Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold375
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: 465583
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 1 of 3
Found at i:1103 original size:27 final size:28
Alignment explanation
Indices: 1049--1104 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1039 AAAGCCCACC
*
1049 TTTGTTTGTAAAAATGGTGGTTATTTTG
1 TTTGTTTGTAAAAATGGTGGTTACTTTG
* * *
1077 TTTGTTTGT-CAAATGGTGTTTCCTTTG
1 TTTGTTTGTAAAAATGGTGGTTACTTTG
1104 T
1 T
1105 ATTTGTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.55
Consensus pattern (28 bp):
TTTGTTTGTAAAAATGGTGGTTACTTTG
Found at i:5203 original size:2 final size:2
Alignment explanation
Indices: 5155--5184 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5145 AAAGTTCCAA
5155 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
5185 GAAAAACGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7718 original size:2 final size:2
Alignment explanation
Indices: 7711--7748 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
7701 AAAATTTTTC
7711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7749 TTCCTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8754 original size:2 final size:2
Alignment explanation
Indices: 8747--8772 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8737 ACTTACATAA
8747 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
8773 GCTGTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13650 original size:15 final size:16
Alignment explanation
Indices: 13624--13653 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13614 GCTTTGATAG
13624 ATAAACAAGAAAGAAA
1 ATAAACAAGAAAGAAA
13640 ATAAA-AAGAAAGAA
1 ATAAACAAGAAAGAA
13654 GGAAGGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (16 bp):
ATAAACAAGAAAGAAA
Found at i:16750 original size:2 final size:2
Alignment explanation
Indices: 16743--16785 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
16733 CCTCAACTCT
*
16743 TA TA TA TA TA TA TA TA TA TA CA 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
16785 T
1 T
16786 GAAAAACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19394 original size:18 final size:18
Alignment explanation
Indices: 19345--19397 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
19335 TATATATCTC
19345 AAAATTTATAT-AATAT-
1 AAAATTTATATAAATATA
*
19361 -AAA-TTATA-AATGTATA
1 AAAATTTATATAA-ATATA
19377 AAAATTTATATAAATATA
1 AAAATTTATATAAATATA
19395 AAA
1 AAA
19398 TACTTTATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 6 0.21
15 6 0.21
17 3 0.10
18 12 0.41
19 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATTTATATAAATATA
Found at i:22396 original size:24 final size:27
Alignment explanation
Indices: 22323--22393 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
22313 AAACAAGCCT
* *
22323 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
22351 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
22378 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
22394 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:24315 original size:21 final size:22
Alignment explanation
Indices: 24277--24322 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
24267 ATCTGTTGAA
* **
24277 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
24298 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
24320 ACT
1 ACT
24323 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:26972 original size:27 final size:28
Alignment explanation
Indices: 26911--26979 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
26901 AAACAAGCCT
*
26911 CCATATTTGACAAATACAAAAGAAACCA
1 CCATTTTTGACAAATACAAAAGAAACCA
* *
26939 CCATTTTTGATAAATACAAAA-TAACCA
1 CCATTTTTGACAAATACAAAAGAAACCA
26966 CCATTTTTGACAAA
1 CCATTTTTGACAAA
26980 CAAATGGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 18 0.49
28 19 0.51
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (28 bp):
CCATTTTTGACAAATACAAAAGAAACCA
Found at i:35501 original size:6 final size:6
Alignment explanation
Indices: 35492--35523 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
35482 ATAAATTAAG
*
35492 TTGTTA TTGTAA TTGTAA TTGTAA TTGTAA TT
1 TTGTAA TTGTAA TTGTAA TTGTAA TTGTAA TT
35524 TTGAGTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (6 bp):
TTGTAA
Found at i:37203 original size:3 final size:3
Alignment explanation
Indices: 37195--37242 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
37185 ATATATACTT
37195 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
37243 ATTGTTTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38416 original size:19 final size:20
Alignment explanation
Indices: 38392--38435 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
38382 GAAAAGAAAA
38392 AAAATG-GAAAATGATTTTC
1 AAAATGTGAAAATGATTTTC
* *
38411 AAAATGTTACAATGATTTTC
1 AAAATGTGAAAATGATTTTC
38431 AAAAT
1 AAAAT
38436 AAAACAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (20 bp):
AAAATGTGAAAATGATTTTC
Found at i:38442 original size:20 final size:20
Alignment explanation
Indices: 38401--38442 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
38391 AAAAATGGAA
***
38401 AATGATTTTCAAAATGTTAC
1 AATGATTTTCAAAATAAAAC
38421 AATGATTTTCAAAATAAAAC
1 AATGATTTTCAAAATAAAAC
38441 AA
1 AA
38443 ATGCTTGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (20 bp):
AATGATTTTCAAAATAAAAC
Found at i:44353 original size:22 final size:21
Alignment explanation
Indices: 44324--44368 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
44314 TTAAGCTTTA
44324 AACTTTAATTTACATCCAAAT
1 AACTTTAATTTACATCCAAAT
**
44345 AACTATTAATTTGTATCCAAAT
1 AACT-TTAATTTACATCCAAAT
44367 AA
1 AA
44369 GTTCTTAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (21 bp):
AACTTTAATTTACATCCAAAT
Found at i:45297 original size:2 final size:2
Alignment explanation
Indices: 45290--45324 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
45280 TGGACATAGT
45290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45325 TTAAAACCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47350 original size:32 final size:32
Alignment explanation
Indices: 47309--47375 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
47299 AATAGCTACT
47309 AACTACTTTGATATGATAGAAAACTAAAATCA
1 AACTACTTTGATATGATAGAAAACTAAAATCA
*
47341 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAACTAAAATCA
47373 AAC
1 AAC
47376 GATGAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.27
Consensus pattern (32 bp):
AACTACTTTGATATGATAGAAAACTAAAATCA
Found at i:49160 original size:2 final size:2
Alignment explanation
Indices: 49155--49179 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49145 TATTTTTTTG
49155 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
49180 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51526 original size:18 final size:16
Alignment explanation
Indices: 51505--51548 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
51495 ATTTTAATTA
51505 TTCTTTACTTTTTTCCAT
1 TTCTTT-CTTTTTTCC-T
*
51523 TTCTTTTTTTTTTCCT
1 TTCTTTCTTTTTTCCT
51539 TT-TTTCTTTT
1 TTCTTTCTTTT
51549 ATTTTTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 8 0.33
18 6 0.25
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTCTTTTTTCCT
Found at i:54362 original size:2 final size:2
Alignment explanation
Indices: 54350--54383 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
54340 ATAAATAGAC
*
54350 AT AT TT 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
54384 TTAAAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:54718 original size:36 final size:38
Alignment explanation
Indices: 54654--54728 Score: 127
Period size: 36 Copynumber: 2.0 Consensus size: 38
54644 GGATTACAAA
54654 GCCTACTTCCGCGTCGTCTGAATGGTCCCATTCTTTATT
1 GCCTACTTCCGCGTCG-CTGAATGGTCCCATTCTTTATT
54693 GCCTACTTCCGCG-C-CTGAATGGTCCCATTCTTTATT
1 GCCTACTTCCGCGTCGCTGAATGGTCCCATTCTTTATT
