAGGT-AACTG
21978817 AGTTAGGGCACTAGGTAACTG
1 AGTTAGGGCACTAGGTAACTG
*
21978838 AGTTGGGGCA
1 AGTTAGGGCA
21978848 GCTTGTTGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
20 3 0.07
21 36 0.88
22 2 0.05
ACGTcount: A:0.25, C:0.11, G:0.37, T:0.27
Consensus pattern (21 bp):
AGTTAGGGCACTAGGTAACTG
Found at i:21978882 original size:21 final size:21
Alignment explanation
Indices: 21978849--21978904 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
21978839 GTTGGGGCAG
*
21978849 CTTGTTGAGTTGGGGTA-CTCT
1 CTTGCTGAGTTGGGGTAGCT-T
*
21978870 CTTGCTGATTTGGGGTAGCTT
1 CTTGCTGAGTTGGGGTAGCTT
*
21978891 GTTGCTGAGTTGGG
1 CTTGCTGAGTTGGG
21978905 ATACCAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.09, C:0.12, G:0.38, T:0.41
Consensus pattern (21 bp):
CTTGCTGAGTTGGGGTAGCTT
Found at i:21979355 original size:21 final size:21
Alignment explanation
Indices: 21979331--21979399 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
21979321 TATTATGATT
21979331 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
21979352 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
21979372 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
*
21979392 ATTGTTAT
1 ATTATTAT
21979400 TATTAGCATT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.28
20 3 0.08
21 17 0.47
22 3 0.08
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:21979548 original size:8 final size:8
Alignment explanation
Indices: 21979535--21979559 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21979525 AGATATTTGT
21979535 TAATTAAA
1 TAATTAAA
21979543 TAATTAAA
1 TAATTAAA
21979551 TAATTAAA
1 TAATTAAA
21979559 T
1 T
21979560 TATGAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATTAAA
Found at i:21979812 original size:12 final size:12
Alignment explanation
Indices: 21979795--21979825 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21979785 GAAGCAGGGG
21979795 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
21979807 AGAAAAAGGGAA
1 AGAAAAAGAGAA
21979819 AGAAAAA
1 AGAAAAA
21979826 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:21984165 original size:15 final size:15
Alignment explanation
Indices: 21984133--21984182 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
21984123 CTATCCTATT
**
21984133 AGACACATCACTTTC
1 AGACACATCACTACC
**
21984148 AGATGCATCACTACC
1 AGACACATCACTACC
21984163 AGACACATCACTACC
1 AGACACATCACTACC
21984178 AGACA
1 AGACA
21984183 TGTCTTATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (15 bp):
AGACACATCACTACC
Found at i:21984513 original size:88 final size:89
Alignment explanation
Indices: 21984397--21984562 Score: 228
Period size: 89 Copynumber: 1.9 Consensus size: 89
21984387 ACACAACCAT
* * * * *
21984397 TTTTGCAACATACAATATAGCAGTTTGGATA-AAACAA-TGACAAATATATATAACAAACATCAG
1 TTTTGCAACATACAATATAACAGCTTGGATACAAAAAATTG-CAAATATACACAACAAACATCAG
21984460 TTTGATAATGACATTCAAATTTTGA
65 TTTGATAATGACATTCAAATTTTGA
* * * *
21984485 TTTTGCCATATACAATATAACAGCTTGGATACAAAAAATTGCAGATATACACAATAAACATCAGT
1 TTTTGCAACATACAATATAACAGCTTGGATACAAAAAATTGCAAATATACACAACAAACATCAGT
21984550 TTGATAATGACAT
66 TTGATAATGACAT
21984563 CCATACAATT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
88 27 0.40
89 38 0.57
90 2 0.03
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (89 bp):
TTTTGCAACATACAATATAACAGCTTGGATACAAAAAATTGCAAATATACACAACAAACATCAGT
TTGATAATGACATTCAAATTTTGA
Found at i:21984589 original size:48 final size:48
Alignment explanation
Indices: 21984521--21984643 Score: 183
Period size: 48 Copynumber: 2.6 Consensus size: 48
21984511 GGATACAAAA
* * *
21984521 AATTGCAGATATACACAATAAACATCAGTTTGATAATGACATCCATAC
1 AATTGCAGATACAAAAAATAAACATCAGTTTGATAATGACATCCATAC
* *
21984569 AATTGCAGATACAAAAAATAAACATTAGTTTGATAATGGCATCCATAC
1 AATTGCAGATACAAAAAATAAACATCAGTTTGATAATGACATCCATAC
* *
21984617 AATGGCAGATACAAATAATAAACATCA
1 AATTGCAGATACAAAAAATAAACATCA
21984644 TGCATATGGC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.25
Consensus pattern (48 bp):
AATTGCAGATACAAAAAATAAACATCAGTTTGATAATGACATCCATAC
Found at i:21984694 original size:6 final size:6
Alignment explanation
Indices: 21984679--21984844 Score: 91
