Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 7 of 19
Found at i:1211404 original size:4 final size:4
Alignment explanation
Indices: 1211397--1211443 Score: 58
Period size: 4 Copynumber: 10.8 Consensus size: 4
1211387 TGGCTATTAA
1211397 AAAT AAAT AAAT AAAAT AAAT AAAT AAAT AAAAT AAAAT AAAAT AAA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT AAA
1211444 ACATTGCACA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 23 0.56
5 18 0.44
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:1211414 original size:13 final size:13
Alignment explanation
Indices: 1211396--1211443 Score: 71
Period size: 13 Copynumber: 3.6 Consensus size: 13
1211386 ATGGCTATTA
1211396 AAAATAAATAAAT
1 AAAATAAATAAAT
1211409 AAAATAAATAAAT
1 AAAATAAATAAAT
1211422 -AAATAAAATAAAAT
1 AAAAT-AAAT-AAAT
1211436 AAAATAAA
1 AAAATAAA
1211444 ACATTGCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.12
13 17 0.53
14 7 0.22
15 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1211415 original size:5 final size:5
Alignment explanation
Indices: 1211396--1211444 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
1211386 ATGGCTATTA
1211396 AAAAT -AAAT -AAAT AAAAT -AAAT -AAAT -AAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1211441 AAAA
1 AAAA
1211445 CATTGCACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 20 0.48
5 22 0.52
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1215542 original size:20 final size:21
Alignment explanation
Indices: 1215519--1215557 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1215509 TATTCGTTTT
*
1215519 TTTAATATATTATA-ATTATA
1 TTTAAAATATTATATATTATA
1215539 TTTAAAATATTATATATTA
1 TTTAAAATATTATATATTA
1215558 ATATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAATATTATATATTATA
Found at i:1215564 original size:20 final size:20
Alignment explanation
Indices: 1215525--1215564 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1215515 TTTTTTTAAT
*
1215525 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
1215545 ATATTATATATTA-ATATAAA
1 ATATTATA-ATTATATATAAA
1215565 TTTTAATACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:1215618 original size:33 final size:33
Alignment explanation
Indices: 1215531--1215624 Score: 100
Period size: 32 Copynumber: 2.8 Consensus size: 33
1215521 TAATATATTA
*
1215531 TAATTATATTTAAAATATTATATATTAATATAAATTT
1 TAATT-TATTT-ATATATT-TATATT-ATATAAATTT
*** *
1215568 TAATACGTTAATA-ATTTATATTATATAAATTT
1 TAATTTATTTATATATTTATATTATATAAATTT
1215600 TAATTTATTTATATATTTATATTAT
1 TAATTTATTTATATATTTATATTAT
1215625 TTTTTATGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
32 19 0.40
33 17 0.36
34 3 0.06
35 2 0.04
36 2 0.04
37 4 0.09
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (33 bp):
TAATTTATTTATATATTTATATTATATAAATTT
Found at i:1215942 original size:23 final size:22
Alignment explanation
Indices: 1215896--1215946 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1215886 AAAATTAAAA
1215896 AAAATAAAATAAAAGTCAAAATT
1 AAAA-AAAATAAAAGTCAAAATT
* **
1215919 ATAAAAAAATAAAATTCATTATT
1 A-AAAAAAATAAAAGTCAAAATT
1215942 AAAAA
1 AAAAA
1215947 TATTAGCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 17 0.71
24 3 0.12
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAAAAAATAAAAGTCAAAATT
Found at i:1217677 original size:16 final size:16
Alignment explanation
Indices: 1217658--1217691 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1217648 GATTAACTTC
* *
1217658 AATCTGAAATTATTTA
1 AATCTAAAATAATTTA
1217674 AATCTAAAATAATTTA
1 AATCTAAAATAATTTA
1217690 AA
1 AA
1217692 CTCGAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AATCTAAAATAATTTA
Found at i:1218135 original size:29 final size:29
Alignment explanation
Indices: 1218103--1218166 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1218093 TATGAGTATG
*
1218103 AAATTTTTCAAATTTATTTATAAAATAAA
1 AAATATTTCAAATTTATTTATAAAATAAA
1218132 AAATATTTCAAATTTATTTATAAAATAAA
1 AAATATTTCAAATTTATTTATAAAATAAA
1218161 AAATAT
1 AAATAT
1218167 AAACAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATATTTCAAATTTATTTATAAAATAAA
Found at i:1218174 original size:30 final size:29
Alignment explanation
Indices: 1218111--1218174 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1218101 TGAAATTTTT
**
1218111 CAAATTTATTTATAAAATAAAAAATATTT
1 CAAATTTATTTATAAAATAAAAAATATAA
1218140 CAAATTTATTTATAAAATAAAAAATATAAA
1 CAAATTTATTTATAAAATAAAAAATAT-AA
1218170 CAAAT
1 CAAAT
1218175 AATAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (29 bp):
CAAATTTATTTATAAAATAAAAAATATAA
Found at i:1219017 original size:27 final size:27
Alignment explanation
Indices: 1218987--1219044 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
1218977 TTTATTTAGA
*
1218987 TAAAAATTAA-AAAATTAAAAAATTATT
1 TAAAAA-TAATAAAAATAAAAAATTATT
*
1219014 TAAATATAATAAAAATAAAAAATTATT
1 TAAAAATAATAAAAATAAAAAATTATT
1219041 TAAA
1 TAAA
1219045 TAAAAGCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAAAATAATAAAAATAAAAAATTATT
Found at i:1220217 original size:28 final size:29
Alignment explanation
Indices: 1220186--1220270 Score: 70
Period size: 30 Copynumber: 2.9 Consensus size: 29
1220176 TATCTTAAAA
1220186 TATAAAAATTTATTTTTATATTAATAT-T
1 TATAAAAATTTATTTTTATATTAATATAT
**
1220214 TATATAATTTTATATTTTTATAATTAA-ATAT
1 TATA-AAAATT-TATTTTTAT-ATTAATATAT
*
1220245 AAGTAAAAATATTA-TTTTA-ATTAATA
1 TA-TAAAAAT-TTATTTTTATATTAATA
1220271 AACAATAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
28 9 0.20
29 5 0.11
30 16 0.36
31 12 0.27
32 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
TATAAAAATTTATTTTTATATTAATATAT
Found at i:1220244 original size:16 final size:15
Alignment explanation
Indices: 1220196--1220240 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
1220186 TATAAAAATT
1220196 TATTTTTAT-ATTAA
1 TATTTTTATAATTAA
* *
1220210 TATTTATATAATTTTA
1 TATTTTTATAA-TTAA
1220226 TATTTTTATAATTAA
1 TATTTTTATAATTAA
1220241 ATATAAGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 8 0.32
15 4 0.16
16 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTTATAATTAA
Found at i:1220735 original size:17 final size:18
Alignment explanation
Indices: 1220705--1220753 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
1220695 ATAGTTGTGC
1220705 AATTATATAATATAA-AAA
1 AATTATA-AATATAATAAA
1220723 TAATTA-AAATATAATAAA
1 -AATTATAAATATAATAAA
1220741 AATTATAAATATA
1 AATTATAAATATA
1220754 TTAATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 12 0.43
18 11 0.39
19 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTATAAATATAATAAA
Found at i:1220754 original size:20 final size:21
Alignment explanation
Indices: 1220716--1220759 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1220706 ATTATATAAT
1220716 ATAAAAATAATTAAAATA-TA
1 ATAAAAATAATTAAAATATTA
*
1220736 ATAAAAATTA-TAAATATATTA
1 ATAAAAATAATTAAA-ATATTA
1220757 ATA
1 ATA
1220760 TATAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAAATAATTAAAATATTA
Found at i:1221498 original size:9 final size:9
Alignment explanation
Indices: 1221471--1221503 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1221461 CCTTTGTTAA
1221471 TTATTAATTT
1 TTATT-ATTT
1221481 TTATT-TTT
1 TTATTATTT
1221489 TTATTATTT
1 TTATTATTT
1221498 TTATTA
1 TTATTA
1221504 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 9 0.41
10 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTATTT
Found at i:1221898 original size:17 final size:17
Alignment explanation
Indices: 1221862--1221900 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1221852 TAAAAATATT
*
1221862 ATTTTTTATTTTAATTA
1 ATTTTTTATTTTAATAA
1221879 ATTTTTTATTTTTAA-AA
1 ATTTTTTA-TTTTAATAA
1221896 ATTTT
1 ATTTT
1221901 AAAATCATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTATTTTAATAA
Found at i:1224415 original size:18 final size:20
Alignment explanation
Indices: 1224373--1224415 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
1224363 ACACGTGTAT
1224373 ATGAAATTATATTAAAAATA
1 ATGAAATTATATTAAAAATA
1224393 A--AAATTA-ATTAAAAA-A
1 ATGAAATTATATTAAAAATA
1224409 ATGAAAT
1 ATGAAAT
1224416 ATGTGATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.10
17 8 0.38
18 10 0.48
20 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
ATGAAATTATATTAAAAATA
Found at i:1224608 original size:3 final size:3
Alignment explanation
Indices: 1224600--1224641 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1224590 GATCACTTTA
*
1224600 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1224642 TCATTGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1225187 original size:6 final size:6
Alignment explanation
Indices: 1225172--1225204 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1225162 TTTTATCATC
1225172 TTTTTA -TTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1225205 GTAGAGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:1226733 original size:12 final size:12
Alignment explanation
Indices: 1226716--1226741 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1226706 AGAAAATGTA
1226716 TCGATACATTTT
1 TCGATACATTTT
1226728 TCGATACATTTT
1 TCGATACATTTT
1226740 TC
1 TC
1226742 TGTGTATCGA
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:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (12 bp):
TCGATACATTTT
Found at i:1229358 original size:79 final size:79
Alignment explanation
Indices: 1229210--1229413 Score: 207
Period size: 79 Copynumber: 2.6 Consensus size: 79
1229200 GTTATCTCAT
* *
1229210 CGGGGATACTCCAACCCCGTTACTTCCG-AGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
1229274 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** **
1229288 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TGATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
1229352 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * ** *
1229367 CAGGGATACTCCAGCCTTGTTATTTTC-AAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCCCG
1229414 TTATTATCTC
Statistics
Matches: 103, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
78 32 0.31
79 71 0.69
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:1230474 original size:20 final size:21
Alignment explanation
Indices: 1230429--1230478 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1230419 TTTTATAATT
*
1230429 AAATTTAAATAATATATTTTT
1 AAATTTAAATAATATATTTTC
*
1230450 TAATTTAAA-AATA-ATATTTC
1 AAATTTAAATAATATAT-TTTC
1230470 AAA-TTAAAT
1 AAATTTAAAT
1230479 TGATTTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.29
20 9 0.38
21 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATTTAAATAATATATTTTC
Found at i:1233334 original size:2 final size:2
Alignment explanation
Indices: 1233327--1233357 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1233317 TCAAGGATTC
*
1233327 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1233358 CTAATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1237019 original size:28 final size:31
Alignment explanation
Indices: 1236926--1237043 Score: 163
Period size: 31 Copynumber: 3.9 Consensus size: 31
1236916 ATGCCTTAAT
1236926 TAGAGCCATCTACATCCTTCTACTATACTTG
1 TAGAGCCATCTACATCCTTCTACTATACTTG
*
1236957 TAGAGCCATCTGCATCCTTCTACTATACTTG
1 TAGAGCCATCTACATCCTTCTACTATACTTG
*
1236988 TAGAGCCATCTGCATCC-T-T-CTATACGTT-
1 TAGAGCCATCTACATCCTTCTACTATAC-TTG
* *
1237016 TAGAGCCATCAACATCCTTGTACTATAC
1 TAGAGCCATCTACATCCTTCTACTATAC
1237044 ATTTAGGACC
Statistics
Matches: 80, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
28 21 0.26
29 4 0.05
30 2 0.03
31 53 0.66
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (31 bp):
TAGAGCCATCTACATCCTTCTACTATACTTG
Found at i:1237032 original size:59 final size:62
Alignment explanation
Indices: 1236926--1237043 Score: 163
Period size: 59 Copynumber: 2.0 Consensus size: 62
1236916 ATGCCTTAAT
**
1236926 TAGAGCCATCTACATCCTTCTACTATACTTGTAGAGCCATCTGCATCCTTCTACTATACTTG
1 TAGAGCCATCTACATCCTTCTACTATACTTGTAGAGCCATCAACATCCTTCTACTATACTTG
* *
1236988 TAGAGCCATCTGCATCC-T-T-CTATACGTT-TAGAGCCATCAACATCCTTGTACTATAC
1 TAGAGCCATCTACATCCTTCTACTATAC-TTGTAGAGCCATCAACATCCTTCTACTATAC
1237044 ATTTAGGACC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
59 31 0.61
60 3 0.06
61 1 0.02
62 16 0.31
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (62 bp):
TAGAGCCATCTACATCCTTCTACTATACTTGTAGAGCCATCAACATCCTTCTACTATACTTG
Found at i:1238394 original size:3 final size:3
Alignment explanation
Indices: 1238386--1238414 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1238376 ACGCTAATGA
1238386 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1238415 ATAAGAGAAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1238777 original size:19 final size:19
Alignment explanation
Indices: 1238753--1238789 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1238743 CAGATAAAAA
*
1238753 AAGTATATATATTTATATG
1 AAGTATATATATATATATG
1238772 AAGTATATATATATATAT
1 AAGTATATATATATATAT
1238790 ATGTGTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
AAGTATATATATATATATG
Found at i:1238929 original size:2 final size:2
Alignment explanation
Indices: 1238922--1238954 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1238912 ACAGACAAAC
*
1238922 AT AT AT AT AT AT AT AT AT GT 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
1238955 CACGCACGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1241096 original size:14 final size:14
Alignment explanation
Indices: 1241066--1241115 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1241056 ACACAGAGGA
*
1241066 AGAAAGAAAAGAGAG
1 AGAAAG-AAAGAAAG
1241081 AGAAAGAAAGAAAG
1 AGAAAGAAAGAAAG
*
1241095 AGAGAA-AAGGAAAG
1 AGA-AAGAAAGAAAG
1241109 AGAAAGA
1 AGAAAGA
1241116 GAAAGAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 2 0.06
14 21 0.68
15 8 0.26
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAGAAAG
Found at i:1241096 original size:18 final size:18
Alignment explanation
Indices: 1241060--1241122 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
1241050 CATCAAACAC
*
1241060 AGAGGAAGAAAGAAAAGAG
1 AGAGAAAGAAAG-AAAGAG
1241079 AGAGAAAGAAAGAAAGAG
1 AGAGAAAGAAAGAAAGAG
*
1241097 AGA-AAAGGAAAG--AGAA
1 AGAGAAA-GAAAGAAAGAG
1241113 AGAGAAAGAA
1 AGAGAAAGAA
1241123 TAAACTAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.22
17 6 0.15
18 14 0.35
19 11 0.28
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAGAAAGAG
Found at i:1243881 original size:16 final size:16
Alignment explanation
Indices: 1243844--1243882 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1243834 AAAATTTTTT
*
1243844 ATTTAAATTTTAAATA
1 ATTTAAATTTGAAATA
* *
1243860 AATTAAATTTGAATTA
1 ATTTAAATTTGAAATA
1243876 ATTTAAA
1 ATTTAAA
1243883 AATTTTGAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
ATTTAAATTTGAAATA
