Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005434.1 Hibiscus syriacus cultivar Beakdansim tig00012460_pilon, whole genome shotgun sequence
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: 125156
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1218 original size:7 final size:7
Alignment explanation
Indices: 1206--1354 Score: 56
Period size: 7 Copynumber: 19.9 Consensus size: 7
1196 CGATATAACA
1206 AAAAAAG
1 AAAAAAG
*
1213 AAAAAAAT
1 -AAAAAAG
1221 ATAGAAAAG
1 A-A-AAAAG
* *
1230 AGAGAAG
1 AAAAAAG
1237 AAAAAGAG
1 AAAAA-AG
*
1245 AGAAAATG
1 A-AAAAAG
1253 -AAAAAG
1 AAAAAAG
1259 AAAAAAG
1 AAAAAAG
*
1266 AAAAAAAT
1 -AAAAAAG
1274 AAAAAATTG
1 AAAAAA--G
1283 AAAAAA-
1 AAAAAAG
*
1289 ATAAAAATA
1 A-AAAAA-G
1298 ACAAAAAG
1 A-AAAAAG
*
1306 AAAATAAC
1 AAAA-AAG
1314 AACAAAAGG
1 AA-AAAA-G
*
1323 GAAAAAG
1 AAAAAAG
1330 -AAAAAG
1 AAAAAAG
1336 --AAAAG
1 AAAAAAG
1341 AAAAAAG
1 AAAAAAG
1348 AAGAAAA
1 AA-AAAA
1355 ATCGATCAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
5 5 0.05
6 12 0.11
7 36 0.33
8 32 0.29
9 24 0.22
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:1285 original size:17 final size:15
Alignment explanation
Indices: 1253--1295 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
1243 AGAGAAAATG
*
1253 AAAAAGAAAAAAGAA
1 AAAAATAAAAAAGAA
1268 AAAAATAAAAAATTGAA
1 AAAAATAAAAAA--GAA
1285 AAAAATAAAAA
1 AAAAATAAAAA
1296 TAACAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (15 bp):
AAAAATAAAAAAGAA
Found at i:1308 original size:23 final size:23
Alignment explanation
Indices: 1253--1355 Score: 77
Period size: 23 Copynumber: 4.5 Consensus size: 23
1243 AGAGAAAATG
1253 AAAAAGAAAAAAGAAAAAAATAA
1 AAAAAGAAAAAAGAAAAAAATAA
* *
1276 AAAATTGAAAAAA-ATAAAAATAA
1 AAAA-AGAAAAAAGAAAAAAATAA
* * ***
1299 CAAAAAGAAAATAACAACAAAAGGG
1 -AAAAAGAAAA-AAGAAAAAAATAA
*
1324 AAAAAG-AAAAAGAAAAGAA-AA
1 AAAAAGAAAAAAGAAAAAAATAA
*
1345 AAGAAGAAAAA
1 AAAAAGAAAAA
1356 TCGATCAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
21 5 0.08
22 11 0.18
23 21 0.34
24 19 0.31
25 5 0.08
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.06
Consensus pattern (23 bp):
AAAAAGAAAAAAGAAAAAAATAA
Found at i:4700 original size:139 final size:139
Alignment explanation
Indices: 4464--5081 Score: 921
Period size: 139 Copynumber: 4.5 Consensus size: 139
4454 ACATTTCCGA
* *
4464 TGGAGAGTTCATAATGAGAAGAACTCAT-TCGATGAGGGATAAGAAGTTCAAAATGAGAAGAACT
1 TGGAGAGTTCATAATGAGAAGAACTCATCT-GATGAGGGAGAAGAAGTTCATAATGAGAAGAACT
*
4528 TGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCAAGGGATCA
65 TGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCA
*
4593 ATATTTATAG
130 ACATTTATAG
*
4603 TGGAGAGAGTTCATAATGAGAA-AACTCATCTGATGAGGGAGAA-AAGTTCATAGTGAGAAGAAC
1 T-G-GAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAAC
4666 TTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATC
64 TTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATC
4731 AACATTT-TCAG
129 AACATTTAT-AG
* *
4742 TGGAGAGTTCATAATGAGAAGAACTCATCCGATGA-GGAGAAGAAGTTCATAATGAAAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* * *
4806 GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTCGAGAGATTAA
66 GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAA
*
4871 CATTTCTAG
131 CATTTATAG
* * * *
4880 TAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGATAAGAATTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* * *
4945 GTTCAACCTTAACTCGATTCATCGCATATGGAGTCGAATCAGCAACACCTCACTCGAGGGATCAA
66 GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAA
5010 CATTTCCA-AG
131 CATTT--ATAG
* * * *
5020 GGGATAGTTCA-AATGATAAGAACTCATCTGA--CGGGAGAAGAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
5082 CATAATGAGA
Statistics
Matches: 439, Mismatches: 30, Indels: 22
0.89 0.06 0.04
Matches are distributed among these distances:
137 52 0.12
138 138 0.31
139 201 0.46
140 29 0.07
141 19 0.04
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (139 bp):
TGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAA
CATTTATAG
Found at i:4945 original size:277 final size:276
Alignment explanation
Indices: 4450--5081 Score: 966
Period size: 277 Copynumber: 2.3 Consensus size: 276
4440 GGGTAAACCA
* * *
4450 ATCAACA-TTTCCGATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAGGGATAAGAAGTTCA
1 ATCAACATTTTCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCGATGA-GGAGAAGAAGTTCA
* *
4514 AAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCT
64 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCT
* * *
4579 CACTCAAGGGATCAATATTTATAGTGGAGAGAGTTCATAATGAGAAAACTCATCTGATGAGGGAG
129 CACTCAAGAGATCAACATTTATAGT-GAGAGAGTTCATAATGAGAAAACTCATCCGATGAGGGAG
* * *
4644 AAAAGTTCATAGTGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCA
193 AAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTCGAATCA
4709 GCAACACCTCACTCGAGGG
258 GCAACACCTCACTCGAGGG
4728 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAGAAGAAGTTCATA
1 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAGAAGAAGTTCATA
*
4793 ATGAAAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCA
* * * *
4858 CTCGAGAGATTAACATTTCTAGT-AGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGATAA
131 CTCAAGAGATCAACATTTATAGTGAGAGAGTTCATAATGAGAA-AACTCATCCGATGAGGGAGAA
* *
4922 GAATTTCATAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCGCATATGGAGTCGAATCAG
195 -AAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTCGAATCAG
4987 CAACACCTCACTCGAGGG
259 CAACACCTCACTCGAGGG
* * * * * *
5005 ATCAACATTTCCAAGGGGATAGTTCA-AATGATAAGAACTCATCTGACG-GGAGAAGAAGTTCAT
1 ATCAACATTTTC-AGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAGAAGAAGTTCAT
5068 AATGAGAAGAACTT
65 AATGAGAAGAACTT
5082 CATAATGAGA
Statistics
Matches: 325, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
275 19 0.06
276 47 0.14
277 202 0.62
278 52 0.16
279 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (276 bp):
ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTCA
CTCAAGAGATCAACATTTATAGTGAGAGAGTTCATAATGAGAAAACTCATCCGATGAGGGAGAAA
AGTTCATAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTCGAATCAGCA
ACACCTCACTCGAGGG
Found at i:5074 original size:17 final size:17
Alignment explanation
Indices: 5054--5098 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
5044 CATCTGACGG
*
5054 GAGAAGAAGTTCATAAT
1 GAGAAGAACTTCATAAT
5071 GAGAAGAACTTCATAAT
1 GAGAAGAACTTCATAAT
5088 GAGAAGAACTT
1 GAGAAGAACTT
5099 GTTCAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (17 bp):
GAGAAGAACTTCATAAT