Period size: 6 Copynumber: 26.7 Consensus size: 6
21984669 TGTGTCATAC
* * * * * * **
21984679 AAATCG AAATCC AAATCG AAATCA AAATCA AAATCT AAAGCT AAATTG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* **
21984727 AGATCA AAATTG AAATCA AAATCA AAATCA AAATCA AAATCA ATGAGTATTTCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA A--A--A--TCA
** ** *
21984781 AAATTG AAATCA AAATCA AAAT-A GAAATTG AAATCA AAATCA GAATCA
1 AAATCA AAATCA AAATCA AAATCA -AAATCA AAATCA AAATCA AAATCA
* * *
21984829 GAATCA GAATCG AAAT
1 AAATCA AAATCA AAAT
21984845 AACCTTAAAT
Statistics
Matches: 126, Mismatches: 26, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
5 1 0.01
6 117 0.93
8 2 0.02
10 2 0.02
12 4 0.03
ACGTcount: A:0.56, C:0.13, G:0.09, T:0.22
Consensus pattern (6 bp):
AAATCA
Found at i:21984782 original size:48 final size:48
Alignment explanation
Indices: 21984691--21984802 Score: 149
Period size: 48 Copynumber: 2.3 Consensus size: 48
21984681 ATCGAAATCC
* *
21984691 AAATCGAAATCAAAATCAAAATCTAAAGCTAAATTGAGATCAAAATTG
1 AAATCAAAATCAAAATCAAAATCTAAAGATAAATTGAGATCAAAATTG
*
21984739 AAATCAAAATCAAAATCAAAATC-AAA-ATCAA-TGAGTATTTCAAAATTG
1 AAATCAAAATCAAAATCAAAATCTAAAGATAAATTGAG-A--TCAAAATTG
21984787 AAATCAAAATCAAAAT
1 AAATCAAAATCAAAAT
21984803 AGAAATTGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
45 4 0.07
46 4 0.07
47 3 0.05
48 47 0.81
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (48 bp):
AAATCAAAATCAAAATCAAAATCTAAAGATAAATTGAGATCAAAATTG
Found at i:21985436 original size:30 final size:31
Alignment explanation
Indices: 21985369--21985439 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
21985359 AAACTGGTAA
* * *
21985369 TTAGTGACTATTTTGTCACTTTTTCATAACG
1 TTAGTGACTGTTTTGTAACTTTTTCATAAAG
21985400 TTAGTGACTGTTTTGTAAC-TTTTCA-AAAG
1 TTAGTGACTGTTTTGTAACTTTTTCATAAAG
21985429 TTGAGTGACTG
1 TT-AGTGACTG
21985440 AAATGAAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.14
30 14 0.39
31 17 0.47
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (31 bp):
TTAGTGACTGTTTTGTAACTTTTTCATAAAG
Found at i:21988948 original size:2 final size:2
Alignment explanation
Indices: 21988941--21988965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21988931 TTGAATTGGT
21988941 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
21988966 TTTTCTGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:22004315 original size:18 final size:21
Alignment explanation
Indices: 22004288--22004366 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 21
22004278 TTAAGAATTG
*
22004288 TTTTAGTA-TTATTTTT-T-T
1 TTTTAATATTTATTTTTATGT
22004306 TTTTAATATTTATTTTTATGT
1 TTTTAATATTTATTTTTATGT
*
22004327 TTTTAAATATATTTGATTTATTATAT
1 TTTT--A-ATATTT-ATTT-TTATGT
22004353 TTTTAA-ATTT-TTTT
1 TTTTAATATTTATTTT
22004367 ATTTAATGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
18 7 0.14
19 9 0.18
20 4 0.08
21 5 0.10
22 4 0.08
23 2 0.04
24 7 0.14
25 4 0.08
26 9 0.18
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTAATATTTATTTTTATGT
Found at i:22004339 original size:20 final size:19
Alignment explanation
Indices: 22004288--22004340 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
22004278 TTAAGAATTG
*
22004288 TTTTAGTAT-TATTTTTTT
1 TTTTAATATATATTTTTTT
*
22004306 TTTTAATATTTATTTTTATGT
1 TTTTAATATATATTTTT-T-T
22004327 TTTTAA-ATATATTT
1 TTTTAATATATATTT
22004341 GATTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 8 0.27
19 7 0.23
20 8 0.27
21 7 0.23
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTTAATATATATTTTTTT
Found at i:22004350 original size:26 final size:24
Alignment explanation
Indices: 22004311--22004370 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
22004301 TTTTTTTTTA
*
22004311 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
22004335 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
22004361 TTTTTTATTT
1 ATATTTATTT
22004371 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:22007589 original size:2 final size:2
Alignment explanation
Indices: 22007584--22007608 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22007574 CATTATACTT
22007584 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 T