Found at i:1247431 original size:25 final size:25
Alignment explanation
Indices: 1247380--1247432 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1247370 TAATTTAGTT
* *
1247380 AATAAAATTGATATTCAAAATATTA
1 AATAAAATTGATACTAAAAATATTA
*
1247405 AATAAAATTTATACTAATAAATA-TA
1 AATAAAATTGATACTAA-AAATATTA
1247430 AAT
1 AAT
1247433 TTAAGGGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (25 bp):
AATAAAATTGATACTAAAAATATTA
Found at i:1249055 original size:24 final size:24
Alignment explanation
Indices: 1249005--1249056 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1248995 CTCGATCAAC
*
1249005 TAAAATTATTATTTATTTTAATAA
1 TAAAATTATTATTTATTATAATAA
1249029 TAAAA-TA-TATTTATATATAATATA
1 TAAAATTATTATTTAT-TATAATA-A
1249053 TAAA
1 TAAA
1249057 TAATAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 7 0.28
23 8 0.32
24 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAATTATTATTTATTATAATAA
Found at i:1250108 original size:21 final size:22
Alignment explanation
Indices: 1250058--1250115 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
1250048 ATACGATGGT
*
1250058 ATAATATAA-AAATATATTAAA
1 ATAATATAATATATATATTAAA
*
1250079 AT-ATGATAATATA-ATATTAAC
1 ATAAT-ATAATATATATATTAAA
1250100 ATAATATAA-ATATATA
1 ATAATATAATATATATA
1250116 AATTTATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 5 0.16
21 22 0.71
22 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAATATAATATATATATTAAA
Found at i:1258192 original size:3 final size:3
Alignment explanation
Indices: 1258186--1258212 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1258176 TCAACGCTCC
1258186 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1258213 ACCTTGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1259380 original size:3 final size:3
Alignment explanation
Indices: 1259372--1259402 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1259362 ATTTCAAACC
*
1259372 AAG AAG AAG AAG AAG CAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1259403 CGACTTGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1263139 original size:16 final size:16
Alignment explanation
Indices: 1263120--1263166 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1263110 TTTTAATTTT
1263120 TTATATATTTAAATAA
1 TTATATATTTAAATAA
* *
1263136 TTATATTTTTATATAA
1 TTATATATTTAAATAA
* *
1263152 ATATATATTCAAATA
1 TTATATATTTAAATA
1263167 GTTTATAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATATTTAAATAA
Found at i:1263183 original size:26 final size:25
Alignment explanation
Indices: 1263143--1263203 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
1263133 TAATTATATT
*
1263143 TTTATATAAATATATAT-TCAAATAG
1 TTTATAAAAATATATATGT-AAATAG
*
1263168 TTTATAAAACATATATATGTAAATAT
1 TTTATAAAA-ATATATATGTAAATAG
*
1263194 TTTTTAAAAA
1 TTTATAAAAA
1263204 ATAAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 9 0.29
26 21 0.68
27 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (25 bp):
TTTATAAAAATATATATGTAAATAG
Found at i:1264712 original size:20 final size:19
Alignment explanation
Indices: 1264676--1264723 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1264666 AATATTTTTT
**
1264676 AATTAAATTAAGCTAAATA
1 AATTAAATTAAAATAAATA
*
1264695 AATTTAAATTAAAATAAATT
1 AA-TTAAATTAAAATAAATA
1264715 AATTAAATT
1 AATTAAATT
1264724 TTTAAATTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTAAATTAAAATAAATA
Found at i:1264942 original size:3 final size:3
Alignment explanation
Indices: 1264934--1264969 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1264924 AAAGAACAAT
1264934 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1264970 ATTTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1264978 original size:3 final size:3
Alignment explanation
Indices: 1264972--1264998 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1264962 AATAATAAAT
1264972 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1264999 AAAAAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1265288 original size:19 final size:21
Alignment explanation
Indices: 1265254--1265299 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1265244 TTCGAGTCAA
* *
1265254 TAAAAAATTATTTTATT-TTT
1 TAAAAAATTATCTTATTCTTC
1265274 TAAAAAATT-TCTTATTCTTC
1 TAAAAAATTATCTTATTCTTC
1265294 TAAAAA
1 TAAAAA
1265300 TAGTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAAAATTATCTTATTCTTC
Found at i:1273225 original size:3 final size:3
Alignment explanation
Indices: 1273217--1273257 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1273207 ATGTATATTG
1273217 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1273258 TTTAATTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1273395 original size:16 final size:16
Alignment explanation
Indices: 1273317--1273444 Score: 50
Period size: 16 Copynumber: 8.1 Consensus size: 16
1273307 GAGTTAATTT
*
1273317 ATTTTAAATT-TTTAAA
1 ATTTTAAATTATTT-TA
1273333 ATTTTAAATTATTTTTTA
1 ATTTTAAATTA--TTTTA
* * *
1273351 GTTTT-GATCATTTTA
1 ATTTTAAATTATTTTA
* ** *
1273366 AATTCGAATCATTTTA
1 ATTTTAAATTATTTTA
1273382 ATTTTAAATTA-TTTA
1 ATTTTAAATTATTTTA
** * *
1273397 AAGTTAAAGTTA-ATCA
1 ATTTTAAA-TTATTTTA
*
1273413 AATTT-AATTATTTTA
1 ATTTTAAATTATTTTA
* *
1273428 AGTTTAAATCATTTTA
1 ATTTTAAATTATTTTA
1273444 A
1 A
1273445 GTTAATTGTT
Statistics
Matches: 84, Mismatches: 21, Indels: 14
0.71 0.18 0.12
Matches are distributed among these distances:
14 3 0.04
15 25 0.30
16 45 0.54
17 3 0.04
18 5 0.06
19 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTAAATTATTTTA
Found at i:1273445 original size:16 final size:16
Alignment explanation
Indices: 1273357--1273447 Score: 53
Period size: 16 Copynumber: 5.8 Consensus size: 16
1273347 TTTAGTTTTG
* **
1273357 ATCATTTTAAATTCGA
1 ATCATTTTAAGTTTAA
*
1273373 ATCATTTTAATTTTAA
1 ATCATTTTAAGTTTAA
* *
1273389 ATTATTTAAAG-TTAA
1 ATCATTTTAAGTTTAA
* * * *
1273404 AGTTA-ATCAAATTT-A
1 A-TCATTTTAAGTTTAA
*
1273419 ATTATTTTAAGTTTAA
1 ATCATTTTAAGTTTAA
1273435 ATCATTTTAAGTT
1 ATCATTTTAAGTT
1273448 AATTGTTCAG
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
14 3 0.05
15 16 0.28
16 39 0.67
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (16 bp):
ATCATTTTAAGTTTAA
Found at i:1274448 original size:19 final size:19
Alignment explanation
Indices: 1274421--1274462 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1274411 TAAATTTTAA
* *
1274421 ATTTTATTTAAATATTTTT
1 ATTTAATTTAAATAATTTT
*
1274440 ATTTAATTTTAATAATTTT
1 ATTTAATTTAAATAATTTT
1274459 ATTT
1 ATTT
1274463 TTATTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTAATTTAAATAATTTT
Found at i:1280887 original size:93 final size:93
Alignment explanation
Indices: 1280721--1280905 Score: 237
Period size: 93 Copynumber: 2.0 Consensus size: 93
1280711 CAGGTTCCTT
* * * * * *
1280721 TTTCACTAATGGAAGGTTTCGATTATCTGATTTTGACTCTGCATTTTCAGAGGCCTTGACCAGAG
1 TTTCACCAATGGAAGGTTTCGATCATCCGATTTTAACTCTGCAGTTTCACAGGCCTTGACCAGAG
* * *
1280786 CAAGAGAAAAAT-AATCAGGAGCCTCTTC
66 AAACAG-AAAATGAATCAAGAGCCTCTTC
* * *
1280814 TTTCACCAATGGAGGGTTTTGATCATCCGATTTTAACTCTGCAGTTTCACAGGCCTTGACCTGAG
1 TTTCACCAATGGAAGGTTTCGATCATCCGATTTTAACTCTGCAGTTTCACAGGCCTTGACCAGAG
*
1280879 AAACAGAAACTGAATCAAGAGCCTCTT
66 AAACAGAAAATGAATCAAGAGCCTCTT
1280906 TAATCTGGGT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
92 4 0.05
93 74 0.95
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (93 bp):
