Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 94 of 103
Found at i:34545478 original size:9 final size:9
Alignment explanation
Indices: 34545464--34545530 Score: 57
Period size: 9 Copynumber: 7.1 Consensus size: 9
34545454 TGTGCTTTGT
34545464 TTCTTTCTC
1 TTCTTTCTC
*
34545473 TTCTTTGTC
1 TTCTTTCTC
34545482 TTTCTTCTTCTC
1 -TTC-T-TTCTC
*
34545494 TTTTTTCTC
1 TTCTTTCTC
34545503 TTCTTTCTC
1 TTCTTTCTC
34545512 TT-TCTTCTTC
1 TTCT-TTC-TC
34545522 TTC-TTCTC
1 TTCTTTCTC
34545530 T
1 T
34545531 CCTACCTCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
8 4 0.08
9 29 0.60
10 8 0.17
11 3 0.06
12 4 0.08
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (9 bp):
TTCTTTCTC
Found at i:34545516 original size:24 final size:27
Alignment explanation
Indices: 34545471--34545530 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 27
34545461 TGTTTCTTTC
*
34545471 TCTTCTTTGTCTTTCTTCTTC-TCTT-T
1 TCTTCTCT-TCTTTCTTCTTCTTCTTCT
34545497 T-TTCTCTTCTTTC-TCTTTCTTCTTCT
1 TCTTCTCTTCTTTCTTC-TTCTTCTTCT
34545523 TCTTCTCT
1 TCTTCTCT
34545531 CCTACCTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 9 0.31
25 9 0.31
26 3 0.10
27 6 0.21
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (27 bp):
TCTTCTCTTCTTTCTTCTTCTTCTTCT
Found at i:34545594 original size:23 final size:21
Alignment explanation
Indices: 34545560--34545606 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
34545550 CCTTGTGCTT
*
34545560 CTTTTCTTT-CT-TC-TTCTC
1 CTTTTCTTTCCTGTCTTTTTC
34545578 CTTTTCTTTCCTGTCTTTTTC
1 CTTTTCTTTCCTGTCTTTTTC
*
34545599 TTTTTCTT
1 CTTTTCTT
34545607 CCTCTTTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.38
19 2 0.08
20 2 0.08
21 11 0.46
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (21 bp):
CTTTTCTTTCCTGTCTTTTTC
Found at i:34545832 original size:19 final size:17
Alignment explanation
Indices: 34545808--34545865 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 17
34545798 TTGTGCTTTG
34545808 TTTCTTTCTCCTCTTTGTC
1 TTTCTTTCTCCT-TTT-TC
34545827 TTTCTTTTTCTCCTTTTTC
1 TTTC--TTTCTCCTTTTTC
34545846 TCTTCTTTCT-CTTTCTTC
1 T-TTCTTTCTCCTTT-TTC
34545864 TT
1 TT
34545866 CTTCTTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 7 0.20
20 6 0.17
21 8 0.23
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTCTTTCTCCTTTTTC
Found at i:34545836 original size:21 final size:20
Alignment explanation
Indices: 34545812--34545853 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
34545802 GCTTTGTTTC
34545812 TTTCTCCTCTTTGTCT-TTCTT
1 TTTCTCCT-TTT-TCTCTTCTT
34545833 TTTCTCCTTTTTCTCTTCTT
1 TTTCTCCTTTTTCTCTTCTT
34545853 T
1 T
34545854 CTCTTTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 9 0.45
21 8 0.40
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTCTCCTTTTTCTCTTCTT
Found at i:34545860 original size:24 final size:24
Alignment explanation
Indices: 34545810--34545870 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
34545800 GTGCTTTGTT
*
34545810 TCTTTCTCC-TCTT-T-GTCTTTC
1 TCTTTCTCCTTCTTCTCTTCTTTC
* *
34545831 TTTTTCTCCTTTTTCTCTTCTTTC
1 TCTTTCTCCTTCTTCTCTTCTTTC
*
34545855 TCTTTCTTCTTCTTCT
1 TCTTTCTCCTTCTTCT
34545871 TCTCTCCTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 8 0.26
22 3 0.10
23 1 0.03
24 19 0.61
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (24 bp):
TCTTTCTCCTTCTTCTCTTCTTTC
Found at i:34545951 original size:9 final size:9
Alignment explanation
Indices: 34545903--34545971 Score: 50
Period size: 10 Copynumber: 7.2 Consensus size: 9
34545893 ATCCTTGTGC
34545903 TTCTTTTCT
1 TTCTTTTCT
34545912 TTCTTCTTC-
1 TTCTT-TTCT
*
34545921 TCCTTTTCT
1 TTCTTTTCT
* *
34545930 TTCCTGTCTT
1 TTCTTTTC-T
34545940 TTCTTTTCT
1 TTCTTTTCT
*
34545949 TTCTCTTTGCC
1 TTCT-TTT-CT
34545960 TTCTTTTGCT
1 TTCTTTT-CT
34545970 TT
1 TT
34545972 ACCCTTCTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
8 3 0.06
9 19 0.40
10 20 0.43
11 5 0.11
ACGTcount: A:0.00, C:0.28, G:0.04, T:0.68
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:34546118 original size:343 final size:345
Alignment explanation
Indices: 34545238--34546271 Score: 1889
Period size: 345 Copynumber: 3.0 Consensus size: 345
34545228 CTTTTCTCTC
*
34545238 CTTTCTTGTCTTTTTCTTTTTCTTTCTCTTTGCCTTCTTTTGCTTTACCCTTCTGCTTCTCTTCC
1 CTTTCCTGTCTTTTTCTTTTTCTTTCTCTTTGCCTTCTTTTGCTTTACCCTTCTGCTTCTCTTCC
34545303 TCTCCTTCACCTTCTGATTCTTTCTCAAAATCTACTATTTCAATTTCCCTGGAGGTTATGTCAGT
66 TCTCCTTCACCTTCTGATTCTTTCTCAAAATCTACTATTTCAATTTCCCTGGAGGTTATGTCAGT
34545368 CTCACACTTCATGTCATTTGCTCCATCTTCGTGTTTCTTCTTCTCCTTCTCATCAGTTTCTTTCT
131 CTCACACTTCATGTCATTTGCTCCATCTTCGTGTTTCTTCTTCTCCTTCTCATCAGTTTCTTTCT
* * *
34545433 TCTTGCTCTTCTCTTCGTCCTTGTGCTTTGTTTCTTTCTCTTCTTTGTCTTTCTTCTTCTCTTTT
196 TCTTGCTCTTCTCTTCGTCCTTGTGCTTTGTTTCTTTCTCCTCTTTGTCTTTCTTTTTCTCCTTT
34545498 TTCTCTTCTTTCTCTTTCTTCTTCTTCTTCTCTCCTACCTCTTCATCTTCATCCTTGTGCTTCTT
261 TTCTCTTCTTTCTCTTTCTTCTTCTTCTTCTCTCCTACCTCTTCATCTTCATCCTTGTGCTTCTT
34545563 TTCTTTCTTCTTCTCCTTTT
326 TTCTTTCTTCTTCTCCTTTT
*
34545583 CTTTCCTGTCTTTTTCTTTTTCTTCCTCTTTGCCTTCTTTTGCTTTACCCTTCTGCTTCTCTTCC
1 CTTTCCTGTCTTTTTCTTTTTCTTTCTCTTTGCCTTCTTTTGCTTTACCCTTCTGCTTCTCTTCC
34545648 TCTCCTTCACCTTCTGATTCTTTCTCAAAATCTACTATTTCAATTTCCCTGGAGGTTATGTCAGT
66 TCTCCTTCACCTTCTGATTCTTTCTCAAAATCTACTATTTCAATTTCCCTGGAGGTTATGTCAGT
* *
34545713 CTCACACTTCATGTCATTTGCTCCATCTTTGTGTTTCTTCTTCTCCTCCTCATCAGTTTCTTTCT
131 CTCACACTTCATGTCATTTGCTCCATCTTCGTGTTTCTTCTTCTCCTTCTCATCAGTTTCTTTCT
34545778 TCTTGCTCTTCTCTTCGTCCTTGTGCTTTGTTTCTTTCTCCTCTTTGTCTTTCTTTTTCTCCTTT
196 TCTTGCTCTTCTCTTCGTCCTTGTGCTTTGTTTCTTTCTCCTCTTTGTCTTTCTTTTTCTCCTTT
34545843 TTCTCTTCTTTCTCTTTCTTCTTCTTCTTCTCTCCTACCTCTTCATCTTCATCCTTGTGCTTCTT
261 TTCTCTTCTTTCTCTTTCTTCTTCTTCTTCTCTCCTACCTCTTCATCTTCATCCTTGTGCTTCTT
34545908 TTCTTTCTTCTTCTCCTTTT
326 TTCTTTCTTCTTCTCCTTTT
34545928 CTTTCCTGTC-TTTTC-TTTTCTTTCTCTTTGCCTTCTTTTGCTTTACCCTTCTGCTTCTCTTCC
1 CTTTCCTGTCTTTTTCTTTTTCTTTCTCTTTGCCTTCTTTTGCTTTACCCTTCTGCTTCTCTTCC
34545991 TCTCCTTCACCTTCTGATTCTTTCTCAAAATCTACTATTTCAATTTCCCTGGAGGTTATGTCAGT
66 TCTCCTTCACCTTCTGATTCTTTCTCAAAATCTACTATTTCAATTTCCCTGGAGGTTATGTCAGT
34546056 CTCACACTTCATGTCATTTGCTCCATCTTCGTGTTTCTTCTTCTCCTTCTCATCAGTTTCTTTCT
131 CTCACACTTCATGTCATTTGCTCCATCTTCGTGTTTCTTCTTCTCCTTCTCATCAGTTTCTTTCT
**
34546121 TCTTGCTCTTCTCTTCGTCCTTGTGCTTTGTTTCNCTCTCCTCTCTTTTGTC-TTCTTTCTT-TC
196 TCTTGCTCTTCTCTTCGTCCTTGTGCTTTGTTTCTTTCT-C-CTC-TTTGTCTTTCTTT-TTCTC
*
34546184 TCTTTTTCTCTTCTTTCTCTTTCTTCTTCTTCTTCTTCTCCTAGCTC-TCATCTTCATCCTTGTG
257 -CTTTTTCTCTTCTTTCTCTTTCTTCTTCTTCTTC-TCTCCTACCTCTTCATCTTCATCCTTGTG
34546248 CTTCTTTTCTTTCTTCTTCTCCTT
320 CTTCTTTTCTTTCTTCTTCTCCTT
34546272 ATCATCCTTG
Statistics
Matches: 670, Mismatches: 13, Indels: 11
0.97 0.02 0.02
Matches are distributed among these distances:
343 212 0.32
344 6 0.01
345 359 0.54
346 83 0.12
347 10 0.01
ACGTcount: A:0.07, C:0.31, G:0.07, T:0.55
Consensus pattern (345 bp):
CTTTCCTGTCTTTTTCTTTTTCTTTCTCTTTGCCTTCTTTTGCTTTACCCTTCTGCTTCTCTTCC
TCTCCTTCACCTTCTGATTCTTTCTCAAAATCTACTATTTCAATTTCCCTGGAGGTTATGTCAGT
CTCACACTTCATGTCATTTGCTCCATCTTCGTGTTTCTTCTTCTCCTTCTCATCAGTTTCTTTCT
TCTTGCTCTTCTCTTCGTCCTTGTGCTTTGTTTCTTTCTCCTCTTTGTCTTTCTTTTTCTCCTTT
TTCTCTTCTTTCTCTTTCTTCTTCTTCTTCTCTCCTACCTCTTCATCTTCATCCTTGTGCTTCTT
TTCTTTCTTCTTCTCCTTTT
Found at i:34546187 original size:10 final size:9
Alignment explanation
Indices: 34546173--34546217 Score: 51
Period size: 8 Copynumber: 5.1 Consensus size: 9
34546163 CTCTTTTGTC
34546173 TTCT-TTCT
1 TTCTCTTCT
34546181 TTCTCTT-T
1 TTCTCTTCT
34546189 TTCTCTTCT
1 TTCTCTTCT
34546198 TTCTCTT-T
1 TTCTCTTCT
34546206 CTTCTTCTTCT
1 -TTC-TCTTCT
34546217 T
1 T
34546218 CTTCTCCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 13 0.41
9 13 0.41
10 5 0.16
11 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (9 bp):
TTCTCTTCT
Found at i:34546195 original size:21 final size:22
Alignment explanation
Indices: 34546156--34546220 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
34546146 CTTTGTTTCN
* *
34546156 CTCTCCTCTCTTTTGTCTTCTTT
1 CTCTTCTCT-TTTTCTCTTCTTT
34546179 CT-TTCTCTTTTTCTCTTCTTT
1 CTCTTCTCTTTTTCTCTTCTTT
*
34546200 CTCTT-TCTTCTTCTTCTTCTT
1 CTCTTCTCTTTTTC-TCTTCTT
34546221 CTCCTAGCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 21 0.57
22 14 0.38
23 2 0.05
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (22 bp):
CTCTTCTCTTTTTCTCTTCTTT
Found at i:34546387 original size:21 final size:21
Alignment explanation
Indices: 34546363--34546405 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34546353 TTCTTTTTTC
34546363 TTCTCCTTCTCCTCTTTGTCT
1 TTCTCCTTCTCCTCTTTGTCT
** * *
34546384 TTCTTTTTCTCTTCTTTTTCT
1 TTCTCCTTCTCCTCTTTGTCT
34546405 T
1 T
34546406 CAACTTTTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (21 bp):
TTCTCCTTCTCCTCTTTGTCT
Found at i:34546434 original size:99 final size:96
Alignment explanation
Indices: 34546184--34547102 Score: 377
Period size: 99 Copynumber: 9.8 Consensus size: 96
34546174 TCTTTCTTTC
* *
34546184 TCTTTTTCTCTTCTTTCTCTTTCTTCTTCTTCTTCTTCT-CCTAGCTCTCATCTTCATCCTTGTG
1 TCTTTTTCTCTTCTTTTTC-TTC-TCTTCTTCTTCTTCTACCTCG-TC-C-TCTTCATCCTTG-G
* *
34546248 CTTCTTTTCTTTCTTCTTCTCCTTATCATCCTTGTCTT
60 CTTCTTTTCTTTCTTCTTCTCCTT-TCCTCTTTGTCTT
* ** * *
34546286 TCTTTGTCTCTTTCTTCTTT-TTCTCTTCAACATCTGC-ACTCTC-TCCCTCTTCATCCTTGAGC
1 TCTTTTTCTC-TTCTT-TTTCTTCTCTTCTTCTTCTTCTAC-CTCGT-CCTCTTCATCCTTG-GC
*
34546348 TT-TCTTTCTTTTTTCTTCTCCTTCTCCTCTTTGTCTT
61 TTCT-TTTCTTTCTTCTTCTCCTT-TCCTCTTTGTCTT
* * *
34546385 TCTTTTTCTCTTCTTTTTCTTCAACTTTTTCTTCTTCTACCTCGTCCTCTTTATCCTT--CTTCT
1 TCTTTTTCTCTTCTTTTTCTTC-TCTTCTTCTTCTTCTACCTCGTCCTCTTCATCCTTGGCTTCT
* *
34546448 TTTCTTTCTTCTTCT-CTTT-CTTTTTATC-T
65 TTTCTTTCTTCTTCTCCTTTCCTCTTTGTCTT
* * * * * *
34546477 TCTTTTTCTTCGTCTTTTTCTAC-C-TCATCCTCTT-TA--TC--CTTCTTC-T--TT-TCTT-T
1 TCTTTTTC-TCTTCTTTTTCTTCTCTTCTTCTTCTTCTACCTCGTCCTCTTCATCCTTGGCTTCT
* * * * *
34546530 CTTC-TTCTCCTTGT-CTTTCTTC-TTCTCTT
65 TTTCTTTCTTCTTCTCCTTTCCTCTTTGTCTT
* * * ** * *
34546559 TCTTTTTCTCTTCTTTTTCTCCATTTTCATCTTCTTCTACCTTATCCTCTTTA-AC----CTTCT