54729 AGCTTTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
36 22 0.61
38 1 0.03
39 13 0.36
ACGTcount: A:0.13, C:0.32, G:0.17, T:0.37
Consensus pattern (38 bp):
GCCTACTTCCGCGTCGCTGAATGGTCCCATTCTTTATT
Found at i:54939 original size:28 final size:27
Alignment explanation
Indices: 54885--54965 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
54875 GCCACCCATT
*
54885 TGTTTGTAAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
54912 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* * *
54940 TATTTGTCAAATATGGAGGCTTATTT
1 TGTTTGTCAAAAATGGTGG-TTATTT
54966 ATTTGTCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.02
27 20 0.43
28 22 0.48
29 2 0.04
30 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:59511 original size:28 final size:27
Alignment explanation
Indices: 59457--59537 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
59447 GCCACCCATT
*
59457 TGTTTGTAAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
59484 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* * *
59512 TATTTGTCAAATATGGAGGCTTATTT
1 TGTTTGTCAAAAATGGTGG-TTATTT
59538 ATTTGTCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.02
27 20 0.43
28 22 0.48
29 2 0.04
30 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:61873 original size:34 final size:34
Alignment explanation
Indices: 61827--62045 Score: 266
Period size: 34 Copynumber: 6.5 Consensus size: 34
61817 GTAAAAACCA
*
61827 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
61861 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * *
61895 CCATTTAATCAACAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
61929 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
61963 CCATTTAGTCAATAATGGCAAACC-ACCAAAT-TAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCT-C
* * *
61997 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
62030 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
62046 TCTCCCACTT
Statistics
Matches: 159, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
33 21 0.13
34 133 0.84
35 5 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:61941 original size:68 final size:68
Alignment explanation
Indices: 61827--62045 Score: 305
Period size: 68 Copynumber: 3.2 Consensus size: 68
61817 GTAAAAACCA
* * * *
61827 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCAAAT
61892 CAC
66 CAC
* * *
61895 CCATTTAATCAACAATGGTAAGCTACCAAATTTTCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCAAAT
*
61960 CTC
66 CAC
* * * * * *
61963 CCATTTAGTCAATAATGGCAAACCACCAAATTACCCATTTAATCAACAATGGTAAACTACTAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCAAAT
62028 CA-
66 CAC
62030 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
62046 TCTCCCACTT
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 14 0.11
68 118 0.89
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:62003 original size:102 final size:101
Alignment explanation
Indices: 61825--62045 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
61815 TGGTAAAAAC
* *
61825 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
*
61890 ATCACCCATTTAATCAACAATGGTAAGCTACCAAATT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAA-T
** * * *
61927 TTCCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAATAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
* *
61992 ATTACCCATTTAATCAACAATGGTAAACTACTAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
62028 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
62046 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 17 0.16
102 90 0.84
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:66138 original size:19 final size:19
Alignment explanation
Indices: 66111--66154 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
66101 TCACGTGTAC
* *
66111 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACATGAAT
66130 AGTACCCGTATACATGAAT
1 AGTACCCGTATACATGAAT
66149 AGTACC
1 AGTACC
66155 TCGACAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (19 bp):
AGTACCCGTATACATGAAT
Found at i:66507 original size:34 final size:34
Alignment explanation
Indices: 66461--66677 Score: 260
Period size: 34 Copynumber: 6.4 Consensus size: 34
66451 GTAAAAACCA
*
66461 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
66495 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * *
66529 CCATTTAATCAACAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
66563 TCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
66597 CCATTTAGTCAATAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
66631 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
66664 CCATTTAATCAACA
1 CCATTTAATCAACA
66678 TTTTTTATTT
Statistics
Matches: 156, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
33 18 0.12
34 133 0.85
35 5 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:66575 original size:68 final size:68
Alignment explanation
Indices: 66461--66677 Score: 292
Period size: 68 Copynumber: 3.2 Consensus size: 68
66451 GTAAAAACCA
* * *
66461 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
66526 CAC
66 CAC
* * * **
66529 CCATTTAATCAACAATGGTAAGCTACCAAATTTTTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
*
66594 CTC
66 CAC
* * * * * *
66597 CCATTTAGTCAATAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
66662 CA-
66 CAC
66664 CCATTTAATCAACA
1 CCATTTAATCAACA
66678 TTTTTTATTT
Statistics
Matches: 127, Mismatches: 22, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
67 12 0.09
68 115 0.91
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:66638 original size:102 final size:102
Alignment explanation
Indices: 66462--66661 Score: 337
Period size: 102 Copynumber: 2.0 Consensus size: 102
66452 TAAAAACCAC
* *
66462 CATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
*
66527 ACCCATTTAATCAACAATGGTAAGCTACCAAATTTTT
66 ACCCATTTAATCAACAATGGTAAACTACCAAATTTTT
* * *
66564 CATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAATAATGGCAAACCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
*
66629 ACCCATTTAATCAACAATGGTAAACTACTAAAT
66 ACCCATTTAATCAACAATGGTAAACTACCAAAT
66662 CACCATTTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (102 bp):
CATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
ACCCATTTAATCAACAATGGTAAACTACCAAATTTTT
Found at i:69152 original size:13 final size:14
Alignment explanation
Indices: 69134--69162 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
69124 CAACAATTTT
69134 AATAAA-ATGTATA
1 AATAAAGATGTATA
69147 AATAAAGATGTATA
1 AATAAAGATGTATA
69161 AA
1 AA
69163 CATATAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (14 bp):
AATAAAGATGTATA
Found at i:72821 original size:12 final size:14
Alignment explanation
Indices: 72798--72833 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
72788 TTCTTCTTTA
72798 CTTTTTCTCTTTTT
1 CTTTTTCTCTTTTT
72812 -TTTTTC-CTTTTT
1 CTTTTTCTCTTTTT
72824 CTTTTT-TCTT
1 CTTTTTCTCTT
72834 CTATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
CTTTTTCTCTTTTT
Found at i:75047 original size:12 final size:11
Alignment explanation
Indices: 75007--75048 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
74997 AAAACTTTTT
75007 TTAAAAAATAA
1 TTAAAAAATAA
75018 TTATAAAAATAA
1 TTA-AAAAATAA
*
75030 AT-AAAAATAA
1 TTAAAAAATAA
75040 TTGAAAAAA
1 TT-AAAAAA
75049 GGAACAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.35
11 3 0.12
12 14 0.54
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
TTAAAAAATAA
Found at i:77954 original size:28 final size:28
Alignment explanation
Indices: 77892--77946 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
77882 CAAATGCCAC
77892 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
77920 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
77947 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:77987 original size:24 final size:24