TTTCACCAATGGAAGGTTTCGATCATCCGATTTTAACTCTGCAGTTTCACAGGCCTTGACCAGAG
AAACAGAAAATGAATCAAGAGCCTCTTC
Found at i:1281793 original size:18 final size:20
Alignment explanation
Indices: 1281749--1281796 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
1281739 TTTTTATTTT
*
1281749 ATAAATTTTAATTATTATTA
1 ATAAATTTTAATTATTATAA
1281769 ATAAAATTTTAATTA-TA-AA
1 AT-AAATTTTAATTATTATAA
1281788 ATAAATTTT
1 ATAAATTTT
1281797 GTTTTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 7 0.27
19 3 0.12
20 4 0.15
21 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAATTTTAATTATTATAA
Found at i:1281890 original size:15 final size:15
Alignment explanation
Indices: 1281870--1281907 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1281860 ATGAGTTCAC
*
1281870 TTTAAAATTTATTAT
1 TTTAAAATATATTAT
1281885 TTT-AAATATATTAT
1 TTTAAAATATATTAT
*
1281899 TTAAAAATA
1 TTTAAAATA
1281908 AAATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAAATATATTAT
Found at i:1282624 original size:18 final size:18
Alignment explanation
Indices: 1282597--1282634 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1282587 TTTATATAAA
*
1282597 TATTTATATATTAATAATT
1 TATTTATATATAAAT-ATT
1282616 TATTT-TATATAAATATT
1 TATTTATATATAAATATT
1282633 TA
1 TA
1282635 CATATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTATATATAAATATT
Found at i:1282624 original size:32 final size:33
Alignment explanation
Indices: 1282587--1282649 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1282577 GTATTCTAAA
*
1282587 TTTATATAAATATTTATATATTAATA-ATTTAT
1 TTTATATAAATATTTACATATTAATATATTTAT
*
1282619 TTTATATAAATATTTACATATTTATATATTT
1 TTTATATAAATATTTACATATTAATATATTT
1282650 TTGTCATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTATATAAATATTTACATATTAATATATTTAT
Found at i:1282642 original size:20 final size:19
Alignment explanation
Indices: 1282586--1282646 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 19
1282576 AGTATTCTAA
1282586 ATTTATATAAATATTT-AT
1 ATTTATATAAATATTTAAT
1282604 A--TAT-T-AATAATTT-AT
1 ATTTATATAAAT-ATTTAAT
1282619 -TTTATATAAATATTTACAT
1 ATTTATATAAATATTTA-AT
1282638 ATTTATATA
1 ATTTATATA
1282647 TTTTTGTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
14 3 0.09
15 7 0.20
16 6 0.17
17 5 0.14
18 4 0.11
19 2 0.06
20 8 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTATATAAATATTTAAT
Found at i:1282831 original size:16 final size:16
Alignment explanation
Indices: 1282801--1282851 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1282791 ATTTTTAAAT
1282801 AAATTTTAT-TAATTA
1 AAATTTTATATAATTA
* *
1282816 TAATTTTATATCATTA
1 AAATTTTATATAATTA
* *
1282832 AAAATTTATAAATATTA
1 AAATTTTATATA-ATTA
1282849 AAA
1 AAA
1282852 CCTGACAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 8 0.29
16 13 0.46
17 7 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTTATATAATTA
Found at i:1283409 original size:14 final size:14
Alignment explanation
Indices: 1283392--1283424 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1283382 TAAAATATAA
1283392 TTTTTAATAAATAT
1 TTTTTAATAAATAT
*
1283406 TTTTTAATATATAT
1 TTTTTAATAAATAT
1283420 TTTTT
1 TTTTT
1283425 TATGAATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTAATAAATAT
Found at i:1288421 original size:21 final size:21
Alignment explanation
Indices: 1288370--1288422 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1288360 CTCTATTCTA
*
1288370 TTTATTTTTTAAAATTATTAT
1 TTTATATTTTAAAATTATTAT
*
1288391 TTTATTTTTTAAAA-TATT-T
1 TTTATATTTTAAAATTATTAT
1288410 TTATATAATTTTA
1 TT-TAT-ATTTTA
1288423 GTATATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.10
20 7 0.24
21 19 0.66
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATATTTTAAAATTATTAT
Found at i:1289890 original size:21 final size:21
Alignment explanation
Indices: 1289851--1289891 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1289841 ATCTAGCAAC
* *
1289851 TTATGTATTTTTTTATTATAT
1 TTATATATTTTTGTATTATAT
*
1289872 TTATATATTTTTGTGTTATA
1 TTATATATTTTTGTATTATA
1289892 ATCGTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TTATATATTTTTGTATTATAT
Found at i:1296531 original size:2 final size:2
Alignment explanation
Indices: 1296524--1296568 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1296514 TTCTTTCTTT
1296524 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
1296566 TA T
1 TA T
1296569 TATTTTTCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1297549 original size:18 final size:18
Alignment explanation
Indices: 1297497--1297549 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1297487 ATGAATTCAT
*
1297497 TATCAAAATCTATAT-AA
1 TATCAAAATTTATATAAA
1297514 TA--AAAA-TTAT-TAACA
1 TATCAAAATTTATATAA-A
1297529 TATCAAAATTTATATAAA
1 TATCAAAATTTATATAAA
1297547 TAT
1 TAT
1297550 ATAATAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
13 1 0.03
14 4 0.14
15 7 0.24
17 6 0.21
18 8 0.28
19 3 0.10
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
TATCAAAATTTATATAAA
Found at i:1298805 original size:22 final size:22
Alignment explanation
Indices: 1298758--1298810 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1298748 TATTTAAAAT
* *
1298758 TTTAATTAATTATAAAATTATC
1 TTTAATTAATTATAAAATAATA
1298780 TTTAATT-ATTATCAAAATAATA
1 TTTAATTAATTAT-AAAATAATA
*
1298802 TTTATTTAA
1 TTTAATTAA
1298811 ATTGTACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 20 0.77
23 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAATTAATTATAAAATAATA
Found at i:1310321 original size:23 final size:24
Alignment explanation
Indices: 1310278--1310371 Score: 88
Period size: 24 Copynumber: 4.0 Consensus size: 24
1310268 TATTAATATA
*
1310278 TTATTTATGAAAAAAATTTATAATT
1 TTATTTATGATAAAAA-TTATAATT
*
1310303 TTATTTAT-ATAAAAATTATAA-A
1 TTATTTATGATAAAAATTATAATT
*
1310325 TTATTTATGAATAAAATTTAT-ATT
1 TTATTTATG-ATAAAAATTATAATT
* *
1310349 TTATTTGTGCA-AAAAATTTTAAT
1 TTATTTATG-ATAAAAATTATAAT
1310372 AATTTTATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
22 8 0.14
23 14 0.25
24 27 0.47
25 8 0.14
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (24 bp):
TTATTTATGATAAAAATTATAATT
Found at i:1310366 original size:47 final size:47
Alignment explanation
Indices: 1310262--1310354 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
1310252 AAAAAAAGTT
* *
1310262 TATAAATATTAATATATTATTTATGAAAAAAATTTATAATTTTATTTA
1 TATAAAAATT-ATAAATTATTTATGAAAAAAATTTATAATTTTATTTA
*
1310310 TATAAAAATTATAAATTATTTATGAATAAAATTTAT-ATTTTATTT
1 TATAAAAATTATAAATTATTTATGAAAAAAATTTATAATTTTATTT
1310355 GTGCAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
46 9 0.21
47 24 0.57
48 9 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (47 bp):
TATAAAAATTATAAATTATTTATGAAAAAAATTTATAATTTTATTTA
Found at i:1310407 original size:27 final size:26
Alignment explanation
Indices: 1310377--1310430 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1310367 TTAATAATTT
*
1310377 TATAAGTATTTAATTATAAATATAAAA
1 TATAAGTATTTAAATATAAATA-AAAA
* * *
1310404 TATAATTTTTTAAATATATATAAAAA
1 TATAAGTATTTAAATATAAATAAAAA
1310430 T
1 T
1310431 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TATAAGTATTTAAATATAAATAAAAA
Found at i:1313644 original size:30 final size:27
Alignment explanation
Indices: 1313581--1313653 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
1313571 TATTAGATAT
* * *
1313581 AATAATTTATATTTAT-GTTATATTTA