1 TCTTTTTCTCTTCTTTTTCTTC-TCTTCTTCTTCTTCTACCTCGTCCTCTTCATCCTTGGCTTCT
34546619 TTTCTTTCTTCTTCT-CTTT-CT-TTT-TC--
65 TTTCTTTCTTCTTCTCCTTTCCTCTTTGTCTT
* * * * * *
34546645 TC---TTCT-TT-TTCTTCATC-C-TCATCGTCTTCTACCTCTTCCTCTTTC-TCCTTCTGCTTC
1 TCTTTTTCTCTTCTTTTTCTTCTCTTCTTCTTCTTCTACCTCGTCCTC-TTCATCCTT-GGCTTC
* *
34546702 TTTTCTTTCTTCTTCT-CTTTCCCCCCCTTGTCTT
64 TTTTCTTTCTTCTTCTCCTTT--CCTCTTTGTCTT
* * * *
34546736 TCTTTTTCT-TCTCTTCTTTC-TCTC--CCTCTTC--CT-CTTCAT-C-CTTCA------GCTTT
1 TCTTTTTCTCT-TCTT-TTTCTTCTCTTCTTCTTCTTCTACCTCGTCCTCTTCATCCTTGGCTTC
*
34546786 TTTTCTTTCTTCTTCTCCTTCTCCTCTTTGTTTT
64 TTTTCTTTCTTCTTCTCCTT-TCCTCTTTGTCTT
* * * * *
34546820 TCTTCTTCTCCTTCTTCTCTTCTTTCTCTTCATCATCTTCTACCTCATCCTCTTTATCC-T-GCT
1 TCTTTTTCT-CTTCTT-T-TTC-TTCTCTTCTTCTTCTTCTACCTCGTCCTCTTCATCCTTGGCT
* * * *
34546883 TCTTTTCTTTCTTTTTCTCCTTATACTCCTCGTCTT
62 TCTTTTCTTTCTTCTTCTCCTT-TCCTCTTTGTCTT
* * * * *
34546919 TCTTCTTTTTCTTCTTATCTTCTGTCTCTTCATCTTCTCCTACCTCATGCTCCTT-ATCCTTGTG
1 TCTT-TTTCTCTTCTT-T-TTCT-TCTCTTCTTCTTCTTCTACCTCGTCCT-CTTCATCCTTG-G
* *
34546983 CTTCTTTTCTTTCTTTTTCTCCTTCTCCTCCTTGTCTT
60 CTTCTTTTCTTTCTTCTTCTCCTT-TCCTCTTTGTCTT
* * * * ** *
34547021 TCTTCTTCATCTTCTCATCTT-TT-TCTTCATCTTCCTCTACCTCAACCTCTTTATCCTTGTGCT
1 TCTTTTTC-TCTTCT--TTTTCTTCTCTTCTTCTTCTTCTACCTCGTCCTCTTCATCCTTG-GCT
*
34547084 TTTTTTCATTT-TTCTTCTC
62 TCTTTTC-TTTCTTCTTCTC
34547103 TTCTATCTCT
Statistics
Matches: 640, Mismatches: 97, Indels: 163
0.71 0.11 0.18
Matches are distributed among these distances:
78 20 0.03
79 3 0.00
81 34 0.05
82 18 0.03
83 7 0.01
84 71 0.11
85 16 0.03
86 7 0.01
87 4 0.01
88 11 0.02
89 16 0.03
90 27 0.04
91 4 0.01
92 12 0.02
93 28 0.04
94 9 0.01
95 8 0.01
96 26 0.04
97 8 0.01
98 13 0.02
99 197 0.31
100 16 0.03
101 15 0.02
102 62 0.10
103 5 0.01
104 3 0.00
ACGTcount: A:0.05, C:0.33, G:0.03, T:0.59
Consensus pattern (96 bp):
TCTTTTTCTCTTCTTTTTCTTCTCTTCTTCTTCTTCTACCTCGTCCTCTTCATCCTTGGCTTCTT
TTCTTTCTTCTTCTCCTTTCCTCTTTGTCTT
Found at i:34546458 original size:12 final size:12
Alignment explanation
Indices: 34546441--34546578 Score: 53
Period size: 12 Copynumber: 11.6 Consensus size: 12
34546431 CTCTTTATCC
34546441 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
34546453 TTCTTCTTCTCT
1 TTCTTCTTTTCT
34546465 TTCTT-TTTATC-
1 TTCTTCTTT-TCT
34546476 TTC-T-TTTTCT
1 TTCTTCTTTTCT
34546486 TCGTCTT-TTTCTACCT
1 T--TCTTCTTT-T--CT
* * *
34546502 CATCCTCTTTATCC
1 -TTCTTCTTT-TCT
34546516 TTCTTCTTTTCT
1 TTCTTCTTTTCT
* *
34546528 TTCTTCTTCTCC
1 TTCTTCTTTTCT
*
34546540 TT-GTC-TTTC-
1 TTCTTCTTTTCT
34546549 TTCTTCTCTTTCT
1 TTCTTCT-TTTCT
*
34546562 TT-TTCTCTTCT
1 TTCTTCTTTTCT
34546573 TT-TTCT
1 TTCTTCT
34546579 CCATTTTCAT
Statistics
Matches: 97, Mismatches: 15, Indels: 29
0.69 0.11 0.21
Matches are distributed among these distances:
9 4 0.04
10 10 0.10
11 17 0.18
12 42 0.43
13 13 0.13
14 2 0.02
15 3 0.03
16 6 0.06
ACGTcount: A:0.03, C:0.29, G:0.01, T:0.67
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:34546477 original size:17 final size:15
Alignment explanation
Indices: 34546440--34546722 Score: 84
Period size: 15 Copynumber: 17.8 Consensus size: 15
34546430 CCTCTTTATC
34546440 CTTCTTCTTTTCTTT
1 CTTCTTCTTTTCTTT
34546455 CTTCTTCTCTTTCTTT
1 CTTCTTCT-TTTCTTT
*
34546471 -TT-ATCTTCTT-TTT
1 CTTCTTCTT-TTCTTT
* *
34546484 CTTCGTCTTTTTCTACCT
1 CTTCTTC-TTTTCT--TT
* *
34546502 CATCCTCTTTATC---
1 CTTCTTCTTT-TCTTT
34546515 CTTCTTCTTTTCTTT
1 CTTCTTCTTTTCTTT
34546530 CTTCTTCTCCTTGTCTTT
1 CTTCTTCT--TT-TCTTT
34546548 CTTCTTCTCTTTCTTT
1 CTTCTTCT-TTTCTTT
34546564 -TTC-TC--TTCTTT
1 CTTCTTCTTTTCTTT
*
34546575 -TTCTCCATTTTCATCTT
1 CTTCTTC-TTTTC-T-TT
*
34546592 CTTCTACCTTATCCTCTTT
1 CTTCT-TCTT-T--TCTTT
***
34546611 AACCTTCTTTTCTTT
1 CTTCTTCTTTTCTTT
34546626 CTTCTTCTCTTTCTTT
1 CTTCTTCT-TTTCTTT
*
34546642 TTCTCTTCTTTTTCTTCAT
1 CT-TCTTC-TTTTCTT--T
* * * *
34546661 CCTCATCGTCTTCTACCT
1 CTTCTTC-TTTTCT--TT
* *
34546679 CTTCCTCTTTCTCCTT
1 CTTCTTCTTT-TCTTT
*
34546695 CTGCTTCTTTTCTTT
1 CTTCTTCTTTTCTTT
34546710 CTTCTTCTCTTTC
1 CTTCTTCT-TTTC
34546723 CCCCCCTTGT
Statistics
Matches: 202, Mismatches: 31, Indels: 69
0.67 0.10 0.23
Matches are distributed among these distances:
11 9 0.04
12 3 0.01
13 12 0.06
14 9 0.04
15 49 0.24
16 37 0.18
17 24 0.12
18 48 0.24
19 8 0.04
20 1 0.00
21 2 0.01
ACGTcount: A:0.05, C:0.32, G:0.01, T:0.62
Consensus pattern (15 bp):
CTTCTTCTTTTCTTT
Found at i:34546478 original size:57 final size:52
Alignment explanation
Indices: 34546348--34546479 Score: 124
Period size: 57 Copynumber: 2.4 Consensus size: 52
34546338 ATCCTTGAGC
* *
34546348 TTTCTTTCTTTTTTCTTCTCCTTCTCCTCTTTGTCTTTCTTTTTCTCTTCTT
1 TTTCTTTCTTTTTTCTTCTCCTTCTCCTCTTTATCCTTCTTTTTCTCTTCTT
*
34546400 TTTCTTCAACTTTTTCTTCTTCTACC-TCGTCCTCTTTATCCTTCTTCTTT-TCTTTCTT
1 TTTCTT--TC-TTTT-TTCTTCT-CCTTC-TCCTCTTTATCCTTCTT-TTTCTC-TTCTT
34546458 CTTCTCTTTCTTTTTATCTTCT
1 -TT-TCTTTCTTTTT-TCTTCT
34546480 TTTTCTTCGT
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
52 6 0.09
54 1 0.02
55 4 0.06
56 10 0.15
57 29 0.45
58 9 0.14
59 2 0.03
60 4 0.06
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.65
Consensus pattern (52 bp):
TTTCTTTCTTTTTTCTTCTCCTTCTCCTCTTTATCCTTCTTTTTCTCTTCTT
Found at i:34546499 original size:75 final size:76
Alignment explanation
Indices: 34546414--34546562 Score: 239
Period size: 75 Copynumber: 2.0 Consensus size: 76
34546404 TTCAACTTTT
* *
34546414 TCTTCTTCTACCTCGTCCTCTTTATCCTTCTTCTTTTCTTTCTTCTTCT-CTT-TCTTTTTATCT
1 TCTTCTTCTACCTCATCCTCTTTATCCTTCTTCTTTTCTTTCTTCTTCTCCTTGTCTTTCT-TCT
*
34546477 TCTTTTTCTTCG
65 TCTCTTTCTTCG
*
34546489 TCTTTTTCTACCTCATCCTCTTTATCCTTCTTCTTTTCTTTCTTCTTCTCCTTGTCTTTCTTCTT
1 TCTTCTTCTACCTCATCCTCTTTATCCTTCTTCTTTTCTTTCTTCTTCTCCTTGTCTTTCTTCTT
34546554 CTCTTTCTT
66 CTCTTTCTT
34546563 TTTCTCTTCT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 47 0.69
76 15 0.22
77 6 0.09
ACGTcount: A:0.04, C:0.32, G:0.02, T:0.62
Consensus pattern (76 bp):
TCTTCTTCTACCTCATCCTCTTTATCCTTCTTCTTTTCTTTCTTCTTCTCCTTGTCTTTCTTCTT
CTCTTTCTTCG
Found at i:34546572 original size:23 final size:21
Alignment explanation
Indices: 34546523--34546578 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 21
34546513 TCCTTCTTCT
* *
34546523 TTTCTTTCTTCTTCTCCTTGTC
1 TTTCTTT-TTCTTCTCTTTTTC
34546545 TTTCTTCTTCTCTT-TCTTTTTC
1 TTTCTT-TT-TCTTCTCTTTTTC
34546567 TCTTCTTTTTCT
1 T-TTCTTTTTCT
34546579 CCATTTTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 3 0.10
22 16 0.55
23 10 0.34
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTCTTTTTCTTCTCTTTTTC
Found at i:34546628 original size:93 final size:90
Alignment explanation
Indices: 34546381--34546657 Score: 147
Period size: 81 Copynumber: 3.1 Consensus size: 90
34546371 CTCCTCTTTG
* *
34546381 TCTTTCTTTTTCTCTTCTTTTTCTTCAACTTTTTCTTCTTCTACCTCGTCCTCTTTATCCTTCTT
1 TCTTTCTTTTTCTCTTCTTTTTCTTC-A-----TCTTCTTCTACCTCATCCTCTTTATAC-TCTT
* *
34546446 CTTTTC-T-TTC-T-TCTTCTCTTTCTTTTTA
59 CTTTTCTTCTTCTTCTCTTCTCTTTCTTCTTC
* * * * * * * *
34546474 TC-TTCTTTTTCTTCGTCTTTTTCTACCTCATC--CT-CTTTATCCT-TCT-T-CTTTTC-TTTC
1 TCTTTCTTTTTC-TCTTCTTTTTCTTCATCTTCTTCTACCTCATCCTCTTTATACTCTTCTTTTC
*
34546531 TTCTTC-TC-CTTGTCTTTCTTCTTC
65 TTCTTCTTCTCTTCTCTTTCTTCTTC
*
34546555 TCTTTCTTTTTCTCTTCTTTTTCTCCATTTTCATCTTCTTCTACCTTATCCTCTTTA-AC-CTTC
1 TCTTTCTTTTTCTCTTC-TTTT-T-C---TTCATCTTCTTCTACCTCATCCTCTTTATACTCTTC
*
34546618 TTTTCTTTCTTCTTCTCTT-TCTTTTTCTCTTC
60 TTTTC-TTCTTCTTCTCTTCTCTTTCT-TCTTC
*
34546650 TTTTTCTT
1 TCTTTCTT
34546658 CATCCTCATC
Statistics
Matches: 141, Mismatches: 21, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
79 4 0.03
80 5 0.04
81 24 0.17
82 14 0.10
83 3 0.02
84 7 0.05
85 2 0.01
87 10 0.07
89 2 0.01
90 8 0.06
91 5 0.04
92 14 0.10
93 20 0.14
94 8 0.06
95 15 0.11
ACGTcount: A:0.05, C:0.30, G:0.01, T:0.64
Consensus pattern (90 bp):
TCTTTCTTTTTCTCTTCTTTTTCTTCATCTTCTTCTACCTCATCCTCTTTATACTCTTCTTTTCT
TCTTCTTCTCTTCTCTTTCTTCTTC
Found at i:34546631 original size:12 final size:12
Alignment explanation
Indices: 34546614--34546648 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
34546604 CCTCTTTAAC
*
34546614 CTTCTTTTCTTT
1 CTTCTTCTCTTT
34546626 CTTCTTCTCTTT
1 CTTCTTCTCTTT
*
34546638 CTTTTTCTCTT
1 CTTCTTCTCTT
34546649 CTTTTTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (12 bp):
CTTCTTCTCTTT
Found at i:34546646 original size:78 final size:78
Alignment explanation
Indices: 34546543--34546688 Score: 240
Period size: 78 Copynumber: 1.9 Consensus size: 78
34546533 CTTCTCCTTG
** *
34546543 TCTTTCTTCTTCTCTTTCTTTTTCTCTTCTTTTTCTCCATTTTCATCTTCTTCTACCT-TATCCT
1 TCTTTCTTCTTCTCTTTCTTTTTCTCTTCTTTTTCTCCATCCTCATCGTCTTCTACCTCT-TCCT
34546607 CTTTAACCTTCTTT
65 CTTTAACCTTCTTT
*
34546621 TCTTTCTTCTTCTCTTTCTTTTTCTCTTCTTTTTCTTCATCCTCATCGTCTTCTACCTCTTCCTC
1 TCTTTCTTCTTCTCTTTCTTTTTCTCTTCTTTTTCTCCATCCTCATCGTCTTCTACCTCTTCCTC
34546686 TTT
66 TTT
34546689 CTCCTTCTGC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
78 62 0.98
79 1 0.02
ACGTcount: A:0.06, C:0.32, G:0.01, T:0.61
Consensus pattern (78 bp):
TCTTTCTTCTTCTCTTTCTTTTTCTCTTCTTTTTCTCCATCCTCATCGTCTTCTACCTCTTCCTC
TTTAACCTTCTTT
Found at i:34546695 original size:78 final size:83
Alignment explanation
Indices: 34546533--34546720 Score: 194
Period size: 78 Copynumber: 2.3 Consensus size: 83
34546523 TTTCTTTCTT
* ** *
34546533 CTTCTCCTTGTCTTTCTTCTTCTCTT-TCTTTTTCTCTTCTTTTTCTCCATTTTCATCTTCTTCT
1 CTTCT-CTT-TCTTTCTTCTTCTCTTCTCTTTTTCTCTTCTTTTTCTTCATCCTCTTCTTCTTCT
*
34546597 ACCT-TATCCTCTTTA---AC
64 ACCTCT-TCCTCTTTATCCTC
* *
34546614 CTTCT-TTTCTTTCTTCTTCTCTT-TCTTTTTCTCTTCTTTTTCTTCATCCTCATCGTCTTCTAC
1 CTTCTCTTTCTTTCTTCTTCTCTTCTCTTTTTCTCTTCTTTTTCTTCATCCTCTTCTTCTTCTAC
*
34546677 CTCTTCCTCTTTCTCCTTC
66 CTCTTCCTCTTTATCC-TC
34546696 TGCTTCT-TTTCTTTCTTCTTCTCTT
1 --CTTCTCTTTCTTTCTTCTTCTCTT
34546721 TCCCCCCCTT
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
78 62 0.66
79 3 0.03
81 5 0.05
82 1 0.01
84 23 0.24
ACGTcount: A:0.05, C:0.33, G:0.02, T:0.61