22007609 TAATTGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22008570 original size:32 final size:30
Alignment explanation
Indices: 22008517--22008581 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 30
22008507 ACTTATTTTA
*
22008517 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
*
22008547 TTGTTAATTTTTTATTATTATTTTAGAGGCAT
1 TTGTTAA--TTTTATTATTATTTTAAAGGCAT
22008579 TTG
1 TTG
22008582 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 7 0.23
32 24 0.77
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:22011875 original size:28 final size:28
Alignment explanation
Indices: 22011837--22011892 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
22011827 TTAACCAAGA
22011837 AAATCACCTAGGCTTAACGGTTAAGTAG
1 AAATCACCTAGGCTTAACGGTTAAGTAG
*
22011865 AAATCACCTAGGCTTAATGGTTAAGTAG
1 AAATCACCTAGGCTTAACGGTTAAGTAG
22011893 TTAGTGCACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (28 bp):
AAATCACCTAGGCTTAACGGTTAAGTAG
Found at i:22012108 original size:11 final size:11
Alignment explanation
Indices: 22012092--22012122 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
22012082 GATAATATAG
22012092 TAAGTATAAAA
1 TAAGTATAAAA
*
22012103 TAAGTAAAAAA
1 TAAGTATAAAA
22012114 TAAGTATAA
1 TAAGTATAA
22012123 TATACTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
TAAGTATAAAA
Found at i:22014560 original size:34 final size:34
Alignment explanation
Indices: 22014517--22014594 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
22014507 TATTGATCCA
* *
22014517 TTATAAGCATATTATTTGCTA-TCGTATCGAATTG
1 TTATAAGCATATAAATTGCTACT-GTATCGAATTG
* * *
22014551 TTATGAGCATATAAATTGCTACTGTATTGATTTG
1 TTATAAGCATATAAATTGCTACTGTATCGAATTG
22014585 TTATAAGCAT
1 TTATAAGCAT
22014595 TCTATATTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (34 bp):
TTATAAGCATATAAATTGCTACTGTATCGAATTG
Found at i:22016402 original size:5 final size:5
Alignment explanation
Indices: 22016392--22016416 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
22016382 CGGGATTGGC
22016392 CCCAT CCCAT CCCAT CCCAT CCCAT
1 CCCAT CCCAT CCCAT CCCAT CCCAT
22016417 ACAGATTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCAT
Found at i:22016789 original size:26 final size:26
Alignment explanation
Indices: 22016704--22016780 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 26
22016694 TAATATTATG
22016704 ATATTTTAATAAAAGTATAAAAACTA
1 ATATTTTAATAAAAGTATAAAAACTA
* *
22016730 ATATTATTTATAAAAGTATAAAAAATA
1 ATATT-TTAATAAAAGTATAAAAACTA
22016757 ATATTTTAATAAAAGTATAAAAAC
1 ATATTTTAATAAAAGTATAAAAAC
22016781 CAAAGTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 22 0.48
27 24 0.52
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (26 bp):
ATATTTTAATAAAAGTATAAAAACTA
Found at i:22016790 original size:27 final size:25
Alignment explanation
Indices: 22016707--22016792 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 25
22016697 TATTATGATA
22016707 TTTTAATAAAAGTATAAAAACTAATAT
1 TTTTAATAAAAGTATAAAAAC-AA-AT
22016734 TATTT-ATAAAAGTATAAAAA-ATAAT
1 T-TTTAATAAAAGTATAAAAACA-AAT
22016759 ATTTTAATAAAAGTATAAAAACCAAAGT
1 -TTTTAATAAAAGTATAAAAA-CAAA-T
22016787 TTTTAA
1 TTTTAA
22016793 AATTCTGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
25 6 0.12
26 17 0.33
27 24 0.46
28 5 0.10
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (25 bp):
TTTTAATAAAAGTATAAAAACAAAT
Found at i:22034752 original size:25 final size:23
Alignment explanation
Indices: 22034700--22034754 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
22034690 TATAAATAGT
22034700 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
22034723 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
22034748 AATAGTG
1 AATAGTG
22034755 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:22034811 original size:26 final size:27
Alignment explanation
Indices: 22034780--22034853 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
22034770 ATGTTAAGAT
*
22034780 ATATATAATATATACATATGT-ATAAA
1 ATATATAATATATAAATATGTAATAAA
* * * *
22034806 ATATATATTAAAAAAATATGTACATAAC
1 ATATATAATATATAAATATGTA-ATAAA
22034834 ATATATGAATATATATAATA
1 ATATAT-AATATATA-AATA