Found at i:5318 original size:18 final size:18
Alignment explanation
Indices: 5277--5325 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
5267 GAAGAGTTCA
* *
5277 TAATAAGAAGAAATCATT
1 TAATTAGAAGAAATCATC
* *
5295 TGATTAGAATAAATCATC
1 TAATTAGAAGAAATCATC
5313 TAATTA-AAGAAAT
1 TAATTAGAAGAAAT
5326 TGGAGCTCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (18 bp):
TAATTAGAAGAAATCATC
Found at i:10790 original size:105 final size:105
Alignment explanation
Indices: 10582--10801 Score: 264
Period size: 105 Copynumber: 2.1 Consensus size: 105
10572 GTGACAGAGT
* * * * ** ** *
10582 TATTGTTAATAGTGTCAAACATTTGGTCACTAAAAAACACTTATTGTGACAACATTGGTGGTCAC
1 TATTGATAATAGTATCAAACATTTGGTCACTAAAAAACACTTAGTGTAACAACATTAATAATCAA
*
10647 AAAATATACTTTCAGTGTCAAATAAATGTATCACAATTTC
66 AAAATATACTTTCAGTGTCAAATAAATGTATCACAATTTA
* *
10687 TATTGATAATAGTATCAAACATTTGGTCACTAAAAAATACTTAGTGTAACAATATTAATAATCAA
1 TATTGATAATAGTATCAAACATTTGGTCACTAAAAAACACTTAGTGTAACAACATTAATAATC-A
* * * *
10752 AAAAATATATTTTTAGTGTGAAAT-AA-GTCATCATAATTTA
65 AAAAATATACTTTCAGTGTCAAATAAATGT-ATCACAATTTA
10792 TATTGATAAT
1 TATTGATAAT
10802 TGTGTCGAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
104 2 0.02
105 74 0.76
106 21 0.22
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (105 bp):
TATTGATAATAGTATCAAACATTTGGTCACTAAAAAACACTTAGTGTAACAACATTAATAATCAA
AAAATATACTTTCAGTGTCAAATAAATGTATCACAATTTA
Found at i:13011 original size:21 final size:21
Alignment explanation
Indices: 12971--13011 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12961 GCTCACCAAA
**
12971 GCATTGTTAATACTTGTCAAG
1 GCATTGTTAATACTAATCAAG
*
12992 GCATTGTTTATACTAATCAA
1 GCATTGTTAATACTAATCAA
13012 AAGTCTCCCT
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:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (21 bp):
GCATTGTTAATACTAATCAAG
Found at i:18925 original size:16 final size:16
Alignment explanation
Indices: 18904--18964 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
18894 GGGTCTCCAA
18904 CATTTATGTTCGTGTT
1 CATTTATGTTCGTGTT
18920 CATTTATGTTCGTGTT
1 CATTTATGTTCGTGTT
*
18936 CGTTTATGTTCGTGTT
1 CATTTATGTTCGTGTT
*
18952 CTTTTATGTTCGT
1 CATTTATGTTCGT
18965 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (16 bp):
CATTTATGTTCGTGTT
Found at i:22462 original size:57 final size:57
Alignment explanation
Indices: 22399--22590 Score: 224
Period size: 57 Copynumber: 3.4 Consensus size: 57
22389 ACGGCACTAA
* * *
22399 GTGTGCAAAAAGCTAAGAAATTCATAATTTGTTTATGAATTTTCTTATGGGCACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATAATTTGTTTATGAATTTCCATATGGGAACTTT
* * * * **
22456 GTGTGCAAAAAGTTAAGAAATCCATAATTGGTTTATGAATTTCCGTATGGGAACTGA
1 GTGTGCAAAAAGCTAAGAAATTCATAATTTGTTTATGAATTTCCATATGGGAACTTT
** * * **
22513 GTGTTAAAAAAGATAAGAAATTCATAATTTGTTTACGAATTTCCATATAAGAACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATAATTTGTTTATGAATTTCCATATGGGAACTTT
**
22570 AAGTGCAAAAA-CTAAGAAATT
1 GTGTGCAAAAAGCTAAGAAATT
22591 ATATGAATTT
Statistics
Matches: 111, Mismatches: 24, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
56 9 0.08
57 102 0.92
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (57 bp):
GTGTGCAAAAAGCTAAGAAATTCATAATTTGTTTATGAATTTCCATATGGGAACTTT
Found at i:22868 original size:60 final size:59
Alignment explanation
Indices: 22775--22940 Score: 154
Period size: 68 Copynumber: 2.7 Consensus size: 59
22765 CATCTAACTG
* * * *
22775 TGCA-TTGACAGAAAGGAGTCAATTATGCCAGTTAGATGAGTGCCTTTGAGGCCTAGCTA
1 TGCATTTGAAAGAAAAGTGTCAATTATG-CAGTTAGATGAGTGCCTTTGAGGCCAAGCTA
*
22834 TGCATTTGAAAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGATGCCAAG
1 TGCATTTGAAAGAAAAGTGTCAATTATGC-AGTTAGAT-----G---AGTGCCTTTGAGGCCAAG
* *
22899 TTG
57 CTA
* *
22902 TGCATTTGAGAGAAATGTGTCAATTATGCAGTTAGATGA
1 TGCATTTGAAAGAAAAGTGTCAATTATGCAGTTAGATGA
22941 AAGGCTAAGT
Statistics
Matches: 88, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
59 6 0.07
60 28 0.32
62 1 0.01
65 1 0.01
67 8 0.09
68 44 0.50
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (59 bp):
TGCATTTGAAAGAAAAGTGTCAATTATGCAGTTAGATGAGTGCCTTTGAGGCCAAGCTA
Found at i:22968 original size:67 final size:68
Alignment explanation
Indices: 22813--22978 Score: 262
Period size: 67 Copynumber: 2.5 Consensus size: 68
22803 CAGTTAGATG
* * *
22813 AGTGCCTTTGAGGCCTAGCTATGCATTTGAAAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGG
1 AGTGCCTTTGAGGCCTAGTTGTGCATTTGAGAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGG
22878 CTA
66 CTA
* * *
22881 AGTGCCTTTGATGCCAAGTTGTGCATTTGAGAGAAATGTGTCAATTATGC-AGTTAGATGAAAGG
1 AGTGCCTTTGAGGCCTAGTTGTGCATTTGAGAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGG
22945 CTA
66 CTA
*
22948 AGTGCCTTCGAGGCCTAGTTGTGCATTTGAG
1 AGTGCCTTTGAGGCCTAGTTGTGCATTTGAG
22979 GCCTAGTTGT
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 45 0.51
68 44 0.49
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (68 bp):
AGTGCCTTTGAGGCCTAGTTGTGCATTTGAGAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGG
CTA
Found at i:22979 original size:19 final size:19
Alignment explanation
Indices: 22957--22996 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
22947 AAGTGCCTTC
22957 GAGGCCTAGTTGTGCATTT
1 GAGGCCTAGTTGTGCATTT
22976 GAGGCCTAGTTGTGCATTT
1 GAGGCCTAGTTGTGCATTT
22995 GA
1 GA
22997 AAGAAAGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.33, T:0.35
Consensus pattern (19 bp):
GAGGCCTAGTTGTGCATTT
Found at i:23060 original size:87 final size:86
Alignment explanation
Indices: 22882--23064 Score: 285
Period size: 87 Copynumber: 2.1 Consensus size: 86
22872 GAAAGGCTAA
* * * *
22882 GTGCCTTTGATGCCAAGTTGTGCATTTGAGAGAAATGTGTCAATTATGCAGTTAGATGAAAGGCT
1 GTGCATTTGAGGCCAAGTTGTGCATTTGAAAGAAAGGTGTCAATTATGCAGTTAGATGAAAGGCT
*
22947 AAGTGCCTTCGAGGCCTAGTT
66 AAGTGCCTTCGACGCCTAGTT
*
22968 GTGCATTTGAGGCCTAGTTGTGCATTTGAAAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGC
1 GTGCATTTGAGGCCAAGTTGTGCATTTGAAAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGC
* *
23033 TAAGTGTCTTTGACGCCTAGTT
65 TAAGTGCCTTCGACGCCTAGTT
23055 GTGCATTTGA
1 GTGCATTTGA
23065 CAGAAAGGTG
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 43 0.49
87 45 0.51
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (86 bp):
GTGCATTTGAGGCCAAGTTGTGCATTTGAAAGAAAGGTGTCAATTATGCAGTTAGATGAAAGGCT
AAGTGCCTTCGACGCCTAGTT
Found at i:23070 original size:154 final size:154
Alignment explanation
Indices: 22814--23131 Score: 494
Period size: 154 Copynumber: 2.1 Consensus size: 154
22804 AGTTAGATGA
*
