Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 4 of 189
Found at i:1251284 original size:29 final size:30
Alignment explanation
Indices: 1251244--1251383 Score: 112
Period size: 29 Copynumber: 4.8 Consensus size: 30
1251234 GTGTATATTA
*
1251244 TATGCGAGCCTATAGT-CGAACCCTAGGAT
1 TATGCGAGCCTATAGTGCGAACCCTAAGAT
* * *
1251273 TATGCGAGCCTATA-TGTGAACCTTAAAAT
1 TATGCGAGCCTATAGTGCGAACCCTAAGAT
* * * * *
1251302 TATACGAGGCTATA-TGCGAACCTTAGGAA
1 TATGCGAGCCTATAGTGCGAACCCTAAGAT
* * *
1251331 CATGCAAGCCTACA-TGCGAACCCTAAG-T
1 TATGCGAGCCTATAGTGCGAACCCTAAGAT
*
1251359 ATATGCGTGCCTAT-GTGCGAACCCT
1 -TATGCGAGCCTATAGTGCGAACCCT
1251384 TGGTGCATGC
Statistics
Matches: 86, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
28 1 0.01
29 85 0.99
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
TATGCGAGCCTATAGTGCGAACCCTAAGAT
Found at i:1251412 original size:34 final size:34
Alignment explanation
Indices: 1251374--1251448 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
1251364 CGTGCCTATG
* * ***
1251374 TGCGAACCCTTGGTGCATGCGTGCCTATATGTCA
1 TGCGAACCCTAGGTACATGCAAACCTATATGTCA
*
1251408 TGCGAACCCTAGGTACATGTAAACCTATATGTCA
1 TGCGAACCCTAGGTACATGCAAACCTATATGTCA
1251442 TGCGAAC
1 TGCGAAC
1251449 TTGTAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (34 bp):
TGCGAACCCTAGGTACATGCAAACCTATATGTCA
Found at i:1253137 original size:3 final size:3
Alignment explanation
Indices: 1253123--1253172 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
1253113 AAATGACATT
* * *
1253123 TTA TTA TT- TTA TTA TTA TTG TTA TTA TTA ATA TTA TTG TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1253169 TTA T
1 TTA T
1253173 GAAATAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1253158 original size:18 final size:18
Alignment explanation
Indices: 1253126--1253167 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1253116 TGACATTTTA
*
1253126 TTATT-TTATTATTATTG
1 TTATTATTAATATTATTG
1253143 TTATTATTAATATTATTG
1 TTATTATTAATATTATTG
1253161 TTATTAT
1 TTATTAT
1253168 ATTATGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATTATTAATATTATTG
Found at i:1254910 original size:21 final size:21
Alignment explanation
Indices: 1254844--1254911 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1254834 CCTTCTGGGT
* *
1254844 TTCAGTTCAGCTATTTTGAGC
1 TTCAGTTTAGCTCTTTTGAGC
* * ** *
1254865 TTCAGTTTAACCCTAAT-AGGT
1 TTCAGTTTAGCTCTTTTGA-GC
1254886 TTCAGTTTAGCTCTTTTGAGC
1 TTCAGTTTAGCTCTTTTGAGC
1254907 TTCAG
1 TTCAG
1254912 ATTAACCCTT
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.43
Consensus pattern (21 bp):
TTCAGTTTAGCTCTTTTGAGC
Found at i:1254936 original size:42 final size:42
Alignment explanation
Indices: 1254818--1254938 Score: 163
Period size: 42 Copynumber: 2.9 Consensus size: 42
1254808 TTAACTCATA
* * *
1254818 TGAGTTTCAGATTAACCCTTCTGGGTTTCAGTTCAGCTATTT
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTTAGCTATTT
* * * *
1254860 TGAGCTTCAGTTTAACCCTAATAGGTTTCAGTTTAGCTCTTT
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTTAGCTATTT
1254902 TGAGCTTCAGATTAACCCTTATGGGTTTTC-GTTTAGC
1 TGAGCTTCAGATTAACCCTTATGGG-TTTCAGTTTAGC
1254939 ACTTATGTGC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 64 0.94
43 4 0.06
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (42 bp):
TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTTAGCTATTT
Found at i:1258705 original size:10 final size:11
Alignment explanation
Indices: 1258679--1258711 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1258669 CTCTACACTA
1258679 TTTCTCTTCAC
1 TTTCTCTTCAC
*
1258690 TTTCTCTT-AT
1 TTTCTCTTCAC
1258700 TTTCTCTTCAC
1 TTTCTCTTCAC
1258711 T
1 T
1258712 AACATATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTCTCTTCAC
Found at i:1260719 original size:18 final size:16
Alignment explanation
Indices: 1260694--1260727 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
1260684 TTTTTTTTTG
1260694 AAAAAATATTTATAAAA
1 AAAAAATATTTA-AAAA
1260711 AAAATAATATTTAAAAA
1 AAAA-AATATTTAAAAA
1260728 TCATACAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATATTTAAAAA
Found at i:1276881 original size:19 final size:18
Alignment explanation
Indices: 1276846--1276881 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1276836 GAAATTTTCA
*
1276846 TTAAATTAATCCTAAAAC
1 TTAAATTAAACCTAAAAC
1276864 TTAAATTAAACACTAAAA
1 TTAAATTAAAC-CTAAAA
1276882 AGTTAGCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAATTAAACCTAAAAC
Found at i:1277731 original size:19 final size:20
Alignment explanation
Indices: 1277701--1277738 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1277691 TTTAAAAATA
1277701 TTGAAAATATTTAAATTGAG
1 TTGAAAATATTTAAATTGAG
1277721 TTGAAAA-ATTTAAATTGA
1 TTGAAAATATTTAAATTGA
1277739 AGTGGAGCGA
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:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (20 bp):
TTGAAAATATTTAAATTGAG
Found at i:1279618 original size:21 final size:24
Alignment explanation
Indices: 1279594--1279638 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1279584 GAATCAAATT
1279594 ATTAT-TATTT-T-TATTAATTTA
1 ATTATATATTTCTATATTAATTTA
1279615 ATTATACTATTTCTATATTAATTT
1 ATTATA-TATTTCTATATTAATTT
1279639 TTTTATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
23 5 0.25
24 1 0.05
25 9 0.45
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATATATTTCTATATTAATTTA
Found at i:1280766 original size:19 final size:19
Alignment explanation
Indices: 1280712--1280768 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
1280702 AAAATAAAAG
1280712 AAAAAATTT-ATAAAAATC
1 AAAAAATTTAATAAAAATC
* * * *
1280730 ATAAAAATATATTTAAAATT
1 A-AAAAATTTAATAAAAATC
1280750 AAAAAATTTAATGAAAAAT
1 AAAAAATTTAAT-AAAAAT
1280769 TTATAATATA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 1 0.03
19 16 0.55
20 12 0.41
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAAATTTAATAAAAATC
Found at i:1282781 original size:30 final size:30
Alignment explanation
Indices: 1282747--1282805 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1282737 CAAATGGTCA
1282747 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
* *
1282777 TTGAACTATTTGAAAGTTTTTATTTAAGT
1 TTGAACTATTTAAAAGTTTTCATTTAAGT
1282806 TATTGGATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (30 bp):
TTGAACTATTTAAAAGTTTTCATTTAAGTC
Found at i:1284581 original size:17 final size:15
Alignment explanation
Indices: 1284549--1284583 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
1284539 GACAATTTTT
1284549 ATTTTAAAATTTTAA
1 ATTTTAAAATTTTAA
1284564 ATTTTATAAATTTATAA
1 ATTTTA-AAATTT-TAA
1284581 ATT
1 ATT
1284584 AATACGTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTAAAATTTTAA
Found at i:1290708 original size:15 final size:15
Alignment explanation
Indices: 1290688--1290722 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1290678 AAGTTAATCG
* *
1290688 AATGTGATTTTTTGT
1 AATGTGATTATTAGT
1290703 AATGTGATTATTAGT
1 AATGTGATTATTAGT
1290718 AATGT
1 AATGT
1290723 AATTGTCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (15 bp):
AATGTGATTATTAGT
Found at i:1292897 original size:15 final size:15
Alignment explanation
Indices: 1292879--1292908 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1292869 TAGCCCAACT
*
1292879 TTATTTACTAAAATA
1 TTATTTACCAAAATA
1292894 TTATTTACCAAAATA
1 TTATTTACCAAAATA
1292909 ATACGAGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATTTACCAAAATA
Found at i:1306352 original size:14 final size:14
Alignment explanation
Indices: 1306333--1306360 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1306323 TTAAAATTTC
1306333 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
1306347 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
1306361 TGCATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:1306400 original size:5 final size:5
Alignment explanation
Indices: 1306390--1306432 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
1306380 CATTTATATT
*
1306390 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTCAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1306433 TTATTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:1306642 original size:23 final size:22
Alignment explanation
Indices: 1306608--1306651 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1306598 TCGCGTTTCG
1306608 AAATTTTCGTGTCTTCAAAAAA
1 AAATTTTCGTGTCTTCAAAAAA
*
1306630 AAATTTCTCGTGTTTTCAAAAA
1 AAATTT-TCGTGTCTTCAAAAA
1306652 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTCGTGTCTTCAAAAAA
Found at i:1306650 original size:21 final size:21
Alignment explanation
Indices: 1306608--1306651 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1306598 TCGCGTTTCG
1306608 AAATTTTCGTGTCTTCAAAAAA
1 AAATTTTCGTGTCTTC-AAAAA
*
1306630 AAATTTCTCGTGTTTTCAAAAA
1 AAATTT-TCGTGTCTTCAAAAA
1306652 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
AAATTTTCGTGTCTTCAAAAA
Found at i:1306785 original size:18 final size:18
Alignment explanation
Indices: 1306764--1307252 Score: 185
Period size: 17 Copynumber: 26.8 Consensus size: 18
1306754 AGAAAATTTT
1306764 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
1306782 TCGTGTTTTCAAAAAATT-
1 TCGTGTTTTC-AAAAATTC
** * *
1306800 TTAT-TTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTC
1306817 TCGTGTTTTCTAAAAATT-