22034854 ATATTAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 17 0.47
28 10 0.28
29 5 0.14
30 4 0.11
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (27 bp):
ATATATAATATATAAATATGTAATAAA
Found at i:22035077 original size:22 final size:24
Alignment explanation
Indices: 22035057--22035106 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
22035047 AAAAGCATAT
22035057 TACATATATGTATATAACATAATA
1 TACATATATGTATATAACATAATA
** * *
22035081 TTTATATATGTATATAAGATGATA
1 TACATATATGTATATAACATAATA
22035105 TA
1 TA
22035107 AAAAATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (24 bp):
TACATATATGTATATAACATAATA
Found at i:22035173 original size:9 final size:9
Alignment explanation
Indices: 22035159--22035195 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
22035149 ATAACATTAA
22035159 AATATATAT
1 AATATATAT
*
22035168 AATATATAA
1 AATATATAT
*
22035177 AATACATAT
1 AATATATAT
22035186 AATATATAT
1 AATATATAT
22035195 A
1 A
22035196 TTAGAAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATATAT
Found at i:22035179 original size:18 final size:18
Alignment explanation
Indices: 22035156--22035193 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
22035146 CTAATAACAT
*
22035156 TAAAATATATATAATATA
1 TAAAATACATATAATATA
22035174 TAAAATACATATAATATA
1 TAAAATACATATAATATA
22035192 TA
1 TA
22035194 TATTAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATACATATAATATA
Found at i:22035291 original size:19 final size:19
Alignment explanation
Indices: 22035267--22035303 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22035257 ATATAATAAT
*
22035267 AATGATGTTAGAAATATAC
1 AATGATATTAGAAATATAC
22035286 AATGATATTAGAAATATA
1 AATGATATTAGAAATATA
22035304 TATAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:22035419 original size:29 final size:29
Alignment explanation
Indices: 22035387--22035460 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
22035377 TTGAAAACAT
*
22035387 ATATACATAATATATACAAAAATATATAG
1 ATATACATAATATATACAAAAATATATAC
** *
22035416 ATATACATAATATAATATTAAAATATTTAC
1 ATATACATAATAT-ATACAAAAATATATAC
22035446 ATAATACATAA-ATAT
1 AT-ATACATAATATAT
22035461 TAGGGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.38
30 16 0.41
31 8 0.21
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (29 bp):
ATATACATAATATATACAAAAATATATAC
Found at i:22035506 original size:12 final size:12
Alignment explanation
Indices: 22035489--22035564 Score: 50
Period size: 12 Copynumber: 6.2 Consensus size: 12
22035479 ATAATAATGC
*
22035489 TACATAAGTATA
1 TACATAAATATA
22035501 TACATAAATATA
1 TACATAAATATA
*
22035513 TTA-A-AAACATA
1 -TACATAAATATA
22035524 TACATATATATATA
1 TACATA-A-ATATA
* *
22035538 TAAATAAAAAATA
1 TACAT-AAATATA
22035551 TACACT-AATATA
1 TACA-TAAATATA
22035563 TA
1 TA
22035565 GTAATCATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.04
11 7 0.14
12 20 0.40
13 10 0.20
14 10 0.20
15 1 0.02
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (12 bp):
TACATAAATATA
Found at i:22041432 original size:46 final size:46
Alignment explanation
Indices: 22041365--22041539 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
22041355 TGTAACCCGC
*
22041365 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
22041411 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
22041461 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
22041504 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
22041540 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 61 0.56
47 27 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:22041484 original size:93 final size:93
Alignment explanation
Indices: 22041372--22041543 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
22041362 CGCCCATAAG
* * *
22041372 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
22041437 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
22041465 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
22041530 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
22041544 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:22070690 original size:29 final size:29
Alignment explanation
Indices: 22070607--22070691 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