22814 GTGCCTTTGAGGCCTAGCTATGCATTTGAAAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGC
1 GTGCATTTGAGGCCTAGCTATGCATTTGAAAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGC
* * * *
22879 TAAGTGCCTTTGATGCCAAGTTGTGCATTTGAGAGAAATGTGTCAATTATGCAGTTAGATGAAAG
66 TAAGTGCCTTTGACGCCAAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCAGTTAGATGAAAG
*
22944 GCTAAGTGCCTTCGAGGCCTAGTT
131 GCTAAGTGCCTTCGAGGCCTAGAT
* * *
22968 GTGCATTTGAGGCCTAGTTGTGCATTTGAAAGAAAGGTGTCAATTATG-TCAGTTAGATGAAAGG
1 GTGCATTTGAGGCCTAGCTATGCATTTGAAAGAAAAGTGTCAATTATGCT-AGTTAGATGAAAGG
* *
23032 CTAAGTGTCTTTGACGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCAGTTAGATGAAA
65 CTAAGTGCCTTTGACGCCAAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCAGTTAGATGAAA
* * *
23097 GGCTTAGTTCCTTTGAGGCCTAGAT
130 GGCTAAGTGCCTTCGAGGCCTAGAT
23122 GTGCATTTGA
1 GTGCATTTGA
23132 CAGAAAGGTG
Statistics
Matches: 149, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
153 1 0.01
154 148 0.99
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (154 bp):
GTGCATTTGAGGCCTAGCTATGCATTTGAAAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGC
TAAGTGCCTTTGACGCCAAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCAGTTAGATGAAAG
GCTAAGTGCCTTCGAGGCCTAGAT
Found at i:23193 original size:68 final size:68
Alignment explanation
Indices: 22968--23385 Score: 561
Period size: 68 Copynumber: 6.2 Consensus size: 68
22958 AGGCCTAGTT
* * * *
22968 GTGCATTTGAGGCCTAGTTGTGCATTTGAAAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGC
1 GTGCCTTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
23033 TAA
66 TAA
* * * *
23036 GTGTCTTTGACGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATG-CAGTTAGATGAAAGGC
1 GTGCCTTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
*
23100 TTA
66 TAA
* * * *
23103 GTTCCTTTGAGGCCTAGATGTGCATTTGACAGAAAGGTGTTAATTATGCCAGTTAGATGAAATGC
1 GTGCCTTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
23168 TAA
66 TAA
* * * * *
23171 GTGACTTTGAGGCCAAGCTGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGATAAAAGGC
1 GTGCCTTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
23236 TAA
66 TAA
* * * * *
23239 GTGCCTTCGAGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGACAGATAGATGAAATGC
1 GTGCCTTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
23304 TAA
66 TAA
* *
23307 GTGCCTTTGAGGTCC-AGCTATGCATTTGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1 GTGCCTTTGAGG-CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
*
23371 TTAA
65 CTAA
* *
23375 ATACCTTTGAG
1 GTGCCTTTGAG
23386 TAAAAGATAA
Statistics
Matches: 308, Mismatches: 40, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
67 60 0.19
68 246 0.80
69 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (68 bp):
GTGCCTTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
TAA
Found at i:23619 original size:45 final size:45
Alignment explanation
Indices: 23529--23717 Score: 288
Period size: 45 Copynumber: 4.2 Consensus size: 45
23519 AAAGACAATG
*
23529 ATGAAATTTATAATAGTGTATAAAAGGGCATGAAAGGATGCCATAA
1 ATGAAATGTATAATAGTGTATAAAA-GGCATGAAAGGATGCCATAA
*
23575 ATGAAATGTATAATAGTGTATATAAGGCATGAAAGGATGCCATAA
1 ATGAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
* * * *
23620 ATGAAATATATAATAGTATATAAAAGGCATGAAATGATGTCATAA
1 ATGAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
* * *
23665 ATGAAATGTATAATAGTGTATAAAAGGCATGCAATGATGTCATAA
1 ATGAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
23710 ATGAAATG
1 ATGAAATG
23718 CATATGGGTG
Statistics
Matches: 133, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 110 0.83
46 23 0.17
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.28
Consensus pattern (45 bp):
ATGAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
Found at i:23665 original size:22 final size:22
Alignment explanation
Indices: 23639--23710 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
23629 ATAATAGTAT
23639 ATAAAAGGCATGAAATGATGTC
1 ATAAAAGGCATGAAATGATGTC
* **
23661 ATAAATGAAATGTATAAT-AGTGT-
1 ATAAAAGGCATG-A-AATGA-TGTC
*
23684 ATAAAAGGCATGCAATGATGTC
1 ATAAAAGGCATGAAATGATGTC
23706 ATAAA
1 ATAAA
23711 TGAAATGCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
21 6 0.16
22 15 0.39
23 11 0.29
24 6 0.16
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.26
Consensus pattern (22 bp):
ATAAAAGGCATGAAATGATGTC
Found at i:23746 original size:45 final size:44
Alignment explanation
Indices: 23648--23833 Score: 155
Period size: 45 Copynumber: 4.1 Consensus size: 44
23638 TATAAAAGGC
* * * * *
23648 ATGAAATGATGTCATAAATGAAATGTATAAT-AGTGTA-TAAAAGGC
1 ATGAAATGATGTCATAAATGAAATGCAT-ATGGGTGCATTATAA--T
*
23693 ATGCAATGATGTCATAAATGAAATGCATATGGGTGCATTATCAAT
1 ATGAAATGATGTCATAAATGAAATGCATATGGGTGCATTAT-AAT
* * ***
23738 ATGAAATGATGTTATAATTGAAATGCATATGGGTGCATTATTGGC
1 ATGAAATGATGTCATAAATGAAATGCATATGGGTGCATTA-TAAT
*
23783 ATGAAA-GAATGCCATAAATGAAAATGCATAAT-GGTGCATTATAAGT
1 ATGAAATG-ATGTCATAAATG-AAATGCAT-ATGGGTGCATTATAA-T
23829 ATGAA
1 ATGAA
23834 TGGATGCTCT
Statistics
Matches: 115, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
44 3 0.03
45 83 0.72
46 25 0.22
47 4 0.03
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (44 bp):
ATGAAATGATGTCATAAATGAAATGCATATGGGTGCATTATAAT
Found at i:31924 original size:23 final size:23
Alignment explanation
Indices: 31898--31950 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
31888 TCCCAAATAA
* *
31898 CCACATAGGTTTACACTGAAGTG
1 CCACATAGATTTACACCGAAGTG
*
31921 CCACATAGATTTGCACCGAAGTG
1 CCACATAGATTTACACCGAAGTG
31944 CCACATA
1 CCACATA
31951 ATTGTCCTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (23 bp):
CCACATAGATTTACACCGAAGTG
Found at i:32805 original size:19 final size:22
Alignment explanation
Indices: 32760--32811 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 22
32750 TACCCCTACA
*
32760 GTATCGATACTTTCCTTCAAGG
1 GTATCGATACTCTCCTTCAAGG
32782 GTATCGATAC-CTCC-TCAA-G
1 GTATCGATACTCTCCTTCAAGG
32801 GTATCGATACT
1 GTATCGATACT
32812 AATTTGGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.39
20 4 0.14
21 3 0.11
22 10 0.36
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (22 bp):
GTATCGATACTCTCCTTCAAGG
Found at i:36116 original size:19 final size:22
Alignment explanation
Indices: 36092--36145 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 22
36082 TGCAAAAATG
36092 GTATCGATACCATA-T-TAG-A
1 GTATCGATACCATAGTATAGTA
*
36111 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAGTATAGTA
36133 GTATCGATACCAT
1 GTATCGATACCAT