1 TCGTGTTTTC-AAAAATTC
* * * *
1306835 TCCAT-ATTTCTAAAATTT
1 T-CGTGTTTTCAAAAATTC
**
1306853 TCGTGTTTAAAAAAATT-
1 TCGTGTTTTCAAAAATTC
* *
1306870 TCGTATTTTCAAAAATTTTTTA
1 TCGTGTTTTCAAAAA----TTC
** * *
1306892 TTTTTTTTTCAACAATTC
1 TCGTGTTTTCAAAAATTC
* *
1306910 TCGAG-TTTCACAAATTC
1 TCGTGTTTTCAAAAATTC
* *
1306927 TCGTGTTTT-AAAATTTT
1 TCGTGTTTTCAAAAATTC
** *
1306944 TTATGTTTTAAAAAATAAATTTC
1 TCGTGTTTT---CAA-AAA-TTC
*
1306967 TCGTG-TTTCAAAAAAATTG
1 TCGTGTTTTC--AAAAATTC
* *
1306986 TCATGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
1307003 TCATG-TTTCTAAAATGT-
1 TCGTGTTTTCAAAAAT-TC
*
1307020 T--TGTATTTCAAAAAATCC
1 TCGTGT-TTTC-AAAAATTC
1307038 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* *
1307056 TCATG-TTT-AAAAAATC
1 TCGTGTTTTCAAAAATTC
1307072 TTCGTGTTTTC-AAAATTC
1 -TCGTGTTTTCAAAAATTC
* *
1307090 TAGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
*
1307107 TCATGTTTTCAAAAATTTC
1 TCGTGTTTTCAAAAA-TTC
* *
1307126 CCCTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
1307144 TCGTATTTT-GAAAATTT
1 TCGTGTTTTCAAAAATTC
*
1307161 TCTTGTTTTCAAAAAAAAAACTT-
1 TCGTGTTTTC-----AAAAA-TTC
*
1307184 TCGTGTTTT-ATAAA-TC
1 TCGTGTTTTCAAAAATTC
1307200 TCCGTGTTTTCAAAAAAATTC
1 T-CGTGTTTTC--AAAAATTC
* *
1307221 TCGT-CTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
1307238 TCGTGTTTTCAAAAA
1 TCGTGTTTTCAAAAA
1307253 ATTGACCTTG
Statistics
Matches: 350, Mismatches: 71, Indels: 100
0.67 0.14 0.19
Matches are distributed among these distances:
15 3 0.01
16 21 0.06
17 131 0.37
18 91 0.26
19 44 0.13
20 16 0.05
21 9 0.03
22 16 0.05
23 17 0.05
24 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:1306811 original size:35 final size:36
Alignment explanation
Indices: 1306769--1307175 Score: 154
Period size: 35 Copynumber: 11.3 Consensus size: 36
1306759 ATTTTTCGTG
*
1306769 TTTTCAAAAATTCTCGTGTTTTCAAAAAATTT-TAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
* * *
1306804 TTTTCAAAATTTTTCGTGTTTTCTAAAAATTTCCAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
* * *
1306840 ATTTCTAAAATTTTCGTG-TTTAAAAAAATTTCGTA-
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTC-TAT
** * * *
1306875 TTTTCAAAAATTTTTTATTTTTTTTTC-AACAATTCTCGA-
1 TTTTCAAAAA---TTT-TCGTGTTTTCAAAAAATT-TCTAT
* * * * *
1306914 GTTTCACAAATTCTCGTGTTTT--AAAATTTTTTAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
*
1306948 GTTTTAAAAAATAAATTTC-TCGTGTTTCAAAAAAATTGTC-AT
1 -TTTTCAAAAAT---TTTCGT-GT-TTTC-AAAAAATT-TCTAT
* * *
1306990 GTTTT-AAAAATTTTCATG-TTTC-TAAAATGTT-TGT
1 -TTTTCAAAAATTTTCGTGTTTTCAAAAAAT-TTCTAT
* **
1307024 ATTTCAAAAAATCCTCGTGTTTTC-AAAAA-TTCTCAT
1 TTTTC-AAAAATTTTCGTGTTTTCAAAAAATTTCT-AT
* * *
1307060 GTTTAAAAAATCTTCGTGTTTTC--AAAA-TTCTAGT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTA-T
* * **
1307094 GTTTCAAAAATTTTCATGTTTTC-AAAAATTTCCCCT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTT-CTAT
* * * *
1307130 GTTTTCAAAAATTCTCGTATTTT-GAAAATTTTCT-T
1 -TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
1307165 GTTTTCAAAAA
1 -TTTTCAAAAA
1307176 AAAAACTTTC
Statistics
Matches: 283, Mismatches: 56, Indels: 66
0.70 0.14 0.16
Matches are distributed among these distances:
33 6 0.02
34 43 0.15
35 108 0.38
36 40 0.14
37 27 0.10
38 13 0.05
39 21 0.07
40 5 0.02
41 6 0.02
42 13 0.05
43 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (36 bp):
TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
Found at i:1306895 original size:17 final size:17
Alignment explanation
Indices: 1306762--1306887 Score: 87
Period size: 18 Copynumber: 7.2 Consensus size: 17
1306752 TCAGAAAATT
*
1306762 TTTCGTGTTTTCAAAAA
1 TTTCGTATTTTCAAAAA
*
1306779 TTCTCGTGTTTTCAAAAAA
1 TT-TCGTATTTTC-AAAAA
*
1306798 TTT--TATTTTTCAAAATT
1 TTTCGTA-TTTTCAAAA-A
*
1306815 TTTCGTGTTTTCTAAAAA
1 TTTCGTATTTTC-AAAAA
* *
1306833 TTTC-CATATTTCTAAAAT
1 TTTCGTAT-TTTC-AAAAA
* **
1306851 TTTCGTGTTTAAAAAAA
1 TTTCGTATTTTCAAAAA
1306868 TTTCGTATTTTCAAAAA
1 TTTCGTATTTTCAAAAA
1306885 TTT
1 TTT
1306888 TTTATTTTTT
Statistics
Matches: 85, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
16 5 0.06
17 32 0.38
18 35 0.41
19 13 0.15
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (17 bp):
TTTCGTATTTTCAAAAA
Found at i:1307060 original size:70 final size:69
Alignment explanation
Indices: 1306978--1307142 Score: 172
Period size: 70 Copynumber: 2.3 Consensus size: 69
1306968 CGTGTTTCAA
* * *
1306978 AAAAATTGTCATGTTTTAAAAATTTTCATG-TTTCTAAAATGT-TTGTATTTCAAAAAATCCTCG
1 AAAAATTCTCATGTTTTAAAAATTTTCATGTTTTC-AAAAT-TCTAGTATTTC-AAAAATCCTCA
1307041 TGTTTTC
63 TGTTTTC
* * * * **
1307048 AAAAATTCTCATGTTTAAAAAATCTTCGTGTTTTCAAAATTCTAGTGTTTCAAAAATTTTCATGT
1 AAAAATTCTCATGTTTTAAAAATTTTCATGTTTTCAAAATTCTAGTATTTCAAAAATCCTCATGT
1307113 TTTC
66 TTTC
* *
1307117 AAAAATTTCCCCTGTTTTCAAAAATT
1 AAAAA-TTCTCATGTTTT-AAAAATT
1307143 CTCGTATTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
69 21 0.27
70 47 0.60
71 10 0.13
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.44
Consensus pattern (69 bp):
AAAAATTCTCATGTTTTAAAAATTTTCATGTTTTCAAAATTCTAGTATTTCAAAAATCCTCATGT
TTTC
Found at i:1307290 original size:37 final size:37
Alignment explanation
Indices: 1307099--1307308 Score: 128
Period size: 37 Copynumber: 5.6 Consensus size: 37
1307089 CTAGTGTTTC
* * * *
1307099 AAAAATTTTCATGTTTTCAAAAATTTCCCCTGTTTTC--
1 AAAAATTCTCGTG-TTTCATAAATTT-CCGTGTTTTCAA
* * * *
1307136 AAAAATTCTCGTATTTTGA-AAATTTTCTTGTTTTCAAAAA
1 AAAAATTCTCGT-GTTTCATAAATTTCCGTGTTTTC---AA
* *
1307176 AAAAACTT-TCGTGTTTTATAAATCTCCGTGTTTTCAA
1 AAAAA-TTCTCGTGTTTCATAAATTTCCGTGTTTTCAA
* * *
1307213 AAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTC-A
1 AAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTCAA
* *
1307249 AAAAATTGAC-CTTGTTTCATAAATTTCCGCG-TTTCAAAA
1 AAAAATT--CTCGTGTTTCATAAATTTCCGTGTTTTC--AA
*
1307288 AAAAATCCTCGTGTTTCATAA
1 AAAAATTCTCGTGTTTCATAA
1307309 TTTATCAAAA
Statistics
Matches: 135, Mismatches: 23, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
35 8 0.06
36 20 0.15
37 60 0.44
38 12 0.09
39 11 0.08
40 22 0.16
41 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (37 bp):
AAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTCAA
Found at i:1307346 original size:21 final size:19
Alignment explanation
Indices: 1307315--1307361 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
1307305 ATAATTTATC
*
1307315 AAAATTTTTGTGTTTTCAAA
1 AAAAATTTTGTGTTTT-AAA
1307335 ATAAAATTTTGTGTTTTAAA
1 A-AAAATTTTGTGTTTTAAA
1307355 AAAAATT
1 AAAAATT
1307362 CTCATGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 6 0.24
20 5 0.20
21 14 0.56
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (19 bp):
AAAAATTTTGTGTTTTAAA
Found at i:1307375 original size:17 final size:18
Alignment explanation
Indices: 1307355--1307397 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1307345 GTGTTTTAAA
1307355 AAAAATTCTCATG-TTTC
1 AAAAATTCTCATGTTTTC
* * *
1307372 AAAAACTGTCGTGTTTTC
1 AAAAATTCTCATGTTTTC
1307390 AAAAATTC
1 AAAAATTC
1307398 CCGTGTTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (18 bp):
AAAAATTCTCATGTTTTC
Found at i:1307436 original size:33 final size:32
Alignment explanation
Indices: 1307399--1307462 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1307389 CAAAAATTCC
*
1307399 CGTGTTAAAAAAATTTTGTGTTTTCGTGTTTTT
1 CGTGTTAAAAAAATTTCGTG-TTTCGTGTTTTT
**
1307432 CGTGTTTCAAAAATTTCGTGTTTCGTGTTTT
1 CGTGTTAAAAAAATTTCGTGTTTCGTGTTTT
1307463 CAAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.19, C:0.09, G:0.19, T:0.53
Consensus pattern (32 bp):
CGTGTTAAAAAAATTTCGTGTTTCGTGTTTTT
Found at i:1307459 original size:23 final size:25
Alignment explanation
Indices: 1307420--1307470 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
1307410 AATTTTGTGT
1307420 TTTCGTGTTTTTCGTG-TTTCAAAAA
1 TTTCGTG-TTTTCGTGTTTTCAAAAA
1307445 TTTCGTG-TTTCGTGTTTTCAAAAA
1 TTTCGTGTTTTCGTGTTTTCAAAAA
1307469 TT
1 TT
1307471 ATTATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.28
24 11 0.44
25 7 0.28
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.53
Consensus pattern (25 bp):
TTTCGTGTTTTCGTGTTTTCAAAAA
Found at i:1310518 original size:25 final size:25
Alignment explanation
Indices: 1310484--1310535 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1310474 TATGCTGCAA
1310484 TCTCGTCAACAACAATTAGATAACC
1 TCTCGTCAACAACAATTAGATAACC
1310509 TCTCGTCAACAACAATTAGATAACC
1 TCTCGTCAACAACAATTAGATAACC
1310534 TC
1 TC
1310536 GAGATTATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.29, G:0.08, T:0.25
Consensus pattern (25 bp):
TCTCGTCAACAACAATTAGATAACC
Found at i:1317675 original size:69 final size:68
Alignment explanation
Indices: 1317503--1317675 Score: 222
Period size: 68 Copynumber: 2.5 Consensus size: 68
1317493 CTTTCCAAGG
* **
1317503 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAGTTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAGTTTTT
1317568 TTC
66 TTC
* ** *
1317571 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAGTTT-T
1317636 GTTT-
65 -TTTC
* ** *
1317640 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1317676 TTTTCAATTT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
68 56 0.62
69 32 0.35
70 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (68 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAGTTTTT
TTC
Found at i:1317954 original size:75 final size:74
Alignment explanation
Indices: 1317677--1318257 Score: 669
Period size: 72 Copynumber: 7.8 Consensus size: 74
1317667 GTTAAGCCTT
* *
1317677 TTTCAATTTCTGTTTTTC---AAAATCAACTCATATTGCTAGAGGTGAGTTGGGCCTCAGGACAC
1 TTTCAATTTCTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1317739 GCTGAGGTAA
65 GCTGAGGTAA
* ** ** *
1317749 TTTCAATTTCTATTGTAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTCGAGCCTCAGGACA
1 TTTCAATTTCTGTT-T-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1317814 CGCTGAGGTAA
64 CGCTGAGGTAA
* * *
1317825 TTTCAATTTTTGTTTTTC---AAAATCAACTCATATTGCTAGAGGTGAGTTGGGCCTCAGGACAC
1 TTTCAATTTCTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1317887 GCTGAGGTAA
65 GCTGAGGTAA
* *
1317897 TTTCAATTTCTGTTGTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTCAATTTCTGTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
** *
1317962 ATTGAGGTAT
65 GCTGAGGTAA
* *
1317972 TTTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTCAATTTCTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* *
1318037 GTTGAGGTAT
65 GCTGAGGTAA
* * *
1318047 TTTCAATTCCTGTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTCAATTTCTGTT---TTCA-------AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1318112 TCAGGACACGCTGAGGTAA
56 TCAGGACACGCTGAGGTAA
* *
1318131 TTTCAATTTCTGTTTTTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
1 TTTCAATTTCTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* *
1318193 GCCGAGGTAT
65 GCTGAGGTAA
** *
1318203 TTTCAA-TTCTACTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCT
1 TTTCAATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1318258 TGGCTCACGT
Statistics
Matches: 440, Mismatches: 44, Indels: 49
0.83 0.08 0.09
Matches are distributed among these distances:
70 4 0.01
71 10 0.02
72 128 0.29
73 35 0.08
74 2 0.00
75 126 0.29
76 64 0.15
77 5 0.01
82 2 0.00
84 62 0.14
85 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (74 bp):
TTTCAATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
CTGAGGTAA
Found at i:1318120 original size:84 final size:84
Alignment explanation
Indices: 1317973--1318462 Score: 358
Period size: 73 Copynumber: 6.0 Consensus size: 84
1317963 TTGAGGTATT
* * *
1317973 TTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
1 TTCAATTTATGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
* *
1318038 TTGAGGTATTTTCAATTCCTG
64 CTGAGGTATTTTCAATTTCTG
1318059 TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1318124 GAGG-----T-AA----T-
66 GAGGTATTTTCAATTTCTG
* * * *
1318132 TTCAATTTCTGTTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCC
1 TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1318196 GAGGTATTTTCAATTCTACT-
66 GAGGTATTTTCAATT-T-CTG
* * *
1318216 TTC-A---A--------AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCT-TGGCTCACG-
1 TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGC
* *
1318267 TGTTGAGTCACTTTCAATTTCTG
65 TG-AG-GT-ATTTTCAATTTCTG
* * * *
1318290 TT---TTTATGTCTGTTTTC-TAAATCAACTCATGTTGCAAGAGGTGAGTTGAGCCTCAGGACAT
1 TTCAATTTATG--T-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
1318351 GCTGAGGTATTTTCCATTTCTG
63 GCTGAGGTATTTTCAATTTCTG
** * ** * * *
1318373 TTTTCGTTATTATGTTTTTGAAAGAATCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACA
1 --TTCAAT-TTATGTTTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
** *
1318438 CATTGAGGTAATTTCAATTTCTG
62 CGCTGAGGTATTTTCAATTTCTG
1318461 TT
1 TT
1318463 TTCAAAATTC
Statistics
Matches: 323, Mismatches: 39, Indels: 84
0.72 0.09 0.19
Matches are distributed among these distances:
72 51 0.16
73 58 0.18
74 6 0.02
75 10 0.03
77 1 0.00
78 4 0.01
79 1 0.00
83 13 0.04
84 55 0.17
85 39 0.12
86 25 0.08
87 2 0.01
88 53 0.16
89 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (84 bp):
TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
GAGGTATTTTCAATTTCTG
Found at i:1318284 original size:306 final size:299
Alignment explanation
Indices: 1317677--1318741 Score: 1086
Period size: 306 Copynumber: 3.5 Consensus size: 299
1317667 GTTAAGCCTT
* *
1317677 TTTCAATTTCTGTTTTTC---AAAATCAACTCATATTGCTAGAGGTGAGTTGGGCCTCAGGACAC
1 TTTCAATTTCTG-TTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * ****
1317739 GCTGAGGTAATTTCAA---T-TTCTAT-TGTAAAAAAAAAATCAACTCATATTGCGAGAAATGAG
65 GCTGAGGTATTTTCAATTCTGTTCTTTATGTTTTTAAAAAATCAACTCATATTGCGAGAAATGAG
* * *
1317799 TCGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTGTTTTTCAAAATCAACTCATATTGCTAG
130 TTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAG
* * *
1317864 AGGTGAGTTGGGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAAATCAACTC
195 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTCTT-TC-AAAAAAATCAACTC
* ** * *
1317929 ATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTAT
258 ATATTGCGAAAGGTGAGTTGAGCCT-TGGACACGTTGAGGTAA
*
1317972 TTTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTCAATTTCTG-TTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * **
1318037 GTTGAGGTATTTTCAATTCCTGTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGT
65 GCTGAGGTATTTTCAATT-CTGTTC--TTTATGTTTTTAAAAAATCAACTCATATTGCGAGAAAT
1318102 GAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAATCAACTCATATTGC
127 GAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAATCAACTCATATTGC
* * *
1318167 GAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAA-TTCTACTTTCAAAAAAATCAAC
192 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-CTTTCAAAAAAATCAAC
* *
1318231 TCATATTGCGAAAGGTGAGTTGAGCCTTGGCTCACGTGTTGA-GTCAC
256 TCATATTGCGAAAGGTGAGTTGAGCCTTGG-ACAC--GTTGAGGT-AA
* * * * *
1318278 TTTCAATTTCTGTTTTTATGTCTGTTTTCTAAATCAACTCATGTTGCAAGAGGTGAGTTGAGCCT
1 TTTCAATTTCTGTTTTCA----AG-----AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
1318343 CAGGACATGCTGAGGTATTTTCCATTTCTGTTTTCGTTATTATGTTTTTGAAAGAATCAACTCAT
57 CAGGACACGCTGAGGTATTTT-CAATTCTG--TTC--T-TTATGTTTTT-AAAAAATCAACTCAT
* * * **
1318408 ATTGCGAGAAATAAGTTGAGCCCCAAGACACATTGAGGTAATTTCAATTTCTG-TTTTCAAAATT
115 ATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAA-T
** * *
1318472 CAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTTT
179 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-C-TT
* *
1318537 TC--AAAATTCAACTCATATTGCAAGAAA--TGAGTTGAGCCTTAGGACACGCTGAGGTAA
242 TCAAAAAAATCAACTCATATTGC--GAAAGGTGAGTTGAGCCTT-GGACACGTTGAGGTAA
* * * * *
1318594 TTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGGCTCAC
1 TTTCAATTTCTGTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC
* * * * *
1318658 GTGCTGAGCTATTTTCAATTTCTATT-TTTAATGTCTAGTTTTAAAGAGTCAATTCATATTGCGA
65 --GCTGAGGTATTTTCAA-TTCTGTTCTTT-ATG--T--TTTTAAAAAATCAACTCATATTGCGA
1318722 GAAATGAGTTGAG-CTCAGGA
122 GAAATGAGTTGAGCCTCAGGA
1318742 TCACATGCCG
Statistics
Matches: 644, Mismatches: 80, Indels: 81
0.80 0.10 0.10
Matches are distributed among these distances:
295 17 0.03
298 55 0.09
302 1 0.00
303 6 0.01
304 45 0.07
305 15 0.02
306 153 0.24
307 68 0.11
308 6 0.01
309 17 0.03
314 54 0.08
315 4 0.01
316 25 0.04
317 21 0.03
318 142 0.22
319 7 0.01
320 8 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (299 bp):
TTTCAATTTCTGTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
CTGAGGTATTTTCAATTCTGTTCTTTATGTTTTTAAAAAATCAACTCATATTGCGAGAAATGAGT
TGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGA
GGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTCTTTCAAAAAAATCAACTCATA
TTGCGAAAGGTGAGTTGAGCCTTGGACACGTTGAGGTAA
Found at i:1318477 original size:318 final size:313
Alignment explanation
Indices: 1317994--1318576 Score: 814
Period size: 318 Copynumber: 1.8 Consensus size: 313
1317984 CTTTTCAAGA
* *
1317994 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTCCTG
1 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTCCTG
** * * * *
1318059 TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
66 TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACACACT
** **
1318124 GAGGTAATTTCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
131 GAGGTAATTTCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
*
1318189 GCACGCCGAGGTATTTTCAA-TTCTAC-TTTCAAAAAAATCAACTCATATTGC-GAAAGGTGAGT
196 ACACGCCGAGGTATTTTCAATTTCTACTTTTC--AAAAATCAACTCATATTGCAGAAA--TGAGT
1318251 TGAGCCTTGGCTCACGTGTTGAGTCACTTTCAATTTCTGTTTTTATGTCTGTTTTCT
257 TGAGCCTTGGCTCACGTGTTGAGTCACTTTCAATTTCTGTTTTTATGTCTGTTTTCT
* * * * *
1318308 AAATCAACTCATGTTGCAAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCCATTTCTG
1 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTCCTG
** *
1318373 TTTTCGTTATTATGTTTTTGAAAGAATCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACA
66 --TTCAAT-TTATGTTTTTCAAA-AATCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACA
*
1318438 CATTGAGGTAATTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCC
127 CACTGAGGTAATTTCAATTTCTGTTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCC
** * *
1318502 TCAAGACACGTTGAGGTATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCAAGAAATGA
191 TCAAGACACGCCGAGGTATTTTCAATTTCTACTTTTCAAAAATCAACTCATATTGC-AGAAATGA
1318567 GTTGAGCCTT
255 GTTGAGCCTT
1318577 AGGACACGCT
Statistics
Matches: 234, Mismatches: 26, Indels: 14
0.85 0.09 0.05
Matches are distributed among these distances:
314 58 0.25