Alignment explanation
Indices: 77928--77996 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
77918 TTCCTTTGTA
* * *
77928 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
*
77954 TTTGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
77978 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
77997 AATTTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 22 0.59
26 15 0.41
ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:80530 original size:21 final size:22
Alignment explanation
Indices: 80501--80546 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
80491 TATTCAGACA
**
80501 AGTAGTACTCCGCAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
80523 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
80544 AGT
1 AGT
80547 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:82512 original size:28 final size:28
Alignment explanation
Indices: 82450--82504 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
82440 CAAATGCCAC
82450 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
82478 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
82505 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:82545 original size:24 final size:24
Alignment explanation
Indices: 82486--82554 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
82476 TTCCTTTGTA
* * *
82486 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
*
82512 TTTGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
82536 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
82555 AATTTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 22 0.59
26 15 0.41
ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:82935 original size:24 final size:25
Alignment explanation
Indices: 82874--82935 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
82864 TATTTTAGTA
*
82874 TTTTTAATGTAATTTTAATTATTAT
1 TTTTTAATATAATTTTAATTATTAT
*
82899 TTAGTTAATATAA-TTTAA-TATATAT
1 TT-TTTAATATAATTTTAATTAT-TAT
82924 TTTTTAATATAA
1 TTTTTAATATAA
82936 ATATAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 12 0.38
25 12 0.38
26 8 0.25
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTTTAATATAATTTTAATTATTAT
Found at i:82951 original size:39 final size:40
Alignment explanation
Indices: 82908--82988 Score: 96
Period size: 39 Copynumber: 2.0 Consensus size: 40
82898 TTTAGTTAAT
*
82908 ATAATTTA-ATATATATTTTTTA-ATATAAATATA-ATTTTA
1 ATAATTTATA-AT-TATTTATTATATATAAATATACATTTTA
* *
82947 ATAATTTTTAATTATTTATTATATATATATATACATTTTA
1 ATAATTTATAATTATTTATTATATATAAATATACATTTTA
82987 AT
1 AT
82989 CCAATGTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 8 0.22
39 19 0.53
40 9 0.25
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (40 bp):
ATAATTTATAATTATTTATTATATATAAATATACATTTTA
Found at i:84617 original size:21 final size:21
Alignment explanation
Indices: 84593--84632 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
84583 AAAATAATTT
84593 TATTTAAAT-TTAATTATAATA
1 TATTTAAATATTAA-TATAATA
84614 TATTTAAATATTAATATAA
1 TATTTAAATATTAATATAA
84633 AAATAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTAAATATTAATATAATA
Found at i:85966 original size:24 final size:24
Alignment explanation
Indices: 85938--85983 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
85928 AATAAAAATT
85938 AGCCACCAATTTTGACAAACAATA
1 AGCCACCAATTTTGACAAACAATA
* *
85962 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
85984 AAATAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAATA
Found at i:86011 original size:28 final size:29
Alignment explanation
Indices: 85952--86040 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 29
85942 ACCAATTTTG
* *
85952 ACAAACAATAAGCCACCATTTTTTAC-AA-
1 ACAAACAATAA-CCACCATATTTGACAAAT
85980 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAACAATAACCACCATATTTGACAAAT
**
86008 ACAAAGGA-AACCACCATATTTGACAAAT
1 ACAAACAATAACCACCATATTTGACAAAT
86036 ACAAA
1 ACAAA
86041 GGGTGGCATT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
26 12 0.22
27 7 0.13
28 35 0.64
29 1 0.02
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (29 bp):
ACAAACAATAACCACCATATTTGACAAAT
Found at i:86041 original size:28 final size:28
Alignment explanation
Indices: 85988--86042 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
85978 AAACAAAAAT
85988 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
86016 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
86043 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:90466 original size:20 final size:20
Alignment explanation
Indices: 90441--90486 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
90431 ATGAATTGAA
90441 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
* **
90461 GAGGGATGCTTGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
*
90481 TAGGGA
1 GAGGGA
90487 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.48, T:0.15
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:90561 original size:24 final size:24
Alignment explanation
Indices: 90533--90578 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
90523 AATAAAAATT
90533 AGCCACCAATTTTGACAAACAATA
1 AGCCACCAATTTTGACAAACAATA
* *
90557 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
90579 AAATAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAATA
Found at i:90606 original size:28 final size:29
Alignment explanation
Indices: 90547--90635 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 29
90537 ACCAATTTTG
* *
90547 ACAAACAATAAGCCACCATTTTTTAC-AA-
1 ACAAACAATAA-CCACCATATTTGACAAAT
90575 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAACAATAACCACCATATTTGACAAAT
**
90603 ACAAAGGA-AACCACCATATTTGACAAAT
1 ACAAACAATAACCACCATATTTGACAAAT
90631 ACAAA
1 ACAAA
90636 GGGTAGCATT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
26 12 0.22
27 7 0.13
28 35 0.64
29 1 0.02
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (29 bp):
ACAAACAATAACCACCATATTTGACAAAT
Found at i:90636 original size:28 final size:28
Alignment explanation
Indices: 90583--90637 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
90573 AAACAAAAAT
90583 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
90611 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
90638 GTAGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:91177 original size:17 final size:17
Alignment explanation
Indices: 91157--91189 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
91147 TTTCATTCTC
91157 CCTTT-CTTTTTCTTTTT
1 CCTTTACTTTTT-TTTTT
91174 CCTTTACTTTTTTTTT
1 CCTTTACTTTTTTTTT
91190 CTTCTCTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
CCTTTACTTTTTTTTTT
Found at i:91934 original size:29 final size:29
Alignment explanation
Indices: 91881--92147 Score: 175
Period size: 29 Copynumber: 9.3 Consensus size: 29
91871 CATTGATCAT
* * **
91881 TAAACTTTTCAAAATTATACTTTGATTCC
1 TAAACTTTTCAAAATTACACATTGACCCC
*
91910 TAAACTCTTCAAAATTACACATTGACCCC
1 TAAACTTTTCAAAATTACACATTGACCCC
* *
91939 T-AACATTTT-AAAATT-CTAGATT-AGCCCT
1 TAAAC-TTTTCAAAATTAC-ACATTGA-CCCC
* *
91967 TAAACTTTTCGAAATTACACTTTGACCCC
1 TAAACTTTTCAAAATTACACATTGACCCC
* * * *
91996 TAAACTTTTCACAATTACATATTGATCTC
1 TAAACTTTTCAAAATTACACATTGACCCC
* *
92025 AAAACTTTTTAAAATTACACATT-ACCCC
1 TAAACTTTTCAAAATTACACATTGACCCC
* * *** *
92053 TAAATTTTTTAAAATTATGGATTGACCTC
1 TAAACTTTTCAAAATTACACATTGACCCC
** ** * * * *
92082 TAAACTTTAAAAAATTATGCACTAATCTC
1 TAAACTTTTCAAAATTACACATTGACCCC
* * *
92111 TAAACTTTTTAAAATTATAGATTGACCCC
1 TAAACTTTTCAAAATTACACATTGACCCC
*
92140 AAAACTTT
1 TAAACTTT
92148 AAAATGGTTA
Statistics
Matches: 184, Mismatches: 46, Indels: 16
0.75 0.19 0.07
Matches are distributed among these distances:
27 2 0.01
28 42 0.23
29 138 0.75
30 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (29 bp):
TAAACTTTTCAAAATTACACATTGACCCC
Found at i:92068 original size:86 final size:86