1 AATATTTTATATTTATAATCATATTTA
*
1313607 TATATTTTATTATATTATAATCATATTTAA
1 AATATTTTA-TAT-TTATAATCATATTT-A
1313637 AATATTTTATATTTATA
1 AATATTTTATATTTATA
1313654 TAAATTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 7 0.18
27 3 0.08
28 9 0.24
29 10 0.26
30 9 0.24
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
AATATTTTATATTTATAATCATATTTA
Found at i:1313670 original size:37 final size:36
Alignment explanation
Indices: 1313629--1313722 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 36
1313619 TATTATAATC
1313629 ATATTTAAAATATTTTATATTTATAT-AAATTTTAA
1 ATATTTAAAATATTTTATATTTATATAAAATTTTAA
* * * *
1313664 AAATATTAATAATAATTCATA-TTATTTAAAATTTTAA
1 ATAT-TTAA-AATATTTTATATTTATATAAAATTTTAA
*
1313701 ATATTTATATATATTTT-TATTT
1 ATATTTA-AAATATTTTATATTT
1313723 TTTTTACATA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
35 5 0.11
36 19 0.41
37 22 0.48
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (36 bp):
ATATTTAAAATATTTTATATTTATATAAAATTTTAA
Found at i:1315020 original size:153 final size:153
Alignment explanation
Indices: 1314737--1315047 Score: 570
Period size: 153 Copynumber: 2.0 Consensus size: 153
1314727 AATGTGGGGT
1314737 TTTATTTGAATAGATCTTGTAAAGTTACTAGCTTTGTCGGATAATTAGTTCAATTTAAGGTGTTA
1 TTTATTTGAATAGATCTTGTAAAGTTACTAGCTTTGTCGGATAATTAGTTCAATTTAAGGTGTTA
* *
1314802 TTAAGAGTAAACATTTTATGTAAAAATATGGAAAATTTATATTGCCGGTGAGCATGTTAGGATTT
66 TTAAGAGTAAACATTTCATGTAAAAATATGGAAAATTTATATTGCCGGTGAGCATGTTAGAATTT
1314867 CTTACATGTATATGTTTTGTGGC
131 CTTACATGTATATGTTTTGTGGC
*
1314890 TTTATTTGAATAGATCTTGTAAAGTTACTAGCTTTGTCGGATAATTAGTTCAATTTAAGTTGTTA
1 TTTATTTGAATAGATCTTGTAAAGTTACTAGCTTTGTCGGATAATTAGTTCAATTTAAGGTGTTA
1314955 TTAAGAGTAAAC-TTGTCATGTAAAAATATGGAAAATTTATATTGCCGGTGAGCATGTTAGAATT
66 TTAAGAGTAAACATT-TCATGTAAAAATATGGAAAATTTATATTGCCGGTGAGCATGTTAGAATT
*
1315019 TCTTACATGTTTATGTTTTGTGGC
130 TCTTACATGTATATGTTTTGTGGC
1315043 TTTAT
1 TTTAT
1315048 ATATATATAT
Statistics
Matches: 153, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
152 2 0.01
153 151 0.99
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (153 bp):
TTTATTTGAATAGATCTTGTAAAGTTACTAGCTTTGTCGGATAATTAGTTCAATTTAAGGTGTTA
TTAAGAGTAAACATTTCATGTAAAAATATGGAAAATTTATATTGCCGGTGAGCATGTTAGAATTT
CTTACATGTATATGTTTTGTGGC
Found at i:1316203 original size:2 final size:2
Alignment explanation
Indices: 1316196--1316223 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1316186 CTAAAACATA
1316196 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
1316224 GTTAAAATCA
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:1318327 original size:29 final size:28
Alignment explanation
Indices: 1318248--1318328 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
1318238 AAAGTATTAA
* * *
1318248 ATATATAATAATATATATATT-AAAATTT
1 ATATAAAATAAAATAT-TATTAAAAAATT
*
1318276 ATATAAAATAAATTATTAATTAAAAAATT
1 ATATAAAATAAAATATT-ATTAAAAAATT
1318305 ATATAAATTATAAAATATT-TTAAA
1 ATATAAA--ATAAAATATTATTAAA
1318329 TATGATTATG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.02
28 16 0.36
29 18 0.41
31 9 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATAAAATAAAATATTATTAAAAAATT
Found at i:1319084 original size:13 final size:13
Alignment explanation
Indices: 1319053--1319099 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
1319043 ACGCTGACAC
1319053 AATATTTATTTTAA
1 AATATTTATTTT-A
*
1319067 AATATTTATATTA
1 AATATTTATTTTA
*
1319080 AATATTTATTTTT
1 AATATTTATTTTA
1319093 AATATTT
1 AATATTT
1319100 CAAATCACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATTTTA
Found at i:1319237 original size:2 final size:2
Alignment explanation
Indices: 1319230--1319258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1319220 CTGATGAAGA
1319230 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
1319259 ACAATATGAA
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:1320554 original size:15 final size:16
Alignment explanation
Indices: 1320530--1320571 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1320520 AATTAAATAT
*
1320530 TAAAAAATAAAT-AAA
1 TAAAATATAAATAAAA
*
1320545 TAAAATATAATTAAAA
1 TAAAATATAAATAAAA
1320561 TAAAAATATAA
1 T-AAAATATAA
1320572 TTGTATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATATAAATAAAA
Found at i:1324384 original size:29 final size:28
Alignment explanation
Indices: 1324334--1324413 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
1324324 AATAAATTTA
*
1324334 TATTAATTTTTATTTAAAAATTTTAAGTT
1 TATTTATTTTTATTTAAAAA-TTTAAGTT
*** *
1324363 TATTTATTTTTATTTTTTAATTTAATTT
1 TATTTATTTTTATTTAAAAATTTAAGTT
*
1324391 TATATATTATTATAATTTAAAAA
1 TATTTATT-TT-T-ATTTAAAAA
1324414 GAATTAAAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 14 0.36
29 18 0.46
30 1 0.03
31 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (28 bp):
TATTTATTTTTATTTAAAAATTTAAGTT
Found at i:1324409 original size:28 final size:28
Alignment explanation
Indices: 1324355--1324410 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1324345 ATTTAAAAAT
* * **
1324355 TTTAAGTTTATTTATTTTTATTTTTTAA
1 TTTAAGTTTATATATTATTATAATTTAA
*
1324383 TTTAATTTTATATATTATTATAATTTAA
1 TTTAAGTTTATATATTATTATAATTTAA
1324411 AAAGAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTAAGTTTATATATTATTATAATTTAA
Found at i:1325423 original size:22 final size:22
Alignment explanation
Indices: 1325382--1325422 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1325372 TTATTTGAAT
*
1325382 TAATTTAATATTATTTAAAACA
1 TAATTTAATATTATTAAAAACA
1325404 TAATTTAAT-TTATTAAAAA
1 TAATTTAATATTATTAAAAA
1325423 ATTATGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATTTAATATTATTAAAAACA
Found at i:1328078 original size:50 final size:50
Alignment explanation
Indices: 1327976--1328178 Score: 232
Period size: 49 Copynumber: 4.1 Consensus size: 50
1327966 TTATTATATA
* * * *
1327976 ATTTTTTTATTACTATCTCTTATCGTAACCGTCTTTTACTATAT-AAAAT
1 ATTTTTTTATTACTATCTCTTATCGTAACTGTATCTTAATATATAAAAAT
* * *
1328025 ATTTTTTTATTACTATTTCTTATCGTAACTTTATCTCAATATATAAAAAT
1 ATTTTTTTATTACTATCTCTTATCGTAACTGTATCTTAATATATAAAAAT
* * * * *
1328075 A-TTTTATATTATTGTCTCTTGTCGTAACTCTATCTTAATATATAAAAAT
1 ATTTTTTTATTACTATCTCTTATCGTAACTGTATCTTAATATATAAAAAT
* * * *
1328124 ATTTTTTTATTATTGTCTCTTGTCGTAA-TCGTATCTTAATATATCAAAAT
1 ATTTTTTTATTACTATCTCTTATCGTAACT-GTATCTTAATATATAAAAAT
1328174 ATTTT
1 ATTTT
1328179 ATATATTATT
Statistics
Matches: 134, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
49 80 0.60
50 54 0.40
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.52
Consensus pattern (50 bp):
ATTTTTTTATTACTATCTCTTATCGTAACTGTATCTTAATATATAAAAAT
Found at i:1329516 original size:18 final size:18
Alignment explanation
Indices: 1329495--1329530 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1329485 TAAATTTTTG
1329495 ATTTTAAT-TTAGTTTTAA
1 ATTTTAATCTTA-TTTTAA
1329513 ATTTTAATCTTATTTTAA
1 ATTTTAATCTTATTTTAA
1329531 TAAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTTTAATCTTATTTTAA
Found at i:1329614 original size:23 final size:23
Alignment explanation
Indices: 1329587--1329631 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1329577 TTTATAATTC
*
1329587 AAAAATTTATAATTTTATTTTTTT
1 AAAAA-TTATAATATTATTTTTTT
1329611 AAAAATTATAATATTATTTTT
1 AAAAATTATAATATTATTTTT
1329632 ATTGATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AAAAATTATAATATTATTTTTTT