316 4 0.02
317 22 0.09
318 137 0.59
319 5 0.02
320 8 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (313 bp):
AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTCCTG
TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACACACT
GAGGTAATTTCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
ACACGCCGAGGTATTTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCAGAAATGAGTTGAG
CCTTGGCTCACGTGTTGAGTCACTTTCAATTTCTGTTTTTATGTCTGTTTTCT
Found at i:1318571 original size:73 final size:72
Alignment explanation
Indices: 1318399--1318649 Score: 376
Period size: 73 Copynumber: 3.4 Consensus size: 72
1318389 TTTGAAAGAA
* * *
1318399 TCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
1318464 TCAAAAT
66 TCAAAAT
*
1318471 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT
1318536 TTCAAAAT
65 TTCAAAAT
* * * * *
1318544 TCAACTCATATTGCAAGAAATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
*
1318609 TCAAAAAAA
66 TC--AAAAT
*
1318618 TCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCT
1318650 TGGCTCACGT
Statistics
Matches: 163, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
72 62 0.38
73 67 0.41
74 34 0.21
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:1318963 original size:5 final size:5
Alignment explanation
Indices: 1318953--1318985 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1318943 CATTTATATT
*
1318953 TTTAA TTTAA TTTAA TTTAA TTTAA TTCAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1318986 TTATTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:1318992 original size:5 final size:5
Alignment explanation
Indices: 1318984--1319014 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1318974 TTAATTCAAT
1318984 TTTTA TTTTA TTTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA
1319015 AATACTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1318998 original size:11 final size:11
Alignment explanation
Indices: 1318982--1319014 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
1318972 ATTTAATTCA
1318982 ATTTTTATTTT
1 ATTTTTATTTT
1318993 ATTTTTATTTT
1 ATTTTTATTTT
1319004 A-TTTTATTTT
1 ATTTTTATTTT
1319014 A
1 A
1319015 AATACTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:1319215 original size:23 final size:22
Alignment explanation
Indices: 1319181--1319224 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1319171 TCGCGTTTCG
1319181 AAATTTTCGTGTCTTCAAAAAA
1 AAATTTTCGTGTCTTCAAAAAA
*
1319203 AAATTTCTCGTGTTTTCAAAAA
1 AAATTT-TCGTGTCTTCAAAAA
1319225 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTCGTGTCTTCAAAAAA
Found at i:1319223 original size:21 final size:21
Alignment explanation
Indices: 1319181--1319224 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1319171 TCGCGTTTCG
1319181 AAATTTTCGTGTCTTCAAAAAA
1 AAATTTTCGTGTCTTC-AAAAA
*
1319203 AAATTTCTCGTGTTTTCAAAAA
1 AAATTT-TCGTGTCTTCAAAAA
1319225 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
AAATTTTCGTGTCTTCAAAAA
Found at i:1319358 original size:18 final size:18
Alignment explanation
Indices: 1319337--1319824 Score: 174
Period size: 17 Copynumber: 26.8 Consensus size: 18
1319327 AGAAAATTTT
1319337 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
1319355 TCGTGTTTTCAAAAAATT-
1 TCGTGTTTTC-AAAAATTC
** * *
1319373 TTAT-TTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTC
1319390 TCGTGTTTTCTAAAAATT-
1 TCGTGTTTTC-AAAAATTC
* * * *
1319408 TCCAT-ATTTCTAAAATTT
1 T-CGTGTTTTCAAAAATTC
**
1319426 TCGTGTTTAAAAAAATT-
1 TCGTGTTTTCAAAAATTC
* * *
1319443 TCATATTTTCAAAAATTTTT
1 TCGTGTTTTCAAAAA--TTC
** * *
1319463 TATTTTTTTTCAACAATTC
1 T-CGTGTTTTCAAAAATTC
* *
1319482 TCGAG-TTTCACAAATTC
1 TCGTGTTTTCAAAAATTC
* *
1319499 TCGTGTTTT-AAAATTTT
1 TCGTGTTTTCAAAAATTC
** *
1319516 TTATGTTTTAAAAAATAAATTTC
1 TCGTGTTTT---CAA-AAA-TTC
*
1319539 TCGTG-TTTCAAAAAAATTG
1 TCGTGTTTTC--AAAAATTC
* *
1319558 TCATGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
1319575 TCATG-TTTCTAAAATGT-
1 TCGTGTTTTCAAAAAT-TC
*
1319592 T--TGTATTTCAAAAAATCC
1 TCGTGT-TTTC-AAAAATTC
1319610 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* *
1319628 TCATG-TTT-AAAAAATC
1 TCGTGTTTTCAAAAATTC
1319644 TTCGTGTTTTC-AAAATTC
1 -TCGTGTTTTCAAAAATTC
* *
1319662 TAGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
*
1319679 TCATGTTTTCAAAAATTTC
1 TCGTGTTTTCAAAAA-TTC
* *
1319698 CCCTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
1319716 TCGTATTTT-GAAAATTT
1 TCGTGTTTTCAAAAATTC
*
1319733 TCTTGTTTTCAAAAAAAAAACTT-
1 TCGTGTTTTC-----AAAAA-TTC
*
1319756 TCGTGTTTT-ATAAA-TC
1 TCGTGTTTTCAAAAATTC
*
1319772 TCCGTATTTTCAAAAAAATTC
1 T-CGTGTTTTC--AAAAATTC
* *
1319793 TCGTCTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTC
1319810 TCGTGTTTTCAAAAA
1 TCGTGTTTTCAAAAA
1319825 ATTGACCTTG
Statistics
Matches: 348, Mismatches: 73, Indels: 98
0.67 0.14 0.19
Matches are distributed among these distances:
15 3 0.01
16 21 0.06
17 133 0.38
18 84 0.24
19 45 0.13
20 21 0.06
21 17 0.05
22 5 0.01
23 17 0.05
24 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.47
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:1319380 original size:17 final size:17
Alignment explanation
Indices: 1319360--1319469 Score: 53
Period size: 18 Copynumber: 6.2 Consensus size: 17
1319350 AATTCTCGTG
1319360 TTTTCAAAAAATTTTAT
1 TTTTCAAAAAATTTTAT
* *
1319377 TTTTC-AAAATTTTTCGT
1 TTTTCAAAAAATTTT-AT
* *
1319394 GTTTTCTAAAAATTTCCAT
1 -TTTTCAAAAAATTT-TAT
* * *
1319413 ATTTC-TAAAATTTTCGT
1 TTTTCAAAAAATTTT-AT
* * *
1319430 GTTTAAAAAAATTTCAT
1 TTTTCAAAAAATTTTAT
*
1319447 ATTTTCAAAAATTTTTTAT
1 -TTTTCAAAAA-ATTTTAT
1319466 TTTT
1 TTTT
1319470 TTTCAACAAT
Statistics
Matches: 67, Mismatches: 18, Indels: 15
0.67 0.18 0.15
Matches are distributed among these distances:
16 8 0.12
17 18 0.27
18 28 0.42
19 13 0.19
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTTCAAAAAATTTTAT
Found at i:1319384 original size:35 final size:35
Alignment explanation
Indices: 1319342--1319747 Score: 165
Period size: 35 Copynumber: 11.3 Consensus size: 35
1319332 ATTTTTCGTG
* *
1319342 TTTTCAAAAATTCTCGTGTTTTCAAAAAATTTTAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCAT
* *
1319377 TTTTCAAAATTTTTCGTGTTTTCTAAAAATTTCCAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTT-CAT
* * *
1319413 ATTTCTAAAATTTTCGTG-TTTAAAAAAATTTCAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCAT
** * *
1319447 ATTTTCAAAAATTTTTTATTTTTTTTC-AACAATTCTCGA-
1 -TTTTCAAAAA--TTTT-CGTGTTTTCAAAAAATT-TC-AT
* * * ** *
1319486 GTTTCACAAATTCTCGTGTTTT-AAAATTTTTTAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCAT
*
1319520 GTTTTAAAAAATAAATTTC-TCGTGTTTCAAAAAAATTGTCAT
1 -TTTTCAAAAAT---TTTCGT-GT-TTTC-AAAAAATT-TCAT
* * **
1319562 GTTTT-AAAAATTTTCATG-TTTC-TAAAATGTTTGT
1 -TTTTCAAAAATTTTCGTGTTTTCAAAAAAT-TTCAT
* **
1319596 ATTTCAAAAAATCCTCGTGTTTTC-AAAAATTCTCAT
1 TTTTC-AAAAATTTTCGTGTTTTCAAAAAATT-TCAT
* * *
1319632 GTTTAAAAAATCTTCGTGTTTTC--AAAA-TTCTAGT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTC-A-T
* * *
1319666 GTTTCAAAAATTTTCATGTTTTC-AAAAATTTCCCCT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTT--CAT
* * * * *
1319702 GTTTTCAAAAATTCTCGTATTTT-GAAAATTTTCTT
1 -TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCAT
1319737 GTTTTCAAAAA
1 -TTTTCAAAAA
1319748 AAAAACTTTC
Statistics
Matches: 282, Mismatches: 56, Indels: 66
0.70 0.14 0.16
Matches are distributed among these distances:
32 2 0.01
33 6 0.02
34 36 0.13
35 111 0.39
36 41 0.15
37 30 0.11
38 26 0.09
39 9 0.03
40 1 0.00
41 12 0.04
42 8 0.03
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (35 bp):
TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCAT
Found at i:1319913 original size:21 final size:19
Alignment explanation
Indices: 1319887--1319932 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 19
1319877 ATAATTTATC
1319887 AAAATTTTGTGTTTTCAAAA
1 AAAATTTTGTGTTTT-AAAA
1319907 TAAAATTTTGTGTTTTAAAA
1 -AAAATTTTGTGTTTTAAAA
1319927 AAAATT
1 AAAATT
1319933 CTCATGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 15 0.60
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (19 bp):
AAAATTTTGTGTTTTAAAA
Found at i:1319946 original size:17 final size:18
Alignment explanation
Indices: 1319926--1319968 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1319916 GTGTTTTAAA
1319926 AAAAATTCTCATG-TTTC
1 AAAAATTCTCATGTTTTC
* * *
1319943 AAAAACTGTCGTGTTTTC
1 AAAAATTCTCATGTTTTC
1319961 AAAAATTC
1 AAAAATTC
1319969 CCGTGTTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (18 bp):
AAAAATTCTCATGTTTTC
Found at i:1320022 original size:18 final size:19
Alignment explanation
Indices: 1319990--1320043 Score: 85
Period size: 17 Copynumber: 2.9 Consensus size: 19
1319980 AAATTTTGTG
1319990 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
1320009 TTTTCGTG-TTTC-AAAAA
1 TTTTCGTGTTTTCAAAAAA
*
1320026 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
1320044 TTATTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 12 0.38
18 8 0.25
19 12 0.38
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (19 bp):
TTTTCGTGTTTTCAAAAAA
Found at i:1320026 original size:17 final size:18
Alignment explanation
Indices: 1319990--1320045 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
1319980 AAATTTTGTG
1319990 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