Alignment explanation
Indices: 91881--92069 Score: 211
Period size: 86 Copynumber: 2.2 Consensus size: 86
91871 CATTGATCAT
* ** **
91881 TAAACTTTTCAAAATTATACTTTGATTCCTAAACTCTTCAAAATTACACATTGACCCCTAACATT
1 TAAACTTTTCAAAATTACACTTTGACCCCTAAACTCTTCAAAATTACACATTGACCCAAAACATT
* *
91946 TTAAAATTCTAGATTAGCCCT
66 TTAAAATTCTACATTAGCCCC
* * * * * *
91967 TAAACTTTTCGAAATTACACTTTGACCCCTAAACTTTTCACAATTACATATTGATCTCAAAACTT
1 TAAACTTTTCAAAATTACACTTTGACCCCTAAACTCTTCAAAATTACACATTGA-CCCAAAACAT
92032 TTTAAAATTAC-ACATTA-CCCC
65 TTTAAAATT-CTACATTAGCCCC
* *
92053 TAAATTTTTTAAAATTA
1 TAAACTTTTCAAAATTA
92070 TGGATTGACC
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
86 64 0.75
87 20 0.24
88 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (86 bp):
TAAACTTTTCAAAATTACACTTTGACCCCTAAACTCTTCAAAATTACACATTGACCCAAAACATT
TTAAAATTCTACATTAGCCCC
Found at i:92077 original size:57 final size:58
Alignment explanation
Indices: 91881--92147 Score: 216
Period size: 57 Copynumber: 4.6 Consensus size: 58
91871 CATTGATCAT
* ** ** * *
91881 TAAACTTTTCAAAATTATACTTTGATTCCTAAACTCTTCAAAATTACACATTGACCCC
1 TAAACTTTTTAAAATTATAGATTGACCCCAAAACTTTTCAAAATTACACATTGACCCC
* * ** * *
91939 T-AACATTTTAAAATTCTAGATT-AGCCCTTAAACTTTTCGAAATTACACTTTGACCCC
1 TAAACTTTTTAAAATTATAGATTGA-CCCCAAAACTTTTCAAAATTACACATTGACCCC
* * * * * * *
91996 TAAACTTTTCACAATTACATATTGATCTCAAAACTTTTTAAAATTACACATT-ACCCC
1 TAAACTTTTTAAAATTATAGATTGACCCCAAAACTTTTCAAAATTACACATTGACCCC
* * * * ** ** * * * *
92053 TAAATTTTTTAAAATTATGGATTGACCTCTAAACTTTAAAAAATTATGCACTAATCTC
1 TAAACTTTTTAAAATTATAGATTGACCCCAAAACTTTTCAAAATTACACATTGACCCC
92111 TAAACTTTTTAAAATTATAGATTGACCCCAAAACTTT
1 TAAACTTTTTAAAATTATAGATTGACCCCAAAACTTT
92148 AAAATGGTTA
Statistics
Matches: 162, Mismatches: 43, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
56 1 0.01
57 88 0.54
58 72 0.44
59 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (58 bp):
TAAACTTTTTAAAATTATAGATTGACCCCAAAACTTTTCAAAATTACACATTGACCCC
Found at i:93562 original size:5 final size:5
Alignment explanation
Indices: 93552--93586 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
93542 CTAAATATCG
*
93552 AATAA AATAA AATAA AATAA AATAA ATTAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA
93587 TGTAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:93592 original size:15 final size:15
Alignment explanation
Indices: 93552--93627 Score: 73
Period size: 15 Copynumber: 4.9 Consensus size: 15
93542 CTAAATATCG
*
93552 AATAAAATAAAATAA
1 AATAAAATAAATTAA
93567 AATAAAATAAATTAA
1 AATAAAATAAATTAA
**
93582 AATAATGTAAATTTAA
1 AATAAAATAAA-TTAA
93598 AATTAAGAA-AAATTAAA
1 AA-TAA-AATAAATT-AA
*
93615 AATAAAATCAATT
1 AATAAAATAAATT
93628 CTCAGCAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
15 25 0.50
16 15 0.30
17 10 0.20
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (15 bp):
AATAAAATAAATTAA
Found at i:93620 original size:22 final size:22
Alignment explanation
Indices: 93570--93622 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
93560 AAAATAAAAT
*
93570 AAAAT-AAATTAAAATAATGTA
1 AAAATAAAATTAAAAAAATGTA
**
93591 AATTTAAAATTAAGAAAAAT-TA
1 AAAATAAAATTAA-AAAAATGTA
93613 AAAATAAAAT
1 AAAATAAAAT
93623 CAATTCTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.12
22 17 0.68
23 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (22 bp):
AAAATAAAATTAAAAAAATGTA
Found at i:94144 original size:167 final size:167
Alignment explanation
Indices: 93758--94307 Score: 541
Period size: 166 Copynumber: 3.3 Consensus size: 167
93748 GAAATAATTG
* * * * * *
93758 GAATTTTTTAAAACTGATTTAATGTGAATTTAATGACAATATTTGATGAATTTTAAAAATTTTAA
1 GAATTTTTTAAAATTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTATAA
* ** * * * *
93823 ACCAAGAAAAAT-CCCTCCGAAAACATATGGAGTAGAAAACTC-GATT-TTTCAAAACTAGGGAG
66 ACCAAGAAAAATCCCCT-CGAAAACATTTACAGAAAAAAACTCTG-TTATTTCAAAACTAAGGAA
* * *
93885 ATTT-TA-AAGAAAAAATGAAAAACTTATGAAAATAAAT
129 ATTTCAAGAAAAAAAAATGAAAAACTTATGAAAATGAAT
* * * *
93922 G-ATTTTTTTAAATTTATTTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAA
1 GAATTTTTTAAAATTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTATAA
**
93986 ACCAAGAAAAATCCCCTCGAAAACATTTACAGAACAAAAACTCTGTTATTTGGAAA-TAAGGAAA
66 ACCAAGAAAAATCCCCTCGAAAACATTTACAGAA-AAAAACTCTGTTATTTCAAAACTAAGGAAA
*
94050 TTTCAAGAAAAAAAAATGAAAAACTCATGAAAATGAAT
130 TTTCAAGAAAAAAAAATGAAAAACTTATGAAAATGAAT
* * * *
94088 GAATTTTTAAAAAATAATTTAATATGAATTAAATAATAATATTTGATGGATTTTAAAAATTATAA
1 GAATTTTTTAAAATTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTATAA
* ** * * * * *
94153 ATCAAGAAAAATCCTCC-AAAAAATATTTACGGAGTAGAAACTTTG-TATTTCAAAAGC-AA-GA
66 ACCAAGAAAAATCC-CCTCGAAAACATTTACAGA-AAAAAACTCTGTTATTTCAAAA-CTAAGGA
* * *
94214 GAATTTCAAG-GAAAAAAATGAAAAACTTATAAAAATGATT
128 -AATTTCAAGAAAAAAAAATGAAAAACTTATGAAAATGAAT
* * * * * *
94254 GAATTTTTCAAAATTGATTTAAT-GGTCATTAAAAAATAATATTTAAAGAATTTT
1 GAATTTTTTAAAATTGATTTAATATG-AATTAAATAATAATATTTGATGAATTTT
94308 GGCATTAAAA
Statistics
Matches: 320, Mismatches: 53, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
163 78 0.24
164 23 0.07
165 9 0.03
166 108 0.34
167 100 0.31
168 2 0.01
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (167 bp):
GAATTTTTTAAAATTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTATAA
ACCAAGAAAAATCCCCTCGAAAACATTTACAGAAAAAAACTCTGTTATTTCAAAACTAAGGAAAT
TTCAAGAAAAAAAAATGAAAAACTTATGAAAATGAAT
Found at i:95994 original size:19 final size:20
Alignment explanation
Indices: 95946--95998 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
95936 TGCTATTATT
* *
95946 AATATTTTTATTTTTAATAA
1 AATATTTTAATTTATAATAA
*
95966 AATTTATTTAATTTATAATAA
1 AATAT-TTTAATTTATAATAA
95987 AA-ATTTTAATTT
1 AATATTTTAATTT
95999 CATTCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 8 0.29
20 5 0.18
21 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATTTTAATTTATAATAA
Found at i:97612 original size:27 final size:27
Alignment explanation
Indices: 97574--97648 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
97564 AAACAACATG
97574 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTGACAAATAAAAAGAAA
* * * *
97601 CTACCATTTTTGACAAACACAAAGTAA
1 CCACCATTTTTGACAAATAAAAAGAAA
*
97628 CCACCATATTTGACAAATAAA
1 CCACCATTTTTGACAAATAAA
97649 TGGTGGCTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (27 bp):
CCACCATTTTTGACAAATAAAAAGAAA
Found at i:102165 original size:27 final size:27
Alignment explanation
Indices: 102133--102205 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
102123 AAACAACATG
*
102133 CCACCATTTTTGACAAATTA-AAAGAAA
1 CCACCATTTTTGACAAA-CACAAAGAAA
* *
102160 CTACCATTTTTGACAAACACAAAGTAA
1 CCACCATTTTTGACAAACACAAAGAAA
*
102187 CCACCATATTTGACAAACA
1 CCACCATTTTTGACAAACA
102206 AATGGTGACT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (27 bp):
CCACCATTTTTGACAAACACAAAGAAA
Found at i:103374 original size:2 final size:2
Alignment explanation
Indices: 103367--103401 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
103357 AGTGGTTATC
*
103367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
103402 ACAAAAAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:103900 original size:16 final size:16
Alignment explanation
Indices: 103879--103911 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
103869 ATCGATCTTG
103879 AGTTTGAATTATTTTA
1 AGTTTGAATTATTTTA
*
103895 AGTTTGAATTTTTTTA
1 AGTTTGAATTATTTTA
103911 A
1 A
103912 TTTAAGTATT
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:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (16 bp):
AGTTTGAATTATTTTA
Found at i:106778 original size:2 final size:2
Alignment explanation
Indices: 106771--106814 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
106761 TAAGGTTCCA
106771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106813 AT
1 AT
106815 TAGAAAAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108414 original size:2 final size:2