Consensus pattern (83 bp):
CTTCTCTTTCTTTCTTCTTCTCTTCTCTTTTTCTCTTCTTTTTCTTCATCCTCTTCTTCTTCTAC
CTCTTCCTCTTTATCCTC
Found at i:34546822 original size:84 final size:86
Alignment explanation
Indices: 34546614--34546842 Score: 240
Period size: 84 Copynumber: 2.7 Consensus size: 86
34546604 CCTCTTTAAC
* * *
34546614 CTTCTTTTCTTTCTTCTTCT-CTT-T-CT-TTT-TCTCTTCTTTTTCTTCATCCTCATCGTCTTC
1 CTTCTTTTCTTTCTTCTTCTCCTTCTCCTCTTTGT-TTTTCTTTTTCTTCATCTTC-TCTTC-TC
*
34546674 TACCTCTTCCTCTTTCTCCTTCTG
63 TACCTCTTCCTCTTTCTCCTTCAG
* * * * * *
34546698 CTTCTTTTCTTTCTTCTTCTCTTTCCCCCCCTTGTCTTTCTTTTTCTTC-TCTTCT-TTCTCTCC
1 CTTCTTTTCTTTCTTCTTCTCCTTCTCCTCTTTGTTTTTCTTTTTCTTCATCTTCTCTTCTCTAC
34546761 CTCTTCCTC-TTCATCCTTCAG
66 CTCTTCCTCTTTC-TCCTTCAG
* * * *
34546782 CTTTTTTTCTTTCTTCTTCTCCTTCTCCTCTTTGTTTTTCTTCTTCTCCTTCTTCTCTTCT
1 CTTCTTTTCTTTCTTCTTCTCCTTCTCCTCTTTGTTTTTCTTTTTCTTCATCTTCTCTTCT
34546843 TTCTCTTCAT
Statistics
Matches: 119, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
83 3 0.03
84 81 0.68
85 10 0.08
86 5 0.04
87 5 0.04
88 14 0.12
89 1 0.01
ACGTcount: A:0.02, C:0.36, G:0.02, T:0.60
Consensus pattern (86 bp):
CTTCTTTTCTTTCTTCTTCTCCTTCTCCTCTTTGTTTTTCTTTTTCTTCATCTTCTCTTCTCTAC
CTCTTCCTCTTTCTCCTTCAG
Found at i:34546828 original size:30 final size:31
Alignment explanation
Indices: 34546785--34546844 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
34546775 CCTTCAGCTT
*
34546785 TTTTTCTTTCTTCTTCTCCTTCTCCTCTTTG
1 TTTTTCTTTCTTCTCCTCCTTCTCCTCTTTG
* *
34546816 TTTTTC-TTCTTCTCCTTCTTCTCTTCTTT
1 TTTTTCTTTCTTCTCCTCCTTCTCCTCTTT
34546845 CTCTTCATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTTTCTTTCTTCTCCTCCTTCTCCTCTTTG
Found at i:34546846 original size:9 final size:8
Alignment explanation
Indices: 34546440--34546860 Score: 52
Period size: 7 Copynumber: 53.6 Consensus size: 8
34546430 CCTCTTTATC
34546440 CTTCTTCT
1 CTTCTTCT
*
34546448 TTTCTT-T
1 CTTCTTCT
34546455 CTTCTTCT
1 CTTCTTCT
34546463 C-T-TTCT
1 CTTCTTCT
*
34546469 -TT-TTAT
1 CTTCTTCT
34546475 CTTCTT-T
1 CTTCTTCT
34546482 -TTCTTCGT
1 CTTCTTC-T
*
34546490 CTTTTTCT
1 CTTCTTCT
* *
34546498 ACCTCATCCT
1 -CTTC-TTCT
34546508 CTT-TATC-
1 CTTCT-TCT
34546515 CTTCTTCT
1 CTTCTTCT
*
34546523 TTTCTT-T
1 CTTCTTCT
34546530 CTTCTTCT
1 CTTCTTCT
34546538 CCTTGTCTT-T
1 -C-T-TCTTCT
34546548 CTTCTTCT
1 CTTCTTCT
34546556 C-T-TTCT
1 CTTCTTCT
34546562 -TT-TTCT
1 CTTCTTCT
34546568 CTTCTT-T
1 CTTCTTCT
34546575 -TTC-TC-
1 CTTCTTCT
34546580 CATT-TTCAT
1 C-TTCTTC-T
34546589 CTTCTTCT
1 CTTCTTCT
* *
34546597 ACCTTATCCT
1 --CTTCTTCT
34546607 CTTTAACCTTCT
1 C-TT---CTTCT
*
34546619 TTTCTT-T
1 CTTCTTCT
34546626 CTTCTTCT
1 CTTCTTCT
34546634 C-T-TTCT
1 CTTCTTCT
34546640 -TT-TTCT
1 CTTCTTCT
34546646 CTTCTT-T
1 CTTCTTCT
34546653 -TTCTTCAT
1 CTTCTTC-T
* *
34546661 CCTCATCGT
1 CTTCTTC-T
*
34546670 CTTCTACCT
1 CTTCT-TCT
*
34546679 CTTCCTCT
1 CTTCTTCT
*
34546687 -TTCTCCTT
1 CTTCTTC-T
*
34546695 CTGCTTCT
1 CTTCTTCT
*
34546703 TTTCTT-T
1 CTTCTTCT
34546710 CTTCTTCT
1 CTTCTTCT
* *
34546718 CTT-TCCC
1 CTTCTTCT
** *
34546725 CCCCTTGT
1 CTTCTTCT
34546733 CTTTCTT-T
1 C-TTCTTCT
34546741 -TTCTTCT
1 CTTCTTCT
34546748 CTTCTTTCT
1 CTTC-TTCT
34546757 CTCCCTCTTCCT
1 CT---TCTT-CT
*
34546769 CTTCATC-
1 CTTCTTCT
**
34546776 CTTCAGCT
1 CTTCTTCT
* *
34546784 TTTTTTCT
1 CTTCTTCT
34546792 -TTCTTCTT
1 CTTCTTC-T
*
34546800 CTCCTTCT
1 CTTCTTCT
*
34546808 CCTCTT-T
1 CTTCTTCT
*
34546815 GTT-TT-T
1 CTTCTTCT
34546821 CTTCTTCT
1 CTTCTTCT
34546829 CCTTCTTCT
1 -CTTCTTCT
34546838 CTTCTTTCT
1 CTTC-TTCT
*
34546847 CTTCATCAT
1 CTTCTTC-T
34546856 CTTCT
1 CTTCT
34546861 ACCTCATCCT
Statistics
Matches: 296, Mismatches: 56, Indels: 121
0.63 0.12 0.26
Matches are distributed among these distances:
5 1 0.00
6 49 0.17
7 73 0.25
8 72 0.24
9 72 0.24
10 12 0.04
11 8 0.03
12 9 0.03
ACGTcount: A:0.04, C:0.33, G:0.02, T:0.61
Consensus pattern (8 bp):
CTTCTTCT
Found at i:34546888 original size:102 final size:100
Alignment explanation
Indices: 34546744--34547106 Score: 393
Period size: 99 Copynumber: 3.7 Consensus size: 100
34546734 TTTCTTTTTC
* * * **
34546744 TTCTCTTC-T-TTC-TCTCCCTCTTCCTCTTCATCCTTCAGCTTTTTTTCTTTCTTCTTCTCCTT
1 TTCTCTTCATCTTCTTCTACCTCATCCTCTTTATCCTTGTGCTTTTTTTCTTTCTTCTTCTCCTT
* *
34546806 CTCCTCTTTGTTTTTCTTCTTCTCCTTCTTCTCTTCT
66 CTCCTCCTTGTCTTTCTTCTT-T-CTTCTTCTCTTCT
* * *
34546843 TTCTCTTCATCATCTTCTACCTCATCCTCTTTATCC---TGCTTCTTTTCTTTCTTTTTCTCCTT
1 TTCTCTTCATCTTCTTCTACCTCATCCTCTTTATCCTTGTGCTTTTTTTCTTTCTTCTTCTCCTT
* * * *
34546905 ATACTCCTCGTCTTTCTTCTTTTTCTTCTTATCTTCT
66 CTCCTCCTTGTCTTTCTTC--TTTCTTCTTCTCTTCT
* * * * * *
34546942 GTCTCTTCATCTTCTCCTACCTCATGCTCCTTATCCTTGTGCTTCTTTTCTTTCTTTTTCTCCTT
1 TTCTCTTCATCTTCTTCTACCTCATCCTCTTTATCCTTGTGCTTTTTTTCTTTCTTCTTCTCCTT
* *
34547007 CTCCTCCTTGTCTTTCTTC-TTCATCTTCTCATCT
66 CTCCTCCTTGTCTTTCTTCTTTCTTCTTCTCTTCT
* * *
34547041 TTTTCTTCATCTTCCTCTACCTCAACCTCTTTATCCTTGTGCTTTTTTTCATTT-TTCTTCT-CT
1 TTCTCTTCATCTTCTTCTACCTCATCCTCTTTATCCTTGTGCTTTTTTTC-TTTCTTCTTCTCCT
34547104 TCT
65 TCT
34547107 ATCTCTTCAT
Statistics
Matches: 222, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
98 5 0.02
99 148 0.67
100 5 0.02
101 4 0.02
102 60 0.27
ACGTcount: A:0.06, C:0.34, G:0.03, T:0.57
Consensus pattern (100 bp):
TTCTCTTCATCTTCTTCTACCTCATCCTCTTTATCCTTGTGCTTTTTTTCTTTCTTCTTCTCCTT
CTCCTCCTTGTCTTTCTTCTTTCTTCTTCTCTTCT
Found at i:34547047 original size:27 final size:27
Alignment explanation
Indices: 34546986--34547047 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
34546976 CCTTGTGCTT
* *
34546986 CTTTTCTTTCTTTTTCTCCTTCTCCTC
1 CTTTTCTTTCTTCTTCTCCTTCTCATC
*
34547013 CTTGTCTTTCTTCTTCAT-CTTCTCATC
1 CTTTTCTTTCTTCTTC-TCCTTCTCATC
*
34547040 TTTTTCTT
1 CTTTTCTT
34547048 CATCTTCCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.03, C:0.32, G:0.02, T:0.63
Consensus pattern (27 bp):
CTTTTCTTTCTTCTTCTCCTTCTCATC
Found at i:34547078 original size:72 final size:69
Alignment explanation
Indices: 34547002--34547147 Score: 154
Period size: 72 Copynumber: 2.1 Consensus size: 69
34546992 TTTCTTTTTC
*
34547002 TCCTTCTCCTCCTTGTC-TTTCTTCTTCATCTTCTCATCT-TT-TTCTTCATCTTCCTCTACCTC
1 TCCTTCTCCTCCTTGTCATTT-TTCTTC-TCTTCT-ATCTCTTCATCTTCATCTTCCTCTA---C
34547064 AACCTCTTTA
60 AACCTCTTTA
* * ** * *
34547074 TCCTTGTGCTTTTTTTCATTTTTCTTCTCTTCTATCTCTTCATCTTCATCTTCCTCTACGACCTC
1 TCCTTCTCCTCCTTGTCATTTTTCTTCTCTTCTATCTCTTCATCTTCATCTTCCTCTACAACCTC
34547139 TTTA
66 TTTA
34547143 TCCTT
1 TCCTT
34547148 ATGATTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
69 15 0.23
70 4 0.06
71 8 0.12
72 34 0.53
73 3 0.05
ACGTcount: A:0.10, C:0.34, G:0.03, T:0.53
Consensus pattern (69 bp):
TCCTTCTCCTCCTTGTCATTTTTCTTCTCTTCTATCTCTTCATCTTCATCTTCCTCTACAACCTC
TTTA
Found at i:34547114 original size:66 final size:67
Alignment explanation
Indices: 34547030--34547163 Score: 173
Period size: 66 Copynumber: 2.0 Consensus size: 67
34547020 TTCTTCTTCA
* * * * *
34547030 TCTTCTCATCTTTTTCTTCATCTTCCTCTACCTC-A-ACCTCTTTATCCTTGTGCTTTTTTTCAT
1 TCTTCTCATCTATCTCTTCATCTTCATCTACCTCTACACCTCTTTATCCTTATGATTTTTTTC-T
34547093 TTT
65 TTT
* *
34547096 TCTTCTCTTCTATCTCTTCATCTTCATCTTCCTCTACGACCTCTTTATCCTTATGATTTTTTTCT
1 TCTTCTCATCTATCTCTTCATCTTCATCTACCTCTAC-ACCTCTTTATCCTTATGATTTTTTTCT
34547161 TTT
65 TTT
34547164 ATCTCTTTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 29 0.50
67 1 0.02
68 4 0.07
69 24 0.41
ACGTcount: A:0.11, C:0.30, G:0.03, T:0.56
Consensus pattern (67 bp):
TCTTCTCATCTATCTCTTCATCTTCATCTACCTCTACACCTCTTTATCCTTATGATTTTTTTCTT
TT
Found at i:34551394 original size:17 final size:17
Alignment explanation
Indices: 34551374--34551411 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
34551364 AGGTAGATTT
*
34551374 TATTAAAAATATTTATA
1 TATTAAAAATATTTAAA
*
34551391 TATTAATAATATTTAAA
1 TATTAAAAATATTTAAA
34551408 TATT
1 TATT
34551412 CTTGTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAAAATATTTAAA
Found at i:34551449 original size:22 final size:21
Alignment explanation
Indices: 34551398--34551457 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
34551388 ATATATTAAT
* *
34551398 AATATTTAAATATTCTTGTAAAA
1 AATATTTAAATATT-AT-CAAAA
34551421 AATATTTAAATATTATCAAAA
1 AATATTTAAATATTATCAAAA
*
34551442 AATAATTTATATATTA
1 AAT-ATTTAAATATTA
34551458 ATATTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.21
22 12 0.36
23 14 0.42
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATTTAAATATTATCAAAA
Found at i:34554264 original size:1 final size:1
Alignment explanation
Indices: 34554258--34554288 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
34554248 AAATCACTTT
34554258 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
34554289 TTGTCAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:34567575 original size:3 final size:3
Alignment explanation
Indices: 34567567--34567591 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34567557 ATTAGAAACT
34567567 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
34567592 ATACAGGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:34573069 original size:2 final size:2
Alignment explanation
Indices: 34573064--34573096 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34573054 TTAAAAAAGA
34573064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34573097 AAACAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34578278 original size:18 final size:18
Alignment explanation
Indices: 34578255--34578293 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
34578245 TTGGGAAAGT
34578255 AAGATAAGATGACTTCGA
1 AAGATAAGATGACTTCGA
*
34578273 AAGATAAGATGACTTTGA
1 AAGATAAGATGACTTCGA
34578291 AAG
1 AAG
34578294 CAGCCAGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (18 bp):
AAGATAAGATGACTTCGA
Found at i:34583295 original size:23 final size:23
Alignment explanation
Indices: 34583252--34583300 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
34583242 TTATATTTAA
*
34583252 ATTATATATATTAAAAATATTTT
1 ATTATATATATTAAAAATATTAT
*
34583275 ATTATATATA-TAATAATTATTAT
1 ATTATATATATTAA-AAATATTAT