1320009 TTTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
1320026 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
1320044 TT
1 TT
1320046 ATTATTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 12 0.35
18 14 0.41
19 8 0.24
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:1328931 original size:16 final size:18
Alignment explanation
Indices: 1328910--1328945 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1328900 TTTAATAATA
1328910 AAAG-AAATTTGG-AAAC
1 AAAGAAAATTTGGTAAAC
1328926 AAAGAAAATTTGGTAAAC
1 AAAGAAAATTTGGTAAAC
1328944 AA
1 AA
1328946 GCCTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (18 bp):
AAAGAAAATTTGGTAAAC
Found at i:1337744 original size:7 final size:7
Alignment explanation
Indices: 1337720--1337753 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1337710 CTCAAACATA
1337720 TTATTTT
1 TTATTTT
* *
1337727 TAATATT
1 TTATTTT
1337734 TTATTTT
1 TTATTTT
1337741 TTATTTT
1 TTATTTT
1337748 TTATTT
1 TTATTT
1337754 AGTCATTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
TTATTTT
Found at i:1343690 original size:16 final size:16
Alignment explanation
Indices: 1343666--1343706 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1343656 TTTGGATCGG
*
1343666 GTTAATTTGAGTTTAA
1 GTTATTTTGAGTTTAA
*
1343682 GTTATTTTGAGTTTAG
1 GTTATTTTGAGTTTAA
1343698 GTTAATTTT
1 GTT-ATTTT
1343707 TAGCTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (16 bp):
GTTATTTTGAGTTTAA
Found at i:1348819 original size:10 final size:10
Alignment explanation
Indices: 1348788--1348820 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1348778 CATCATTGTA
1348788 TTAAATT-AT
1 TTAAATTAAT
1348797 TTAAATATAAT
1 TTAAAT-TAAT
1348808 TTAAATTAAT
1 TTAAATTAAT
1348818 TTA
1 TTA
1348821 TATTTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 8 0.36
11 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:1350693 original size:6 final size:6
Alignment explanation
Indices: 1350687--1350752 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
1350677 CTCATCGTCG
* * * * * * * *
1350687 TCATCG TCATCT TCATCT TCATCT TCATCA TCGTCC TCGTCC ACATCA
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
1350735 TCATCT TCATCT TCATCT
1 TCATCT TCATCT TCATCT
1350753 ACTATCTCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.18, C:0.36, G:0.05, T:0.41
Consensus pattern (6 bp):
TCATCT
Found at i:1350708 original size:18 final size:18
Alignment explanation
Indices: 1350666--1350751 Score: 73
Period size: 18 Copynumber: 4.8 Consensus size: 18
1350656 GGTCTTACTT
* * *
1350666 TCTTCATCATCCTCATCG
1 TCTTCATCTTCATCATCA
* * *
1350684 TCGTCATCGTCATCTTCA
1 TCTTCATCTTCATCATCA
*
1350702 TCTTCATCTTCATCATCG
1 TCTTCATCTTCATCATCA
* * **
1350720 TCCTCGTCCACATCATCA
1 TCTTCATCTTCATCATCA
1350738 TCTTCATCTTCATC
1 TCTTCATCTTCATC
1350752 TACTATCTCT
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (18 bp):
TCTTCATCTTCATCATCA
Found at i:1350718 original size:36 final size:36
Alignment explanation
Indices: 1350666--1350751 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
1350656 GGTCTTACTT
* * * ** *
1350666 TCTTCATCATCCTCATCGTCGTCATCGTCATCTTCA
1 TCTTCATCTTCATCATCGTCCTCATCCACATCATCA
*
1350702 TCTTCATCTTCATCATCGTCCTCGTCCACATCATCA
1 TCTTCATCTTCATCATCGTCCTCATCCACATCATCA
1350738 TCTTCATCTTCATC
1 TCTTCATCTTCATC
1350752 TACTATCTCT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (36 bp):
TCTTCATCTTCATCATCGTCCTCATCCACATCATCA
Found at i:1350727 original size:42 final size:42
Alignment explanation
Indices: 1350666--1350752 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
1350656 GGTCTTACTT
** *
1350666 TCTTCATCATCCTCATCGTCGTCATCGTCATCTTCATCTTCA
1 TCTTCATCATCCTCATCGTCCACATCATCATCTTCATCTTCA
* *
1350708 TCTTCATCATCGTCCTCGTCCACATCATCATCTTCATCTTCA
1 TCTTCATCATCCTCATCGTCCACATCATCATCTTCATCTTCA
1350750 TCT
1 TCT
1350753 ACTATCTCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (42 bp):
TCTTCATCATCCTCATCGTCCACATCATCATCTTCATCTTCA
Found at i:1351717 original size:39 final size:39
Alignment explanation
Indices: 1351674--1351755 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
1351664 TTTTCATGGC
1351674 AGTAAGCCAAAAATCAGGTACTCCTTTCTCTGCATATAA
1 AGTAAGCCAAAAATCAGGTACTCCTTTCTCTGCATATAA
1351713 AGTAAGCCAAAAATCAGGTACTCCTTTCTCTGCATATAA
1 AGTAAGCCAAAAATCAGGTACTCCTTTCTCTGCATATAA
1351752 AGTA
1 AGTA
1351756 TAATTGCATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (39 bp):
AGTAAGCCAAAAATCAGGTACTCCTTTCTCTGCATATAA
Found at i:1364385 original size:13 final size:13
Alignment explanation
Indices: 1364367--1364393 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1364357 TAGCATGATA
1364367 TAGTAAAAACGCC
1 TAGTAAAAACGCC
1364380 TAGTAAAAACGCC
1 TAGTAAAAACGCC
1364393 T
1 T
1364394 CAAACTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (13 bp):
TAGTAAAAACGCC
Found at i:1365558 original size:53 final size:54
Alignment explanation
Indices: 1365445--1365558 Score: 203
Period size: 54 Copynumber: 2.1 Consensus size: 54
1365435 ATTACAATGA
*
1365445 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATATTTTT
1 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATAATTTT
*
1365499 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGTATTTCA-AATTTT
1 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATAATTTT
1365552 TATTTTC
1 TATTTTC
1365559 CAAAATTGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 12 0.21
54 46 0.79
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (54 bp):
TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATAATTTT
Found at i:1365846 original size:47 final size:47
Alignment explanation
Indices: 1365772--1365861 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
1365762 AGTATTTTCT
* * *
1365772 GTCAAAATTTGCCATCAATACAGCTATGCTATCATACTAACTTTAGA
1 GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTTTAGA
* * *
1365819 GTCAAAATTTACCATCAATGCACCTATGCAATGATATTAACTT
1 GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTT
1365862 CCAGAAGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (47 bp):
GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTTTAGA
Found at i:1374591 original size:19 final size:19
Alignment explanation
Indices: 1374567--1374612 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1374557 TCACAAAAAT
1374567 AAAAAAATTAAATTTTCAA
1 AAAAAAATTAAATTTTCAA
1374586 AAAAAAATTAAATTTTCAA
1 AAAAAAATTAAATTTTCAA
*
1374605 ATAAAAAT
1 AAAAAAAT
1374613 AAGGAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAAATTAAATTTTCAA
Found at i:1374887 original size:20 final size:20
Alignment explanation
Indices: 1374848--1374887 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1374838 TTTCTAAAAA
**
1374848 ATTTTATGAACTTTTTATAT
1 ATTTTATGAACTTTGAATAT
*
1374868 ATTTTTTGAACTTTGAATAT
1 ATTTTATGAACTTTGAATAT
1374888 TATTGTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (20 bp):
ATTTTATGAACTTTGAATAT
Found at i:1375762 original size:21 final size:20
Alignment explanation
Indices: 1375736--1375774 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1375726 TTACAATTCC
*
1375736 ATTTTAAACATAATGTTAAAA
1 ATTTTAAAAATAAT-TTAAAA
1375757 ATTTTAAAAATAATTTAA
1 ATTTTAAAAATAATTTAA
1375775 TGTAGTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
ATTTTAAAAATAATTTAAAA
Found at i:1380501 original size:6 final size:6
Alignment explanation
Indices: 1380492--1380519 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1380482 CCTCTCTAGA
1380492 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1380520 ATTTTTCGTC
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:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:1390428 original size:21 final size:18
Alignment explanation
Indices: 1390381--1390439 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
1390371 TATTATGCCA
1390381 AAAAAATAATTTAAAAATT
1 AAAAAAT-ATTTAAAAATT
*
1390400 ACAAAATATTTAAAGAAATCT
1 AAAAAATATTT-AA-AAAT-T
1390421 AAAAAATA--TAAAAATT
1 AAAAAATATTTAAAAATT
1390437 AAA
1 AAA
1390440 GATTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 6 0.17
19 9 0.26
20 4 0.11
21 8 0.23
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAAATATTTAAAAATT
Found at i:1391502 original size:22 final size:20
Alignment explanation
Indices: 1391454--1391490 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1391444 TATATGAATA
*
1391454 AAATATATAAAAATTATTTT
1 AAATATATAAAAATGATTTT
1391474 AAATATATAAAAA-GATT
1 AAATATATAAAAATGATT
1391491 ATTAGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATATAAAAATGATTTT
Found at i:1402813 original size:14 final size:15
Alignment explanation
Indices: 1402774--1402815 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1402764 AGAAAAACTA
*
1402774 AATGAAAAATAGAGG
1 AATGAAAAAAAGAGG
1402789 AA-GAAACAAAAGA-G
1 AATGAAA-AAAAGAGG
1402803 AATGAAAAAAAGA
1 AATGAAAAAAAGA
1402816 AAAAAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.69, C:0.02, G:0.21, T:0.07
Consensus pattern (15 bp):
AATGAAAAAAAGAGG
Found at i:1408343 original size:19 final size:19
Alignment explanation
Indices: 1408319--1408355 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1408309 AGTCACCATA
1408319 CAAGAAAA-CAACCAAAAAG
1 CAAGAAAATCAA-CAAAAAG
1408338 CAAGAAAATCAACAAAAA
1 CAAGAAAATCAACAAAAA