22070597 AAAAGTTATT
*
22070607 AAAA-TATAAT-ATAATATATAAATACATAA
1 AAAATTATAATAATAATA-ATAAAAAC-TAA
* *
22070636 AAAATTATAAGAA-AATAAAAAAAAACTAA
1 AAAATTATAATAATAAT-AATAAAAACTAA
**
22070665 AACTTTATAATAATAATAATAAAAACT
1 AAAATTATAATAATAATAATAAAAACT
22070692 TCGATAAACA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
29 26 0.58
30 17 0.38
31 2 0.04
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (29 bp):
AAAATTATAATAATAATAATAAAAACTAA
Found at i:22071024 original size:13 final size:13
Alignment explanation
Indices: 22070988--22071037 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
22070978 TTGGCAATGT
22070988 TTTTAAAAAGTGC
1 TTTTAAAAAGTGC
* *
22071001 TGTAAAAAAGTGC
1 TTTTAAAAAGTGC
*
22071014 TTTTAAGAAGTGC
1 TTTTAAAAAGTGC
*
22071027 TTTTGAAAAGT
1 TTTTAAAAAGT
22071038 TTAGTTTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (13 bp):
TTTTAAAAAGTGC
Found at i:22073331 original size:20 final size:20
Alignment explanation
Indices: 22073302--22073351 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
22073292 ATATAAACAT
22073302 TAAA-ATATAAAAAAGTAAA
1 TAAATATATAAAAAAGTAAA
22073321 TAAATATATAAAAAAGTAAA
1 TAAATATATAAAAAAGTAAA
22073341 -AATATATATAA
1 TAA-ATATATAA
22073352 TATGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (20 bp):
TAAATATATAAAAAAGTAAA
Found at i:22073404 original size:17 final size:16
Alignment explanation
Indices: 22073356--22073406 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 16
22073346 ATATAATATG
22073356 AAAAAATATAATTTAT
1 AAAAAATATAATTTAT
22073372 ----AA-ATAATTTAT
1 AAAAAATATAATTTAT
22073383 AAAAAATATAATTTATT
1 AAAAAATATAATTTA-T
22073400 AAAAAAT
1 AAAAAAT
22073407 TCAATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
11 9 0.31
12 2 0.07
15 2 0.07
16 8 0.28
17 8 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAAATATAATTTAT
Found at i:22076481 original size:20 final size:22
Alignment explanation
Indices: 22076456--22076500 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
22076446 ACATTAGAAA
22076456 ATAT-AAAAAT-AGAAATAAAT
1 ATATAAAAAATCAGAAATAAAT
*
22076476 ATATAAAAAATCAGAAATATAT
1 ATATAAAAAATCAGAAATAAAT
22076498 ATA
1 ATA
22076501 ATCTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 12 0.55
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
ATATAAAAAATCAGAAATAAAT
Found at i:22076501 original size:20 final size:20
Alignment explanation
Indices: 22076456--22076501 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
22076446 ACATTAGAAA
22076456 ATAT-AAAAATAGAAATAAAT
1 ATATAAAAAATAGAAAT-AAT
22076476 ATATAAAAAATCAGAAAT-AT
1 ATATAAAAAAT-AGAAATAAT
22076496 ATATAA
1 ATATAA
22076502 TCTAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.50
21 6 0.25
22 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
ATATAAAAAATAGAAATAAT
Found at i:22076652 original size:8 final size:7
Alignment explanation
Indices: 22076623--22076650 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
22076613 AGAAATTATA
22076623 AATTTTT
1 AATTTTT
22076630 AATTTTT
1 AATTTTT
22076637 AATTTTT
1 AATTTTT
22076644 AATTTTT
1 AATTTTT
22076651 TATATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:22076708 original size:17 final size:18
Alignment explanation
Indices: 22076686--22076729 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
22076676 ATTTCAAGTT
* *
22076686 TTTTTATACCTTTTTC-A
1 TTTTTATACATTTATCAA
22076703 TTTTTATAACATTTATCAA
1 TTTTTAT-ACATTTATCAA
22076722 TTTTTATA
1 TTTTTATA
22076730 TATTATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 8 0.35
19 8 0.35
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATACATTTATCAA
Found at i:22076761 original size:8 final size:8
Alignment explanation
Indices: 22076740--22076780 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
22076730 TATTATTTTG
22076740 AATTTTA-
1 AATTTTAT
22076747 AATTTTTAT
1 AA-TTTTAT
22076756 AATTTTAT
1 AATTTTAT
22076764 -ATTTTAT
1 AATTTTAT
22076771 AATTTTAT
1 AATTTTAT
22076779 AA
1 AA
22076781 AAAAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 9 0.29
8 20 0.65
9 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTTTAT
Found at i:22076768 original size:15 final size:16
Alignment explanation
Indices: 22076740--22076779 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
22076730 TATTATTTTG
*
22076740 AATTTTAAATTTTTAT
1 AATTTTATATTTTTAT
22076756 AATTTTATA-TTTTAT
1 AATTTTATATTTTTAT
22076771 AATTTTATA
1 AATTTTATA
22076780 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTATATTTTTAT
Found at i:22077093 original size:31 final size:32
Alignment explanation
Indices: 22077057--22077125 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
22077047 TTTTTAATAT
* * *
22077057 TATATATTATATGGATTAAAATGTAAAAAAA-
1 TATATATAATATAGATAAAAATGTAAAAAAAG
* *
22077088 TATATATAATATATATAAAAATTTAAAAAAAG
1 TATATATAATATAGATAAAAATGTAAAAAAAG
22077120 TATATA
1 TATATA
22077126 AATTTCAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (32 bp):
TATATATAATATAGATAAAAATGTAAAAAAAG
Found at i:22077193 original size:15 final size:15
Alignment explanation
Indices: 22077173--22077203 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22077163 ATTTTTTAGA
22077173 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
22077188 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
22077203 A
1 A
22077204 AAAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:22078377 original size:39 final size:39
Alignment explanation
Indices: 22078291--22078403 Score: 163
Period size: 39 Copynumber: 2.8 Consensus size: 39
22078281 ACAATATCGG
* *
22078291 TGGCATGCTTTACATGCAATCAACATGTACGGTAATATTCAA
1 TGGCATGC-TTACATGCAATC-A-ATATACGATAATATTCAA
* *
22078333 TGGCATGCTTACATGCAATCAATATACGATAATATTTAT
1 TGGCATGCTTACATGCAATCAATATACGATAATATTCAA
22078372 TGGCATGCTTACATGCAATCAATATACGATAA
1 TGGCATGCTTACATGCAATCAATATACGATAA
22078404 CAATCAGCAC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
39 46 0.69
40 1 0.01
41 12 0.18
42 8 0.12
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (39 bp):
TGGCATGCTTACATGCAATCAATATACGATAATATTCAA
Found at i:22079173 original size:26 final size:25
Alignment explanation
Indices: 22079144--22079225 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 25
22079134 TCAAACCTAA
22079144 TTTCTCCTTTTTCTTTTCTTTTCTTC
1 TTTCT-CTTTTTCTTTTCTTTTCTTC
*
22079170 TTTCT-TTCTTTCTATTTCGTTTCTTC
1 TTTCTCTT-TTTCT-TTTCTTTTCTTC
* *
22079196 TTTGTTTCTTTTTCTTGT-TTTTCTTTC
1 -TT-TCTCTTTTTCTTTTCTTTTC-TTC
22079223 TTT
1 TTT
22079226 TTATTTATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
24 2 0.04
25 6 0.13
26 22 0.48
27 7 0.15
28 7 0.15
29 2 0.04
ACGTcount: A:0.01, C:0.21, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTCTCTTTTTCTTTTCTTTTCTTC
Found at i:22079177 original size:11 final size:11
Alignment explanation
Indices: 22079158--22079243 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 11
22079148 TCCTTTTTCT
22079158 TTTCTTTTCTTC
1 TTTC-TTTCTTC
22079170 TTTCTTTCTTTC
1 TTTCTTTC-TTC
22079182 TATTTCGTTTCTTC
1 --TTTC-TTTCTTC
*
22079196 TTTGTTTCTT-
1 TTTCTTTCTTC
*
22079206 TTTC-TTGTT-
1 TTTCTTTCTTC
22079215 TTTCTTTCTT-
1 TTTCTTTCTTC
* *
22079225 TTTATTTATTC
1 TTTCTTTCTTC
*
22079236 TTTATTTC
1 TTTCTTTC
22079244 ATTTTATTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
9 8 0.13
10 15 0.25
11 17 0.28
12 10 0.16
14 7 0.11
15 4 0.07
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTCTTTCTTC
Found at i:22079403 original size:3 final size:3
Alignment explanation
Indices: 22079395--22079425 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
22079385 TTGATAAAAT
*
22079395 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
22079426 GTAAATATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:22082871 original size:27 final size:27
Alignment explanation
Indices: 22082814--22082865 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
22082804 AATATTTTTC
*
22082814 ATAT-TATAATTATATATTTATAACAA
1 ATATATATAATTATATAATTATAACAA
*
22082840 ATATATATAATTA-ATAATTATTACAA
1 ATATATATAATTATATAATTATAACAA
22082866 CCTATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATATATAATTATATAATTATAACAA
Found at i:22083617 original size:20 final size:19
Alignment explanation
Indices: 22083579--22083621 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