34583298 ATT
1 ATT
34583301 TTTTATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTATATATATTAAAAATATTAT
Found at i:34583610 original size:21 final size:21
Alignment explanation
Indices: 34583579--34583628 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
34583569 TTTAAAAAAA
* *
34583579 TTAAAATATTTTTTTTATTAATT
1 TTAAAAT-TTATTATTA-TAATT
*
34583602 TTAAAATTTATTATTATATTT
1 TTAAAATTTATTATTATAATT
34583623 TTAAAA
1 TTAAAA
34583629 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 7 0.29
23 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAAATTTATTATTATAATT
Found at i:34593631 original size:31 final size:30
Alignment explanation
Indices: 34593596--34593687 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
34593586 AATCATTAGT
* * **
34593596 TATAAGAGTTTATTTGATTTGAAATAAAAAA
1 TATAAGAGCTTATTTGACTCAAAAT-AAAAA
*
34593627 TATAAAAGCTTATTTGACTCAAAATAAAAA
1 TATAAGAGCTTATTTGACTCAAAATAAAAA
* * *
34593657 TATAAGAGCTTAATTGAAT-ACAATAAAAA
1 TATAAGAGCTTATTTGACTCAAAATAAAAA
34593686 TA
1 TA
34593688 CAAAAATTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.21
30 21 0.40
31 20 0.38
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (30 bp):
TATAAGAGCTTATTTGACTCAAAATAAAAA
Found at i:34620172 original size:16 final size:18
Alignment explanation
Indices: 34620147--34620189 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
34620137 TTTTTTATAA
*
34620147 TTTAAATATTAATA-T-T
1 TTTAATTATTAATAGTAT
*
34620163 TTTAATTATTATTAGTAT
1 TTTAATTATTAATAGTAT
34620181 TTTAATTAT
1 TTTAATTAT
34620190 GACTCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.52
17 1 0.04
18 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTAATTATTAATAGTAT
Found at i:34620181 original size:19 final size:18
Alignment explanation
Indices: 34620153--34620189 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
34620143 ATAATTTAAA
34620153 TATTAATATTTTTAATTAT
1 TATTAATA-TTTTAATTAT
*
34620172 TATTAGTATTTTAATTAT
1 TATTAATATTTTAATTAT
34620190 GACTCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTAATATTTTAATTAT
Found at i:34632363 original size:89 final size:88
Alignment explanation
Indices: 34632205--34632389 Score: 230
Period size: 89 Copynumber: 2.1 Consensus size: 88
34632195 CTCTTTAAAT
* * * *
34632205 TGTTTTTTTTTGGTATGAACTTTAAATTTTCACATTTATGCAAATTTGTGTTAAATTAAGGTTGA
1 TGTTTTTTTTTCGTATGAACTTTAAATTTTCACACTCATGCAAATTTGTGTTAAATTAAGATTGA
34632270 TGTCATTTAGTACTAAAGTGGG-
66 TGTCATTTAGTACTAAAGTGGGA
* * *
34632292 TGTTTTTTCTTTCGTATGAAGTTTGAATTTTGATCACTCATGCAAATTTGTGTTAAAATT-AGAT
1 TGTTTTTT-TTTCGTATGAACTTTAAATTTTCA-CACTCATGCAAATTTGTGTT-AAATTAAGAT
* **
34632356 TGGTGTCATTTAGTTGTAAAGTGGGA
63 TGATGTCATTTAGTACTAAAGTGGGA
34632382 TTGTTTTT
1 -TGTTTTT
34632390 AACTCTTAAC
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
87 8 0.10
88 20 0.24
89 43 0.52
90 5 0.06
91 7 0.08
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.48
Consensus pattern (88 bp):
TGTTTTTTTTTCGTATGAACTTTAAATTTTCACACTCATGCAAATTTGTGTTAAATTAAGATTGA
TGTCATTTAGTACTAAAGTGGGA
Found at i:34642887 original size:61 final size:61
Alignment explanation
Indices: 34642792--34642916 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
34642782 CATTTAACTA
34642792 AGATCCTTTATTATGAAATAAACGATCATTGCATGCAAAAAAATTAAACCAAAAATAAATC
1 AGATCCTTTATTATGAAATAAACGATCATTGCATGCAAAAAAATTAAACCAAAAATAAATC
34642853 AGATCCTTTATTATGAAATAAACGATCATTGCATGCAAAAAAATTAAACCAAAAATAAATC
1 AGATCCTTTATTATGAAATAAACGATCATTGCATGCAAAAAAATTAAACCAAAAATAAATC
34642914 AGA
1 AGA
34642917 AAATTGTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (61 bp):
AGATCCTTTATTATGAAATAAACGATCATTGCATGCAAAAAAATTAAACCAAAAATAAATC
Found at i:34648705 original size:19 final size:19
Alignment explanation
Indices: 34648650--34648706 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
34648640 ACAAAACAAC
* *
34648650 AAATTATTATATTTTT-GT
1 AAATTTTTATATTTTTATT
34648668 AAATTTTT-TATTATATTATT
1 AAATTTTTATATT-T-TTATT
*
34648688 AAGTTTTTATATTTTTATT
1 AAATTTTTATATTTTTATT
34648707 TTGAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.12
18 8 0.25
19 7 0.22
20 9 0.28
21 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
AAATTTTTATATTTTTATT
Found at i:34650572 original size:22 final size:22
Alignment explanation
Indices: 34650547--34650592 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
34650537 CTTAAAAGAT
34650547 AAACTACAACCGTTGCCTTTAA
1 AAACTACAACCGTTGCCTTTAA
34650569 AAACTACAACCGTTGCCTTTAA
1 AAACTACAACCGTTGCCTTTAA
34650591 AA
1 AA
34650593 GTTATTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (22 bp):
AAACTACAACCGTTGCCTTTAA
Found at i:34656023 original size:26 final size:26
Alignment explanation
Indices: 34655994--34656048 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
34655984 ATACTTTTAT
* * *
34655994 AAACTTCTCTTTTATTATATTCAATC
1 AAACTTCTATATTATTATATTAAATC
* *
34656020 AAACTTTTATATTATTATTTTAAATC
1 AAACTTCTATATTATTATATTAAATC
34656046 AAA
1 AAA
34656049 TAAATTCTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (26 bp):
AAACTTCTATATTATTATATTAAATC
Found at i:34656212 original size:27 final size:28
Alignment explanation
Indices: 34656182--34656241 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
34656172 CAACGTCACA
34656182 TAAATAT-A-AAAAAATAAAAAATTTAAT
1 TAAATATAATAAAAAAT-AAAAATTTAAT
* *
34656209 TAAACATAATAAAAAATAAAAATTTATT
1 TAAATATAATAAAAAATAAAAATTTAAT
34656237 TAAAT
1 TAAAT
34656242 TTATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 15 0.54
29 7 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAATATAATAAAAAATAAAAATTTAAT
Found at i:34659463 original size:15 final size:15
Alignment explanation
Indices: 34659443--34659482 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
34659433 GTTATCATCA
34659443 AATACTATTTATCTT
1 AATACTATTTATCTT
34659458 AATACT-TTTAT-TT
1 AATACTATTTATCTT
*
34659471 CA-ACTATTTATC
1 AATACTATTTATC
34659483 CAAACATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
12 3 0.14
13 8 0.36
14 5 0.23
15 6 0.27
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (15 bp):
AATACTATTTATCTT
Found at i:34662615 original size:29 final size:28
Alignment explanation
Indices: 34662545--34662617 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
34662535 CTAAGAAAAT
34662545 TTAAATAAATTTTTATTTTTTTATTACA
1 TTAAATAAATTTTTATTTTTTTATTACA
* *
34662573 TTGAATCAAGTTTTTATATTTTATT-TTGA-A
1 TTAAAT-AAATTTTTAT-TTTT-TTATT-ACA
34662603 TTAAATAAATTTTTA
1 TTAAATAAATTTTTA
34662618 CAAGTAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
28 5 0.14
29 17 0.46
30 12 0.32
31 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.58
Consensus pattern (28 bp):
TTAAATAAATTTTTATTTTTTTATTACA
Found at i:34662925 original size:2 final size:2
Alignment explanation
Indices: 34662920--34662953 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34662910 CTTTAATAGA
34662920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34662954 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34662966 original size:12 final size:12
Alignment explanation
Indices: 34662951--34662975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34662941 TATATATATA
34662951 TATGTGTGTGTG
1 TATGTGTGTGTG
34662963 TATGTGTGTGTG
1 TATGTGTGTGTG
34662975 T
1 T
34662976 GCGCGCATGC
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:0.08, C:0.00, G:0.40, T:0.52
Consensus pattern (12 bp):
TATGTGTGTGTG
Found at i:34670304 original size:16 final size:17
Alignment explanation
Indices: 34670265--34670311 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
34670255 CTCCCAAGGA
34670265 AAGGGAGCATC-GATCG
1 AAGGGAGCATCAGATCG
*
34670281 AGAGGGAGCACCAGATC-
1 A-AGGGAGCATCAGATCG
34670298 AAGGGAGCATCAGA
1 AAGGGAGCATCAGA
34670312 GGGAGCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 13 0.48
17 10 0.37
18 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.36, T:0.09
Consensus pattern (17 bp):
AAGGGAGCATCAGATCG
Found at i:34670955 original size:21 final size:20
Alignment explanation
Indices: 34670937--34670979 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
34670927 ATAAAATACC
*
34670937 AATATATCATTTTTAAATAAA
1 AATATAT-ATGTTTAAATAAA
34670958 AATATATATGTTTAATATAAA
1 AATATATATGTTTAA-ATAAA
34670979 A
1 A
34670980 TAATATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AATATATATGTTTAAATAAA
Found at i:34670974 original size:19 final size:21
Alignment explanation
Indices: 34670937--34670985 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
34670927 ATAAAATACC
*
34670937 AATATATCATTTTTAAATA-AA
1 AATATAT-ATGTTTAAATATAA
34670958 AATATATATGTTT-AATATAA
1 AATATATATGTTTAAATATAA
34670978 AATA-ATAT
1 AATATATAT
34670986 TATTTTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.31
20 11 0.42
21 7 0.27
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATATATGTTTAAATATAA
Found at i:34670992 original size:21 final size:19
Alignment explanation
Indices: 34670937--34670992 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 19
34670927 ATAAAATACC
34670937 AATATATCATTTTTAAATAAA
1 AATATAT-A-TTTTAAATAAA
34670958 AATATATATGTTT-AATATAA
1 AATATATAT-TTTAAATA-AA
34670978 AATAATATTATTTTA
1 AAT-ATA-TATTTTA
34670993 TTCAACAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
19 5 0.17
20 9 0.30
21 13 0.43
22 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
AATATATATTTTAAATAAA
Found at i:34671049 original size:2 final size:2
Alignment explanation
Indices: 34671042--34671092 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
34671032 AACTTCATAA
*
34671042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
34671084 AT GT AT AT A
1 AT AT AT AT A
34671093 CTTTTATTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34683323 original size:2 final size:2
Alignment explanation
Indices: 34683316--34683346 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34683306 TTATTATTAT
34683316 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 T