1408356 TTGAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.70, C:0.19, G:0.08, T:0.03
Consensus pattern (19 bp):
CAAGAAAATCAACAAAAAG
Found at i:1424097 original size:30 final size:30
Alignment explanation
Indices: 1424061--1424145 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
1424051 CTTGACATTA
1424061 AGATGCTTGTGTCTTTCTATTTTCTACTTC
1 AGATGCTTGTGTCTTTCTATTTTCTACTTC
1424091 AGATGCTTGTGTCTTTCTATTTTCTACTTC
1 AGATGCTTGTGTCTTTCTATTTTCTACTTC
*
1424121 AGATGCTTGTGTCTTTCTAGTTTCT
1 AGATGCTTGTGTCTTTCTATTTTCT
1424146 TCTCTATCTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.13, C:0.19, G:0.15, T:0.53
Consensus pattern (30 bp):
AGATGCTTGTGTCTTTCTATTTTCTACTTC
Found at i:1430987 original size:19 final size:19
Alignment explanation
Indices: 1430963--1431002 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1430953 TGGGTTCGAG
1430963 ATAGTTTCAAGTTCAAGTT
1 ATAGTTTCAAGTTCAAGTT
1430982 ATAGTTTCAAGTTCAAGTT
1 ATAGTTTCAAGTTCAAGTT
1431001 AT
1 AT
1431003 TTCAGGGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (19 bp):
ATAGTTTCAAGTTCAAGTT
Found at i:1444504 original size:15 final size:16
Alignment explanation
Indices: 1444484--1444513 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1444474 TTGATGGTGA
1444484 AATTAAA-TTAAATTG
1 AATTAAATTTAAATTG
1444499 AATTAAATTTAAATT
1 AATTAAATTTAAATT
1444514 TATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATTAAATTTAAATTG
Found at i:1445223 original size:7 final size:8
Alignment explanation
Indices: 1445205--1445229 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1445195 ATTGTTAAGA
1445205 TTTTATGT
1 TTTTATGT
1445213 TTTTATGT
1 TTTTATGT
1445221 TTTTATGT
1 TTTTATGT
1445229 T
1 T
1445230 AGTATAATTA
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:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TTTTATGT
Found at i:1448450 original size:3 final size:3
Alignment explanation
Indices: 1448442--1448467 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1448432 AACCATTTCA
1448442 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1448468 AAAAAACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1454753 original size:23 final size:23
Alignment explanation
Indices: 1454715--1454760 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1454705 GAGACCAAAT
*
1454715 TTAATTTGAAAAAAAATA-AAAA
1 TTAAATTGAAAAAAAATATAAAA
1454737 TTAAATTGAAAAAAAAATATAAAA
1 TTAAATTG-AAAAAAAATATAAAA
1454761 ATTGGGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (23 bp):
TTAAATTGAAAAAAAATATAAAA
Found at i:1461034 original size:11 final size:11
Alignment explanation
Indices: 1461020--1461045 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1461010 TTTTTTTTAA
1461020 TTTTAAAATAC
1 TTTTAAAATAC
1461031 TTTTAAAATAC
1 TTTTAAAATAC
1461042 TTTT
1 TTTT
1461046 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:1461084 original size:29 final size:29
Alignment explanation
Indices: 1461031--1461137 Score: 135
Period size: 29 Copynumber: 3.6 Consensus size: 29
1461021 TTTAAAATAC
*
1461031 TTTTAAAATACTTTTTTTAAAATTTTTTTAA
1 TTTTAAAATAC--ATTTTAAAATTTTTTTAA
1461062 TTTTAAAATACATTTTAAAATTTTTTTAA
1 TTTTAAAATACATTTTAAAATTTTTTTAA
*
1461091 TTTTAAAATA-TTTTTAAAATATTTTTTTAA
1 TTTTAAAATACATTTT-AAA-ATTTTTTTAA
*
1461121 TTTTTAAAATATATTTT
1 -TTTTAAAATACATTTT
1461138 TGGTATTTAT
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
28 4 0.06
29 30 0.43
30 10 0.14
31 21 0.30
32 4 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTAAAATACATTTTAAAATTTTTTTAA
Found at i:1461119 original size:13 final size:11
Alignment explanation
Indices: 1461091--1461137 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1461081 ATTTTTTTAA
1461091 TTTTAAAATAT
1 TTTTAAAATAT
1461102 TTTTAAAATAT
1 TTTTAAAATAT
**
1461113 TTTT-TTA-AT
1 TTTTAAAATAT
1461122 TTTTAAAATAT
1 TTTTAAAATAT
1461133 ATTTT
1 -TTTT
1461138 TGGTATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 17 0.59
12 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1461123 original size:20 final size:21
Alignment explanation
Indices: 1461100--1461138 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1461090 ATTTTAAAAT
1461100 ATTTTTAAAATAT-TTTTTTA
1 ATTTTTAAAATATATTTTTTA
1461120 ATTTTTAAAATATATTTTT
1 ATTTTTAAAATATATTTTT
1461139 GGTATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTAAAATATATTTTTTA
Found at i:1465841 original size:29 final size:29
Alignment explanation
Indices: 1465809--1465866 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1465799 GAATAGTTAA
* *
1465809 GTGACCATTTTATAACTTTTCACAGTTGG
1 GTGACAATTTTACAACTTTTCACAGTTGG
* *
1465838 GTGACAATTTTGCAACTTTTCATAGTTGG
1 GTGACAATTTTACAACTTTTCACAGTTGG
1465867 ATGATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (29 bp):
GTGACAATTTTACAACTTTTCACAGTTGG
Found at i:1467817 original size:29 final size:29
Alignment explanation
Indices: 1467783--1467838 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1467773 TTTGATTCTT
* *
1467783 TTTAATGGTATAGGGACTAAATTGATCCA
1 TTTAATAGTAGAGGGACTAAATTGATCCA
*
1467812 TTTAATAGTAGAGGGACTAATTTGATC
1 TTTAATAGTAGAGGGACTAAATTGATC
1467839 AGATCTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TTTAATAGTAGAGGGACTAAATTGATCCA
Found at i:1467858 original size:31 final size:29
Alignment explanation
Indices: 1467794--1467859 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1467784 TTAATGGTAT
*
1467794 AGGGACTAAATTGATCCATTTAATAGTAG
1 AGGGACTAAATTGATCCATTTAATAATAG
* * *
1467823 AGGGACTAATTTGATCAGATCTTTATAATAG
1 AGGGACTAAATTGATC-CAT-TTAATAATAG
1467854 AGGGAC
1 AGGGAC
1467860 CTCCCAGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.48
30 2 0.06
31 14 0.45
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (29 bp):
AGGGACTAAATTGATCCATTTAATAATAG
Found at i:1469779 original size:29 final size:28
Alignment explanation
Indices: 1469735--1469806 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
1469725 ACACTAAATT
* *
1469735 TTTTTA-ATTT-AGAATTTAGTCCACTTA
1 TTTTTATATTTAAAAATTTAATCC-CTTA
* * *
1469762 TTTTTATTTTTAAAAATTTAATCCTTTT
1 TTTTTATATTTAAAAATTTAATCCCTTA
1469790 TTTTTATATTTAAAAAT
1 TTTTTATATTTAAAAAT
1469807 GTAAATTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 6 0.16
28 21 0.57
29 10 0.27
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTTATATTTAAAAATTTAATCCCTTA
Found at i:1469848 original size:138 final size:138
Alignment explanation
Indices: 1469600--1469851 Score: 343
Period size: 138 Copynumber: 1.8 Consensus size: 138
1469590 AGATTCTTAA
* *
1469600 TTAATTTAGAATTTAGTTCATCTATTTTTACTTTTAGAAATTTAATCTCTTTATTTTTCGAATTT
1 TTAATTTAGAATTTAGTCCATCTATTTTTACTTTTAAAAATTTAATCTCTTTATTTTTCGAATTT
* * *
1469665 AAAACGTAAGTCTAATTATTAATATTATTAAAATTCTTTTTTAAATTCAAATAAATTACAACACT
66 AAAACGTAAGTCTAATTACTAATACTATTAAAATTCTTTTCTAAATTCAAATAAATTACAACACT
1469730 AAATTTTT
131 AAATTTTT
* *
1469738 TTAATTTAGAATTTAGTCCA-CTTATTTTTATTTTTAAAAATTTAATC-CTTT-TTTTT-TATAT
1 TTAATTTAGAATTTAGTCCATC-TATTTTTACTTTTAAAAATTTAATCTCTTTATTTTTCGA-AT
* *
1469799 TTAAAAATGTAAAT-TCAATTACTAATACTATTAAAATTCTTTTGCTAAATTCA
64 TT-AAAACGTAAGTCT-AATTACTAATACTATTAAAATTCTTTT-CTAAATTCA
1469852 GATCCATTAT
Statistics
Matches: 100, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
135 1 0.01
136 10 0.10
137 39 0.39
138 50 0.50
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.50
Consensus pattern (138 bp):
TTAATTTAGAATTTAGTCCATCTATTTTTACTTTTAAAAATTTAATCTCTTTATTTTTCGAATTT
AAAACGTAAGTCTAATTACTAATACTATTAAAATTCTTTTCTAAATTCAAATAAATTACAACACT
AAATTTTT
Found at i:1485059 original size:20 final size:20
Alignment explanation
Indices: 1485034--1485073 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1485024 GTTCTTGTCA
1485034 TAACATGTC-AGATGTGATTC
1 TAACATGTCGA-ATGTGATTC
1485054 TAACATGTCGAATGTGATTC
1 TAACATGTCGAATGTGATTC
1485074 CGACATGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
TAACATGTCGAATGTGATTC
Found at i:1485079 original size:20 final size:20
Alignment explanation
Indices: 1485035--1485080 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1485025 TTCTTGTCAT
*
1485035 AACATGTCAGATGTGATTCT
1 AACATGTCAGATGTGATTCC
1485055 AACATGTC-GAATGTGATTCC
1 AACATGTCAG-ATGTGATTCC
*
1485075 GACATG
1 AACATG
1485081 CTAGACACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (20 bp):
AACATGTCAGATGTGATTCC
Found at i:1485237 original size:6 final size:6
Alignment explanation
Indices: 1485226--1485252 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1485216 CTACTTTACC
1485226 AGGTTT AGGTTT AGGTTT AGGTTT AGG
1 AGGTTT AGGTTT AGGTTT AGGTTT AGG
1485253 AGTACGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (6 bp):
AGGTTT
Found at i:1485966 original size:16 final size:17
Alignment explanation
Indices: 1485922--1485966 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1485912 AACCAAACCC
1485922 AAAATATTTTTTATTTCA
1 AAAATA-TTTTTATTTCA
* *
1485940 AGAATAATTTTATTT-A
1 AAAATATTTTTATTTCA
1485956 AAAATATTTTT
1 AAAATATTTTT
1485967 TCTTCGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.43
17 8 0.35
18 5 0.22
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
AAAATATTTTTATTTCA
Found at i:1485967 original size:17 final size:18
Alignment explanation
Indices: 1485922--1485967 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
1485912 AACCAAACCC
1485922 AAAATATTTTTTATTTCA