36146 GGTAGGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 13 0.43
20 1 0.03
21 3 0.10
22 13 0.43
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (22 bp):
GTATCGATACCATAGTATAGTA
Found at i:36556 original size:58 final size:57
Alignment explanation
Indices: 36494--36679 Score: 232
Period size: 57 Copynumber: 3.3 Consensus size: 57
36484 TGAGTGTGTC
*
36494 AAAAGTTAAGAAAATTCATAATTTGTTTATGAATATTCGTATGGGCACTTTGTGTGCA
1 AAAAGTTAAG-AAATTCATAATTTGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA
* * * *
36552 AAAAGTTACGAAATCCATAATTGGTTTATGAATTTTCGTATGGGCA-TTGAGTGTGCA
1 AAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTCGTATGGGCACTT-TGTGTGCA
* * ** * *
36609 AAAAGTTAAGAAACTCATAATTTGTTTACGAATTTTCGTATAAGAACTTTATGTGCA
1 AAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA
*
36666 AAAA-ATAAGAAATT
1 AAAAGTTAAGAAATT
36680 ATATGAATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
56 10 0.09
57 88 0.81
58 11 0.10
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (57 bp):
AAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA
Found at i:36947 original size:68 final size:68
Alignment explanation
Indices: 36855--37398 Score: 734
Period size: 68 Copynumber: 8.0 Consensus size: 68
36845 AAAGATTAAA
** *
36855 AGGCCTAACTGTGCA-TTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
36919 TTG
66 TTG
* ** * *
36922 AGGCCTAGATGTGCATTTGACAGAAAAATATCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
36987 TTG
66 TTG
* * *
36990 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTTAATTATGCCAATTAGATGAAAGACTAAGTGCCT
1 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
37055 TTG
66 TTG
* * * * **
37058 AGACCTAGCTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAACGCCT
1 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
37123 TTG
66 TTG
** * * *
37126 AGGTGTAGCTATGCATTTGACAGAAAGATGTCAATTATGCCA-TGTAGATGAAAGGCTAAGTGCC
1 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGT-TAGATGAAAGGCTAAGTGCC
37190 TTTG
65 TTTG
* * * * *
37194 AGGCCTAGTTGTGCATTTGATAGAAATGTGTCAATTATG-CAGATAGATGAAAGGTTATGTGCCT
1 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
37258 TTG
66 TTG
* * *
37261 AGGCCTAGTTGTGCATTTGAGAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTTCCT
1 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
37326 TTG
66 TTG
* * * * * *
37329 AGGCATAGTTGTGCATGTGACAGAAAGGTGTCAATTTTGCCAGTTAGATGAAAGGTTAAATACCT
1 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
37394 TTG
66 TTG
37397 AG
1 AG
37399 TAAAAGATAA
Statistics
Matches: 420, Mismatches: 53, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
67 75 0.18
68 345 0.82
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (68 bp):
AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:37563 original size:45 final size:45
Alignment explanation
Indices: 37513--37826 Score: 337
Period size: 45 Copynumber: 6.9 Consensus size: 45
37503 GTGTAACGTG
* * *
37513 GTATAAATGGCATGAATGGATGTCA-ATAATGAAATGTATATTAGT
1 GTATAAAAGGCATGAAAGGATGTCATA-AATGAAATGTATAATAGT
* **
37558 ATATAAAAGGGCATGAAAGGATACCATAAATGAAATGTATAATAGT
1 GTATAAAA-GGCATGAAAGGATGTCATAAATGAAATGTATAATAGT
*
37604 GTATAAAAAGCATGAAAGGATGTCATAAATGAAATGTATAATAGT
1 GTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAATAGT
*
37649 GTACAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAATAGT
1 GTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAATAGT
* * *
37694 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGCAT-ATGGGT
1 GTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAAT-AGT
* * ** * * * *
37739 GCATTATCGGCATGAAAGGATGTCATAATTTAAATGCAT-ATGGGT
1 GTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAAT-AGT
* * ** * *
37784 GCATTATTGGCATGAAAGAATGTCATAAATGAAAATGCATAAT
1 GTATAAAAGGCATGAAAGGATGTCATAAATG-AAATGTATAAT
37827 GGTGCATTAT
Statistics
Matches: 237, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
44 2 0.01
45 186 0.78
46 46 0.19
47 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (45 bp):
GTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAATAGT
Found at i:41989 original size:16 final size:16
Alignment explanation
Indices: 41970--42025 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
41960 TTAAGCGTTA
41970 AATGATTTAAATGTTG
1 AATGATTTAAATGTTG
* *
41986 AATGA-TTAAACGCTG
1 AATGATTTAAATGTTG
*
42001 AATGATTCAAATGTTG
1 AATGATTTAAATGTTG
42017 AATGATTTA
1 AATGATTTA
42026 GAGACTCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (16 bp):
AATGATTTAAATGTTG
Found at i:41990 original size:31 final size:31
Alignment explanation
Indices: 41954--42023 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
41944 GTTTACTTCA
* * *
41954 GAATGATTAAGCGTTAAATGATTTAAATGTT
1 GAATGATTAAACGCTAAATGATTCAAATGTT
*
41985 GAATGATTAAACGCTGAATGATTCAAATGTT
1 GAATGATTAAACGCTAAATGATTCAAATGTT
42016 GAATGATT
1 GAATGATT
42024 TAGAGACTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.36
Consensus pattern (31 bp):
GAATGATTAAACGCTAAATGATTCAAATGTT
Found at i:41994 original size:15 final size:15
Alignment explanation
Indices: 41954--42023 Score: 77
Period size: 16 Copynumber: 4.5 Consensus size: 15
41944 GTTTACTTCA
*
41954 GAATGATTAAGCGTT
1 GAATGATTAAACGTT
* *
41969 AAATGATTTAAATGTT
1 GAATGA-TTAAACGTT
*
41985 GAATGATTAAACGCT
1 GAATGATTAAACGTT
*
42000 GAATGATTCAAATGTT
1 GAATGATT-AAACGTT
42016 GAATGATT
1 GAATGATT
42024 TAGAGACTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
15 20 0.44
16 25 0.56
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.36
Consensus pattern (15 bp):
GAATGATTAAACGTT
Found at i:42753 original size:16 final size:16
Alignment explanation
Indices: 42724--42778 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
42714 ATATATATTA
42724 AAATAAGTAA-ATAAAT
1 AAATAA-TAATATAAAT
42740 AAATAATAATATAATAAT
1 AAATAATAATAT-A-AAT
*
42758 AAATATTAATAGT-AAT
1 AAATAATAATA-TAAAT
42774 AAATA
1 AAATA
42779 TAAAAGGGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 3 0.09
16 16 0.47
17 1 0.03
18 13 0.38
19 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
AAATAATAATATAAAT
Found at i:42760 original size:18 final size:19
Alignment explanation
Indices: 42737--42775 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
42727 TAAGTAAATA
42737 AATAAATAATAATA-TAAT
1 AATAAATAATAATAGTAAT
*
42755 AATAAATATTAATAGTAAT
1 AATAAATAATAATAGTAAT
42774 AA
1 AA
42776 ATATAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATAAATAATAATAGTAAT
Found at i:42855 original size:23 final size:23
Alignment explanation