Alignment explanation
Indices: 108407--108431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
108397 AGATATCTTT
108407 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
108432 GAGCAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:121079 original size:15 final size:16
Alignment explanation
Indices: 121053--121082 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
121043 GCTTTGATAG
121053 ATAAACAAGAAAGAAA
1 ATAAACAAGAAAGAAA
121069 ATAAA-AAGAAAGAA
1 ATAAACAAGAAAGAA
121083 GAAAGGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (16 bp):
ATAAACAAGAAAGAAA
Found at i:123496 original size:15 final size:15
Alignment explanation
Indices: 123451--123501 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
123441 AAATTAAAAT
123451 TAAAAT-TAATAT-A
1 TAAAATATAATATCA
123464 TCAAAA-ATAATTATTCA
1 T-AAAATATAA-TA-TCA
123481 TAAAATATAATATCA
1 TAAAATATAATATCA
123496 TAAAAT
1 TAAAAT
123502 GTATTTATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 7 0.22
15 11 0.34
16 7 0.22
17 6 0.19
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAATATAATATCA
Found at i:124783 original size:15 final size:15
Alignment explanation
Indices: 124757--124797 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
124747 TAATATTAAT
124757 ATATCA-AAAATA-A
1 ATATCATAAAATATA
*
124770 TTATTCATAAAATATA
1 ATA-TCATAAAATATA
124786 ATATCATAAAAT
1 ATATCATAAAAT
124798 GTATTTATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 3 0.13
15 15 0.65
16 3 0.13
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATCATAAAATATA
Found at i:125599 original size:17 final size:18
Alignment explanation
Indices: 125577--125610 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
125567 ACAAGTATAT
125577 AATGAT-ATTTTATTATC
1 AATGATAATTTTATTATC
*
125594 AATGATAATTTTGTTAT
1 AATGATAATTTTATTAT
125611 TTGAAGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (18 bp):
AATGATAATTTTATTATC
Found at i:125782 original size:20 final size:20
Alignment explanation
Indices: 125741--125784 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
125731 GAGTTTCCTA
*
125741 TCTTCTTTTCTTTTTCTTTT
1 TCTTCTTTTCTTTTTCTCTT
*
125761 TCTTTTTTTCTTTTT-TGCTT
1 TCTTCTTTTCTTTTTCT-CTT
125781 TCTT
1 TCTT
125785 GTTTATGTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (20 bp):
TCTTCTTTTCTTTTTCTCTT
Found at i:126708 original size:15 final size:16
Alignment explanation
Indices: 126682--126734 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
126672 CCTTTGATAG
126682 ATAAACAAGAAAGAAA
1 ATAAACAAGAAAGAAA
126698 ATAAA-AAGAAAGAAGAA
1 ATAAACAAGAAAG-A-AA
* *
126715 AGGAAACAAGAAGGAAA
1 A-TAAACAAGAAAGAAA
126732 ATA
1 ATA
126735 GAAAAAGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 7 0.23
16 7 0.23
17 6 0.20
18 4 0.13
19 6 0.20
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.06
Consensus pattern (16 bp):
ATAAACAAGAAAGAAA
Found at i:127042 original size:6 final size:6
Alignment explanation
Indices: 127027--127061 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
127017 TTAATAATAT
* *
127027 ATATAG ATATAA ATATAG ATATAG ATAGAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
127062 TAAATAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (6 bp):
ATATAG
Found at i:130805 original size:20 final size:19
Alignment explanation
Indices: 130776--130851 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 19
130766 AAAAATACAT
130776 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
130795 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
130816 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
130836 AATGTATCGATACATT
1 AATGTATCGATACATT
130852 TGGGTAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 44 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:130833 original size:40 final size:39
Alignment explanation
Indices: 130773--130851 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 39
130763 GGTAAAAATA
*
130773 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
130812 CATACATGTATCGATATATTGAAAAATGTATCGATACATT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACATT
130852 TGGGTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:133169 original size:15 final size:15
Alignment explanation
Indices: 133124--133172 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
133114 TTTAAAAAAT
133124 TAAAAT-TAATAT-A
1 TAAAATATAATATCA
133137 TTAAAA-ATAATTATTCA
1 -TAAAATATAA-TA-TCA
133154 TAAAATATAATATCA
1 TAAAATATAATATCA
133169 TAAA
1 TAAA
133173 TGTATTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 8 0.27
15 9 0.30
16 8 0.27
17 5 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATATAATATCA
Found at i:134661 original size:21 final size:21
Alignment explanation
Indices: 134635--134682 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
134625 TATAATATAA
134635 ATTATA-AATATATTAAAAT-TT
1 ATTATATAA-ATA-TAAAATATT
134656 ATTATATAAATATAAAATATT
1 ATTATATAAATATAAAATATT
134677 -TTATAT
1 ATTATAT
134683 GATCGAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 12 0.48
21 11 0.44
22 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTATATAAATATAAAATATT
Found at i:134665 original size:30 final size:30
Alignment explanation
Indices: 134596--134676 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 30
134586 ATGAGATAAA
*
134596 ATATATAAATA-AACATATATCAAAATTTAT
1 ATATATAAATATAA-ATATATTAAAATTTAT
134626 ATAATATAAATTATAAATATATTAAAATTTAT
1 AT-ATATAAA-TATAAATATATTAAAATTTAT
134658 -TATATAAATATAAA-ATATT
1 ATATATAAATATAAATATATT
134677 TTATATGATC
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
28 5 0.11
29 6 0.13
30 9 0.19
31 8 0.17
32 17 0.36
33 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (30 bp):
ATATATAAATATAAATATATTAAAATTTAT
Found at i:142018 original size:2 final size:2
Alignment explanation
Indices: 142011--142039 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
142001 GAATTTAAAA
142011 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 A
142040 GCACTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:143707 original size:12 final size:12
Alignment explanation
Indices: 143690--143715 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
143680 GTAATGATAT
143690 ATTAAATATTAA
1 ATTAAATATTAA
143702 ATTAAATATTAA
1 ATTAAATATTAA
143714 AT
1 AT
143716 ATTTTGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTAAATATTAA
Found at i:146052 original size:20 final size:21
Alignment explanation
Indices: 146027--146071 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
146017 GATTAAAATG
146027 TTTCTTTCATC-A-ATTATATA
1 TTTCTTTC-TCTACATTATATA
146047 TTTCTTTCTCTACATTATATA
1 TTTCTTTCTCTACATTATATA
146068 TTTC
1 TTTC
146072 CCAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.09
20 9 0.39
21 12 0.52
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTCTTTCTCTACATTATATA
Found at i:150092 original size:26 final size:27
Alignment explanation
Indices: 150063--150119 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
150053 ATTTTTTTAC
150063 ATAAAAATA-AATTTTATTCAAACA-AA
1 ATAAAAATATAATTTT-TTCAAACATAA
* *
150089 ATAAATATATTATTTTTTCAAACATAA
1 ATAAAAATATAATTTTTTCAAACATAA
150116 ATAA
1 ATAA
150120 TTGACATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (27 bp):
ATAAAAATATAATTTTTTCAAACATAA
Found at i:151042 original size:20 final size:21
Alignment explanation
Indices: 151017--151064 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
151007 TTACAAAGTT
151017 TAATTTTAT-AAT-ATAATTA
1 TAATTTTATGAATAATAATTA
*
151036 TATATTTTATGAATAATAGTTA
1 TA-ATTTTATGAATAATAATTA
151058 TAATTTT
1 TAATTTT
151065 TTTATACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 7 0.28
21 8 0.32
22 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TAATTTTATGAATAATAATTA
Found at i:151186 original size:19 final size:19