34683347 GTTATTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34683852 original size:2 final size:2
Alignment explanation
Indices: 34683845--34683876 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34683835 TGCATATCAA
34683845 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
34683877 TTCATATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34684773 original size:24 final size:23
Alignment explanation
Indices: 34684746--34684793 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
34684736 AGCAAAAGAG
*
34684746 AAGCAATGCCAAGAAGCGAAAGCC
1 AAGCAATGACAAGAAGC-AAAGCC
* *
34684770 AAGCAGTGAGAAGAAGCAAAGCC
1 AAGCAATGACAAGAAGCAAAGCC
34684793 A
1 A
34684794 GAGAAACAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.48, C:0.21, G:0.27, T:0.04
Consensus pattern (23 bp):
AAGCAATGACAAGAAGCAAAGCC
Found at i:34686327 original size:18 final size:19
Alignment explanation
Indices: 34686304--34686339 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34686294 AATATTTAAA
34686304 TAAG-TTTTATATTTTTAT
1 TAAGTTTTTATATTTTTAT
*
34686322 TAAGTTTTTGTATTTTTA
1 TAAGTTTTTATATTTTTA
34686340 ACATATCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TAAGTTTTTATATTTTTAT
Found at i:34686441 original size:30 final size:29
Alignment explanation
Indices: 34686407--34686474 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
34686397 ATCGTCAGTA
34686407 ATAAAG-TTCATTTGACTCAAAATAAAAAGT
1 ATAAAGATTCA-TTGACTCAAAATAAAAA-T
* * *
34686437 ATAAAGATTTATTGATTTAAAATAAAAAT
1 ATAAAGATTCATTGACTCAAAATAAAAAT
34686466 ATAAAGATT
1 ATAAAGATT
34686475 TGATTGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 10 0.29
30 21 0.62
31 3 0.09
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (29 bp):
ATAAAGATTCATTGACTCAAAATAAAAAT
Found at i:34686481 original size:30 final size:30
Alignment explanation
Indices: 34686425--34686481 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
34686415 CATTTGACTC
34686425 AAAATAAAAAGTATAAAGATTTATTGATTT
1 AAAATAAAAAGTATAAAGATTTATTGATTT
34686455 AAAATAAAAA-TATAAAGATTTGATTGA
1 AAAATAAAAAGTATAAAGATTT-ATTGA
34686482 ACGTAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (30 bp):
AAAATAAAAAGTATAAAGATTTATTGATTT
Found at i:34686489 original size:29 final size:28
Alignment explanation
Indices: 34686426--34686507 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
34686416 ATTTGACTCA
**
34686426 AAATAAAAAGTATAAAGATTTATTGATTT
1 AAATAAAAA-TATAAAGATTTATTGACGT
34686455 AAAATAAAAATATAAAGATTTGATTGAACGT
1 -AAATAAAAATATAAAGATTT-ATTG-ACGT
*
34686486 -AATAAAAGTATAAA-AGTTTATT
1 AAATAAAAATATAAAGA-TTTATT
34686508 TGAATTTTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
28 4 0.09
29 27 0.59
30 13 0.28
31 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.11, T:0.34
Consensus pattern (28 bp):
AAATAAAAATATAAAGATTTATTGACGT
Found at i:34694118 original size:29 final size:30
Alignment explanation
Indices: 34694063--34694122 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
34694053 TTAAAGAGAC
* **
34694063 TTATTTGAATAAAAATAAAAATTTAAGAAT
1 TTATTTAAATAAAAATAAAAAGATAAGAAT
*
34694093 TTATTTAAAT-AAAATAAAAGGATAAGAAT
1 TTATTTAAATAAAAATAAAAAGATAAGAAT
34694122 T
1 T
34694123 AAATTAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (30 bp):
TTATTTAAATAAAAATAAAAAGATAAGAAT
Found at i:34713925 original size:38 final size:38
Alignment explanation
Indices: 34713869--34713945 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
34713859 GATCAAACAG
* *
34713869 TGATTTTATAATGTTATAAATATTGTTGTGAATCGATT
1 TGATGTTATAATGTTATAAATATTGTTGTGAATAGATT
34713907 TGATGTTATAATGTTATAAATATTGTTGTGAATAGATT
1 TGATGTTATAATGTTATAAATATTGTTGTGAATAGATT
34713945 T
1 T
34713946 TTACTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.49
Consensus pattern (38 bp):
TGATGTTATAATGTTATAAATATTGTTGTGAATAGATT
Found at i:34714847 original size:22 final size:22
Alignment explanation
Indices: 34714795--34714849 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
34714785 GTATTGCATT
*
34714795 ACTGATTTTTAGACATTGTGTC
1 ACTGATTTTTAGACATTGTGAC
** *
34714817 ACT-AGTTTTTAGGTATTGTGAG
1 ACTGA-TTTTTAGACATTGTGAC
34714839 ACTGATTTTTA
1 ACTGATTTTTA
34714850 AGCATTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (22 bp):
ACTGATTTTTAGACATTGTGAC
Found at i:34715118 original size:22 final size:22
Alignment explanation
Indices: 34715056--34715118 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
34715046 AAAATCAATC
* * *
34715056 ATGTGACTGGTTTTTAAGCATT
1 ATGTGATTGATTTTTAAGCACT
* * *
34715078 ACGTGGTTAGATTTGTAAGCACT
1 ATGTGATT-GATTTTTAAGCACT
34715101 ATGTGATTGATTTTTAAG
1 ATGTGATTGATTTTTAAG
34715119 TAATGTCTAA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (22 bp):
ATGTGATTGATTTTTAAGCACT
Found at i:34715173 original size:20 final size:20
Alignment explanation
Indices: 34715148--34715186 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34715138 TACCTAAATA
*
34715148 CTAGTCACTCAATACCTTAG
1 CTAGTCACGCAATACCTTAG
34715168 CTAGTCACGCAATACCTTA
1 CTAGTCACGCAATACCTTA
34715187 CTAACTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.28
Consensus pattern (20 bp):
CTAGTCACGCAATACCTTAG
Found at i:34715202 original size:23 final size:22
Alignment explanation
Indices: 34715128--34715203 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
34715118 GTAATGTCTA
* *
34715128 AGTCATACAATACC-TAAATACT
1 AGTCATGCAATACCTTATA-ACT
*
34715150 AGTCACT-CAATACC-T-TAGCT
1 AGTCA-TGCAATACCTTATAACT
*
34715170 AGTCACGCAATACCTTACTAACT
1 AGTCATGCAATACCTTA-TAACT
34715193 AGTCATGCAAT
1 AGTCATGCAAT
34715204 GCCTATCAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
20 14 0.32
21 2 0.05
22 13 0.30
23 15 0.34
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (22 bp):
AGTCATGCAATACCTTATAACT
Found at i:34715262 original size:22 final size:22
Alignment explanation
Indices: 34715234--34715288 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
34715224 ATGTCATATC
* *
34715234 AATCAGTTATGTAATACCTAAA
1 AATCAGTCACGTAATACCTAAA
*
34715256 AATCAGTCACGTAATACTTAAA
1 AATCAGTCACGTAATACCTAAA
*
34715278 AATTAGTCACG
1 AATCAGTCACG
34715289 CAATGCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (22 bp):
AATCAGTCACGTAATACCTAAA
Found at i:34715298 original size:21 final size:21
Alignment explanation
Indices: 34715246--34715300 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
34715236 TCAGTTATGT
*
34715246 AATACCTAAAAATCAGTCACGT
1 AATA-CTAAAAATCAGTCACGC
*
34715268 AATACTTAAAAATTAGTCACGC
1 AATAC-TAAAAATCAGTCACGC
*
34715290 AATGCTAAAAA
1 AATACTAAAAA
34715301 ACCAATTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (21 bp):
AATACTAAAAATCAGTCACGC
Found at i:34715515 original size:60 final size:60
Alignment explanation
Indices: 34715417--34715542 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
34715407 CTTGACGAAG
* * *
34715417 AATGCTCAAAATGTTCAAAGATTTTTCTTCATACATCAAAAA-TCACTCTAAAATGCTT-AA
1 AATGCTCAAAATGTACAAAAATTTTTCTTCATACATCAAAAACT-ACTCCAAAATG-TTCAA
* **
34715477 AATGCTCAAAATGTACAAAAATTTTTCTTCGTGTATCAAAAACTACTCCAAAATGTTCAA
1 AATGCTCAAAATGTACAAAAATTTTTCTTCATACATCAAAAACTACTCCAAAATGTTCAA
34715537 AATGCT
1 AATGCT
34715543 TAAAGTTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
59 2 0.03
60 55 0.95
61 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (60 bp):
AATGCTCAAAATGTACAAAAATTTTTCTTCATACATCAAAAACTACTCCAAAATGTTCAA
Found at i:34719143 original size:28 final size:28
Alignment explanation
Indices: 34719103--34719158 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34719093 GTGAACTGAA
34719103 GTAAACCCAATTCCCAACATCTAATTGT
1 GTAAACCCAATTCCCAACATCTAATTGT
34719131 GTAAACCCAATTCCCAACATCTAATTGT
1 GTAAACCCAATTCCCAACATCTAATTGT
34719159 TTTGCTGCTA
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:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (28 bp):
GTAAACCCAATTCCCAACATCTAATTGT
Found at i:34721187 original size:61 final size:61
Alignment explanation
Indices: 34721101--34721218 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
34721091 AATTGTCTCA
34721101 AAATTCGTAAACTCTTTTTAAAAAATACTTGAATAATCACAAAGAGATCATGCCAAGTCAT
1 AAATTCGTAAACTCTTTTTAAAAAATACTTGAATAATCACAAAGAGATCATGCCAAGTCAT
* **
34721162 AAATTCGTGAACTCTTTTTGGAAAATACTTGAATAATCACAAAGAGATCATGCCAAG
1 AAATTCGTAAACTCTTTTTAAAAAATACTTGAATAATCACAAAGAGATCATGCCAAG
34721219 CTTGCCTTGC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (61 bp):
AAATTCGTAAACTCTTTTTAAAAAATACTTGAATAATCACAAAGAGATCATGCCAAGTCAT
Found at i:34723053 original size:18 final size:18
Alignment explanation
Indices: 34723011--34723054 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
34723001 AACATATGGA
34723011 AAAATATAAATAAAAATT
1 AAAATATAAATAAAAATT
* *
34723029 AAGATATAGAT-AAAATT
1 AAAATATAAATAAAAATT
34723046 ATAAATATA
1 A-AAATATA
34723055 TACCTCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATATAAATAAAAATT
Found at i:34725517 original size:16 final size:16
Alignment explanation
Indices: 34725496--34725539 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
34725486 AGCCGACTAC
34725496 GGAGTAACCGACCGCG
1 GGAGTAACCGACCGCG
*
34725512 GGAGTAACCGACCGTG
1 GGAGTAACCGACCGCG
*
34725528 AGA-TAACCGACC
1 GGAGTAACCGACC
34725540 AATACAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.30, C:0.30, G:0.32, T:0.09
Consensus pattern (16 bp):
GGAGTAACCGACCGCG
Found at i:34728091 original size:2 final size:2
Alignment explanation
Indices: 34728084--34728175 Score: 91
Period size: 2 Copynumber: 46.0 Consensus size: 2
34728074 ATCAGGACAG
* * *
34728084 GA GA GA GA GA GA CA GA GA GA GA GA GA GG GA GA GA GA GA -A CTA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -GA
* *
34728126 CGA -A AA NGA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA GG GA
1 -GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34728168 GA GA GA GA
1 GA GA GA GA
34728176 ACTCAAAAGG
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
1 3 0.04
2 70 0.91
3 4 0.05
ACGTcount: A:0.49, C:0.03, G:0.46, T:0.01
Consensus pattern (2 bp):
GA