Found at i:1329858 original size:38 final size:38
Alignment explanation
Indices: 1329816--1330031 Score: 297
Period size: 38 Copynumber: 5.7 Consensus size: 38
1329806 TTTAATTAGT
* *
1329816 TGACGGTTAGAGAATTCAATTTGAAATTAGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
*
1329854 TGACGGCTAGAGAATTTAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
* *
1329892 TGACGACTAAAGAATTCAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
* *
1329930 TGACGGCTAGAGAATTCAATTTGAAATTGACCGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
* * * *
1329968 TGACGACTAGAGAATTCAATTTGGAATTGGCCGGTGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
** *
1330006 TGGTGGCTAGAGAATTCCAAATTGAA
1 TGACGGCTAGAGAATT-CAATTTGAA
1330032 CTCTCTTTGA
Statistics
Matches: 158, Mismatches: 19, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
38 151 0.96
39 7 0.04
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
Found at i:1333610 original size:38 final size:38
Alignment explanation
Indices: 1333559--1333712 Score: 256
Period size: 38 Copynumber: 4.1 Consensus size: 38
1333549 TTGAATTAGT
*
1333559 TGACGGTTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1333597 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1333635 TGACGGCTAGAGAATTCAATTTGAAATTGG-TCGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCT-GGCGGC
* * *
1333673 TGACGACTAGAGAATTCAATTTGAAATTGGCCGGTGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1333711 TG
1 TG
1333713 GTGACTGGTG
Statistics
Matches: 110, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
37 1 0.01
38 109 0.99
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
Found at i:1334340 original size:30 final size:29
Alignment explanation
Indices: 1334290--1334359 Score: 97
Period size: 28 Copynumber: 2.3 Consensus size: 29
1334280 TTGATTTAAT
1334290 TATTTTTAAATTATAATTTAATTTATAAAAAA
1 TATTTTT-AATTATAATTTAA-TTAT-AAAAA
*
1334322 TATTTTTATTTA-AATTTAATTATAAAAA
1 TATTTTTAATTATAATTTAATTATAAAAA
1334350 TATTTTTAAT
1 TATTTTTAAT
1334360 ACTTTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 14 0.39
29 4 0.11
30 7 0.19
31 4 0.11
32 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTTTTAATTATAATTTAATTATAAAAA
Found at i:1336786 original size:48 final size:48
Alignment explanation
Indices: 1336722--1336836 Score: 144
Period size: 48 Copynumber: 2.4 Consensus size: 48
1336712 TATATATTAT
* *
1336722 TATATAAAAATATTTTTATTATCGTCTCTTATCGTAA-TCGTGCTTTAA
1 TATATAAAAATATTTTTATTATCATCTCTTATCATAACT-GTGCTTTAA
* * *
1336770 TATAT-AAAATATTTTTTATTATCATCTTTTATTATAACTGTGTTTTAA
1 TATATAAAAATA-TTTTTATTATCATCTCTTATCATAACTGTGCTTTAA
*
1336818 TATATAAAAATAATTTTAT
1 TATATAAAAATATTTTTAT
1336837 ATATTATTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
47 6 0.10
48 45 0.78
49 7 0.12
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (48 bp):
TATATAAAAATATTTTTATTATCATCTCTTATCATAACTGTGCTTTAA
Found at i:1337369 original size:38 final size:38
Alignment explanation
Indices: 1337233--1337371 Score: 179
Period size: 38 Copynumber: 3.7 Consensus size: 38
1337223 AATTGACAGT
* * * * * *
1337233 TAGAGAATTTAATTTAAAATTGACTGGCAGCTGACGGT
1 TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGGC
* *
1337271 TAGAGAATTCAATTTGAAATTAGCTGGCGGCTGACGGC
1 TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGGC
* * *
1337309 TAGAGAATTCAATTTGGAATTGGCCGGCGGTTGACGAC
1 TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGGC
1337347 TAGAGAATTCAATTTGAAATTGGCC
1 TAGAGAATTCAATTTGAAATTGGCC
1337372 AGTGGCTGGT
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 89 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (38 bp):
TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGGC
Found at i:1341988 original size:38 final size:38
Alignment explanation
Indices: 1341946--1342123 Score: 212
Period size: 38 Copynumber: 4.7 Consensus size: 38
1341936 TTGAATTAGT
* ***
1341946 TGACGGTTAGAGAATTCAATTTGAAATTTATTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1341984 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
* * *
1342022 TGACGGCTAGAGAATTCAATTTGGAATTGGCCGGCGAC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
* * * * *
1342060 TGACGACTAGAGAATTCAATTTGGAATTGGCCGGTGAC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
** *
1342098 TGGTGGCTAGAGAATTCCAAATTGAA
1 TGACGGCTAGAGAATT-CAATTTGAA
1342124 CTCTTTTTGA
Statistics
Matches: 125, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 118 0.94
39 7 0.06
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.28
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
Found at i:1342016 original size:31 final size:31
Alignment explanation
Indices: 1341928--1342022 Score: 75
Period size: 38 Copynumber: 2.9 Consensus size: 31
1341918 AAGTAAATCA
* * * *
1341928 AATTCAAATTG-AATTAGTTGACGGTTAGAG
1 AATTCAATTTGAAATTGGCTGACGGCTAGAG
1341958 AATTCAATTTGAAATTTATTGGCGGCTGACGGCTAGAG
1 AATTCAATTTG-AA---ATT---GGCTGACGGCTAGAG
*
1341996 AATTCAATTTGAAATTGGCTGGCGGCT
1 AATTCAATTTGAAATTGGCTGACGGCT
1342023 GACGGCTAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
30 10 0.19
31 10 0.19
32 1 0.02
34 3 0.06
35 3 0.06
37 2 0.04
38 23 0.44
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (31 bp):
AATTCAATTTGAAATTGGCTGACGGCTAGAG
Found at i:1342751 original size:17 final size:16
Alignment explanation
Indices: 1342722--1342765 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1342712 AATTAAAAAA
1342722 TAAAATA-ATTTATAT
1 TAAAATATATTTATAT
1342737 TAAACATATATTTATAT
1 TAAA-ATATATTTATAT
*
1342754 TTAAATATATTT
1 TAAAATATATTT
1342766 TTAAATAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 11 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAATATATTTATAT
Found at i:1342768 original size:18 final size:17
Alignment explanation
Indices: 1342729--1342765 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1342719 AAATAAAATA
1342729 ATTTATATTAAACATAT
1 ATTTATATTAAACATAT
*
1342746 ATTTATATTTAA-ATAT
1 ATTTATATTAAACATAT
1342762 ATTT
1 ATTT
1342766 TTAAATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATATTAAACATAT
Found at i:1344443 original size:2 final size:2
Alignment explanation
Indices: 1344397--1344425 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1344387 TCTTTCAAGA
1344397 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
1344426 ATGTTTTGAG
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:1344714 original size:14 final size:15
Alignment explanation
Indices: 1344696--1344729 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1344686 ATACAAAAAT
1344696 AATTATATTT-TAAA
1 AATTATATTTATAAA
*
1344710 CATTATATTTATAAA
1 AATTATATTTATAAA
1344725 AATTA
1 AATTA
1344730 ATATACTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATATTTATAAA
Found at i:1345391 original size:16 final size:16
Alignment explanation
Indices: 1345372--1345410 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1345362 TTCAAATATT
1345372 TTATATTTATATAAAA
1 TTATATTTATATAAAA
* * *
1345388 TTATATATATATATAG
1 TTATATTTATATAAAA
1345404 TTATATT
1 TTATATT
1345411 ATTTTTATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTATATTTATATAAAA
Found at i:1345419 original size:21 final size:22
Alignment explanation
Indices: 1345393--1345438 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
1345383 TAAAATTATA
1345393 TATATATATAGTTATATTA-TTTT