Alignment explanation
Indices: 151149--151186 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
151139 AACAAAAAAC
*
151149 TTATTAAAAATATATTTAA
1 TTATTAAAAATATAATTAA
151168 TTATTAAAAACTA-AATTAA
1 TTATTAAAAA-TATAATTAA
151187 AAAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATTAAAAATATAATTAA
Found at i:153067 original size:39 final size:39
Alignment explanation
Indices: 152993--153105 Score: 212
Period size: 38 Copynumber: 2.9 Consensus size: 39
152983 AAAATATAAT
152993 TTTTTTAATTAAATCACTATAACAAATTATG-AAAATTA
1 TTTTTTAATTAAATCACTATAACAAATTATGAAAAATTA
153031 TTTTTTAATTAAATCACTATAACAAATTATGAAAAATTA
1 TTTTTTAATTAAATCACTATAACAAATTATGAAAAATTA
153070 -TTTTTAATTAAATCACTATAACAAATTATGAAAAAT
1 TTTTTTAATTAAATCACTATAACAAATTATGAAAAAT
153106 GTTACAAATT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
38 67 0.91
39 7 0.09
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (39 bp):
TTTTTTAATTAAATCACTATAACAAATTATGAAAAATTA
Found at i:153640 original size:12 final size:12
Alignment explanation
Indices: 153612--153643 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
153602 CAACATATAT
153612 ATAAT-TAAAAA
1 ATAATATAAAAA
153623 AT-ATATAAAAA
1 ATAATATAAAAA
153634 ATAATATAAA
1 ATAATATAAA
153644 CATGCTACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 10 0.53
12 7 0.37
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:153940 original size:14 final size:15
Alignment explanation
Indices: 153921--153961 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
153911 AATTTTCCCT
153921 TTTTCTTTCTTTC-C
1 TTTTCTTTCTTTCTC
*
153935 TTTTCTTTTTTTCTC
1 TTTTCTTTCTTTCTC
*
153950 CTTTCTTTCTTT
1 TTTTCTTTCTTT
153962 TTTTTCAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTCTTTCTC
Found at i:154446 original size:14 final size:15
Alignment explanation
Indices: 154421--154486 Score: 66
Period size: 14 Copynumber: 4.4 Consensus size: 15
154411 AATACATAAT
154421 TTTTTTCTCTTTTTC
1 TTTTTTCTCTTTTTC
154436 TTTTTTC-CTTTTTC
1 TTTTTTCTCTTTTTC
* *
154450 TTTTTTTTCTCCTTTC
1 TTTTTTCTCT-TTTTC
154466 TTTCTTTCT-TTCTTT-
1 TTT-TTTCTCTT-TTTC
154481 TTTTTT
1 TTTTTT
154487 TAGCACTGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
14 16 0.37
15 12 0.28
16 11 0.26
17 4 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTCTTTTTC
Found at i:154456 original size:30 final size:31
Alignment explanation
Indices: 154420--154487 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 31
154410 AAATACATAA
*
154420 TTTTTTTCTCTTTTTCTTT-TTTCCTTT-TTCT
1 TTTTTTTCTC-CTTTCTTTCTTT-CTTTCTTCT
154451 TTTTTTTCTCCTTTCTTTCTTTCTTTCTT-T
1 TTTTTTTCTCCTTTCTTTCTTTCTTTCTTCT
154481 TTTTTTT
1 TTTTTTT
154488 AGCACTGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (31 bp):
TTTTTTTCTCCTTTCTTTCTTTCTTTCTTCT
Found at i:154882 original size:509 final size:511
Alignment explanation
Indices: 153540--154995 Score: 1744
Period size: 509 Copynumber: 2.9 Consensus size: 511
153530 AATTTTTTTA
*
153540 TAAATTGAATCACGGTGATTAGCTATACAAAATATAACATGAATTGAGATATAATACAAACTCAA
1 TAAA-TGAATCACGGTGATTAGCTATGCAAAATATAACATGAATTGAGATATAATACAAACTCAA
* * * * *
153605 CATATAT----ATAATTAAAAA-ATATATAAAAAATAATATAAACATGCTACGAATACACGAATT
65 CATATATAAAAATAATTAAAAATA-ACAT-GAAAATAATATAAACACGGTACGAATACACGAATA
* *
153665 TGTTAAAATATAGATAAATGAATAATTAACGTGTAAAAATTTATA-AAA---ATTTTA----AAC
128 TGTCAAAATATAGATAAATGAATAATTAACGTGTAAAAATTTATATAAATTTATTTTATTTTAAT
* * * * *
153722 ATAAAAAATAACATAAATACAATGTTTATAAAAGAAATTT-AAATATAACATGAAAATGATGTTC
193 AT-AAAAATAATATAAATACGATGTTTATAAAA-AAATTTAAAACATAACATGAAAATGATATGC
* * * *
153786 ACATAATACGGATATATGTACATATAAAAATATATATAAAATAAAATGAATTATTAATATGTAAA
256 ACATAACACGAATATACGTACATATAAAAATATATATGAAATAAAATGAATTATTAATATGT-AA
* ** * **
153851 AAAATATACAAAAATATAATATTTTAAATACAAAAAAATAATACAAATACGAACACATAA-AATT
320 AAAATATACAAAAATATAATA-TTT---TACATAAAAA-AATACAAATATAAAAACATAATTTTT
*
153915 TTCCCTTTTTCTTTCTTTCC-TTTTC-TTTTTT-T-C-TC---CTTTCTTTC-TTTTTTTTCAAC
380 TTCTCTTTTTCTTTCTTTCCTTTTTCTTTTTTTCTCCTTCTTTCTTTCTTTCTTTTTTTTTCAAC
* * * * *
153971 CCTACCTGGCTAAACGCCAAAAAAAAAACTCACTTGTCAGTATCATGTGAGTTTGTGTAGTTGAT
445 ACTACCTGGCTAAACGACAAAAAAAAAACTCACTTGTCAGCATCAAGTGAGTTTATGTAGTTGAT
154036 TT
510 TT
* * * * *
154038 TATATGAATCACGGTGATTAGTTATGCAAAATATAGCATAAATTGAGATATAATATAAACTCAAC
1 TAAATGAATCACGGTGATTAGCTATGCAAAATATAACATGAATTGAGATATAATACAAACTCAAC
*
154103 ATATATATATATATATAATTAAAACAAAACATGAAAAATAATATAAACACGGTACGAATACACGA
66 ATATATA-A-A-A-ATAATTAAAA-ATAACATG-AAAATAATATAAACACGGTACGAATACACGA
*
154168 ATATGTCAAAATATAGATAAATGAATAATTAAC-TATAAAAATTTATATAAATTTATTTTATTTT
125 ATATGTCAAAATATAGATAAATGAATAATTAACGTGTAAAAATTTATATAAATTTATTTTATTTT
* *
154232 AAACATAAAAAAATAATATAAATACGATGTTTATAAAAAAAATTTTAAAACATAACTTGAAAATG
190 --A-ATATAAAAATAATATAAATACGATGTTTAT-AAAAAAA-TTTAAAACATAACATGAAAATG
* * *
154297 ATATGTACATAACACGAATATACGTACATATAAAAACATACATGAAA-AAAATGAATTATTAATA
250 ATATGCACATAACACGAATATACGTACATATAAAAATATATATGAAATAAAATGAATTATTAATA
*
154361 TGTAAAAAATATA-AAAAATATAATATTTTACATAAAAAAATACAAATATAAATACATAATTTTT
315 TGTAAAAAATATACAAAAATATAATATTTTACATAAAAAAATACAAATATAAAAACATAATTTTT
*
154425 TTCTCTTTTTCTTT-TTTCCTTTTTCTTTTTTTTCTCCTTTCTTTCTTTCTTTCTTTTTTTTTTA
380 TTCTCTTTTTCTTTCTTTCCTTTTTC-TTTTTTTCTCC-TTCTTTCTTTCTTTCTTTTTTTTTCA
* * * * *
154489 GCACTGA-CTTGCTGAAC-ATAAAAAAAAAGC-CA-TGTGTCAGCATCAAGTGAGTTTATGTAGT
443 ACACT-ACCTGGCTAAACGACAAAAAAAAAACTCACT-TGTCAGCATCAAGTGAGTTTATGTAGT
154550 TGATTT
506 TGATTT
**
154556 TAAATGAATCACTTTGATTAGCTATGCAAAATATAACATGAATTGAGATATAATACAAACT-AAC
1 TAAATGAATCACGGTGATTAGCTATGCAAAATATAACATGAATTGAGATATAATACAAACTCAAC
* * * * * *
154620 ATATATAAAAAAAATTAAAAATTAACATGAAAATAATATAAATACGGTATGAATATATGAATATA
66 ATATATAAAAATAATTAAAAA-TAACATGAAAATAATATAAACACGGTACGAATACACGAATATG
* *
154685 TCAAAATATAAATAAATAAATAATTAACGTGTAAAAATTTATATAAATTTATTTTATTTTAAGTA
130 TCAAAATATAGATAAATGAATAATTAACGTGTAAAAATTTATATAAATTTATTTTATTTTAA-TA
* *
154750 TAAAAA-AATATAAACACGATATTTATAAAAAATATTTAAAACATAACATGAAAATGATATGCAC
194 TAAAAATAATATAAATACGATGTTTATAAAAAA-ATTTAAAACATAACATGAAAATGATATGCAC
*
154814 ATAACACGAATATACGTACATATAAAAATATATATGAAATAAAATAAATTATTAATATGT-AAAA
258 ATAACACGAATATACGTACATATAAAAATATATATGAAATAAAATGAATTATTAATATGTAAAAA
* * *
154878 ATATACAAAAATATAATATTTTAAATACAAAAAATA-ATATAAATACGAAAAAATAAATTTTTTT
323 ATATACAAAAATATAATATTTTACATA-AAAAAATACA-A-ATATA--AAAACAT-AATTTTTTT
*
154942 CTCTTTTTCTTTCTTTCTTTTTTCTTTTTTTCTCCATTCTTTCTTTCTTT-TTTT
382 CTCTTTTTCTTTCTTTCCTTTTTCTTTTTTTCTCC-TTCTTTCTTTCTTTCTTTT
154996 CTTTCTTTTT
Statistics
Matches: 829, Mismatches: 77, Indels: 88
0.83 0.08 0.09
Matches are distributed among these distances:
497 62 0.07
498 3 0.00
505 23 0.03
506 67 0.08
507 1 0.00
509 109 0.13
510 89 0.11
511 17 0.02
512 68 0.08
513 49 0.06
514 23 0.03
515 85 0.10
516 42 0.05
517 65 0.08
518 86 0.10
519 19 0.02
520 20 0.02
521 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (511 bp):
TAAATGAATCACGGTGATTAGCTATGCAAAATATAACATGAATTGAGATATAATACAAACTCAAC
ATATATAAAAATAATTAAAAATAACATGAAAATAATATAAACACGGTACGAATACACGAATATGT
CAAAATATAGATAAATGAATAATTAACGTGTAAAAATTTATATAAATTTATTTTATTTTAATATA
AAAATAATATAAATACGATGTTTATAAAAAAATTTAAAACATAACATGAAAATGATATGCACATA
ACACGAATATACGTACATATAAAAATATATATGAAATAAAATGAATTATTAATATGTAAAAAATA
TACAAAAATATAATATTTTACATAAAAAAATACAAATATAAAAACATAATTTTTTTCTCTTTTTC
TTTCTTTCCTTTTTCTTTTTTTCTCCTTCTTTCTTTCTTTCTTTTTTTTTCAACACTACCTGGCT
AAACGACAAAAAAAAAACTCACTTGTCAGCATCAAGTGAGTTTATGTAGTTGATTT
Found at i:154920 original size:18 final size:19
Alignment explanation
Indices: 154880--154933 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
154870 ATGTAAAAAT
154880 ATACAAAAATATAATATTTTAA
1 ATACAAAAA-ATAATA--TTAA
154902 ATACAAAAAATAATA-TAA
1 ATACAAAAAATAATATTAA
154920 ATACGAAAAAATAA
1 ATAC-AAAAAATAA
154934 ATTTTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.23
19 9 0.29
21 6 0.19