Found at i:34730217 original size:17 final size:17
Alignment explanation
Indices: 34730183--34730215 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34730173 AATTATTTAA
34730183 AATTTTTTAAATAATTT
1 AATTTTTTAAATAATTT
34730200 AATTTTTTAAA-AATTT
1 AATTTTTTAAATAATTT
34730216 TATGTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTTTTAAATAATTT
Found at i:34735117 original size:183 final size:183
Alignment explanation
Indices: 34734797--34735529 Score: 1092
Period size: 183 Copynumber: 4.0 Consensus size: 183
34734787 GTATTACTTA
34734797 CTTGACTGCCTTTTCTGCTCAAATCTCTTGGTGACCTTCGAGGTTTTAAGCAATCTGTAGTGAGA
1 CTTGACTGCCTTTTCTGCTCAAATCTCTTGGTGACCTTCGAGGTTTTAAGCAATCTGTAGTGAGA
* *
34734862 TCATTTTTCTTGCACTTGTTTGGGGTGTTAACCTTCTGATCACCTGTGTCACCTGAAGTAGAACT
66 TCATTTTTCTTGCACTTGTTTGGGGTGTTAATCTTCTGATCACCTGTGTCACCTGAAGTACAACT
* *
34734927 CTCTTTGGGCTGAGTGAAGTTGGAATCATGTACGTCTCTGACACTATCATCCT
131 TTCTTTGGGCTGAGTGAAGTTGGAATCACGTACGTCTCTGACACTATCATCCT
* * * *
34734980 CTTGACTGCCTCTTCTGTTCAAATCTCTTGGGGACCTTCGAGATTTTAAGCAATCTGTAGTGAGA
1 CTTGACTGCCTTTTCTGCTCAAATCTCTTGGTGACCTTCGAGGTTTTAAGCAATCTGTAGTGAGA
*
34735045 TCGTTTTTCTTGCACTTGTTTGGGGTGTTAATCTTCTGATCACCTGTGTCACCTGAAGTACAACT
66 TCATTTTTCTTGCACTTGTTTGGGGTGTTAATCTTCTGATCACCTGTGTCACCTGAAGTACAACT
* * ** * * *
34735110 TTCTTTGGGTTGAGTGAACTTAAAATCACGCATGTCTCTAACACTATCATCCT
131 TTCTTTGGGCTGAGTGAAGTTGGAATCACGTACGTCTCTGACACTATCATCCT
* **
34735163 CTTGACTGCCTTTTCTGCTCAAATCTCTTGATGAGGTTCGAGGTTTTAAGCAATCTGTAGTGAGA
1 CTTGACTGCCTTTTCTGCTCAAATCTCTTGGTGACCTTCGAGGTTTTAAGCAATCTGTAGTGAGA
* * *
34735228 TCATTTTTCTTGCACTTGTTTGGGGCGTTAATCTTCTGATCACCAGTGTCACCAGAAGTACAACT
66 TCATTTTTCTTGCACTTGTTTGGGGTGTTAATCTTCTGATCACCTGTGTCACCTGAAGTACAACT
* * * * *
34735293 TTCTTTGGGCTGATTGAAGTTGGAATCACATACGTCTTTGACAGC-ATCATTCA
131 TTCTTTGGGCTGAGTGAAGTTGGAATCACGTACGTCTCTGACA-CTATCATCCT
* *
34735346 CTTGACTGACCTTTT-TTCTCAAATCTCTTGGTGACCTTCGAGGTTTTAAGCAATCTGTATTGAG
1 CTTGACTG-CCTTTTCTGCTCAAATCTCTTGGTGACCTTCGAGGTTTTAAGCAATCTGTAGTGAG
*
34735410 ATCATTTTTCTTACACTTGTTTGGGGTGTTAATCTTCTGATCACCTGTGTCACCTGAAGTACAAC
65 ATCATTTTTCTTGCACTTGTTTGGGGTGTTAATCTTCTGATCACCTGTGTCACCTGAAGTACAAC
* * * * * * * *
34735475 TTTCTTTGTGCTGAGTGAGGTTGCACTCATGTATGTCTTTGATACTATCATCCT
130 TTTCTTTGGGCTGAGTGAAGTTGGAATCACGTACGTCTCTGACACTATCATCCT
34735529 C
1 C
34735530 CTTACCATGA
Statistics
Matches: 488, Mismatches: 59, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
182 1 0.00
183 480 0.98
184 7 0.01
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (183 bp):
CTTGACTGCCTTTTCTGCTCAAATCTCTTGGTGACCTTCGAGGTTTTAAGCAATCTGTAGTGAGA
TCATTTTTCTTGCACTTGTTTGGGGTGTTAATCTTCTGATCACCTGTGTCACCTGAAGTACAACT
TTCTTTGGGCTGAGTGAAGTTGGAATCACGTACGTCTCTGACACTATCATCCT
Found at i:34739958 original size:2 final size:2
Alignment explanation
Indices: 34739951--34739992 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
34739941 CATTAAATGA
34739951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34739992 A
1 A
34739993 CTTAAATCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34746433 original size:22 final size:22
Alignment explanation
Indices: 34746408--34746449 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34746398 ATATGTTTAC
*
34746408 TTAATCGTATTATCGTGTTTGT
1 TTAATCATATTATCGTGTTTGT
*
34746430 TTAATCATGTTATCGTGTTT
1 TTAATCATATTATCGTGTTT
34746450 AAATGTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.55
Consensus pattern (22 bp):
TTAATCATATTATCGTGTTTGT
Found at i:34746546 original size:12 final size:12
Alignment explanation
Indices: 34746526--34746557 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34746516 ATATAAATAA
*
34746526 TTTTAAATAATT
1 TTTTTAATAATT
34746538 TTTTTAATAATT
1 TTTTTAATAATT
34746550 TTTTTAAT
1 TTTTTAAT
34746558 TTTATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTAATAATT
Found at i:34746667 original size:20 final size:19
Alignment explanation
Indices: 34746632--34746672 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
34746622 GATATTATTT
**
34746632 TTATTTTTATTTTTTTATAA
1 TTATTTTTATAATTTTA-AA
34746652 TTATTTTTATAATTTTAAA
1 TTATTTTTATAATTTTAAA
34746671 TT
1 TT
34746673 TTAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTTATAATTTTAAA
Found at i:34746735 original size:9 final size:9
Alignment explanation
Indices: 34746718--34746817 Score: 112
Period size: 9 Copynumber: 11.1 Consensus size: 9
34746708 AATTTTTTAT
34746718 TTAATCGTG
1 TTAATCGTG
*
34746727 TTAAACGTG
1 TTAATCGTG
*
34746736 TTAATCGTA
1 TTAATCGTG
*
34746745 TTAAACGTG
1 TTAATCGTG
34746754 TTAATCGTG
1 TTAATCGTG
*
34746763 TTAAACGTG
1 TTAATCGTG
*
34746772 TTAATCGTA
1 TTAATCGTG
*
34746781 TTAAAT-ATG
1 TT-AATCGTG
*
34746790 TTAATCATG
1 TTAATCGTG
*
34746799 TTAAACGTG
1 TTAATCGTG
34746808 TTAATCGTG
1 TTAATCGTG
34746817 T
1 T
34746818 CGTATCGTAT
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
8 3 0.04
9 69 0.92
10 3 0.04
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (9 bp):
TTAATCGTG
Found at i:34746741 original size:18 final size:18
Alignment explanation
Indices: 34746718--34746817 Score: 155
Period size: 18 Copynumber: 5.6 Consensus size: 18
34746708 AATTTTTTAT
34746718 TTAATCGTGTTAAACGTG
1 TTAATCGTGTTAAACGTG
*
34746736 TTAATCGTATTAAACGTG
1 TTAATCGTGTTAAACGTG
34746754 TTAATCGTGTTAAACGTG
1 TTAATCGTGTTAAACGTG
* **
34746772 TTAATCGTATTAAATATG
1 TTAATCGTGTTAAACGTG
*
34746790 TTAATCATGTTAAACGTG
1 TTAATCGTGTTAAACGTG
34746808 TTAATCGTGT
1 TTAATCGTGT
34746818 CGTATCGTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (18 bp):
TTAATCGTGTTAAACGTG
Found at i:34748366 original size:30 final size:32
Alignment explanation
Indices: 34748309--34748376 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
34748299 TGATTTTTTT
*
34748309 TAAAAAATATAATAATAGTAATTTTAAAGTTAA
1 TAAAAAATATAATAATAG-AATTTTAAAATTAA
*
34748342 TAAAAAATAT-ATAATA-ATTTTTAAAATTAA
1 TAAAAAATATAATAATAGAATTTTAAAATTAA
34748372 TAAAA
1 TAAAA
34748377 GTTAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 17 0.52
32 6 0.18
33 10 0.30
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (32 bp):
TAAAAAATATAATAATAGAATTTTAAAATTAA
Found at i:34749140 original size:33 final size:34
Alignment explanation
Indices: 34749076--34749142 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
34749066 GTGAGGGGGA
* * *
34749076 AAGGAGGGGCTGGTGCTGCCGGTTTGTGAGAGAG
1 AAGGAAGGGCTGGTGCCGCCGGTTTGGGAGAGAG
34749110 AAGGAAGGGCT-GTGCCGCCGGTTTGGGAGAGAG
1 AAGGAAGGGCTGGTGCCGCCGGTTTGGGAGAGAG
34749143 CTTAGGAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 20 0.67
34 10 0.33
ACGTcount: A:0.19, C:0.13, G:0.49, T:0.18
Consensus pattern (34 bp):
AAGGAAGGGCTGGTGCCGCCGGTTTGGGAGAGAG
Found at i:34753927 original size:22 final size:22
Alignment explanation
Indices: 34753885--34753927 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
34753875 AAAATTCATA
*
34753885 TGAAAATTATACAAATAAATCT
1 TGAAAATTATACAAAGAAATCT
* *
34753907 TGAAAATTATTCAAAGGAATC
1 TGAAAATTATACAAAGAAATC
34753928 AATATTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
TGAAAATTATACAAAGAAATCT
Found at i:34754744 original size:26 final size:25
Alignment explanation
Indices: 34754729--34754783 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 25
34754719 AAATTATTAT
34754729 AAAAATAAAATTTAAAAATTTTAAA
1 AAAAATAAAATTTAAAAATTTTAAA
34754754 AAAAATAAAAATATGTTAAAAATTTTAAA
1 AAAAAT--AAA-AT-TTAAAAATTTTAAA
34754783 A
1 A
34754784 TATTTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 6 0.23
27 3 0.12
28 2 0.08
29 15 0.58
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAAATAAAATTTAAAAATTTTAAA
Found at i:34762173 original size:23 final size:23
Alignment explanation
Indices: 34762135--34762178 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
34762125 AATTATGAGT
34762135 AAAATTTATATAATTTATAAATAA
1 AAAATTTATATAATTT-TAAATAA
*
34762159 AAAATTTA-ATTATTTTAAAT
1 AAAATTTATATAATTTTAAAT
34762179 GATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATTTATATAATTTTAAATAA
Found at i:34766471 original size:38 final size:39
Alignment explanation
Indices: 34766419--34766507 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 39
34766409 ATACAATATT
* * * *
34766419 CAACTCAAACCAATAAAACCCTAACTTTGTATAACAC-A
1 CAACTCAAATCAATAAAACCCTAACTTTATACAAAACGA
* *
34766457 CAACTCAAATCAATATAACTCTAACTTTATACAAAACGA
1 CAACTCAAATCAATAAAACCCTAACTTTATACAAAACGA
34766496 -AACTCAAATCAA
1 CAACTCAAATCAA
34766508 ATTCAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
38 43 0.98
39 1 0.02
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.22
Consensus pattern (39 bp):
CAACTCAAATCAATAAAACCCTAACTTTATACAAAACGA
Found at i:34766602 original size:95 final size:95
Alignment explanation
Indices: 34766435--34766632 Score: 265
Period size: 95 Copynumber: 2.1 Consensus size: 95
34766425 AAACCAATAA
* * *
34766435 AACCCTAACTTTGTATAACACACAACTCAAATCAATATAACTCTAACTTTATACAAAACGAAACT
1 AACCCTAACTTTATACAACACACAACTCAAATCAATATAACCCTAACTTTATACAAAACGAAACT
*
34766500 CAAATCAAATTCAAATTTAAATCATTATAC
66 CAAATCAAATTCAAACTTAAATCATTATAC
* * * * *
34766530 AACCCTAACTTTATACAATACACAATTCAAA-CTAATATAACCCTAATTTTGTACAACAC-ACAA
1 AACCCTAACTTTATACAACACACAACTCAAATC-AATATAACCCTAACTTTATACAAAACGA-AA
* *
34766593 CTCAGATCAAATTCAAACTTAAATCATTATAT
64 CTCAAATCAAATTCAAACTTAAATCATTATAC
34766625 AACCCTAA
1 AACCCTAA
34766633 TCTCACAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
94 2 0.02
95 88 0.98
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.28
Consensus pattern (95 bp):
AACCCTAACTTTATACAACACACAACTCAAATCAATATAACCCTAACTTTATACAAAACGAAACT
CAAATCAAATTCAAACTTAAATCATTATAC
Found at i:34776403 original size:217 final size:218
Alignment explanation
Indices: 34776028--34776463 Score: 820
Period size: 217 Copynumber: 2.0 Consensus size: 218
34776018 AAAGTTAAAT
34776028 GGATCAGAAACAAAGGCTTTGGTCAGGAAGTAACTAGAAAGTTGCCTACTTTCCTTTTGGGTCTT
1 GGATCAGAAACAAAGGCTTTGGTCAGGAAGTAACTAGAAAGTTGCCTACTTTCCTTTTGGGTCTT
* *
34776093 TGTTTATAGTTTTCTATTACGCGGAGACCAGTTTCCAGTCAGCTTCATCATCATGCAAGCAGCAA