22083569 CACAATGTAA
*
22083579 TAATATATTTTAAAACTAT
1 TAATATATTATAAAACTAT
*
22083598 TAATATATGTATATAACTAT
1 TAATATAT-TATAAAACTAT
22083618 TAAT
1 TAAT
22083622 TAGTCCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (19 bp):
TAATATATTATAAAACTAT
Found at i:22097130 original size:40 final size:39
Alignment explanation
Indices: 22097067--22097199 Score: 129
Period size: 35 Copynumber: 3.6 Consensus size: 39
22097057 GGCAAAGTGC
*
22097067 GAAATGTTGGTATGGTA-TT---ATCCATACTGAGTTGT
1 GAAATGTAGGTATGGTATTTCAAATCCATACTGAGTTGT
**
22097102 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TCAAATCCATACTGAGTTGT
** * *
22097142 GAAATGTAGGTATGACATTTC----CCAAACCGAGTTGT
1 GAAATGTAGGTATGGTATTTCAAATCCATACTGAGTTGT
*
22097177 AAAATGTAGGTATGGTATTTCAA
1 GAAATGTAGGTATGGTATTTCAA
22097200 TGAGGAAAAC
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
35 44 0.56
36 1 0.01
37 1 0.01
39 2 0.03
40 31 0.39
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.34
Consensus pattern (39 bp):
GAAATGTAGGTATGGTATTTCAAATCCATACTGAGTTGT
Found at i:22098533 original size:13 final size:13
Alignment explanation
Indices: 22098517--22098550 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
22098507 TTTAATTAAA
22098517 TTAGTTAATTAGT
1 TTAGTTAATTAGT
*
22098530 TTAGATAATTAGT
1 TTAGTTAATTAGT
*
22098543 TTAATTAA
1 TTAGTTAA
22098551 AACAAACCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:22100044 original size:28 final size:28
Alignment explanation
Indices: 22100012--22100093 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
22100002 CCAATTTTGG
22100012 CCCACTCAACAATACCCAAAACCCCTAA
1 CCCACTCAACAATACCCAAAACCCCTAA
* *
22100040 CCCACTCAACAATACCCAAAACCCTTAG
1 CCCACTCAACAATACCCAAAACCCCTAA
22100068 CCCACTCAA-AATTAAACCCAAAACCC
1 CCCACTCAACAA-T--ACCCAAAACCC
22100094 AATTATATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.04
28 36 0.73
30 11 0.22
ACGTcount: A:0.43, C:0.44, G:0.01, T:0.12
Consensus pattern (28 bp):
CCCACTCAACAATACCCAAAACCCCTAA
Found at i:22101180 original size:3 final size:3
Alignment explanation
Indices: 22101172--22101228 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
22101162 CTTTATTAAA
* * * *
22101172 TAT TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAT CAA TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
22101217 TAT TAT TTT TAT
1 TAT TAT TAT TAT
22101229 ATATATTAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:22101193 original size:18 final size:18
Alignment explanation
Indices: 22101170--22101222 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
22101160 TTCTTTATTA
22101170 AATATTATTATTATT-TC
1 AATATTATTATTATTATC
*
22101187 TAATATTATTAATATTATC
1 -AATATTATTATTATTATC
22101206 AATATTATTATTATTAT
1 AATATTATTATTATTAT
22101223 TTTTATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 30 0.94
19 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTATTATTATC
Found at i:22101223 original size:9 final size:9
Alignment explanation
Indices: 22101164--22101223 Score: 68
Period size: 9 Copynumber: 6.6 Consensus size: 9
22101154 TTTTGTTTCT
22101164 TTATTAAATA
1 TTATT-AATA
*
22101174 TTATTATTA
1 TTATTAATA
22101183 TT-TCTAATA
1 TTAT-TAATA
22101192 TTATTAATA
1 TTATTAATA
*
22101201 TTATCAATA
1 TTATTAATA
*
22101210 TTATTATTA
1 TTATTAATA
22101219 TTATT
1 TTATT
22101224 TTTATATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
8 1 0.02
9 36 0.84
10 6 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATTAATA
Found at i:22101347 original size:12 final size:12
Alignment explanation
Indices: 22101314--22101463 Score: 75
Period size: 12 Copynumber: 12.3 Consensus size: 12
22101304 TTTCATATTG
22101314 TTATTATTAGTAT
1 TTATTATTA-TAT
*
22101327 TATAATATTATAT
1 T-TATTATTATAT
22101340 TTATTATTAATAT
1 TTATTATT-ATAT
22101353 TGGTA-TA-TAT-T
1 T--TATTATTATAT
22101364 TTATTA-TATAT
1 TTATTATTATAT
*
22101375 GTA-TATATATACT
1 TTATTAT-TATA-T
22101388 TT-TTA-TATA-
1 TTATTATTATAT
* **
22101397 GTATTATCGT-T
1 TTATTATTATAT
22101408 TCTATTATTATAT
1 T-TATTATTATAT
22101421 TTATTATTATAT
1 TTATTATTATAT
*
22101433 TTATTATTTTCACT
1 TTATTATTAT-A-T
*
22101447 ATTATTATTATTT
1 -TTATTATTATAT
22101460 TTAT