22 9 0.29
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.26
Consensus pattern (19 bp):
ATACAAAAAATAATATTAA
Found at i:154954 original size:4 final size:4
Alignment explanation
Indices: 154947--155011 Score: 71
Period size: 4 Copynumber: 16.8 Consensus size: 4
154937 TTTTTCTCTT
* * * *
154947 TTTC TTTC TTTC TTT- TTTC TTTT TTTC -TCC ATTC TTTC TTTC TTTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
154993 TTTC TTTC TTTT TTTC TTT
1 TTTC TTTC TTTC TTTC TTT
155012 TTCAGCTGGC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
3 5 0.10
4 45 0.90
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:154966 original size:23 final size:22
Alignment explanation
Indices: 154936--155014 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
154926 AAAAATAAAT
154936 TTTTTTCTCTTTTTCTTTCTTTC
1 TTTTTT-TCTTTTTCTTTCTTTC
*
154959 -TTTTTTCTTTTT-TTCTCCATTC
1 TTTTTTTCTTTTTCTT-T-CTTTC
*
154981 TTTCTTTC-TTTT-TTTCTTTC
1 TTTTTTTCTTTTTCTTTCTTTC
155001 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
155015 AGCTGGCCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
20 13 0.28
21 13 0.28
22 15 0.32
23 6 0.13
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTCTTTTTCTTTCTTTC
Found at i:156539 original size:20 final size:21
Alignment explanation
Indices: 156514--156570 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
156504 ATTGGGCTCA
156514 ATGTATCGATACAATGC-ACT
1 ATGTATCGATACAATGCAACT
* *
156534 ATGTATCGATACAATTCAAGT
1 ATGTATCGATACAATGCAACT
156555 ATGTATCGATACAATG
1 ATGTATCGATACAATG
156571 TATTGATACT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACAATGCAACT
Found at i:157360 original size:21 final size:22
Alignment explanation
Indices: 157334--157375 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
157324 TGATATATAA
157334 CTCCCCCTTAATAAAA-ATTTT
1 CTCCCCCTTAATAAAATATTTT
157355 CTCCCCCTTAATAAAATATTT
1 CTCCCCCTTAATAAAATATTT
157376 AATGTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.38
Consensus pattern (22 bp):
CTCCCCCTTAATAAAATATTTT
Found at i:163855 original size:3 final size:3
Alignment explanation
Indices: 163847--163871 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
163837 TGAGTCAACT
163847 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
163872 TAATGGTTAA
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:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:165481 original size:20 final size:21
Alignment explanation
Indices: 165456--165512 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
165446 GTTGGGCTCA
165456 ATGTATCGATACAATGC-ACT
1 ATGTATCGATACAATGCAACT
* *
165476 ATGTATCGATACAATTCAAGT
1 ATGTATCGATACAATGCAACT
165497 ATGTATCGATACAATG
1 ATGTATCGATACAATG
165513 TATCGATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACAATGCAACT
Found at i:165611 original size:32 final size:33
Alignment explanation
Indices: 165570--165633 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
165560 CAATTCAGTG
165570 TGTATCGATACCAAG-AACT-TGTATCGATACAA
1 TGTATCGATACCAAGCAA-TATGTATCGATACAA
*
165602 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACCAAGCAATATGTATCGATACA
165634 TCTAGGTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (33 bp):
TGTATCGATACCAAGCAATATGTATCGATACAA
Found at i:169632 original size:72 final size:72
Alignment explanation
Indices: 169515--169651 Score: 247
Period size: 72 Copynumber: 1.9 Consensus size: 72
169505 ATCCAAATTC
*
169515 CTATTCTCACTCAGGTCAAGAAGCTGCAAGGCTGATAAGTTCCCAAGATGAGGTGGAATCTCTCC
1 CTATTCCCACTCAGGTCAAGAAGCTGCAAGGCTGATAAGTTCCCAAGATGAGGTGGAATCTCTCC
169580 CCCATTA
66 CCCATTA
**
169587 CTATTCCCACTCAGGTCAAGAATTTGCAAGGCTGATAAGTTCCCAAGATGAGGTGGAATCTCTCC
1 CTATTCCCACTCAGGTCAAGAAGCTGCAAGGCTGATAAGTTCCCAAGATGAGGTGGAATCTCTCC
169652 ATCAAAGCAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (72 bp):
CTATTCCCACTCAGGTCAAGAAGCTGCAAGGCTGATAAGTTCCCAAGATGAGGTGGAATCTCTCC
CCCATTA
Found at i:171556 original size:15 final size:16
Alignment explanation
Indices: 171538--171577 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
171528 ATTTTTTTGA
171538 ATAT-TATTTTAATAT
1 ATATATATTTTAATAT
*
171553 ATATAGTTTTTTAATAT
1 ATATA-TATTTTAATAT
171570 ATATATAT
1 ATATATAT
171578 CATATGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 4 0.19
16 2 0.10
17 15 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATATATATTTTAATAT
Found at i:172227 original size:14 final size:14
Alignment explanation
Indices: 172208--172251 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
172198 TTTTATATAA
*
172208 AAAAATTATAATTT
1 AAAAATTAAAATTT
*
172222 AAAAATAAAAATTT
1 AAAAATTAAAATTT
172236 ATAAATATTAAAATTT
1 A-AAA-ATTAAAATTT
172252 TAATATTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 3 0.12
16 9 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAATTAAAATTT
Found at i:172231 original size:21 final size:23
Alignment explanation
Indices: 172207--172248 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
172197 ATTTTATATA
172207 AAAAAATTAT-AAT-TTAAAAAT
1 AAAAAATTATAAATATTAAAAAT
*
172228 AAAAATTTATAAATATTAAAA
1 AAAAAATTATAAATATTAAAA
172249 TTTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 3 0.17
23 6 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAAATTATAAATATTAAAAAT
Found at i:177855 original size:28 final size:27
Alignment explanation
Indices: 177800--177870 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
177790 GCCACCCATT
177800 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
177827 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
177855 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
177871 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:177972 original size:20 final size:20
Alignment explanation
Indices: 177947--177992 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
177937 AAATAGAGGC
*
177947 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
177967 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
177987 TCCCTC
1 TCCCTC
177993 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:178498 original size:30 final size:29
Alignment explanation
Indices: 178464--178536 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
178454 TATAATCATG
*
178464 TAATAAAATGTAATTATA-ATTTTTTTAAAA
1 TAATAAAAT-TAAATATATA-TTTTTTAAAA
* *
178494 TAATATATATTAAATATTTATTTTTTAAAA
1 TAATA-AAATTAAATATATATTTTTTAAAA
178524 TAAT--AATTAAATA
1 TAATAAAATTAAATA
178537 ATTTTTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 8 0.22
30 25 0.68
31 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (29 bp):
TAATAAAATTAAATATATATTTTTTAAAA
Found at i:178844 original size:26 final size:26
Alignment explanation
Indices: 178814--178893 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 26
178804 ATGAATCGAG
178814 TTATTTATAAATTATTTAAATTTAAT
1 TTATTTATAAATTATTTAAATTTAAT
*
178840 TTA--T-TAAA-TA-TTAAATTAAAT
1 TTATTTATAAATTATTTAAATTTAAT
* *
178861 TTTTTTATGTAATTATATTTAAATTTAAAT
1 TTATTTA--TAAAT-TATTTAAATTT-AAT
178891 TTA
1 TTA
178894 AATTTGATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
21 12 0.30
22 2 0.05
23 5 0.12
24 1 0.03
26 6 0.15
28 2 0.05
29 7 0.17
30 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TTATTTATAAATTATTTAAATTTAAT
Found at i:180169 original size:25 final size:26
Alignment explanation
Indices: 180106--180170 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
180096 TAATATATAA
*
180106 ATTTATATGTTATTAGTAAATAAAATT
1 ATTTATAT-TTATTAGAAAATAAAATT
*
180133 ATATTAT-CTTATTA-AAAATAAAATT
1 AT-TTATATTTATTAGAAAATAAAATT
180158 ATTTATATTTATT
1 ATTTATATTTATT
180171 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 4 0.12
25 17 0.52
26 6 0.18
27 2 0.06
28 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (26 bp):
ATTTATATTTATTAGAAAATAAAATT
Found at i:181001 original size:27 final size:27
Alignment explanation