Indices: 42807--42856 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
42797 ACGTTGTCTT
* *
42807 TAAAATAAAATATAATAATTAAA
1 TAAAAGAAAATATAATAAATAAA
*
42830 TAAAAGAAAA-ATAATTAAATACA
1 TAAAAGAAAATATAA-TAAATAAA
42853 TAAA
1 TAAA
42857 TTAAAGAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
TAAAAGAAAATATAATAAATAAA
Found at i:44935 original size:5 final size:5
Alignment explanation
Indices: 44925--44989 Score: 60
Period size: 5 Copynumber: 12.8 Consensus size: 5
44915 TGTTCAGAGA
* **
44925 AAAAT AAAAT AAAATT AAGCAT CTAAT AAAAT AAAAT AAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAA-T AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
44976 GAAAT GAAAT AAAA
1 AAAAT AAAAT AAAA
44990 CGAAATGGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
4 4 0.08
5 40 0.82
6 4 0.08
7 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:44973 original size:19 final size:19
Alignment explanation
Indices: 44926--44988 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
44916 GTTCAGAGAA
*
44926 AAATAAAATAAAATTAAGCAT
1 AAATAAAATAAAA-TAA-AAT
*
44947 CTAATAAAATAAAATAAAAT
1 -AAATAAAATAAAATAAAAT
* *
44967 AAATAAAATGAAATGAAAT
1 AAATAAAATAAAATAAAAT
44986 AAA
1 AAA
44989 ACGAAATGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 3 0.08
22 12 0.33
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAT
Found at i:44994 original size:15 final size:15
Alignment explanation
Indices: 44953--44996 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
44943 GCATCTAATA
*
44953 AAATAAAATAAAAT-
1 AAATAAAATGAAATG
44967 AAATAAAATGAAATG
1 AAATAAAATGAAATG
*
44982 AAATAAAACGAAATG
1 AAATAAAATGAAATG
44997 GGTTGCCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.18
Consensus pattern (15 bp):
AAATAAAATGAAATG
Found at i:47345 original size:23 final size:23
Alignment explanation
Indices: 47319--47365 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
47309 AATGAGTCAT
47319 GTCTTTAATTGAAACGGAGTCCC
1 GTCTTTAATTGAAACGGAGTCCC
47342 GTCTTTAATTGAAACGGAGTCCC
1 GTCTTTAATTGAAACGGAGTCCC
47365 G
1 G
47366 CCACTAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (23 bp):
GTCTTTAATTGAAACGGAGTCCC
Found at i:47919 original size:18 final size:15
Alignment explanation
Indices: 47898--47937 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 15
47888 GTTATCTTTA
47898 AAATAAAAGATAAGAATT
1 AAATAAAAGA-AA-AA-T
47916 AAATAAAAGAAAAAT
1 AAATAAAAGAAAAAT
47931 AAATAAA
1 AAATAAA
47938 TAAATTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 2 0.09
17 2 0.09
18 10 0.45
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATAAAAGAAAAAT
Found at i:48402 original size:12 final size:12
Alignment explanation
Indices: 48377--48420 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
48367 TTAGCATAAT
48377 AGAAAAATAT-G
1 AGAAAAATATAG
48388 AGAAAAATATAG
1 AGAAAAATATAG
** *
48400 AGAAAGCTAGAG
1 AGAAAAATATAG
48412 AGAAAAATA
1 AGAAAAATA
48421 AGATTTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.64, C:0.02, G:0.20, T:0.14
Consensus pattern (12 bp):
AGAAAAATATAG
Found at i:55126 original size:9 final size:9
Alignment explanation
Indices: 55086--55125 Score: 53
Period size: 9 Copynumber: 4.1 Consensus size: 9
55076 TGATTCATTC
55086 AATAAACAA
1 AATAAACAA
55095 AATCAAAACAA
1 AAT--AAACAA
55106 AATAAACAA
1 AATAAACAA
55115 AATAAAGCAA
1 AATAAA-CAA
55125 A
1 A
55126 TGAAGGGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 15 0.54
10 4 0.14
11 9 0.32
ACGTcount: A:0.75, C:0.12, G:0.03, T:0.10
Consensus pattern (9 bp):
AATAAACAA
Found at i:60238 original size:21 final size:21
Alignment explanation
Indices: 60212--60295 Score: 73
Period size: 21 Copynumber: 3.9 Consensus size: 21
60202 TACAGCAGAG
*
60212 GATGAAAAAGATGCAGAAGAA
1 GATGAAAAAGATGAAGAAGAA
60233 GATGAACAAA-ATGAAGAAGTATAA
1 GATGAA-AAAGATGAAGAAG---AA
* *
60257 GATGAACAAGTTGAA-ATAGAA
1 GATGAAAAAGATGAAGA-AGAA
*
60278 GATGAACAAGATGAAGAA
1 GATGAAAAAGATGAAGAA
60296 AAAACAAGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
21 31 0.60
22 4 0.08
23 3 0.06
24 14 0.27
ACGTcount: A:0.56, C:0.05, G:0.25, T:0.14
Consensus pattern (21 bp):
GATGAAAAAGATGAAGAAGAA
Found at i:61460 original size:15 final size:15
Alignment explanation
Indices: 61440--61470 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
61430 CTTTAGTTAG
61440 TGATACTGATTTTAC
1 TGATACTGATTTTAC
61455 TGATACTGATTTTAC
1 TGATACTGATTTTAC
61470 T
1 T
61471 TTTTTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (15 bp):
TGATACTGATTTTAC
Found at i:63336 original size:17 final size:17
Alignment explanation
Indices: 63314--63353 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
63304 ATACATAACC
63314 TTCACTTTTAACAAAGA
1 TTCACTTTTAACAAAGA
*
63331 TTCACTTTTAACAATGA
1 TTCACTTTTAACAAAGA
63348 TT-ACTT
1 TTCACTT
63354 CCAACATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (17 bp):
TTCACTTTTAACAAAGA
Found at i:67748 original size:3 final size:3
Alignment explanation
Indices: 67742--67808 Score: 82
Period size: 3 Copynumber: 22.7 Consensus size: 3
67732 TTAATAATAA
* * *
67742 TAT TAT T-T TAT TAA TAT TAT TAT TGT TAT TAA TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
67789 TAA TAT AAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
67809 CATACACAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:67759 original size:6 final size:6
Alignment explanation
Indices: 67730--67808 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
67720 TTTTCATTGT
* * * ** *
67730 TATTAA TAATAA TATTATTT TATTAA TATTAT TATTGT TATTAA TATTAT
1 TATTAA TATTAA TATTA--A TATTAA TATTAA TATTAA TATTAA TATTAA
* *
67780 TATTAT TATTAA TA-TAA TTATTAT TATTA
1 TATTAA TATTAA TATTAA -TATTAA TATTA
67809 CATACACAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
5 3 0.05
6 48 0.83
7 2 0.03
8 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (6 bp):
TATTAA
Found at i:67772 original size:18 final size:18
Alignment explanation
Indices: 67729--67808 Score: 117
Period size: 18 Copynumber: 4.5 Consensus size: 18
67719 ATTTTCATTG
* *
67729 TTATTAATAATAATATTA
1 TTATTATTAATATTATTA
67747 TT-TTATTAATATTATTA
1 TTATTATTAATATTATTA
*
67764 TTGTTATTAATATTATTA
1 TTATTATTAATATTATTA
*
67782 TTATTATTAATATAATTA
1 TTATTATTAATATTATTA
67800 TTATTATTA
1 TTATTATTA
67809 CATACACAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
17 15 0.26
18 42 0.74
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (18 bp):
TTATTATTAATATTATTA
Found at i:69384 original size:2 final size:2
Alignment explanation