1 AAAATATTTTTTATTTCA
* *
1485940 AGAATA-ATTTTATTT-A
1 AAAATATTTTTTATTTCA
1485956 AAAATATTTTTT
1 AAAATATTTTTT
1485968 CTTCGAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 6 0.26
17 12 0.52
18 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
AAAATATTTTTTATTTCA
Found at i:1493859 original size:12 final size:12
Alignment explanation
Indices: 1493842--1493866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1493832 ATTTGTTAAA
1493842 TTTATATATATT
1 TTTATATATATT
1493854 TTTATATATATT
1 TTTATATATATT
1493866 T
1 T
1493867 ATAGTGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATATATT
Found at i:1494239 original size:23 final size:24
Alignment explanation
Indices: 1494184--1494240 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1494174 TATAGTATTT
* *
1494184 TTTAATTGTTTGTGAACATGTTCAA
1 TTTAA-TGTTTATGAACATATTCAA
1494209 -TTATATGTTTATGAACATATT-AA
1 TTTA-ATGTTTATGAACATATTCAA
1494232 TTTAATGTT
1 TTTAATGTT
1494241 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 7 0.25
24 20 0.71
25 1 0.04
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (24 bp):
TTTAATGTTTATGAACATATTCAA
Found at i:1503821 original size:13 final size:14
Alignment explanation
Indices: 1503798--1503826 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1503788 TGCTATAAAA
1503798 TATATTATGTTAAT
1 TATATTATGTTAAT
1503812 TATA-TATGTTAAT
1 TATATTATGTTAAT
1503825 TA
1 TA
1503827 AGAATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TATATTATGTTAAT
Found at i:1504038 original size:36 final size:37
Alignment explanation
Indices: 1503956--1504040 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 37
1503946 AAAATTTATA
* * *
1503956 TTTAATACAATAAATATTTATTTATATTTGTTTGTGTT
1 TTTAATATAA-AAACATTTATTTATATTTGTTAGTGTT
1503994 TTTAATATAAAAACATTTA-TTATATTTG-TAGTAGTGT
1 TTTAATATAAAAACATTTATTTATATTTGTTAGT-GT-T
1504031 TTT-ATATAAA
1 TTTAATATAAA
1504041 TAATTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 3 0.07
36 18 0.43
37 12 0.29
38 9 0.21
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.53
Consensus pattern (37 bp):
TTTAATATAAAAACATTTATTTATATTTGTTAGTGTT
Found at i:1514390 original size:24 final size:26
Alignment explanation
Indices: 1514344--1514395 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 26
1514334 TGTTATTGGG
1514344 TTATTAATTTAATATAAATATATATAA
1 TTATTAATTTAATAT-AATATATATAA
*
1514371 TTATT-ATTTAATAT-ATATATTTAA
1 TTATTAATTTAATATAATATATATAA
1514395 T
1 T
1514396 ATAATTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 10 0.42
26 9 0.38
27 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATTAATTTAATATAATATATATAA
Found at i:1514393 original size:13 final size:13
Alignment explanation
Indices: 1514350--1514398 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1514340 TGGGTTATTA
1514350 ATTTAATATAAATAT
1 ATTTAATAT--ATAT
*
1514365 ATATAAT-TAT-T
1 ATTTAATATATAT
1514376 ATTTAATATATAT
1 ATTTAATATATAT
1514389 ATTTAATATA
1 ATTTAATATA
1514399 ATTACTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 7 0.23
12 5 0.17
13 11 0.37
14 1 0.03
15 6 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTTAATATATAT
Found at i:1521690 original size:21 final size:21
Alignment explanation
Indices: 1521664--1521703 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1521654 ACTAAGTGTG
1521664 GGCTTAATTAGTAATTAAAAT
1 GGCTTAATTAGTAATTAAAAT
*
1521685 GGCTTAATTAGTTATTAAA
1 GGCTTAATTAGTAATTAAA
1521704 TTTTAATTTT
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:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (21 bp):
GGCTTAATTAGTAATTAAAAT
Found at i:1521827 original size:81 final size:82
Alignment explanation
Indices: 1521723--1521884 Score: 281
Period size: 82 Copynumber: 2.0 Consensus size: 82
1521713 TGTTAACATA
1521723 TTTTATTTTAATAATTAAATTTAAATAAAAATGTTAAC-TAATAAATAGTAATTAAGCCAGATAC
1 TTTTATTTTAATAATTAAATTTAAATAAAAATGTTAACTTAATAAATAGTAATTAAGCCAGATAC
1521787 GAATTGGATGGAAATAT
66 GAATTGGATGGAAATAT
* * * *
1521804 TTTTATTTTAATAATTAAATTTAAATAAAAGTGTTAACTTAATAAATAGTAATTAAGTCGGATAT
1 TTTTATTTTAATAATTAAATTTAAATAAAAATGTTAACTTAATAAATAGTAATTAAGCCAGATAC
1521869 GAATTGGATGGAAATA
66 GAATTGGATGGAAATA
1521885 GAAGATTGAG
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 37 0.49
82 39 0.51
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (82 bp):
TTTTATTTTAATAATTAAATTTAAATAAAAATGTTAACTTAATAAATAGTAATTAAGCCAGATAC
GAATTGGATGGAAATAT
Found at i:1522216 original size:40 final size:40
Alignment explanation
Indices: 1522189--1522281 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
1522179 ATCTATGGTT
*
1522189 AAATTTTAATTTTAAAATTTTAGATTATATAAAAATTATC
1 AAATTTTAATTTTAAAATTTTAGATTATATAAAAATGATC
* *
1522229 AAATTTTAATTTTAAATTTTTAGATTATATAAAAATTATC
1 AAATTTTAATTTTAAAATTTTAGATTATATAAAAATGATC
1522269 AAATTTTAATTTT
1 AAATTTTAATTTT
1522282 GGTCCTTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (40 bp):
AAATTTTAATTTTAAAATTTTAGATTATATAAAAATGATC
Found at i:1530312 original size:60 final size:60
Alignment explanation
Indices: 1530218--1530335 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
1530208 TTGTTTGATA
*
1530218 GATGTACTTGGACTACCGGAGTTTGAAAAACATTGATGATATGTCCAAGTTGAAAAAATC
1 GATGTACTTGGACTACCGGAGTTTGAAAAACATTGATGACATGTCCAAGTTGAAAAAATC
*
1530278 GATGTACTTGGACTACCGGAGTTTGAAAAGCATTGATGACATGTCCAAGTTGAAAAAA
1 GATGTACTTGGACTACCGGAGTTTGAAAAACATTGATGACATGTCCAAGTTGAAAAAA
1530336 AAAATTTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (60 bp):
GATGTACTTGGACTACCGGAGTTTGAAAAACATTGATGACATGTCCAAGTTGAAAAAATC
Found at i:1536014 original size:122 final size:122
Alignment explanation
Indices: 1535870--1536110 Score: 473
Period size: 122 Copynumber: 2.0 Consensus size: 122
1535860 AATTAACAAC
1535870 ACACTAATGAAAAGACTTGATTGAAATGATATTTTAATCTCGTAATTTAATTATAACATTTAAAA
1 ACACTAATGAAAAGACTTGATTGAAATGATATTTTAATCTCGTAATTTAATTATAACATTTAAAA
1535935 GAATCAATTTAAAAGTTAACCCATACGAGAAATTATTATTTTTAACCCTAATAAAAT
66 GAATCAATTTAAAAGTTAACCCATACGAGAAATTATTATTTTTAACCCTAATAAAAT
1535992 ACACTAATGAAAAGACTTGATTGAAATGATATTTTAATCTCGTAATTTAATTATAACATTTAAAA
1 ACACTAATGAAAAGACTTGATTGAAATGATATTTTAATCTCGTAATTTAATTATAACATTTAAAA
*
1536057 GAATCAATTTAAAAGTTAACCCATACGGGAAATTATTATTTTTAACCCTAATAA
66 GAATCAATTTAAAAGTTAACCCATACGAGAAATTATTATTTTTAACCCTAATAA
1536111 TTAAGGTAGG
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (122 bp):
ACACTAATGAAAAGACTTGATTGAAATGATATTTTAATCTCGTAATTTAATTATAACATTTAAAA
GAATCAATTTAAAAGTTAACCCATACGAGAAATTATTATTTTTAACCCTAATAAAAT
Found at i:1541128 original size:16 final size:16
Alignment explanation
Indices: 1541109--1541139 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1541099 TCAGGTTCAT
*
1541109 ATTATTTTGGGTTTGG
1 ATTATTTAGGGTTTGG
1541125 ATTATTTAGGGTTTG
1 ATTATTTAGGGTTTG
1541140 AATCGTTTCA
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:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (16 bp):
ATTATTTAGGGTTTGG
Found at i:1551000 original size:3 final size:3
Alignment explanation
Indices: 1550994--1551019 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1550984 TATGTGGTGC
1550994 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
1551020 AATCTTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:1554748 original size:16 final size:16
Alignment explanation
Indices: 1554727--1554762 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1554717 CGGAGTATTA
*
1554727 TTATATTATATTAAAT
1 TTATATTACATTAAAT
*
1554743 TTATATTACATTATAT
1 TTATATTACATTAAAT
1554759 TTAT
1 TTAT
1554763 CTATTAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTACATTAAAT
Found at i:1562062 original size:71 final size:71
Alignment explanation
Indices: 1561965--1562108 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
1561955 ATGAATAGCC
*
1561965 AAATTGAGTTGTTATTGTTGAGAAATGAAAGTTAAGAATAAATTAGTTTATTTATGAATTAATTG
1 AAATTGAGTTGTAATTGTTGAGAAATGAAAGTTAAGAATAAATTAGTTTATTTATGAATTAATTG
1562030 TTATAT
66 TTATAT
1562036 AAATTGAGTTGTAATTGTTGAGAAATGAAAGTTAAGAATAAATTAGTTTATTTATGAATTAATTG
1 AAATTGAGTTGTAATTGTTGAGAAATGAAAGTTAAGAATAAATTAGTTTATTTATGAATTAATTG
1562101 TTATAT
66 TTATAT
1562107 AA
1 AA
1562109 TTTGGCATGT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.42
Consensus pattern (71 bp):
AAATTGAGTTGTAATTGTTGAGAAATGAAAGTTAAGAATAAATTAGTTTATTTATGAATTAATTG
TTATAT
Found at i:1564879 original size:24 final size:23
Alignment explanation
Indices: 1564852--1564909 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
1564842 TTTATGTGCT
* *
1564852 TATTTTTAAATTTATTAAATAATA
1 TATTTTTAAATTT-TAAAAAAATA
*
1564876 TATTTTTATCATTTTAAAAAAATA
1 TATTTTTA-AATTTTAAAAAAATA
1564900 TATTTATTAA
1 TATTT-TTAA
1564910 TTAAATGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTTTTAAATTTTAAAAAAATA
Found at i:1569937 original size:39 final size:39
Alignment explanation
Indices: 1569879--1569959 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
1569869 ATTTTGAGAG
*
1569879 TTAAAATATAATTTTACTATATATATACATGCATATTTA
1 TTAAAATATAATTTGACTATATATATACATGCATATTTA
* *
1569918 TTAAAGTATAATTTGACTATATATATACATTCATATTTA
1 TTAAAATATAATTTGACTATATATATACATGCATATTTA
1569957 TTA
1 TTA
1569960 TTTATGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (39 bp):
TTAAAATATAATTTGACTATATATATACATGCATATTTA
Found at i:1571275 original size:102 final size:100