66 TGTTTATAGTTTTCCATTACGCGGAGACCAGTTTCCAGTCAACTTCATCATCATGCAAGCAGCAA
34776158 GAATAGAAATGTTCGGCTTTGTGGGTTTTGGTTTTTGCTGTAAGGTGCGGGCTTTAATC-AAACT
131 GAATAGAAATGTTCGGCTTTGTGGGTTTTGGTTTTTGCTGTAAGGTGCGGGCTTTAATCAAAACT
34776222 CATGAAGGCTAGTTGCAGAATCA
196 CATGAAGGCTAGTTGCAGAATCA
*
34776245 GGATCAGAAAGAAAGGCTTTGGTCAGGAAGTAACTAGAAAGTTGCCTACTTTCCTTTTGGGTCTT
1 GGATCAGAAACAAAGGCTTTGGTCAGGAAGTAACTAGAAAGTTGCCTACTTTCCTTTTGGGTCTT
34776310 TGTTTATAGTTTTCCATTACGCGGAGACCAGTTTCCAGTCAACTTCATCATCATGCAAGCAGCAA
66 TGTTTATAGTTTTCCATTACGCGGAGACCAGTTTCCAGTCAACTTCATCATCATGCAAGCAGCAA
*
34776375 GATTAGAAATGTTCGGCTTTGTGGGTTTTGGTTTTTGCTGTAAGGTGCGGGCTTTAATCAAAACT
131 GAATAGAAATGTTCGGCTTTGTGGGTTTTGGTTTTTGCTGTAAGGTGCGGGCTTTAATCAAAACT
*
34776440 CATGACGGCTAGTTGCAGAATCA
196 CATGAAGGCTAGTTGCAGAATCA
34776463 G
1 G
34776464 CCCAGGTTGT
Statistics
Matches: 213, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
217 185 0.87
218 28 0.13
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (218 bp):
GGATCAGAAACAAAGGCTTTGGTCAGGAAGTAACTAGAAAGTTGCCTACTTTCCTTTTGGGTCTT
TGTTTATAGTTTTCCATTACGCGGAGACCAGTTTCCAGTCAACTTCATCATCATGCAAGCAGCAA
GAATAGAAATGTTCGGCTTTGTGGGTTTTGGTTTTTGCTGTAAGGTGCGGGCTTTAATCAAAACT
CATGAAGGCTAGTTGCAGAATCA
Found at i:34785260 original size:27 final size:29
Alignment explanation
Indices: 34785205--34785265 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
34785195 AATTATATAA
**
34785205 TAAAT-AAAAATTATTTTATATTAATTAT
1 TAAATAAAAAATTATTTTATAAGAATTAT
34785233 TAAATAAAAAATTATTTTA-AAGAA-TAT
1 TAAATAAAAAATTATTTTATAAGAATTAT
34785260 TAAATA
1 TAAATA
34785266 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 9 0.30
28 8 0.27
29 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
TAAATAAAAAATTATTTTATAAGAATTAT
Found at i:34804004 original size:43 final size:43
Alignment explanation
Indices: 34803923--34804004 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
34803913 TTGTTTAGGT
* *
34803923 ATTTTTAATAAAAATTATTAATATTTAGTTTTAGTTTTTATGC
1 ATTTTTAATAAAAATTATTAATATTTAGTTTAAATTTTTATGC
*
34803966 ATTTTTAA-AGAAACTT-TTAATATTTAGTTTCAAATTTTT
1 ATTTTTAATA-AAAATTATTAATATTTAGTTT-AAATTTTT
34804005 TAAAAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 15 0.44
43 19 0.56
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (43 bp):
ATTTTTAATAAAAATTATTAATATTTAGTTTAAATTTTTATGC
Found at i:34811260 original size:28 final size:28
Alignment explanation
Indices: 34811218--34811285 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
34811208 GGATGAGATA
34811218 AAAAGATTTTAACTTGATTACTATATAT
1 AAAAGATTTTAACTTGATTACTATATAT
*
34811246 AAAAGATTTTCACTTGATTACTATATAT
1 AAAAGATTTTAACTTGATTACTATATAT
34811274 AAAAGATTTTAA
1 AAAAGATTTTAA
34811286 GTTTATTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (28 bp):
AAAAGATTTTAACTTGATTACTATATAT
Found at i:34815823 original size:100 final size:100
Alignment explanation
Indices: 34815703--34815924 Score: 295
Period size: 100 Copynumber: 2.2 Consensus size: 100
34815693 CCATAATCAC
* * * *
34815703 ATTTGAAATGCTTTGGATTTTCCATTTTAAAGGAATAAAAGAACCATGTGAAACAGTGGAGTAAC
1 ATTTGATATGCTTTGGATTTTCCATTTTAAAGGAATAAAAAAACCATGTGAAACAGTAGAGCAAC
* *
34815768 AAATTTAGTGGCCATATTTTGTTATATATTTA-TAT
66 AAA-TTAGTGGCCACATTTTGTTATATATATACTAT
* **
34815803 ATTTGATATGCTTTGGATTTTCCTTTTTAAAGGAATAAAAAAACCATGTGAAACAGTAGAGCAGT
1 ATTTGATATGCTTTGGATTTTCCATTTTAAAGGAATAAAAAAACCATGTGAAACAGTAGAGCAAC
* * *
34815868 AAATTAGTGGCCACGTTTTGTTATATCTATACCTCT
66 AAATTAGTGGCCACATTTTGTTATATATATA-CTAT
34815904 ATTTGATATGCCTTT-GATTTT
1 ATTTGATATG-CTTTGGATTTT
34815925 TCTTGTTAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
99 24 0.22
100 61 0.57
101 18 0.17
102 4 0.04
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (100 bp):
ATTTGATATGCTTTGGATTTTCCATTTTAAAGGAATAAAAAAACCATGTGAAACAGTAGAGCAAC
AAATTAGTGGCCACATTTTGTTATATATATACTAT
Found at i:34822277 original size:79 final size:79
Alignment explanation
Indices: 34822146--34822304 Score: 185
Period size: 79 Copynumber: 2.0 Consensus size: 79
34822136 GGCAACAGCC
** * * * * *
34822146 TTCACCATTTTTCTATGTGATCTATACTACACAATATTAGATATGCCAGTAAATAGTTTTACCAA
1 TTCACCATTTTTCTACATGATCTATACTACACAATATTAGACATGCCAGTAAAAAATTCTAACAA
*
34822211 AATGATACATATCT
66 AATGAGACATATCT
* * * *
34822225 TTCACCATTTTTCTACATGATCTTTA-TTCAACAATGTTCGACATGCCAGTAAAAAATTCTAACA
1 TTCACCATTTTTCTACATGATCTATACTAC-ACAATATTAGACATGCCAGTAAAAAATTCTAACA
*
34822289 AAATGAGAGATATCT
65 AAATGAGACATATCT
34822304 T
1 T
34822305 AGATGGTAAC
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
78 2 0.03
79 64 0.97
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (79 bp):
TTCACCATTTTTCTACATGATCTATACTACACAATATTAGACATGCCAGTAAAAAATTCTAACAA
AATGAGACATATCT
Found at i:34838919 original size:32 final size:32
Alignment explanation
Indices: 34838874--34838939 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
34838864 TCATTCTAAT
*
34838874 ATAATCACAATTCCCAAAATATTATATTATTC
1 ATAATCACAATTCCCAAAATATTATATAATTC
** *
34838906 ATAATCATGATTCCCAAAATATTTTATAATTC
1 ATAATCACAATTCCCAAAATATTATATAATTC
34838938 AT
1 AT
34838940 TTTATTAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.39
Consensus pattern (32 bp):
ATAATCACAATTCCCAAAATATTATATAATTC
Found at i:34855001 original size:34 final size:34
Alignment explanation
Indices: 34854954--34855031 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
34854944 AGTTTTGACG
* *
34854954 TGTAATATATGGTGTTGAAGCTTTGACATTGGCA
1 TGTAATATCTGGTGTTGAAGCTTTGACATTAGCA
*
34854988 TGTAATATCTGGTGTTGAAGCTTTGACCTTAGCA
1 TGTAATATCTGGTGTTGAAGCTTTGACATTAGCA
*
34855022 TGTAACATCT
1 TGTAATATCT
34855032 AGTGCTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (34 bp):
TGTAATATCTGGTGTTGAAGCTTTGACATTAGCA
Found at i:34855636 original size:34 final size:34
Alignment explanation
Indices: 34855479--34855861 Score: 257
Period size: 34 Copynumber: 11.5 Consensus size: 34
34855469 AATTAAGTAA
* * * *
34855479 CACCAAATGTTACACGCTAAGGCCAGAGCTTCAG
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
* * * * * *
34855513 CATCAGATATTACATGCCAAGGCCAAAGCTTTAT
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
* * *
34855547 CTCCAGATGTTACATGCTAAAGTCAAAGCTTCAA
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
* * * * *
34855581 CATCTA-ATGCTACACGTTAAGGTCAAAACTTCAG
1 CA-CCAGATGTTACATGCTAAGGTCAAAGCTTCAG
*
34855615 CACCAGATGTTACATGCTAAGGTTAAAGCTTCAG
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
* * *** * *
34855649 CACCTGATATTAC-T-CGTCAAAACCAAAACTTTAG
1 CACCAGATGTTACATGC-T-AAGGTCAAAGCTTCAG
** * * * *
34855683 CATTAGATGCTACATGCCAAGGTCAAAGTTTCAC
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
34855717 CACCAGATGTTACATGCTAA-G-----G-TTCAG
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
* ** *
34855744 CACCAGATGTTACATGCCAAAATCAAAGCTTCAT
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
* * *
34855778 CGCCAGATGTTACATGCT-AGATCAAAGCTTTAG
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
* * * *
34855811 CACCAGATGTTACATGCAAAAGTCAAATCTTCAA
1 CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
* *
34855845 CACCATATATTACATGC
1 CACCAGATGTTACATGC
34855862 CAAAGCTTCC
Statistics
Matches: 262, Mismatches: 73, Indels: 28
0.72 0.20 0.08
Matches are distributed among these distances:
27 23 0.09
28 1 0.00
32 1 0.00
33 34 0.13
34 199 0.76
35 3 0.01
36 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (34 bp):
CACCAGATGTTACATGCTAAGGTCAAAGCTTCAG
Found at i:34858198 original size:2 final size:2
Alignment explanation
Indices: 34858191--34858234 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
34858181 CTCCCCCAAT
34858191 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
34858233 TA
1 TA
34858235 AGCAATTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34859024 original size:16 final size:16
Alignment explanation
Indices: 34858999--34859031 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34858989 CCATCACCGC
*
34858999 ATACATTTTCCATTAG
1 ATACAGTTTCCATTAG
34859015 ATACAGTTTCCATTAG
1 ATACAGTTTCCATTAG
34859031 A
1 A
34859032 CATGGTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (16 bp):
ATACAGTTTCCATTAG
Found at i:34869939 original size:34 final size:34
Alignment explanation
Indices: 34869862--34870238 Score: 265
Period size: 34 Copynumber: 11.3 Consensus size: 34
34869852 TCAACACCAA
* * * ** *
34869862 ATGTTAGATGCTAAGGCCTAAGCTTCAGTACCAG
1 ATGTTACATGCTAAGGTCAAAGCTTCACCACTAG
* * * * *
34869896 ATATAACATGCTAAGGTCAAAGCTTTACCTCTAT
1 ATGTTACATGCTAAGGTCAAAGCTTCACCACTAG
*
34869930 ATGTTACATGCTAAGGTCAAAG-TTCAACATCTA-
1 ATGTTACATGCTAAGGTCAAAGCTTCACCA-CTAG
* * * * *
34869963 ATGTTACATG-TCCAGGCCAAAGCTTCAGCACCAA
1 ATGTTACATGCT-AAGGTCAAAGCTTCACCACTAG
* * * * *
34869997 ATGTTACATGCCACGGCCAAAGTTTCAGCACCTA-
1 ATGTTACATGCTAAGGTCAAAGCTTCACCA-CTAG
* ** *
34870031 ATGTTACACG-TCAAGACCAAAGCTTCAACACTAG
1 ATGTTACATGCT-AAGGTCAAAGCTTCACCACTAG
* *
34870065 ATGTTACATGCCAAGGTCAAAGCTTCACCACCAG
1 ATGTTACATGCTAAGGTCAAAGCTTCACCACTAG
* *
34870099 ATGTTACATGC------C-AAGGTTCAACACTAG
1 ATGTTACATGCTAAGGTCAAAGCTTCACCACTAG
*
34870126 ATGTTACATGCTAAGGTCAAAACTTCACCACTAG
1 ATGTTACATGCTAAGGTCAAAGCTTCACCACTAG
* **
34870160 ATGTTACATGCTAAGGTCAAAGCTTCAGCACCCG
1 ATGTTACATGCTAAGGTCAAAGCTTCACCACTAG
* * * * * *
34870194 ATATTACATGCCAAGGTCAAATCTTCAACACCAT
1 ATGTTACATGCTAAGGTCAAAGCTTCACCACTAG
*
34870228 ATATTACATGC
1 ATGTTACATGC
34870239 CAAAGCTTCC
Statistics
Matches: 274, Mismatches: 53, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
27 23 0.08
28 1 0.00
32 1 0.00
33 28 0.10
34 219 0.80
35 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (34 bp):
ATGTTACATGCTAAGGTCAAAGCTTCACCACTAG
Found at i:34870127 original size:27 final size:27
Alignment explanation
Indices: 34870088--34870142 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
34870078 AGGTCAAAGC
*
34870088 TTCACCACCAGATGTTACATGCCAAGG
1 TTCAACACCAGATGTTACATGCCAAGG
* *
34870115 TTCAACACTAGATGTTACATGCTAAGG
1 TTCAACACCAGATGTTACATGCCAAGG