Indices: 69377--69402 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69367 AGTCACGTTA
69377 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
69403 GAAAAATTCG
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:75269 original size:10 final size:10
Alignment explanation
Indices: 75246--75341 Score: 62
Period size: 9 Copynumber: 10.0 Consensus size: 10
75236 CTCATCCATC
75246 AGAG-AAAAA
1 AGAGAAAAAA
75255 A-AGAAAAAA
1 AGAGAAAAAA
*
75264 AGAGAAAAGA
1 AGAGAAAAAA
75274 AG-GAAAAAA
1 AGAGAAAAAA
*
75283 TAAAGAAAAAA
1 -AGAGAAAAAA
*
75294 TA-A-AGAAAA
1 -AGAGAAAAAA
*
75303 ATAGAAAAAA
1 AGAGAAAAAA
*
75313 AGA-AAAAGA
1 AGAGAAAAAA
*
75322 A-ATAAAAAA
1 AGAGAAAAAA
75331 AGAAGAAAAAA
1 AG-AGAAAAAA
75342 GAAATTGAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
8 4 0.06
9 31 0.45
10 18 0.26
11 16 0.23
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
AGAGAAAAAA
Found at i:75282 original size:11 final size:11
Alignment explanation
Indices: 75248--75345 Score: 67
Period size: 11 Copynumber: 8.8 Consensus size: 11
75238 CATCCATCAG
*
75248 AGAAAAAAAGAA
1 AGAAAGAAA-AA
* *
75260 AAAAAGAGAAA
1 AGAAAGAAAAA
*
75271 AGAAGGAAAAA
1 AGAAAGAAAAA
*
75282 ATAAAGAAAAA
1 AGAAAGAAAAA
*
75293 ATAAAGAAAAA
1 AGAAAGAAAAA
75304 TAGAAA-AAAAGA
1 -AGAAAGAAAA-A
75316 A-AAAGAAATAA
1 AGAAAGAAA-AA
* *
75327 AAAAAGAAGAA
1 AGAAAGAAAAA
75338 A-AAAGAAA
1 AGAAAGAAA
75346 TTGAATTAAG
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
10 9 0.13
11 43 0.61
12 18 0.26
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:75293 original size:22 final size:20
Alignment explanation
Indices: 75268--75341 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
75258 AAAAAAAGAG
75268 AAAAGAAGGAAAAAATAAAGAA
1 AAAAGAA-GAAAAAATAAA-AA
* *
75290 AAAATAA-AGAAAAATAGAAA
1 AAAAGAAGA-AAAAATAAAAA
75310 AAAAGAA-AAAGAAAT--AAA
1 AAAAGAAGAAA-AAATAAAAA
75328 AAAAGAAGAAAAAA
1 AAAAGAAGAAAAAA
75342 GAAATTGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 13 0.28
19 5 0.11
20 14 0.30
21 8 0.17
22 6 0.13
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAAGAAGAAAAAATAAAAA
Found at i:75303 original size:49 final size:48
Alignment explanation
Indices: 75248--75341 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 48
75238 CATCCATCAG
*
75248 AGAAAAAAAGAAAAAAAGAGAAAAGAAGGAAAAAATA-AAGAAAAAATAA
1 AGAAAAAAAGAAAAAAAGA-AAAAGAAAGAAAAAA-AGAAGAAAAAATAA
* *
75297 AGAAAAATAGAAAAAAAGAAAAAGAAATAAAAAAAGAAGAAAAAA
1 AGAAAAAAAGAAAAAAAGAAAAAGAAAGAAAAAAAGAAGAAAAAA
75342 GAAATTGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
47 1 0.02
48 22 0.54
49 18 0.44
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (48 bp):
AGAAAAAAAGAAAAAAAGAAAAAGAAAGAAAAAAAGAAGAAAAAATAA
Found at i:77716 original size:54 final size:54
Alignment explanation
Indices: 77396--77719 Score: 461
Period size: 54 Copynumber: 6.0 Consensus size: 54
77386 CTGATGAGAA
* *
77396 ATCTGGGCAGAAGTCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTAC-AAGC
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAA-C
* * * * * *
77450 ATCTGGGCAGAAGTCACAAGAAATGATAAATATATTGTCAAATGTTTTACGAAT
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * * *
77504 ATATGGGCAGAAGCCACAAGAAAGGATGAATGTATTGTCAAATGTTTTATGAAC
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
**
77558 ATCTGGGCAGAAGCCACAGGAACGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
77612 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTTAAATGTTTTACGGAC
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
77666 ATCTGTGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
77720 CAGTGATTAT
Statistics
Matches: 243, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
54 241 0.99
55 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:78113 original size:22 final size:22
Alignment explanation
Indices: 78083--78192 Score: 145
Period size: 22 Copynumber: 5.0 Consensus size: 22
78073 TATATATCTA
*
78083 CATTCTTCAAAGATGATAGATT
1 CATTTTTCAAAGATGATAGATT
*
78105 CATTATTCAAAGATGATAGATT
1 CATTTTTCAAAGATGATAGATT
78127 C-TCTTTTCAAAGATGATAGATT
1 CAT-TTTTCAAAGATGATAGATT
78149 C-TCTTTTCAAAGATGATAGATT
1 CAT-TTTTCAAAGATGATAGATT
*
78171 C-TATTTTCAAAGATGAAAGATT
1 CAT-TTTTCAAAGATGATAGATT
78193 TATTGGATTT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
21 1 0.01
22 82 0.99
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
CATTTTTCAAAGATGATAGATT
Found at i:78143 original size:44 final size:44
Alignment explanation
Indices: 78088--78192 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
78078 ATCTACATTC
*
78088 TTCAAAGATGATAGATTCAT-TATTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTC-TCTATTCAAAGATGATAGATTCTATT
*
78132 TTCAAAGATGATAGATTCTCTTTTCAAAGATGATAGATTCTATT
1 TTCAAAGATGATAGATTCTCTATTCAAAGATGATAGATTCTATT
*
78176 TTCAAAGATGAAAGATT
1 TTCAAAGATGATAGATT
78193 TATTGGATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
43 1 0.02
44 56 0.98
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.38
Consensus pattern (44 bp):
TTCAAAGATGATAGATTCTCTATTCAAAGATGATAGATTCTATT
Found at i:79294 original size:223 final size:223
Alignment explanation
Indices: 78823--79421 Score: 871
Period size: 223 Copynumber: 2.7 Consensus size: 223
78813 CCCGAATTTG
78823 TAAGACCTCTGGGCCATCCATAAGACCTTCAG-GCAAGATGTTTTCAAATGAGATTTTAGAAACC
1 TAAGACCTCTGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACC
* * * * ***
78887 TAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGTTTTTAAAGGAAGTTAAGCCT-TTTAA-GG
66 AAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGG
* * *
78950 GTTCCTTAACAACCAAGACACTAAGCTTGATTTTCAAGAGTTTCTTGATGTTTAAATCTTACGGG
131 GTTCCTTGACAACCAAGAAACTAAGCTTGATTTTCAAGAGTTTCTTGATGTTTAAATCCTACGGG
*
79015 TTATCTATAAGCCTTCTGAGCAAGATGA
196 TCATCTATAAGCCTTCTGAGCAAGATGA
** * * *
79043 TAAGAAATCTGGGTCATCCATTAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACC
1 TAAGACCTCTGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACC
79108 AAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGG
66 AAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGG
* *
79173 GGTCCTTGACAACCAAGAAACTAAGCTTGATTTTCAAGAGTTTCTTGATGTTTAAATCCTCCGGG
131 GTTCCTTGACAACCAAGAAACTAAGCTTGATTTTCAAGAGTTTCTTGATGTTTAAATCCTACGGG
*
79238 TCATCTGTAAGCCTTCTGAGCAAGATGA
196 TCATCTATAAGCCTTCTGAGCAAGATGA
* * * * * *
79266 TAAGACCTCCGAGCCATCTATAAGACCTTCAGTGCATGATGTTTTTAAATGAGAGTTTAGAAACC
1 TAAGACCTCTGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACC
** * * * **
79331 AAGCCTTCGACGGTTTACTAATTATTTCAAAAGAACTGTTAAAGGAAGCTAAGTCTAACAAAGAA