Indices: 180963--181015 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
180953 TGCAACCTTC
*
180963 ACTGTTTCAAATTGAATTTCATAATTT
1 ACTGTTTCAAATTGAATTTCAAAATTT
180990 ACTGTTTCAAATTGAATTTCAAAATT
1 ACTGTTTCAAATTGAATTTCAAAATT
181016 GACAGCACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (27 bp):
ACTGTTTCAAATTGAATTTCAAAATTT
Found at i:183973 original size:44 final size:43
Alignment explanation
Indices: 183910--184026 Score: 177
Period size: 40 Copynumber: 2.7 Consensus size: 43
183900 TTAGAATTTG
183910 GGTGGCTATGCCAATCCACGGAAAAATAAATAAATATGCAATTA
1 GGTGGCTATGCCAATCCAC-GAAAAATAAATAAATATGCAATTA
*
183954 GGTGGCTATGCCAATCCACG--AAA-AAATAAATATGCAATTG
1 GGTGGCTATGCCAATCCACGAAAAATAAATAAATATGCAATTA
*
183994 GGTGGCTATGCCAATCCACGAAAATGTAAATAA
1 GGTGGCTATGCCAATCCACGAAAA-ATAAATAA
184027 TAAAAACACC
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
40 36 0.54
41 3 0.04
42 2 0.03
43 1 0.01
44 25 0.37
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (43 bp):
GGTGGCTATGCCAATCCACGAAAAATAAATAAATATGCAATTA
Found at i:186813 original size:7 final size:7
Alignment explanation
Indices: 186801--186831 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
186791 TCCACATTTT
186801 TGTGGAA
1 TGTGGAA
186808 TGTGGAA
1 TGTGGAA
*
186815 TGTAGAA
1 TGTGGAA
186822 TGTGGAA
1 TGTGGAA
186829 TGT
1 TGT
186832 CATGACCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.39, T:0.32
Consensus pattern (7 bp):
TGTGGAA
Found at i:187497 original size:50 final size:50
Alignment explanation
Indices: 187443--187730 Score: 495
Period size: 50 Copynumber: 5.8 Consensus size: 50
187433 TATACTTAGA
*
187443 GTCAACAATTATGGCCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
** *
187493 GTCAACAATTGCGGCCACCTCTCTCTATTGTCAAAGGTTGGTAAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
187543 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
187593 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
187643 ATCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
** *
187693 GTCAACAATTGCGGCCATCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
187731 ACTTTCCACC
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 225 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:192171 original size:50 final size:50
Alignment explanation
Indices: 192117--192354 Score: 361
Period size: 50 Copynumber: 4.8 Consensus size: 50
192107 TATACTTAGA
* * *
192117 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAAGTTGATGAAGAATT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
** * *
192167 GTCAACAATTGCGGTCACCTCTCTCTATTGTCAAAGGTTGGTAAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
192217 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
192267 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
192317 GTCAACAATTACGGCCATCTC-CTTCTATTGTAAAAGGT
1 GTCAACAATTATGGCCACCTCTC-TCTATTGTCAAAGGT
192355 ACTTTCCACC
Statistics
Matches: 171, Mismatches: 16, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
49 1 0.01
50 170 0.99
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:195572 original size:25 final size:26
Alignment explanation
Indices: 195534--195588 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
195524 TTGTAATAGT
*
195534 TTTTTTAATGTATAAATGAAGTCATAA
1 TTTTTTAA-GTATAAATAAAGTCATAA
*
195561 TTTTTTAA-TATAAATAAAGTTATAA
1 TTTTTTAAGTATAAATAAAGTCATAA
195586 TTT
1 TTT
195589 GAAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 18 0.69
27 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (26 bp):
TTTTTTAAGTATAAATAAAGTCATAA
Found at i:195595 original size:25 final size:25
Alignment explanation
Indices: 195544--195603 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
195534 TTTTTTAATG
* ***
195544 TATAAATGAAGTCATAATTTTTTAA
1 TATAAATAAAGTCATAATTTGAAAA
*
195569 TATAAATAAAGTTATAATTTGAAAA
1 TATAAATAAAGTCATAATTTGAAAA
*
195594 TA-AAAGAAAG
1 TATAAATAAAG
195604 ATTGTAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (25 bp):
TATAAATAAAGTCATAATTTGAAAA
Found at i:196722 original size:32 final size:32
Alignment explanation
Indices: 196686--196749 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
196676 GACTTAGGGC
*
196686 ATATAATTAATAATGCAAG-CTCATCATTATTT
1 ATATAATTAATAATGCAAGTC-CATCACTATTT
196718 ATATAATTAATAATGCAAGTCCATCACTATTT
1 ATATAATTAATAATGCAAGTCCATCACTATTT
196750 TTTAGTGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (32 bp):
ATATAATTAATAATGCAAGTCCATCACTATTT
Found at i:201757 original size:13 final size:11
Alignment explanation
Indices: 201731--201785 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
201721 TTGTTATTAA
201731 GATAATTATTT
1 GATAATTATTT
201742 GATAATTATTTTT
1 GATAATTA--TTT
*
201755 GATAA--ATTA
1 GATAATTATTT
* *
201764 AATAATCATTT
1 GATAATTATTT
201775 GATAATTATTT
1 GATAATTATTT
201786 AGTTGAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
9 6 0.17
11 21 0.60
13 8 0.23
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (11 bp):
GATAATTATTT
Found at i:202658 original size:28 final size:28
Alignment explanation
Indices: 202627--202685 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
202617 TTTTTTTTAA
* *
202627 TTTTTAGATTTTTTTGATTTTTTAATTTT
1 TTTTTA-ATTTTTATCATTTTTTAATTTT
*
202656 TTTTTAATTTTTATCATTTTTTTATTTT
1 TTTTTAATTTTTATCATTTTTTAATTTT
202684 TT
1 TT
202686 ATAATTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (28 bp):
TTTTTAATTTTTATCATTTTTTAATTTT
Found at i:202662 original size:36 final size:36
Alignment explanation
Indices: 202615--202686 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
202605 AATTTGTCTT
*
202615 ATTTTTTTTTAATTTTTA-GATTTTTTTGATTTTTTA
1 ATTTTTTTTTAATTTTTATCATTTTTTT-ATTTTTTA
202651 ATTTTTTTTTAATTTTTATCATTTTTTTATTTTTTA
1 ATTTTTTTTTAATTTTTATCATTTTTTTATTTTTTA
202687 TAATTATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.76
Consensus pattern (36 bp):
ATTTTTTTTTAATTTTTATCATTTTTTTATTTTTTA
Found at i:202679 original size:18 final size:17
Alignment explanation
Indices: 202613--202688 Score: 80
Period size: 18 Copynumber: 4.3 Consensus size: 17
202603 AAAATTTGTC
*
202613 TTATTTTTTTTTAATTT
1 TTATATTTTTTTAATTT
* *
202630 TTAGATTTTTTTGATTTT
1 TTATATTTTTTT-AATTT
*
202648 TTAATTTTTTTTTAATTT
1 TT-ATATTTTTTTAATTT
*
202666 TTATCATTTTTTTATTTT
1 TTAT-ATTTTTTTAATTT
202684 TTATA
1 TTATA
202689 ATTATTGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 13 0.27
18 27 0.56
19 8 0.17
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (17 bp):
TTATATTTTTTTAATTT
Found at i:205796 original size:18 final size:20
Alignment explanation
Indices: 205773--205809 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
205763 AAACAAAATA
205773 TATTGCA-TTTTT-TTTTGC
1 TATTGCACTTTTTATTTTGC
205791 TATTGCACTTTTTATTTTG
1 TATTGCACTTTTTATTTTG
205810 TTTTCGCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.65
Consensus pattern (20 bp):
TATTGCACTTTTTATTTTGC
Found at i:206628 original size:2 final size:2
Alignment explanation
Indices: 206621--206653 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
206611 AGGTTTCAAA
206621 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
206654 CACATATTAG
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:208302 original size:2 final size:2
Alignment explanation
Indices: 208295--208331 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
208285 GAGATTTCCT
208295 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
208332 GAGCAATGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:209157 original size:13 final size:13
Alignment explanation
Indices: 209136--209171 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
209126 AAGCTTTTTT
*
209136 TTAAAAAAAAAAA
1 TTAAAAAAAAGAA
209149 TCTAAAAAAAAGAA
1 T-TAAAAAAAAGAA
209163 TTAAAAAAA
1 TTAAAAAAA
209172 TCAACAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (13 bp):
TTAAAAAAAAGAA
Done.