34870142 T
1 T
34870143 CAAAACTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (27 bp):
TTCAACACCAGATGTTACATGCCAAGG
Found at i:34870129 original size:61 final size:61
Alignment explanation
Indices: 34870054--34870176 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
34870044 AGACCAAAGC
*
34870054 TTCAACACTAGATGTTACATGCCAAGGTCAAAGCTTCACCACCAGATGTTACATGCCAAGG
1 TTCAACACTAGATGTTACATGCCAAGGTCAAAACTTCACCACCAGATGTTACATGCCAAGG
* * *
34870115 TTCAACACTAGATGTTACATGCTAAGGTCAAAACTTCACCACTAGATGTTACATGCTAAGG
1 TTCAACACTAGATGTTACATGCCAAGGTCAAAACTTCACCACCAGATGTTACATGCCAAGG
34870176 T
1 T
34870177 CAAAGCTTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (61 bp):
TTCAACACTAGATGTTACATGCCAAGGTCAAAACTTCACCACCAGATGTTACATGCCAAGG
Found at i:34870176 original size:95 final size:95
Alignment explanation
Indices: 34869930--34870210 Score: 293
Period size: 95 Copynumber: 2.9 Consensus size: 95
34869920 TTACCTCTAT
* * *
34869930 ATGTTACATGCTAAGGTC-AAAGTTCAACATCTA-ATGTTACATG-TCCAGGCCAAAGCTTCAGC
1 ATGTTACATGCTAAGGTCAAAACTTCAACA-CTAGATGTTACATGCT-AAGGTCAAAGCTTCAGC
* * *
34869992 ACCAAATGTTACATGCCACGGCCAAAGTTTCAGCACCTA
64 ACCAGATGTTACAT------GCC-AAGGTTCAACACCTA
* ** * * *
34870031 ATGTTACACG-TCAAGACCAAAGCTTCAACACTAGATGTTACATGCCAAGGTCAAAGCTTCACCA
1 ATGTTACATGCT-AAGGTCAAAACTTCAACACTAGATGTTACATGCTAAGGTCAAAGCTTCAGCA
34870095 CCAGATGTTACATGCCAAGGTTCAACA-CTA
65 CCAGATGTTACATGCCAAGGTTCAACACCTA
*
34870125 GATGTTACATGCTAAGGTCAAAACTTCACCACTAGATGTTACATGCTAAGGTCAAAGCTTCAGCA
1 -ATGTTACATGCTAAGGTCAAAACTTCAACACTAGATGTTACATGCTAAGGTCAAAGCTTCAGCA
* *
34870190 CCCGATATTACATGCCAAGGT
65 CCAGATGTTACATGCCAAGGT
34870211 CAAATCTTCA
Statistics
Matches: 153, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
94 3 0.02
95 83 0.54
96 4 0.03
100 1 0.01
101 16 0.10
102 46 0.30
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (95 bp):
ATGTTACATGCTAAGGTCAAAACTTCAACACTAGATGTTACATGCTAAGGTCAAAGCTTCAGCAC
CAGATGTTACATGCCAAGGTTCAACACCTA
Found at i:34873566 original size:30 final size:31
Alignment explanation
Indices: 34873532--34873603 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
34873522 TTGAATATGA
*
34873532 CGTGTAACAATAATA-TTTTTTTTAACATAG
1 CGTGTAACAACAATATTTTTTTTTAACATAG
34873562 CGTGTAACAACAATATTTTTTTTTAACAT-G
1 CGTGTAACAACAATATTTTTTTTTAACATAG
*
34873592 ACATGTAACAAC
1 -CGTGTAACAAC
34873604 CTTTTTTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 15 0.39
31 23 0.61
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (31 bp):
CGTGTAACAACAATATTTTTTTTTAACATAG
Found at i:34873582 original size:31 final size:30
Alignment explanation
Indices: 34873510--34873603 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
34873500 ATTAAAGTGT
* * * *
34873510 AACAAAATGTTTTTGAATATGACGTGTAAC
1 AACAATATTTTTTTTAACATGACGTGTAAC
*
34873540 AATAATATTTTTTTTAACAT-AGCGTGTAAC
1 AACAATATTTTTTTTAACATGA-CGTGTAAC
*
34873570 AACAATATTTTTTTTTAACATGACATGTAAC
1 AACAATA-TTTTTTTTAACATGACGTGTAAC
34873601 AAC
1 AAC
34873604 CTTTTTTAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.02
30 29 0.54
31 23 0.43
32 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (30 bp):
AACAATATTTTTTTTAACATGACGTGTAAC
Found at i:34873634 original size:26 final size:25
Alignment explanation
Indices: 34873579--34873652 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 25
34873569 CAACAATATT
* *
34873579 TTTTTTTAACATGACATGTAACAAC
1 TTTTTTTAACATGGCGTGTAACAAC
*
34873604 CTTTTTTAACCATGGCGTGTAACATA-
1 TTTTTTTAA-CATGGCGTGTAACA-AC
* *
34873630 TTTTTGT-ACATGGTGTGTAACAA
1 TTTTTTTAACATGGCGTGTAACAA
34873653 TAGTATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 1 0.02
24 13 0.32
25 9 0.22
26 17 0.41
27 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (25 bp):
TTTTTTTAACATGGCGTGTAACAAC
Found at i:34873837 original size:45 final size:45
Alignment explanation
Indices: 34873718--34873840 Score: 113
Period size: 45 Copynumber: 2.7 Consensus size: 45
34873708 TTGTATATGA
* * * * *
34873718 CGTGTCACATGTTTCTGTACATTGTGTGTAACAACCTAACCATGG
1 CGTGTAACATATTTTTGCACATGGTGTGTAACAACCTAACCATGG
* * * ** *
34873763 CGTGTCACCTGTTTTTGCACATGACGTGTAACAACCTAATCATGG
1 CGTGTAACATATTTTTGCACATGGTGTGTAACAACCTAACCATGG
* *
34873808 CG-GATAACATATTTTTGTATATGGTGTGTAACA
1 CGTG-TAACATATTTTTGCACATGGTGTGTAACA
34873841 TCATAGCGTG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
44 1 0.02
45 62 0.98
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (45 bp):
CGTGTAACATATTTTTGCACATGGTGTGTAACAACCTAACCATGG
Found at i:34874461 original size:16 final size:16
Alignment explanation
Indices: 34874436--34874468 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34874426 CCATCACCGC
*
34874436 ATACATTTTCCATTAG
1 ATACAGTTTCCATTAG
34874452 ATACAGTTTCCATTAG
1 ATACAGTTTCCATTAG
34874468 A
1 A
34874469 CATGGTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (16 bp):
ATACAGTTTCCATTAG
Found at i:34889232 original size:18 final size:16
Alignment explanation
Indices: 34889198--34889261 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 16
34889188 TATATGAATA
34889198 AATAGAATAGAATTAAAT
1 AATA-AATA-AATTAAAT
34889216 GAATAAATAAATATAAAT
1 -AATAAATAAAT-TAAAT
*
34889234 AATAATATAAATTGAAAG
1 AATAA-ATAAATT-AAAT
*
34889252 AAAAAATAAA
1 AATAAATAAA
34889262 AAAACTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 14 0.35
18 22 0.55
19 4 0.10
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (16 bp):
AATAAATAAATTAAAT
Found at i:34898382 original size:24 final size:24
Alignment explanation
Indices: 34898346--34898423 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
34898336 CAAGGAGTTA
**
34898346 AAGCCAGCAAAAGATGTGGAATCG
1 AAGCCAGTGAAAGATGTGGAATCG
34898370 AAGCCAGTGAAAGATGTGGAATCG
1 AAGCCAGTGAAAGATGTGGAATCG
*
34898394 AAGCCAGTGAAAGATGTGGAATCA
1 AAGCCAGTGAAAGATGTGGAATCG
34898418 AAGCCA
1 AAGCCA
34898424 ATGGAGGATA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.14
Consensus pattern (24 bp):
AAGCCAGTGAAAGATGTGGAATCG
Found at i:34906039 original size:17 final size:19
Alignment explanation
Indices: 34906018--34906129 Score: 66
Period size: 20 Copynumber: 5.6 Consensus size: 19
34906008 GAAAAAAAAT
*
34906018 TATATAACAGAAAA-TGTAA
1 TATA-AACAAAAAATTGTAA
34906037 TATGAAACAAAAAATTGTAA
1 TAT-AAACAAAAAATTGTAA
* *
34906057 TACATAA-TAAAAATTCGTAA
1 TATA-AACAAAAAATT-GTAA
* * *
34906077 AATATAACAAAAAGTTATAA
1 TATA-AACAAAAAATTGTAA
* * *
34906097 CACATAACAAAAAATTATAA
1 TATA-AACAAAAAATTGTAA
34906117 TATATAACAAAAA
1 TATA-AACAAAAA
34906130 CTCATTATAC
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
19 19 0.25
20 50 0.67
21 6 0.08
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (19 bp):
TATAAACAAAAAATTGTAA
Found at i:34906068 original size:20 final size:20
Alignment explanation
Indices: 34906042--34906129 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
34906032 TGTAATATGA
*
34906042 AACAAAAAATTGTAATACAT
1 AACAAAAAATTATAATACAT
* * * *
34906062 AA-TAAAAATTCGTAAAATAT
1 AACAAAAAATT-ATAATACAT
* *
34906082 AACAAAAAGTTATAACACAT
1 AACAAAAAATTATAATACAT
*
34906102 AACAAAAAATTATAATATAT
1 AACAAAAAATTATAATACAT
34906122 AACAAAAA
1 AACAAAAA
34906130 CTCATTATAC
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 7 0.13
20 42 0.76
21 6 0.11
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (20 bp):
AACAAAAAATTATAATACAT
Found at i:34906087 original size:40 final size:40
Alignment explanation
Indices: 34906042--34906129 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
34906032 TGTAATATGA
* * * *
34906042 AACAAAAAATTGTAATACATAA-TAAAAATTCGTAAAATAT
1 AACAAAAAATTATAACACATAACAAAAAATT-ATAAAATAT
* *
34906082 AACAAAAAGTTATAACACATAACAAAAAATTATAATATAT
1 AACAAAAAATTATAACACATAACAAAAAATTATAAAATAT
34906122 AACAAAAA
1 AACAAAAA
34906130 CTCATTATAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 34 0.83
41 7 0.17
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (40 bp):
AACAAAAAATTATAACACATAACAAAAAATTATAAAATAT
Found at i:34907341 original size:2 final size:2
Alignment explanation
Indices: 34907336--34907363 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34907326 TTAAGATCAC
34907336 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
34907364 GAATTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34908553 original size:30 final size:31
Alignment explanation
Indices: 34908518--34908582 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
34908508 TTTAATCAAG
*
34908518 TTTTTATATTTTTATTTTAAGTTAAATAA-A
1 TTTTTATATTTTTATTTTAAGTCAAATAATA
*
34908548 TTTTTATATTTTTATTTTGAGTCAAATAATA
1 TTTTTATATTTTTATTTTAAGTCAAATAATA
34908579 TTTT
1 TTTT
34908583 ATAATTAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (31 bp):
TTTTTATATTTTTATTTTAAGTCAAATAATA
Found at i:34908836 original size:30 final size:29
Alignment explanation
Indices: 34908802--34908870 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
34908792 AACTATTTGT
* * *
34908802 TATAAAAATTAATTTATTTTAAAACAAAAA
1 TATAAAAATTAATTGAATGTAAAA-AAAAA
*
34908832 TATAAAAACTTGATTGAATGTAAAAAAAAA
1 TATAAAAA-TTAATTGAATGTAAAAAAAAA
34908862 -ATAAAAATT
1 TATAAAAATT
34908871 TCTTTAAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 7 0.21
30 13 0.38
31 12 0.35
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (29 bp):
TATAAAAATTAATTGAATGTAAAAAAAAA
Found at i:34921459 original size:3 final size:3
Alignment explanation
Indices: 34921453--34921481 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34921443 AAAGTTAGCC
34921453 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
34921482 TTAACATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34925579 original size:21 final size:21
Alignment explanation
Indices: 34925555--34925597 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34925545 TTGTTTCATG
* *
34925555 AAATTATAATAGCTTGATTTT
1 AAATCATAATAACTTGATTTT
* *
34925576 AAATCATATTAACTTGTTTTT
1 AAATCATAATAACTTGATTTT
34925597 A
1 A
34925598 TGGTTGCCAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
AAATCATAATAACTTGATTTT
Done.