1 TATAT-TATA-TTATATTAGTTTT
*
1345416 TATATTATATTTTATTAGTTTT
1 TATATTATATTATATTAGTTTT
1345438 T
1 T
1345439 TTATGTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TATATTATATTATATTAGTTTT
Found at i:1345420 original size:11 final size:12
Alignment explanation
Indices: 1345372--1345430 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
1345362 TTCAAATATT
1345372 TTATA-TTTATA
1 TTATATTTTATA
* * *
1345383 TAAAATTATATA
1 TTATATTTTATA
*
1345395 TATATATAGTTATA
1 T-TATAT-TTTATA
1345409 TTAT-TTTTATA
1 TTATATTTTATA
1345420 TTATATTTTAT
1 TTATATTTTAT
1345431 TAGTTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
11 12 0.33
12 13 0.36
13 6 0.17
14 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:1347376 original size:16 final size:16
Alignment explanation
Indices: 1347333--1347378 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1347323 GGAGGATGAT
*
1347333 AAATTTATATAAAATA
1 AAATTTATATAAATTA
*
1347349 AATTATTA-ATAAATTA
1 AAAT-TTATATAAATTA
1347365 AAATTTATATAAAT
1 AAATTTATATAAAT
1347379 ATATAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTATATAAATTA
Found at i:1347394 original size:32 final size:36
Alignment explanation
Indices: 1347333--1347418 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 36
1347323 GGAGGATGAT
1347333 AAATTTATATAAA-ATA-AATTATTAATAAAT-T-A
1 AAATTTATATAAATATATAATTATTAATAAATATAA
*
1347365 AAATTTATATAAATATATAA-TATT-TTAAATATAAA
1 AAATTTATATAAATATATAATTATTAATAAATAT-AA
* *
1347400 AAAATAATATAAATATATA
1 AAATTTATATAAATATATA
1347419 TGTAATTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
32 18 0.39
33 8 0.17
34 2 0.04
35 18 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (36 bp):
AAATTTATATAAATATATAATTATTAATAAATATAA
Found at i:1348834 original size:16 final size:17
Alignment explanation
Indices: 1348809--1348847 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
1348799 AATTAAAAAA
1348809 TTAA-ATATATTTA-AT
1 TTAATATATATTTATAT
1348824 TTAATATATATTTATAT
1 TTAATATATATTTATAT
1348841 TTAATAT
1 TTAATAT
1348848 TTTCATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATATATATTTATAT
Found at i:1350045 original size:19 final size:19
Alignment explanation
Indices: 1350021--1350061 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1350011 AGTTTATTTG
*
1350021 TTTTTATTTATTAATT-TAA
1 TTTTTATATATT-ATTATAA
1350040 TTTTTATATATTATTATAA
1 TTTTTATATATTATTATAA
1350059 TTT
1 TTT
1350062 AAAAATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTATATATTATTATAA
Found at i:1353689 original size:46 final size:47
Alignment explanation
Indices: 1353588--1353714 Score: 166
Period size: 46 Copynumber: 2.6 Consensus size: 47
1353578 TATAAACTTG
* **
1353588 TCTTAATATATAAAAATATTTTTTATTATCATTTTCTGTCGTAACTTTA
1 TCTTAATATATAAAAATATTTTTTATTAT--TTTTCTGTCGCAACCGTA
1353637 TCTTAATATATAAAAATATTTTTTATTATTTTT-TGTCGCAACCGTA
1 TCTTAATATATAAAAATATTTTTTATTATTTTTCTGTCGCAACCGTA
* *
1353683 TTTTAATATATCAAAATATTTTATATATTATT
1 TCTTAATATATAAAAATATTTT-T-TATTATT
1353715 ATATATAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
46 30 0.42
47 5 0.07
48 7 0.10
49 29 0.41
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (47 bp):
TCTTAATATATAAAAATATTTTTTATTATTTTTCTGTCGCAACCGTA
Found at i:1358806 original size:21 final size:22
Alignment explanation
Indices: 1358764--1358808 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1358754 GATTTCAATA
* **
1358764 AAAAAATTAAAAATCACTTTAT
1 AAAAAATTAAAAATAAAATTAT
1358786 AAAAAATT-AAAATAAAATTAT
1 AAAAAATTAAAAATAAAATTAT
1358807 AA
1 AA
1358809 TTTATAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATTAAAAATAAAATTAT
Found at i:1358918 original size:25 final size:26
Alignment explanation
Indices: 1358890--1358949 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
1358880 TAATAATTAA
* * *
1358890 TTTAAATATTTTTTAT-TCATAAAAT
1 TTTAAATATTTTTAATCTAAAAAAAT
1358915 TTTAAAT-TTTTTAATCTAAAAAAAT
1 TTTAAATATTTTTAATCTAAAAAAAT
*
1358940 TTTATATATT
1 TTTAAATATT
1358950 AATTTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
25 20 0.69
26 2 0.07
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTAAATATTTTTAATCTAAAAAAAT
Found at i:1358937 original size:24 final size:25
Alignment explanation
Indices: 1358888--1358949 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
1358878 TTTAATAATT
* * *
1358888 AATTTAAATATTTTTTATTC-ATAA
1 AATTTTAATATTTTTTAATCAAAAA
1358912 AATTTTAA-ATTTTTTAATCTAAAAA
1 AATTTTAATATTTTTTAATC-AAAAA
1358937 AATTTTATATATT
1 AATTTTA-ATATT
1358950 AATTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 10 0.32
24 7 0.23
25 10 0.32
26 1 0.03
27 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTTTAATATTTTTTAATCAAAAA
Found at i:1359037 original size:27 final size:26
Alignment explanation
Indices: 1358992--1359051 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
1358982 TTTTAAAAAT
*
1358992 TTAATATTATCATAATAATATTTTTA
1 TTAATATTATAATAATAATATTTTTA
* * *
1359018 TATAATTTTATAATATTAATTTTTTTA
1 T-TAATATTATAATAATAATATTTTTA
1359045 TTAATAT
1 TTAATAT
1359052 ACAATTTACT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TTAATATTATAATAATAATATTTTTA
Found at i:1359411 original size:22 final size:20
Alignment explanation
Indices: 1359374--1359414 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
1359364 TAATATTTAT
1359374 TATTTAAATTAATTTAATTA
1 TATTTAAATTAATTTAATTA
1359394 TATTTAAAGTATAATTTAATT
1 TATTTAAA-T-TAATTTAATT
1359415 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TATTTAAATTAATTTAATTA
Found at i:1359470 original size:28 final size:27
Alignment explanation
Indices: 1359365--1359459 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 27
1359355 ACTTAAATAT
* *
1359365 AATATTTATTATTTAAATTAATT-TAAT
1 AATATTT-TTATTTAATTTAATTATAAA
* ** *
1359392 TATATTTAAAGTATAATTTAATTTATAAAA
1 AATATTTTTA-TTTAATTTAA-TTAT-AAA
1359422 AATATTTTTATTTAAATTTAATTATAAA
1 AATATTTTTATTT-AATTTAATTATAAA
1359450 AATATTTTTA
1 AATATTTTTA
1359460 ATATTTTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.02
27 14 0.26
28 15 0.28
29 7 0.13
30 16 0.30
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
AATATTTTTATTTAATTTAATTATAAA
Found at i:1361665 original size:25 final size:25
Alignment explanation
Indices: 1361632--1361681 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1361622 TGTGATAAAT
1361632 TTTTTTATTTTTTTTAAATATGAAA
1 TTTTTTATTTTTTTTAAATATGAAA
1361657 TTTTTTATTTTTTTTAAATATGAAA
1 TTTTTTATTTTTTTTAAATATGAAA
1361682 CCAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTTTTATTTTTTTTAAATATGAAA
Found at i:1361931 original size:48 final size:49
Alignment explanation
Indices: 1361816--1361945 Score: 140
Period size: 48 Copynumber: 2.7 Consensus size: 49
1361806 ATAGTTTTAA
* * *
1361816 TATATATTATTATATAAAAATA-TTTTTATTATCGTCTCTTATTGTAAC
1 TATATTTTAATATATAAAAATATTTTTTATTATCGTCTCTTATTATAAC
** ** *
1361864 CGTGGTTTAATATAT-AAAATATTTTTTATTATCGTCTTTTA-TATAAC
1 TATATTTTAATATATAAAAATATTTTTTATTATCGTCTCTTATTATAAC
*
1361911 TATATTTTAATATCTAAAAATATTTTATATATTAT
1 TATATTTTAATATATAAAAATATTTT-T-TATTAT
1361946 TATATAAAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
47 21 0.32
48 37 0.57
49 1 0.02
50 6 0.09
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (49 bp):
TATATTTTAATATATAAAAATATTTTTTATTATCGTCTCTTATTATAAC
Found at i:1367033 original size:2 final size:2
Alignment explanation