66 AAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGG
* *
79396 GTTCCTTGACCACTAAGAAACTAAGC
131 GTTCCTTGACAACCAAGAAACTAAGC
79422 CTTCGAGGGT
Statistics
Matches: 337, Mismatches: 39, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
220 28 0.08
221 83 0.25
222 2 0.01
223 224 0.66
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (223 bp):
TAAGACCTCTGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACC
AAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGG
GTTCCTTGACAACCAAGAAACTAAGCTTGATTTTCAAGAGTTTCTTGATGTTTAAATCCTACGGG
TCATCTATAAGCCTTCTGAGCAAGATGA
Found at i:79581 original size:177 final size:177
Alignment explanation
Indices: 79278--79611 Score: 501
Period size: 177 Copynumber: 1.9 Consensus size: 177
79268 AGACCTCCGA
* * *
79278 GCCATCTATAAGACCTTCAGTGCATGATGTTTTTAAATGAGAGTTTAGAAACCAAGCCTTCGACG
1 GCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAGTTTAGAAACCAAGCCTTCGACG
* * * *
79343 GTTTACTAATTATTTCAAAAGAACTGTTAAAGGAAGCTAAGTCTAACAAAGAAGTTCCTTGACCA
66 GTTTACTAATTATCTCAAAAGAACTGTTAAAAGAAGCTAAGCCTAACAAAGAAGTTCCTTGACAA
79408 CTAAGAAACTAAGCCTTC-GAGGGTTTCTTGATTCGTACGTCCTACGG
131 CTAAGAAACTAAGCCTTCAG-GGGTTTCTTGATTCGTACGTCCTACGG
* * *
79455 GCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCAATCCTTC-AGG
1 GCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAGTTTAGAAACCAAGCCTTCGA-C
** ** *
79519 GGTTTACTAATTATCTCAAAAGAGTTGTTAAAAGAAGCTAAGCCTAACAAAGGGGTTCCTTGATA
65 GGTTTACTAATTATCTCAAAAGAACTGTTAAAAGAAGCTAAGCCTAACAAAGAAGTTCCTTGACA
79584 ACTAAGAAACTAAGCCTTCAGGGGTTTC
130 ACTAAGAAACTAAGCCTTCAGGGGTTTC
79612 CTAACTATCT
Statistics
Matches: 140, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
176 1 0.01
177 138 0.99
178 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (177 bp):
GCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAGTTTAGAAACCAAGCCTTCGACG
GTTTACTAATTATCTCAAAAGAACTGTTAAAAGAAGCTAAGCCTAACAAAGAAGTTCCTTGACAA
CTAAGAAACTAAGCCTTCAGGGGTTTCTTGATTCGTACGTCCTACGG
Found at i:79647 original size:87 final size:87
Alignment explanation
Indices: 79501--79698 Score: 306
Period size: 87 Copynumber: 2.3 Consensus size: 87
79491 ATGAGATTTT
* * * *
79501 AGAAACCAATCCTTCAGGGGTTTACTAATTATCTCAAAAGAGTTGTTAAAAGAAGCTAAGCCTAA
1 AGAAACTAAGCCTTCAGGGGTTTCCTAACTATCTCAAAAGAGTTGTTAAAAGAAGCTAAGCCTAA
*
79566 CAAAGGGGTTCCTTGATAACTA
66 CAAAGGGGTTCCTTGACAACTA
* * *
79588 AGAAACTAAGCCTTCAGGGGTTTCCTAACTATCTTAAAAGAGTTGTTAAAGGAAGCTAAGTCTAA
1 AGAAACTAAGCCTTCAGGGGTTTCCTAACTATCTCAAAAGAGTTGTTAAAAGAAGCTAAGCCTAA
*
79653 CAAGGGGGTTCCTTGACAACTA
66 CAAAGGGGTTCCTTGACAACTA
*
79675 AGAAACTAAGCCTTCGGGGGTTTC
1 AGAAACTAAGCCTTCAGGGGTTTC
79699 TTGATTTATA
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 101 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (87 bp):
AGAAACTAAGCCTTCAGGGGTTTCCTAACTATCTCAAAAGAGTTGTTAAAAGAAGCTAAGCCTAA
CAAAGGGGTTCCTTGACAACTA
Found at i:80155 original size:3 final size:3
Alignment explanation
Indices: 80135--80241 Score: 126
Period size: 3 Copynumber: 36.0 Consensus size: 3
80125 ATTCTCATTT
* * *
80135 TTA TTT TTA TTG TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
80182 TTG TTA TTA ATA TTA TTA TTG TTA TTA ATA TTA TTA TTA TTA ATA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
80230 TTA TTA TTA TTA
1 TTA TTA TTA TTA
80242 CAGGCCCAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
2 2 0.02
3 83 0.98
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:81691 original size:21 final size:22
Alignment explanation
Indices: 81659--81699 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
81649 AATTAGGGTT
*
81659 ATTAATTTTTATATTTTTAAAA
1 ATTAATTTTTATAGTTTTAAAA
81681 ATTAA-TTTTATAGTTTTAA
1 ATTAATTTTTATAGTTTTAA
81700 TTTTCTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTAATTTTTATAGTTTTAAAA
Found at i:81812 original size:2 final size:2
Alignment explanation
Indices: 81805--81872 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
81795 TTAATTTTAG
81805 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
81847 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
81873 GAAAAATTCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82583 original size:17 final size:17
Alignment explanation
Indices: 82561--82599 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
82551 TATTCATTTG
82561 CATTTCCACCAAAAAAA
1 CATTTCCACCAAAAAAA
82578 CATTTCCACCAAAAAAA
1 CATTTCCACCAAAAAAA
*
82595 TATTT
1 CATTT
82600 GTGACCGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (17 bp):
CATTTCCACCAAAAAAA
Found at i:83334 original size:53 final size:53
Alignment explanation
Indices: 83234--83337 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 53
83224 AAATATACTA
** *
83234 ATTTTTTTATTAAATTTACCAAAAGATTAGTGTAATGATTATGTTTTTTTTTT
1 ATTTTTTTATTAAATACACCAAAAGATTAATGTAATGATTATGTTTTTTTTTT
*
83287 ATTTTTTTATTAAA-ACACTAAAAGATTAATGTAATGATTATGTTTTTTTTT
1 ATTTTTTTATTAAATACACCAAAAGATTAATGTAATGATTATGTTTTTTTTT
83338 ATTAAAACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 33 0.70
53 14 0.30
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.55
Consensus pattern (53 bp):
ATTTTTTTATTAAATACACCAAAAGATTAATGTAATGATTATGTTTTTTTTTT
Found at i:88586 original size:16 final size:16
Alignment explanation
Indices: 88565--88601 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
88555 AATCGTCTTG
88565 CATATGGATGCCCCTC
1 CATATGGATGCCCCTC
88581 CATATGGATGCCCCTC
1 CATATGGATGCCCCTC
88597 CATAT
1 CATAT
88602 TCAACCAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (16 bp):
CATATGGATGCCCCTC
Found at i:89064 original size:5 final size:5
Alignment explanation
Indices: 89040--89107 Score: 57
Period size: 5 Copynumber: 13.8 Consensus size: 5
89030 TTCCTGCAAC
* * * * * *
89040 AAAAT AAAA- AAGAT AGAAT AAAAT ACAAT TATAT AACAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
89089 TATAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
89108 AATTAGACGC
Statistics
Matches: 47, Mismatches: 15, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
4 3 0.06
5 44 0.94
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:89082 original size:20 final size:20
Alignment explanation
Indices: 89056--89107 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
89046 AAAAAGATAG
*
89056 AATAAAATACAATTATATAA
1 AATAAAATAAAATTATATAA
*
89076 CATAAAATAAAATTATATAA
1 AATAAAATAAAATTATATAA
89096 AATAAAATAAAA
1 AATAAAATAAAA
89108 AATTAGACGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
AATAAAATAAAATTATATAA
Found at i:90193 original size:18 final size:18
Alignment explanation