Alignment explanation
Indices: 1571138--1571335 Score: 308
Period size: 102 Copynumber: 2.0 Consensus size: 100
1571128 AAGGATCAAA
* * *
1571138 ATCTACTCTCGTGAAAAAAAATAAAAAAGATATATCATCGTAACTTTTCACCCAATTAAGCCATT
1 ATCTACTCTCGTAAAAAAAAATAAAAAAGATATATCATCGTAACTTCTCACCCAATTAAGACATT
1571203 ATCGA-AAAAAAGAAATAATTGTTTAAACCTTTAC
66 ATCGACAAAAAAGAAATAATTGTTTAAACCTTTAC
* *
1571237 ATCTGCTCTCGTTAAAAAAAAATTAAAAAAAGATATATCATCGTAACTTCTCACCCAATTAAGAT
1 ATCTACTCTCG-TAAAAAAAAA-T-AAAAAAGATATATCATCGTAACTTCTCACCCAATTAAGAC
*
1571302 ATTATTGACAAAAAAGAAATAATTGTTTAAACCT
63 ATTATCGACAAAAAAGAAATAATTGTTTAAACCT
1571336 GTACGTGAGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
99 10 0.11
100 9 0.10
101 1 0.01
102 44 0.49
103 25 0.28
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (100 bp):
ATCTACTCTCGTAAAAAAAAATAAAAAAGATATATCATCGTAACTTCTCACCCAATTAAGACATT
ATCGACAAAAAAGAAATAATTGTTTAAACCTTTAC
Found at i:1573682 original size:42 final size:39
Alignment explanation
Indices: 1573632--1573751 Score: 127
Period size: 42 Copynumber: 3.0 Consensus size: 39
1573622 CGGCCCGAAT
1573632 TATATATTAAATATATTTATTTTTATTTTTAATCAAATA
1 TATATATTAAATATATTTATTTTTATTTTTAATCAAATA
* ** * *
1573671 TACTTTTTATTAAATATATTT-TTTGGACTTTTAATCTGAAT-
1 TA---TATATTAAATATATTTATTTTTATTTTTAATC-AAATA
* *
1573712 TATATATTAAATATATATAATTTTATTTTTAATCAAATA
1 TATATATTAAATATATTTATTTTTATTTTTAATCAAATA
1573751 T
1 T
1573752 GGGCCGAGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
38 17 0.27
39 14 0.22
41 14 0.22
42 18 0.29
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (39 bp):
TATATATTAAATATATTTATTTTTATTTTTAATCAAATA
Found at i:1573694 original size:16 final size:16
Alignment explanation
Indices: 1573655--1573694 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1573645 TATTTATTTT
*
1573655 TATTTTTAATCAAATA
1 TATTTTTTATCAAATA
* *
1573671 TACTTTTTATTAAATA
1 TATTTTTTATCAAATA
1573687 TATTTTTT
1 TATTTTTT
1573695 GGACTTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTTATCAAATA
Found at i:1577503 original size:16 final size:16
Alignment explanation
Indices: 1577482--1577533 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1577472 TTTATGTTAA
1577482 ATTTTTTAATATTTTT
1 ATTTTTTAATATTTTT
*
1577498 ATTTTTGAATATTTTAT
1 ATTTTTTAATATTTT-T
*
1577515 AATTTTTAA-ATTATTT
1 ATTTTTTAATATT-TTT
1577531 ATT
1 ATT
1577534 GATATGCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 20 0.67
17 10 0.33
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTTTTTAATATTTTT
Found at i:1577531 original size:18 final size:17
Alignment explanation
Indices: 1577481--1577532 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1577471 ATTTATGTTA
*
1577481 AATTTTTTAATATTT-T
1 AATTTTTAAATATTTAT
* *
1577497 TATTTTTGAATATTTTAT
1 AATTTTTAAATA-TTTAT
1577515 AATTTTTAAATTATTTAT
1 AATTTTTAAA-TATTTAT
1577533 TGATATGCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 10 0.34
17 3 0.10
18 14 0.48
19 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
AATTTTTAAATATTTAT
Found at i:1582315 original size:16 final size:16
Alignment explanation
Indices: 1582284--1582335 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1582274 GATGTTAACA
*
1582284 TTATTTTGAGTTTCATT
1 TTATTTCGA-TTTCATT
*
1582301 TTATATT-TATTTCATT
1 TTAT-TTCGATTTCATT
*
1582317 TCATTTCGATTTCATT
1 TTATTTCGATTTCATT
1582333 TTA
1 TTA
1582336 CTTTGGGTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 2 0.07
16 20 0.69
17 5 0.17
18 2 0.07
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.63
Consensus pattern (16 bp):
TTATTTCGATTTCATT
Found at i:1590187 original size:113 final size:113
Alignment explanation
Indices: 1590025--1590251 Score: 427
Period size: 113 Copynumber: 2.0 Consensus size: 113
1590015 AATGGATAAG
1590025 GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAATTTGTGACCTTTCTGACTACA
1 GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAATTTGTGACCTTTCTGACTACA
* *
1590090 GGTTAACCCTAATTTGAAAGCTCAAACATTCAATTACCATATTGGAGA
66 GGTTAACCCTAAGTTAAAAGCTCAAACATTCAATTACCATATTGGAGA
*
1590138 GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAGTTTGTGACCTTTCTGACTACA
1 GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAATTTGTGACCTTTCTGACTACA
1590203 GGTTAACCCTAAGTTAAAAGCTCAAACATTCAATTACCATATTGGAGA
66 GGTTAACCCTAAGTTAAAAGCTCAAACATTCAATTACCATATTGGAGA
1590251 G
1 G
1590252 ACCTCTCCAT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (113 bp):
GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAATTTGTGACCTTTCTGACTACA
GGTTAACCCTAAGTTAAAAGCTCAAACATTCAATTACCATATTGGAGA
Found at i:1604136 original size:17 final size:17
Alignment explanation
Indices: 1604114--1604147 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1604104 ATCAACTATT
*
1604114 TTTAAATTATATTAAAA
1 TTTAAATTAAATTAAAA
1604131 TTTAAATTAAATTAAAA
1 TTTAAATTAAATTAAAA
1604148 AAACATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTAAATTAAAA
Found at i:1614620 original size:28 final size:30
Alignment explanation
Indices: 1614551--1614605 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1614541 TTCGTATTTA
*
1614551 AAAATATTAAATATTATTATAAAAATATTG
1 AAAATATAAAATATTATTATAAAAATATTG
1614581 AAAATATAAAAT-TTATTA-AAAAATA
1 AAAATATAAAATATTATTATAAAAATA
1614606 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 7 0.29
29 6 0.25
30 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATATAAAATATTATTATAAAAATATTG
Found at i:1622447 original size:41 final size:41
Alignment explanation
Indices: 1622400--1622489 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
1622390 AAATAAACAC
1622400 AAAAAAATTTAAAAAAAGTATTTTAAAATA-TTTTAAAAATA
1 AAAAAAATTT-AAAAAAGTATTTTAAAATATTTTTAAAAATA
1622441 AAAAAAATTTAAAAAAGTATTTTAAAATATTTTTAAAAATA
1 AAAAAAATTTAAAAAAGTATTTTAAAATATTTTTAAAAATA
1622482 AAAAAAAT
1 AAAAAAAT
1622490 ATATTTATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 19 0.40
41 29 0.60
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (41 bp):
AAAAAAATTTAAAAAAGTATTTTAAAATATTTTTAAAAATA
Found at i:1625125 original size:16 final size:17
Alignment explanation
Indices: 1625083--1625127 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1625073 ACTTTTCGAT
1625083 AAATAAA-AAATATATA
1 AAATAAATAAATATATA
* *
1625099 AAATTACTAAATAT-TA
1 AAATAAATAAATATATA
1625115 AAATAAATAAATA
1 AAATAAATAAATA
1625128 AATTATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAATAAATATATA
Found at i:1632897 original size:17 final size:17
Alignment explanation
Indices: 1632855--1632897 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1632845 ATTATTGAAC
1632855 TAATTTTTTCTATTTTA
1 TAATTTTTTCTATTTTA
*
1632872 AAATATTTTT-TATTTATA
1 TAAT-TTTTTCTATTT-TA
1632890 TAATTTTT
1 TAATTTTT
1632898 AATTAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTTTCTATTTTA
Found at i:1637051 original size:236 final size:231
Alignment explanation
Indices: 1636635--1637105 Score: 888
Period size: 236 Copynumber: 2.0 Consensus size: 231
1636625 TTGTAACCGG
1636635 ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
1 ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
1636700 AATCTACATCATCGAGAAACCTGGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTATAGAG
66 AATCTACATCATCGAGAAACCTGGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTATAGAG
1636765 AGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGAGATTG
131 AGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGAGATTG
1636830 TCACGAACCCGTAAAGAATCAGTTTCTGTGAATTCC
196 TCACGAACCCGTAAAGAATCAGTTTCTGTGAATTCC
1636866 ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
1 ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
1636931 AATCTACATCATCGAGAAACCTGGAGGGGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTA
66 AATCTACATCATCGAGAAACCT-----GGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTA
1636996 TAGAGAGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGA
126 TAGAGAGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGA
*
1637061 GATTGTCACGAACCCGTAAAGAATTAGTTTCTGTGAATTCC
191 GATTGTCACGAACCCGTAAAGAATCAGTTTCTGTGAATTCC
1637102 ATTT
1 ATTT
1637106 AGGAGGGGTA
Statistics
Matches: 234, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
231 87 0.37
236 147 0.63
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (231 bp):
ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
AATCTACATCATCGAGAAACCTGGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTATAGAG
AGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGAGATTG
TCACGAACCCGTAAAGAATCAGTTTCTGTGAATTCC
Found at i:1653287 original size:23 final size:23
Alignment explanation
Indices: 1653261--1653314 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1653251 TGATTTTAAA
* *
1653261 ATTTTGAATTATTTAGTAATAAT
1 ATTTAGAATTATTTAATAATAAT
*
1653284 ATTTAGAATTATTTAATGATAAT
1 ATTTAGAATTATTTAATAATAAT
1653307 ATTTAGAA
1 ATTTAGAA
1653315 AAAATCTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
ATTTAGAATTATTTAATAATAAT
Found at i:1653479 original size:14 final size:15
Alignment explanation
Indices: 1653450--1653483 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1653440 GTCACACATA
*
1653450 TTTTGTTCTTTCAAT
1 TTTTTTTCTTTCAAT
1653465 TTTTTTTCTTT-AAT
1 TTTTTTTCTTTCAAT
1653479 TTTTT
1 TTTTT
1653484 GGTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTTTCAAT
Done.