1 TTAT
22101464 CATTGTTATA
Statistics
Matches: 106, Mismatches: 13, Indels: 37
0.68 0.08 0.24
Matches are distributed among these distances:
9 3 0.03
10 10 0.09
11 10 0.09
12 43 0.41
13 19 0.18
14 10 0.09
15 11 0.10
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:22101360 original size:26 final size:24
Alignment explanation
Indices: 22101308--22101403 Score: 65
Period size: 26 Copynumber: 3.9 Consensus size: 24
22101298 CTTTAATTTC
*
22101308 ATATTGTTATTATTAGTATTATAAT
1 ATATT-TTATTATTAATATTATAAT
*
22101333 ATTATATTTATTATTAATATTGGT-AT
1 A-TAT-TTTATTATTAATATT-ATAAT
22101359 ATATTTTATTA-T-ATATGTATATAT
1 ATATTTTATTATTAATAT-TATA-AT
* *
22101383 ATACTTT-TTATATAGTATTAT
1 ATATTTTATTAT-TAATATTAT
22101404 CGTTTCTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
22 5 0.09
23 5 0.09
24 15 0.26
25 8 0.14
26 22 0.39
27 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (24 bp):
ATATTTTATTATTAATATTATAAT
Found at i:22101378 original size:20 final size:21
Alignment explanation
Indices: 22101318--22101432 Score: 70
Period size: 21 Copynumber: 5.7 Consensus size: 21
22101308 ATATTGTTAT
*
22101318 TATTAGTATTATAATAT-TATA
1 TATTATTATTAT-ATATGTATA
22101339 T-TTATTATTA-ATATTGGTATA
1 TATTATTATTATATA-T-GTATA
22101360 TATT-TTATTATATATGTATA
1 TATTATTATTATATATGTATA
*
22101380 TATATACTTTTTATATA-GTAT-
1 TAT-TA-TTATTATATATGTATA
**
22101401 TATCGTT-TCTAT-TAT-TATA
1 TATTATTAT-TATATATGTATA
22101420 T-TTATTATTATAT
1 TATTATTATTATAT
22101433 TTATTATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 28
0.69 0.06 0.26
Matches are distributed among these distances:
18 15 0.20
19 9 0.12
20 16 0.21
21 17 0.23
22 9 0.12
23 9 0.12
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (21 bp):
TATTATTATTATATATGTATA
Found at i:22101449 original size:21 final size:21
Alignment explanation
Indices: 22101412--22101451 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22101402 ATCGTTTCTA
*
22101412 TTATTATATTTATTATTATAT
1 TTATTATATTTACTATTATAT
22101433 TTATTAT-TTTCACTATTAT
1 TTATTATATTT-ACTATTAT
22101452 TATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTATATTTACTATTATAT
Found at i:22101709 original size:24 final size:25
Alignment explanation
Indices: 22101677--22101724 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
22101667 CATATATTTT
*
22101677 ATTATATTA-TATATATTTTTAATA
1 ATTACATTATTATATATTTTTAATA
*
22101701 ATTACATTATTTATGTATTTTTAA
1 ATTACATTA-TTATATATTTTTAA
22101725 CTCTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTACATTATTATATATTTTTAATA
Found at i:22101988 original size:28 final size:27
Alignment explanation
Indices: 22101929--22101993 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
22101919 TTCCGAATAC
* *
22101929 TATAT-TATTTTTTTTATATTATCTCA
1 TATATATATTTTTTTTATACTATATCA
*
22101955 TGTATATATTTTTTTTATAACTATAT--
1 TATATATATTTTTTTTAT-ACTATATCA
22101981 TATATATATTTTT
1 TATATATATTTTT
22101994 AATACCGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 16 0.48
27 12 0.36
28 5 0.15
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (27 bp):
TATATATATTTTTTTTATACTATATCA
Found at i:22102284 original size:2 final size:2
Alignment explanation
Indices: 22102277--22102325 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
22102267 CATTATCAAC
* * *
22102277 AT AT AT AT AT AT AT AT AT AT AT AT CT GT AT AT AT AT -T TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
22102318 GT AT AT AT
1 AT AT AT AT
22102326 TGTTATTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (2 bp):
AT
Found at i:22105857 original size:5 final size:5
Alignment explanation
Indices: 22105831--22105923 Score: 68
Period size: 5 Copynumber: 17.8 Consensus size: 5
22105821 CCTCTTATTT
22105831 TTTTA -TTTA TTCTTA TTTTTA TTTTA TTTTA TTTTA -TTTA TTTTTA
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
* *
22105877 TTTTTC TTTTGA TTTTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTT-A -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
22105924 GAAAGACATA
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
3 3 0.04
4 8 0.11
5 32 0.44
6 24 0.33
7 6 0.08
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Done.