Indices: 90170--90208 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
90160 CTTCAGGTAA
90170 CTTCTCAATCCCTAATCT
1 CTTCTCAATCCCTAATCT
*
90188 CTTCTCAATCCCTAATTT
1 CTTCTCAATCCCTAATCT
90206 CTT
1 CTT
90209 TCGATCCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (18 bp):
CTTCTCAATCCCTAATCT
Found at i:95157 original size:8 final size:8
Alignment explanation
Indices: 95144--95170 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
95134 CTGGAAGTAC
95144 AACAAAAT
1 AACAAAAT
95152 AACAAAAT
1 AACAAAAT
95160 AACAAAAT
1 AACAAAAT
95168 AAC
1 AAC
95171 TAACTCCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.11
Consensus pattern (8 bp):
AACAAAAT
Found at i:95413 original size:18 final size:18
Alignment explanation
Indices: 95390--95428 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
95380 CTTCAGGTAA
*
95390 CTTCTCAATCCCTAATTT
1 CTTCTCAATCCCTAATCT
*
95408 CTTCTCAATCCTTAATCT
1 CTTCTCAATCCCTAATCT
95426 CTT
1 CTT
95429 TCGATCTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTCTCAATCCCTAATCT
Found at i:98262 original size:6 final size:6
Alignment explanation
Indices: 98251--98276 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
98241 ACACTTGGAC
98251 TGGCTG TGGCTG TGGCTG TGGCTG TG
1 TGGCTG TGGCTG TGGCTG TGGCTG TG
98277 ACCAGACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
TGGCTG
Found at i:98870 original size:6 final size:6
Alignment explanation
Indices: 98859--98900 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
98849 TATCACACCA
98859 ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG
1 ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG
98901 TTGAAGGTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
ACAGAG
Found at i:99236 original size:60 final size:60
Alignment explanation
Indices: 99156--99268 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
99146 ATGGTCTCTC
* * * * * *
99156 GACTATAGGGTATTGCTTTATTAAGTCTATTGACTGTTAAAAGTTATAAAATGATCATTT
1 GACTATAGAGTATTGCTTTATTAAGACCATCGACTATTAAAAGTTACAAAATGATCATTT
* *
99216 GACTATAGAGTGTTGTTTTATTAAGACCATCGACTATTAAAAGTTACAAAATG
1 GACTATAGAGTATTGCTTTATTAAGACCATCGACTATTAAAAGTTACAAAATG
99269 GTCACCGGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (60 bp):
GACTATAGAGTATTGCTTTATTAAGACCATCGACTATTAAAAGTTACAAAATGATCATTT
Found at i:99280 original size:60 final size:59
Alignment explanation
Indices: 99143--99281 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
99133 TAAAAATACA
* * * * * * *
99143 AAAATGGTCTCTCGACTATAGGGTATTGCTTTATTAAGTCTATTGACTGTTAAAAGTTAT
1 AAAATGGTCAC-CGACTATAGAGTATTGCTTTATTAAGACCATCGACTATTAAAAGTTAC
* ** * *
99203 AAAATGATCATTTGACTATAGAGTGTTGTTTTATTAAGACCATCGACTATTAAAAGTTAC
1 AAAATGGTCA-CCGACTATAGAGTATTGCTTTATTAAGACCATCGACTATTAAAAGTTAC
99263 AAAATGGTCACCGGACTAT
1 AAAATGGTCACC-GACTAT
99282 TCATATGTTC
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (59 bp):
AAAATGGTCACCGACTATAGAGTATTGCTTTATTAAGACCATCGACTATTAAAAGTTAC
Found at i:99589 original size:60 final size:60
Alignment explanation
Indices: 99479--99591 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
99469 GTCAAGTGAC
** * *
99479 CATTATGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACTTTATAGTTGAAGGAT
1 CATTATGTAACTTTTAATAGTCGAAAGACTCAACAAAACAACACTCTATAGTTGAAGGAT
* * * *
99539 CATTTTGTAACTTTTAATAGTCGAAAGACTTAATAAAACAATACTCTATAGTT
1 CATTATGTAACTTTTAATAGTCGAAAGACTCAACAAAACAACACTCTATAGTT
99592 AGGGGGCTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (60 bp):
CATTATGTAACTTTTAATAGTCGAAAGACTCAACAAAACAACACTCTATAGTTGAAGGAT
Found at i:106825 original size:26 final size:26
Alignment explanation
Indices: 106751--106826 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
106741 GAATTATTAT
*
106751 ATTTATTAATATTCATATCATTTAAA
1 ATTTATTAATGTTCATATCATTTAAA
** * *
106777 AAATATTAATGATAATATCATTTAAA
1 ATTTATTAATGTTCATATCATTTAAA
* *
106803 ATTTATTAATGTTCCTATTATTTA
1 ATTTATTAATGTTCATATCATTTA
106827 TTCGTCAAGA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.49
Consensus pattern (26 bp):
ATTTATTAATGTTCATATCATTTAAA
Found at i:110722 original size:18 final size:16
Alignment explanation
Indices: 110699--110737 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
110689 AAAGTAACAC
110699 ATATTAATTAATAATAAA
1 ATATTAA-TAA-AATAAA
*
110717 ATATTAATCAAATAAA
1 ATATTAATAAAATAAA
110733 ATATT
1 ATATT
110738 TATCAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 2 0.10
18 7 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATTAATAAAATAAA
Found at i:110732 original size:16 final size:16
Alignment explanation
Indices: 110711--110745 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
110701 ATTAATTAAT
110711 AATAAAATATTAATCA
1 AATAAAATATTAATCA
*
110727 AATAAAATATTTATCA
1 AATAAAATATTAATCA
110743 AAT
1 AAT
110746 CTCCACGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAAATATTAATCA
Found at i:110992 original size:19 final size:20
Alignment explanation
Indices: 110960--110999 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
110950 CTAACTTAAA
110960 TCACGTATTTATTTATAACT
1 TCACGTATTTATTTATAACT
110980 TCACGTA-TTATTTATAACT
1 TCACGTATTTATTTATAACT
110999 T
1 T
111000 GAGTCGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.50
Consensus pattern (20 bp):
TCACGTATTTATTTATAACT
Found at i:114439 original size:90 final size:88
Alignment explanation
Indices: 114288--114463 Score: 271
Period size: 90 Copynumber: 2.0 Consensus size: 88
114278 CCCAACACAC
* * *
114288 CCTTTTATATCCAAGTTACCCTAATTATATTAGGTTTTTTTATTTTAAATTAATTAAATCTATAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGTTTTATTATTTCAAATTAATTAAATCTATAT
* *
114353 TTAATTAATTGGAATTTAATAAT
66 TTAATTAATTGAAATTAAATAAT
* *
114376 CCTTTTATGTCTAAGTTACCCTAATCATATTAGTGGTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTA--GGTTTTATTATTTCAAATTAATTAAATCTAT
114441 ATTTAATTAATTGAAATTAAATA
64 ATTTAATTAATTGAAATTAAATA
114464 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 29 0.37
90 50 0.63
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (88 bp):
CCTTTTATATCCAAGTTACCCTAATCATATTAGGTTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAAATAAT
Found at i:123297 original size:17 final size:18
Alignment explanation
Indices: 123262--123304 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
123252 GACATTTTAT
123262 ATATTATAATTTAAATTA
1 ATATTATAATTTAAATTA
123280 ATATTATAATTT-AATTA
1 ATATTATAATTTAAATTA
*
123297 ATTTTATA
1 ATATTATA
123305 TTATAGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATAATTTAAATTA
Done.