Indices: 1367020--1367049 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1367010 TCTGTTCTAA
*
1367020 AT AT AC 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
1367050 TCCATTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1369417 original size:23 final size:24
Alignment explanation
Indices: 1369391--1369442 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
1369381 TTTTTTATAT
* *
1369391 TTAAATATTAAATTTAA-TATTAA
1 TTAAATATTAAATATAATTAATAA
*
1369414 TTAAGTATTAAATATAATTAATAA
1 TTAAATATTAAATATAATTAATAA
1369438 TTAAA
1 TTAAA
1369443 AATATGCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TTAAATATTAAATATAATTAATAA
Found at i:1369440 original size:17 final size:19
Alignment explanation
Indices: 1369401--1369442 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
1369391 TTAAATATTA
*
1369401 AATTTAATATTAATTAAGT
1 AATTAAATATTAATTAAGT
1369420 -ATTAAATA-TAATTAA-T
1 AATTAAATATTAATTAAGT
1369436 AATTAAA
1 AATTAAA
1369443 AATATGCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTAAATATTAATTAAGT
Found at i:1369818 original size:17 final size:16
Alignment explanation
Indices: 1369796--1369845 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
1369786 TATATTAAAT
1369796 ATTATATTTTAAATATA
1 ATTATATTTTAAAT-TA
1369813 ATTATA---TAAATTTA
1 ATTATATTTTAAA-TTA
*
1369827 ATTAAATTTTAAATTA
1 ATTATATTTTAAATTA
1369843 ATT
1 ATT
1369846 TTTTTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 6 0.21
17 10 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATATTTTAAATTA
Found at i:1371792 original size:21 final size:21
Alignment explanation
Indices: 1371762--1371802 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1371752 AGTATAGATA
1371762 AATTTAATAATATTT-ATATAT
1 AATTTAATAA-ATTTGATATAT
*
1371783 AATTTTATAAATTTGATATA
1 AATTTAATAAATTTGATATA
1371803 AATAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTTAATAAATTTGATATAT
Found at i:1371802 original size:11 final size:10
Alignment explanation
Indices: 1371759--1371805 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
1371749 AAAAGTATAG
1371759 ATAAATTTA-
1 ATAAATTTAT
1371768 ATAATATTTAT
1 ATAA-ATTTAT
1371779 ATATAATTT-T
1 ATA-AATTTAT
1371789 ATAAATTTGAT
1 ATAAATTT-AT
1371800 ATAAAT
1 ATAAAT
1371806 AAAATAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 9 0.27
10 9 0.27
11 14 0.42
12 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
ATAAATTTAT
Found at i:1373661 original size:39 final size:39
Alignment explanation
Indices: 1373585--1373664 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
1373575 AGGACGTAAG
*
1373585 AAATAGATAAAACAATCGTAAGCTAAATGAAATCATTGA
1 AAATAGATAAAACAATCGTAAGCTAAATGAAACCATTGA
**
1373624 AAATAGATAAAACAATCGTAAGCTAAATGATCCCATTGA
1 AAATAGATAAAACAATCGTAAGCTAAATGAAACCATTGA
1373663 AA
1 AA
1373665 TAGTGTTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (39 bp):
AAATAGATAAAACAATCGTAAGCTAAATGAAACCATTGA
Found at i:1437022 original size:17 final size:17
Alignment explanation
Indices: 1436996--1437029 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1436986 ATGATAAACT
1436996 TTATGATAAATTATTAA
1 TTATGATAAATTATTAA
* *
1437013 TTATGTTAAATTTTTAA
1 TTATGATAAATTATTAA
1437030 AGATAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTATGATAAATTATTAA
Found at i:1439541 original size:21 final size:19
Alignment explanation
Indices: 1439517--1439556 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1439507 ATATTTTACT
1439517 ATATAATATATATAAATATAA
1 ATATAAT-TA-ATAAATATAA
*
1439538 ATATAATTAATAGATATAA
1 ATATAATTAATAAATATAA
1439557 TTTAAAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATAATTAATAAATATAA
Found at i:1440216 original size:15 final size:16
Alignment explanation
Indices: 1440190--1440231 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1440180 CATCTATTTG
1440190 AAATTATTATAATTAA-
1 AAATT-TTATAATTAAC
*
1440206 AAGTTTTATAATTAAC
1 AAATTTTATAATTAAC
1440222 AAATTTTATA
1 AAATTTTATA
1440232 TTTATTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATTTTATAATTAAC
Found at i:1445751 original size:52 final size:49
Alignment explanation
Indices: 1445690--1445818 Score: 170
Period size: 49 Copynumber: 2.6 Consensus size: 49
1445680 ATCTCTTATC
*
1445690 TTAATATATAAAAATATTTTTTATTACTGTC-TCCTCCTATCATAACTTTAAT
1 TTAATATATAAAAATATTTTTTATTA---TCAT-CTCCTATCATAACCTTAAT
* *
1445742 TTAATATATAAAAATATTTTTTATGATCATCTCCTATCATAACCTTATT
1 TTAATATATAAAAATATTTTTTATTATCATCTCCTATCATAACCTTAAT
*
1445791 TTAATATATAAAATTATATTTTTATTAT
1 TTAATATATAAAAATAT-TTTTTATTAT
1445819 TGTTACTTGT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
49 35 0.50
50 10 0.14
52 25 0.36
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (49 bp):
TTAATATATAAAAATATTTTTTATTATCATCTCCTATCATAACCTTAAT
Found at i:1446310 original size:107 final size:106
Alignment explanation
Indices: 1446130--1446342 Score: 363
Period size: 107 Copynumber: 2.0 Consensus size: 106
1446120 AGGTTGGATA
*
1446130 GCTGAAAATAATATAAATTAGTTATGATAATAATCTATATTTTAAAATTTTTTAAAATTAAATTA
1 GCTGAAAATAATATAAATTAGTTATGATAATAATCTATATTTTAAAAGTTTTTAAAATTAAATTA
1446195 ATTATGGTCATATGTCACTTTCCTTCGAGGGTAGGTTGTTGG
66 ATTATGGTCATATGTCAC-TTCCTTCGAGGGTAGGTTGTTGG
* * * *
1446237 GCTGAAAATAATATAAATTAGTTATGATAGTTATCTATTTTTTTAAAGTTTTTAAAATTAAATTA
1 GCTGAAAATAATATAAATTAGTTATGATAATAATCTATATTTTAAAAGTTTTTAAAATTAAATTA
*
1446302 ATTGTGGTCATATGTCACTTCCTTCGAGGGTAGGTTGTTGG
66 ATTATGGTCATATGTCACTTCCTTCGAGGGTAGGTTGTTGG
1446343 CTTTGGAAGA
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
106 23 0.23
107 77 0.77
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (106 bp):
GCTGAAAATAATATAAATTAGTTATGATAATAATCTATATTTTAAAAGTTTTTAAAATTAAATTA
ATTATGGTCATATGTCACTTCCTTCGAGGGTAGGTTGTTGG
Found at i:1447530 original size:21 final size:20
Alignment explanation
Indices: 1447498--1447537 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1447488 AGTATAGATA
*
1447498 AATTTAATAATTTTATATAT
1 AATTTAATAATTTGATATAT
*
1447518 AATTTTATAAATTTGATATA
1 AATTTAAT-AATTTGATATA
1447538 AATAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AATTTAATAATTTGATATAT
Found at i:1449412 original size:39 final size:39
Alignment explanation
Indices: 1449336--1449415 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
1449326 AGGACGTAAG
*
1449336 AAATAGATAAAACAATCGTAAGCTAAATGAAATCATTGA
1 AAATAGATAAAACAATCGTAAGCTAAATGAAACCATTGA
**
1449375 AAATAGATAAAACAATCGTAAGCTAAATGATCCCATTGA
1 AAATAGATAAAACAATCGTAAGCTAAATGAAACCATTGA
1449414 AA
1 AA
1449416 TAGTGTTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (39 bp):
AAATAGATAAAACAATCGTAAGCTAAATGAAACCATTGA
Found at i:1449747 original size:21 final size:23
Alignment explanation
Indices: 1449723--1449764 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1449713 CACTATTTAA
1449723 TTAA-TAAAAAAT-TATATAAAT
1 TTAATTAAAAAATATATATAAAT
*
1449744 TTAATTATAAAATATATATAA
1 TTAATTAAAAAATATATATAA
1449765 TATAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAATTAAAAAATATATATAAAT
Found at i:1449747 original size:25 final size:23
Alignment explanation
Indices: 1449717--1449764 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
1449707 TTGAATCACT
1449717 ATTTAATTAATAAAAAATTATATAA
1 ATTTAATT-ATAAAAAA-TATATAA
*
1449742 ATTTAATTATAAAATATATATAA
1 ATTTAATTATAAAAAATATATAA
1449765 TATAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTAATTATAAAAAATATATAA
Done.